Recursos de colección

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Chemistry - Ph.D. / Sc.D.

Mostrando recursos 1 - 20 de 1.030

  1. A freezing point apparatus

    Vonnegut, Bernard
    by Bernard Vonnegut.

  2. Elucidating the pumping mechanism of bacteriorhodopsin using dynamic nuclear polarization enhanced magic angle spinning NMR

    Ni, Qing Zhe
    Bacteriorhodopsin (bR) is comprised of 7 trans-membrane helices that enclose a retinylidene chromophore formed by a Schiff base (SB) between the retinal and Lys216. Due to bR's relative availability, it serves as a model for other members of the rhodopsin family, ion channels and GPCRs. Since its discovery in the 1970's, bR has been intensely studied by various methods including: X-ray crystallography, EM, FT-IR, molecular simulations, and NMR, etc. Despite numerous advances, details of its pump mechanism remain elusive due to experimental limitations in sensitivity and/or resolution. Here, dynamic nuclear polarization (DNP) is employed to boost the ¹H NMR signal....

  3. Using VHHs to study the function and control of the E2 Ubiquitin-conjugating enzyme UBC6e

    Ling, Jingjing, Ph. D. Massachusetts Institute of Technology
    Endoplasmic reticulum-associated degradation (ERAD) is essential for protein quality control both during stress and at steady state. We found that an E2 ubiquitin-conjugating enzyme UBC6e contributes to a new layer of homeostatic control, in which ERAD activity itself is regulated post-transcriptionally and independently of the unfolded protein response. Ablation of UBC6e causes up-regulation of active ERAD enhancers and increases clearance not only of terminally misfolded substrates, but also of wild-type glycoproteins that fold comparatively slowly. Tuning of ERAD component level involves a mechanism that is likely distinct from the conventional ERAD by Hrdl/SEL1L complex. To better understand how UBC6e is...

  4. Total synthesis of cyclotryptamine and diketopiperazine alkaloids and biosynthetic pathway investigation of unsymmetrical diketopiperazine dimers

    Lindovská, Petra
    I. Total Synthesis of (-)-Hodgkinsine, (-)-Calycosidine, (-)-Hodgkinsine B, (-)-Quadrigemine C and (-)-Psycholeine The enantioselective total synthesis of (-)-hodgkinsine, (-)-calycosidine, (-)-hodgkinsine B, (-)- quadrigemine C, and (-)-psycholeine through a diazene-directed assembly of cyclotryptamine fragments is described. Our synthetic strategy enables multiple and directed assembly of intact cyclotryptamine subunits for convergent synthesis of highly complex bis- and tris-diazene intermediates. Photoextrusion of dinitrogen from these intermediates enables completely stereoselective formation of all C3a-C3a' and C3a-C7' carbon-carbon bonds and all the associated quaternary stereogenic centers. The synthesis of these complex diazenes was made possible through a new methodology for synthesis of aryl-alkyl diazenes using...

  5. Modeling non-radiative processes in solar materials

    Kohn, Alexander Wolfe
    In this thesis, we investigate methods and systems for understanding the electronic properties of a variety of systems relevant to organic photovoltaics. The second chapter examines how to predict the radiative and non-radiative decay rates of a large family of naphthalene derivatives. Naphthalene is a common building block in many organic electronic devices and possesses complex photophysics that are difficult to capture. Principally using time-dependent density functional theory, we are able to reproduce the experimental rates and, moreover, the fluorescence quantum yield, quite accurately. The next chapter then goes into extensions of the methodology discussed and analyzed in the prior...

  6. Mechanistic studies of the radical transport pathway in aminotyrosine-substituted class Ia ribonucleotide reductase

    Lee, Wankyu
    Ribonucleotide reductase (RNR) catalyzes the reduction of nucleotides to 2'- deoxynucleotides. The focus of this thesis is the F coli class la RNR, which is comprised of two homodimeric subunits, [alpha]2 and [beta]2, forming an active [alpha]2[beta]2 complex. The [beta]2 subunit harbors the stable diferric-tyrosyl radical cofactor (Y 122*) that reversibly oxidizes the active site cysteine (C₄₃₉) in [alpha]2. This oxidation requires a long-range radical transport (RT) pathway consisting of proton-coupled electron transfer (PCET) events through redox-active aromatic amino acid residues: Y₁₂₂* <--> [W₄₈] <--> Y₃₅₆ in [beta]2 to Y₇₃₁ <--> Y₇₃₀ <--> C₄₃₉ in [alpha]2. Once formed, the transient...

