Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The neuronal synapse is the seat of cognitive computation in the brain, where the minor adjustments in electrical activity between various neuronal circuits results from the sophisticated orchestration of molecules at the synapse. The molecular interplay between the diverse range of synapses and circuits in the brain makes comprehending the full scope of cognition a major challenge for modem neuroscience, one that is limited by crude fractionation schemes for picking apart selective portions of the neuron. While we currently have a strong foundation in our basic understanding of synaptic biology, the challenges we currently face in characterizing precise mechanisms of learning, memory, and cognitive decline will require the ability to finely dissect neurons and synapses into their own distinct subtypes, and understand them from a detailed molecular standpoint. The goal of this thesis is to introduce a novel chemical genetic method, called APEX, into the synapse to enable specific proximity dependent biotinylation of the proteomes at the glutamatergic (excitatory) and GABAergic (inhibitory) postsynaptic densities. In doing so, we provide the first selective and comprehensive survey of the inhibitory postsynaptic density, which has eluded purification by conventional biochemical methods. Furthermore, we demonstrate the use of APEX in state dependent studies of the synapse by exploring the excitatory postsynaptic proteome at early ages and mature ages. Finally, we demonstrate the application of APEX in vivo and illustrate the challenges inherent in such a venture. Thus, we hope to provide the foundation for spatially restricted proteomic mapping of synapses, and demonstrate the utility of such tools designed to enable deeper exploration of neuronal and synaptic diversity. / by Kurt J. Cox. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. / Includes bibliographical references (p. 141-153). / Biomaterials and biomineralization have been successfully utilized in a broad variety of technical applications. Properties of natural biopolymers, such as the ability to control the nucleation, growth, and organization of crystals, have been extended to a much wider array of technologically applicable materials through combinatorial selection techniques. However, detailed mechanisms of peptide adsorption on inorganic surfaces have largely escaped characterization. This knowledge would open new routes for the rational design of nanostructures and composite biomaterials. The development of accurate and computationally efficient methods for the simulation of biopolymer-inorganic surface adsorption could provide a more detailed understanding of adsorption mechanisms. While simple models involving reduced solvent representations and polymer flexibility have found some success in limited applications, robust performance for systems of varying size and composition can generally be expected only through accurate inclusion of these key details. Fully atomistic representations of biopolymer and surface are necessary for detailed molecular recognition, while polymer flexibility is required to capture structural rearrangement and the resulting free energy contributions. Finally, electrostatic interactions between the adsorbing biopolymer and inorganic surface, as well as interactions of the polymer and surface with the surrounding solvent environment will play a dominant role in the adsorption process, and an accurate representation of the solvated system is inherently necessary. Computational efficiency can be increased through the application of implicit solvent models, which replace the numerous solvent molecules with a continuum dielectric, and seek to capture the average effects of the statistical solvent environment. The Poisson-Boltzmann model represents the most rigorous treatment of implicit solvent. / (cont.) This model, however, requires the relatively expensive solution of a second order elliptical differential equation over the space of the system. Here, a method is presented which reduces the scale at which the Poisson-Boltzmann equation must be solved. However, even when combined with an efficient multi-grid solver, the Poisson-Boltzmann model represents a significant computational cost. The modified Generalized Born model, GBr6, based on an approximation to the Poisson-Boltzmann model, offers a computationally efficient alternative. Generalized Born models, however, are often inaccurate in the case of charges positioned near an extended dielectric interface, which is precisely the system we wish to investigate. Here, an analytical integration of the approximate electric displacement is used to calculate Born radii, and tested in application to surface adsorption studies. Replica-exchange Monte Carlo simulations with modified Generalized Born implicit solvent environment is then used to study the adsorption mechanism of a set of rationally designed sapphire-binding peptides. Modulation of binding affinity is predicted to depend on multiple interactions between basic amino acids and the negatively charged sapphire surface. The proximity of charged residues to one another as well as the conformational ability of each peptide to present functional groups towards the surface are shown to control the relative binding affinities. / by Stephen Thomas Kottmann. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references (p. 97-111). / In this thesis, aspects of charge reconbination and charge transport in organic solar cells and light-emitting devices are presented. These devices show promise relative to traditional inorganic semiconductors. We show that the energy splitting between singlet and triplet CT states in organic materials is appreciable and is material and geometry dependent. This prediction is used to guide the development of an OLED with enhanced fluorescence. The effects of nuclear disorder on optical and transport properties in organic semiconductors are examined and a general computational method for carrying out this analysis is described. The function of organic semiconductors is characterized by the interplay between localized and delocalized excited states. We present an ab initio method for obtaining the electronic coupling between CT states and excitons and (discuss the nonadiabatic transitions between these states. / by Seth Difley. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Adenosylcobalamin (AdoCbl, coenzyme B 12) is a complex organometallic enzyme cofactor derived from vitamin B 12 that allows for challenging radical-based chemical transformations. Additionally, the biological role of AdoCbl was recently expanded by the discovery that AdoCbl can serve as a light sensor in light-dependent gene regulation. The use of AdoCbl in living systems, however, comes at a significant price because the cofactor is reactive, prone to side reactions, and very rare. Thus, the acquisition and handling of AdoCbl require specialized machinery such as metallochaperones. In this thesis, I illustrate these different facets of the biochemistry of AdoCbl. Using X-ray crystallography, I determined structures of IcmF, a fusion protein between AdoCbl-dependent isobutyryl-coenzyme A mutase and a G-protein metallochaperone that mediates AdoCbl delivery. Structures determined in the absence and presence of AdoCbl depict large-scale conformational changes mediated by the metallochaperone that expose the mutase active site and allow for cofactor delivery. Collectively, these structures visualize how the precious AdoCbl cofactor is delivered to an enzyme active site with the help of a metallochaperone. I furthermore determined crystal structures of IcmF in complex with different acyl-coenzyme A substrates, revealing how the enzyme positions AdoCbl and substrates for catalysis using specific amino acid residues. These structures combined with bioinformatic analyses allowed me to predict the existence of AdoCbl-dependent enzymes with unique reactivities. Finally, the recent discovery that the CarH transcription factors use AdoCbl as a light sensor was remarkable because light sensitivity is usually detrimental and leads to inactivation of the cofactor, yet here it is the main function of AdoCbl. To investigate the molecular basis for this functional repurposing of AdoCbl, I determined crystal structures of CarH in three states. These structures elucidate how CarH harnesses the light sensitivity of AdoCbl to drive a light-dependent gene expression switch: intact AdoCbl in the dark mediates formation of a CarH tetramer that binds to DNA and represses transcription, whereas light exposure triggers a conformational change that dissociates CarH from DNA and activates transcription. This work provides fundamental insight into a new mode of light-dependent gene regulation and expands the functional repertoire of AdoCbl in living systems. / by Marco Jost. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2007. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Vita. / Includes bibliographical references. / The semiconducting properties of conjugated polymers are finding use in various optoelectronic applications, including chemical sensors and light-emitting diodes. In this thesis, we investigate aggregation in conjugated polymers and how it affects the optical properties of these organic materials. We discuss how aggregation enhances exciton transport properties in fluorescent polymers, thereby increasing the probability of excitons reaching low-energy sites in the polymer. A consequence of this aggregation-enhanced exciton migration is that low-energy defect sites in a conjugated polymer can dramatically alter the polymer's fluorescence properties when it is in an aggregated state. In a poly(pphenylene ethynylene) (PPE) that was previously proposed to form green-emitting