  7. Ligand participation in energy storage electrocatalysis and photocatalysis

    Maher, Andrew Gerard
    The electrochemical or photochemical production of fuels using energy from the sun is an attractive approach for storing solar energy. However, the development of efficient and inexpensive catalysts is necessary to facilitate these reactions. While a number of molecular catalysts do exist for this purpose, a lack of deep understanding of how they operate on a mechanistic level impedes their optimization and rational design. This thesis addresses the key mechanistic issue of ligand participation during energy storage catalysis using electrochemical, spectroscopic (both steady-state and time-resolved), synthetic, and computational techniques. The thesis begins by investigating the reactivity of nickel porphyrins during...

  8. Spectroscopy, relaxation, and transport of molecular excitons in noisy and disordered environments

    Chuang, Chern
    In this thesis contribution we theoretically investigate the spectroscopy, relaxation, and transport properties of Frenkel excitons in molecular aggregates, with extensive comparison to or prediction of experimental observables. Particular emphasis is devoted to the effects of thermal noise, static disorder, and system dimensionality. Our key contributions are summarized as the following. We study the spectroscopic signatures of excitonic molecular aggregates of dimensionality larger than unity as functions of temperature and disorder strength. These findings are applied to the determination of essential system characteristics and quantitatively explain the spectroscopic traits seen in experiments where either the temperature or disorder strength is...

  9. Type I collagen proteostasis

    DiChiara, Andrew Stephen
    The folding, quality control, and secretion of collagen presents a significant challenge to collagen-producing cells. Each monomeric polypeptide must undergo extensive post-translational modifications, folding and assembly of the C-terminal propeptide globular domain, and isomerization of hundreds of prolyl bonds into the trans conformation before the mature triple helix can form. The triple-helical domain lacks a traditional hydrophobic core that often drives the assembly and folding of globular proteins. Even once folded, the triple helix is at best marginally stable at body temperature and is prone to local regions of unwinding. The process must be highly orchestrated by the endoplasmic reticulum's...

  10. Syntheses of biocompatible luminescent nanocrystals for visible and short-wave infrared imaging applications

    Chen, Yue, Ph. D. Massachusetts Institute of Technology
    The primary focus of this thesis is to synthesize biocompatible luminescent nanocrystals for visible and short-wave infrared (1-2 [mu]m, SWIR) imaging applications. Quantum dots (QDs) have been promising fluorescent probes for biomedical imaging due to their high quantum yield (QY), narrow photoluminescence spectra, and excellent photostability. However, challenges remain to be solved to transfer the as-synthesized hydrophobic QD to aqueous solutions while maintaining the high QY and a compact size. This study involves the design and synthesis of a novel ligand that can be introduced to the established QD synthesis, producing norbornene functionalized QDs that can be readily phase transferred...

  11. Development of N-heterocyclic carbene ligands for nanomaterials in aqueous media and expanding the interface of metal-organic framework (MOF) and polymer chemistry via polyMOFs

    MacLeod, Michelle (Michelle Jeanette)
    In the field of coordination chemistry, there are many standard organic ligand designs that are optimized for their ease of synthesis as well as established and favorable properties. Nevertheless, there is still room to add new ligand classes to the toolbox for specific applications. This thesis focuses on expansion of the types of ligands available for (1) metallic nanomaterial surface modification and (2) metal-ligand driven supramolecular assembly. (1) Surface ligands are typically used for surface passivation, imparting new properties such as solubility, or introducing a functional handle for further modification. The different demands in many diverse fields such as catalysis,...

  12. Site-selective modification of cysteine residues

    Dai, Peng, Ph. D. Massachusetts Institute of Technology
    Proteins are biomolecules that carry out essential work in cells and are required for the structure, function, and regulation of biological systems. It is desired to install designer modifications on proteins of interest, in a site-selective manner mimicking nature's post-translational modifications, for various biological and therapeutic applications. Towards this goal, efforts were devoted to develop site-selective protein modification methods. The [pi]-clamp-mediated cysteine perfluoroarylation, a novel sequence-selective protein modification strategy, enabled regioselective cysteine modification in the presence of competing cysteines on protein surface. The major goals of this thesis include improving and understanding the [pi]-clamp-mediated reaction, and discovering new sequence-selective protein...

  13. Macroscopic electrostatics and the molecular theory of dielectric polarization

    Ramshaw, John D
    by John David Ramshaw.