excimers, we found that a small concentration of anthryl defects in the polymer emitted green fluorescence that was only noticeable when the polymer was in an aggregated state (otherwise the polymer was fluorescent blue). After elucidating the origin of the green fluorescence, we purposely added more emissive anthryl units into the polymer to enhance the blue-to-green fluorescence color change that accompanied polymer aggregation. / (cont.) Using this anthryl-doped conjugated polymer, we developed aggregationbased chemical sensors that exhibited a visually noticeable fluorescence color change upon addition of poor solvents or biologically relevant, nonquenching, multicationic analytes (e.g., polyamines, neomycin) to the polymer solution. We also studied the effects of aggregation on the optical properties of a chiral poly(p-phenylene vinylene) (PPV) derivative in solutions and in films. We found that the organizations and functional properties existing in aggregated polymer solutions can be transferred to the film state by controlling the processing conditions. Using the same polymer, we were able to obtain films with different architectures and luminescence properties simply by adjusting the spin-casting solvent and film annealing conditions. Controlling the organizations and functional properties of conjugated polymer films is important in the fabrication of conjugated polymer-based optoelectronic devices. / by Andrew Satrijo. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. / Vita. / Includes bibliographical references. / This thesis addresses two emerging areas in the study of iron-sulfur cluster biochemistry: bioassembly of iron-sulfur clusters, and their involvement in initiation of radical chemistry. The structure of a cysteine desulfurase involved in cluster bioassembly in the cyanobacterium Synechocystis PCC sp. 6803 was solved by X-ray crystallography and analyzed in terms of its mechanistic implications. We found that the active site cysteine responsible for the direct removal of sulfur from substrate cysteine is located on a short, well-ordered loop, consistent with structures solved of homologous proteins. The length of this loop is thought to restrain the active site cysteine, interfering with its ability to affect catalysis. Our results are consistent with the theory that this cysteine desulfurase requires an accessory protein for fully activity in vivo. Two structures of pyruvate formate-lyase activating enzyme from Escherichia coli, an Sadenosylmethionine radical enzyme, were also solved by X-ray crystallography, providing the first structure of an activase from this family of enzymes. These structures revealed the enzyme's active site and the residues involved in binding and orienting substrate for hydrogen atom abstraction. Comparison of the structures of the substrate-free and substrate-bound forms of the enzyme identified a conformational change associated with substrate binding. Detailed analyses of the structure of pyruvate formatelyase activating enzyme were carried out to provide insight into catalysis. These structures were also analyzed in comparison with other S-adenosylmethionine radical enzyme structures to more clearly understand the structural basis for reactivity in this superfamily. / by Jessica L. Vey. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1988. / Vita. / Includes bibliographical references. / by Yun Gao. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Page 257 blank. Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references. / Dynamic Nuclear Polarization (DNP) enhances signal to noise in NMR experiments, by transferring the large electron Boltzmann polarization to nuclear polarization, via application of pulsed or continuous-wave microwave irradiation. This results in increases in NMR sensitivity of 2-3 orders of magnitude. DNP greatly reduces experimental times and makes some experiments possible that are otherwise unfeasible due to lack of sensitivity. DNP methods have undergone vast improvements in recent years. However, continued advancement of DNP methods will rely on having a clear understanding of the underlying mechanisms. We develop instrumentation and software intended for the study of DNP mechanisms. This includes a three-channel (e-, 13C, 1H) probe for observing both electrons and nuclei, and a 140 GHz pulsed-EPR spectrometer. We also have developed DNPsim, a program designed for easy quantum-mechanical simulation of basic DNP experiments, combined with the flexibility to customize simulations for more advanced experiments and mechanistic studies. Using these tools, we develop a theoretical framework for the solid effect DNP mechanism, which considers the roles of quantum mechanical and relaxation processes in many-spin systems. NMR experiments under static conditions that monitor nuclear polarization buildup were fit to models of electronnuclear polarization transfer; the results