  14. The use of modified nucleosides as probes of macromolecular function.

    Hawrelak, Stephen Douglas
    Massachusetts Institute of Technology. Dept. of Chemistry. Thesis. 1974. Ph.D.

  15. Application of RMT-RNN improved decomposition onto defected system

    Xie, Wanqin, Ph. D. Massachusetts Institute of Technology
    This thesis is about the study and application of a stochastic optimization algorithm - Random Matrix Theory coupled with Neural Networks (RMT-RNN) to large static systems with relatively large disorder in mesoscopic systems. It is a new algorithm that can quickly decompose random matrices with real eigenvalues for further study of physical properties, such as transmission probability, conductivity and so on. As a major topic of Random Matrix Theory (RMT), free convolution has managed to approximate the distribution of eigenvalues in the Anderson Model. RMT has proven to work well when looking for the transport properties in slightly defect system....

  16. Solid-state nuclear magnetic resonance investigations of the influenza M2 protein : structure and dynamics characterization of channel gating and conduction

    Williams, Jonathan K. (Jonathan Kyle)
    Solid-state nuclear magnetic resonance (ssNMR) spectroscopy is a powerful technique that can be used to probe the structure and dynamics of biomolecules that are intractable to study by other structural biology methods. In this thesis, the mechanisms of conduction and gating are investigated in the influenza AM2 and BM2 proton channels bound to native-like lipid bilayers. Using pH-dependent 15N chemical shifts of the conserved Histidine residue, we have found that the proton conduction mechanism is the same in all of the M2 channels (WT AM2, S3 IN AM2, BM2) studied, and that the conduction cycle involves proton shuttling via hydrogen-bonding...

  17. Electron- and ion-conducting metal-organic frameworks

    Park, Sarah Sunah
    This thesis focused on designing, characterizing and understanding the electronic or ionic behavior of electron- or ion-conducting metal-organic frameworks (MOFs). Chapter 1 gives a general introduction for electron- or ion-conducting MOFs, including a review of the reported materials exhibiting such behavior. Chapter 2 describes new MOFs designed using through-space charge transport strategies, as introduced in Chapter 1. Chapter 2 discusses four isostructural materials of general formula M2(TTFTB) (M = Mn, Co, Zn, and Cd), which exhibit infinite helical TTF stacks and reveal a correlation between the shortest intermolecular S ... S interaction among neighboring TTF cores and their single crystal...

  18. Bond activation and catalysis by nontrigonal tricoordinate and tetracoordinate phosphorus compounds

    Lin, Yi-Chun, Ph. D. Massachusetts Institute of Technology
    Molecular distortion has a profound impact on the electronic structure and reactivity of molecules. This dissertation describes studies on E-H bond activation and catalytic reactivity of [sigma]³- and [sigma]⁴ -phosphorus compounds with distorted nontrigonal structures. Specifically, a rare example of N-H oxidative addition to a planar, C2v-symmetric P(III) center is described in Chapter 2. The kinetics and computational studies implicate a noncanonical, phosphorus-based electrophilic pathway for this transformation. As detailed in Chapter 3, a Cs-symmetric phosphorous triamide and its P-N cooperative reactivity are presented. B-H activation and catalytic imine hydroboration are achieved via the combination of the electrophilic phosphorus center...

  19. Structure and dynamics of full-length M2 protein of influenza A virus from solid-state NMR

    Liao, Shu-Yu, Ph. D. Massachusetts Institute of Technology
    Solid-state nuclear magnetic resonance (SSNMR) has been frequently used to elucidate the structure and dynamics of membrane proteins and fibrils that are difficult to characterize by Xray crystallography or solution NMR. This thesis focuses on the structure determination and the proton conduction mechanism of the full-length matrix protein 2 (M2) of influenza A virus. The M2 membrane protein can be separated into three domains: an N-terminal ectodomain (1-2 1), an cc-helical transmembrane domain (TM) (22-46) connected to an amphipathic helix (AH) and a Cterminal cytoplasmic tail (63-97). The TM domain of M2 is responsible for proton conduction ant the ectodomain...

  20. Spatially-resolved transcriptomic mapping in live cells using peroxidase-mediated proximity biotinylation

    Kaewsapsak, Pornchai
    The spatial organization of RNA within cells is crucial for the regulation of a wide range of biological functions, spanning all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we developed two methods, termed APEX-RIP and APEX-Seq. APEX-RIP combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking, while APEX-Seq utilizes peroxidase-catalyzed in situ biotinylation on RNA. We demonstrated that APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, bulk cytosol, and...

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