show that nuclei near the electron and the observed (bulk) nuclei compete for electron polarization. Therefore bulk nuclear enhancements are reduced, since nuclei near the electron deplete electron polarization. This result is also reproduced for magic angle spinning NMR experiments. EPR experiments that monitor electron polarization as a function of microwave frequency can be used to measure DNP 'matching conditions'. Experiments utilizing the solid effect show DNP matching conditions that are a result of polarization transfer through many spin, high-order coherences. Previously, it was thought that transfers involving highorder coherences should be highly forbidden, whereas these experiments present strong evidence of their presence. Simulations using DNPsim also show that high-order coherences can play a significant role in DNP polarization transfers in strongly coupled, many-spin systems. / by Albert Andrew Smith. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2001. / Vita. / Includes bibliographical references. / Two-electron mixed-valence complexes of rhodium may be supported by diphosphazane ligands (RN(PY2)2). Whereas diphosphazane ligands with strongly [pi]-acidic phosphine groups (Y = F, OCH2CF3) react with RhI starting materials to afford binuclear Rh20,II complexes, Rh20,II(MeN(PY)2)3X2(L) or Rh2"II(MeN(PY),)3X2 (X = Cl, Br), diphosphazane ligands with weaker [pi]-acid phosphines (Y = OMe, OPh) give only valence-symmetric Rh2I,I complexes, Rh2I,I(MeN(PY2)2X2(L)2. Moreover, the formation of Rh20,II(tfepma)3C12 and [ClRh'(tfepx)]2([mu]-tfepx) (tfepma = MeN[P(OCH2CF3)2]2; tfepx = (3,5-Me2C6H3)N[P(OCH2CF3)2] suggest that delocalization of the nitrogen lone pair into the [pi]-system of the aryl group defeats formation of the two-electron mixed-valence species. These results are interpreted in terms of a polarizable nitrogen lone pair mediating the [pi]-acid properties of the PY2 groups to induce disproportionation of valence-symmetric dirhodium cores. Application of this knowledge to iridium provided the first example of a two-electron mixed-valence complex for this metal, Ir20,II(tfepma)3C12. X-ray diffraction studies reveal a coordination environment with two bridging tfepma ligands and a third tfepma chelating the Ir0 center. Trigonal bipyramidal geometry at the Ir0 is completed by a metal-metal bond to a square pyramidal IrII containing cis-disposed chloride ligands. Ir20-II(tfepma)3C12 is Lewis-acidic, readily accepting donor ligands to form 36 e- complexes. Oxidative addition is also rapid: chlorine and hydrogen chloride react to afford Ir2I-III(tfepma)3C14 and Ir2I,III(tfepma)3HC13, respectively. Hydrogen adds reversibly to Ir20,II(tfepma)3C12, providing the first example of such an addition across a preserved metal-metal single bond. / (cont.) Two electron oxidation and reduction reactions also are facile for Rh20,II(dfpma)X2(L), affording Rh2II-II(dfpma)X4 and Rh20,0(dfpma)(L)2 complexes, respectively. These three species form a homologous series of metal-metal bonded complexes with well characterized trigonal bipyramidal Rh0 and octahedral RhII centers. Preservation of the metal-metal bond across the series supports the multi-electron reactivity of the system, as evidenced by photo-induced halogen elimination. We obtained the mixed-valence complex, Rh20-II(dfpma)X2(L), quantitatively when solutions of Rh2(dfpma)3X4 containing excess L were photolyzed in the presence of a halogen-atom trap such as THF. Further irradiation of the Rh20,II(dfpma)X2(L) photoproduct resulted in a second 2e- elimination reaction to give Rh20,0(dfpma)(L)2 in quantitative yield. In the overall transformation, the two-electron mixed-valence LRh0--RhIIX2 compound sustains the multi-electron photoreactivity of the system by coupling the 2e- M-X chemistry of the individual Rh centers. M-X photoactivation from this two-electron mixed-valence platform provides the basis for the photocatalytic production of H2 from HX in homogeneous solution ... / by Alan F. Heyduk. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004. / Vita. / Includes bibliographical references. / There are numerous advantages to high frequency (high field) electron paramagnetic resonance (EPR) spectroscopy. Two of the most important are improved sensitivity and the improved resolution of field dependent interactions. In addition, there are many attractive features to time domain spectroscopy. Pulsed EPR allows for the design of experiments, which can specifically be used to study structure and dynamics of paramagnetic species and provide utmost resolution by separating interactions from each other. The combination of pulsed techniques and high frequencies is not only complimentary to continuous wave (CW) low frequency EPR but it also greatly increases the accessible information on paramagnetic species. High frequency, time domain EPR is still in its infancy. Spectrometers at W-band ([approximately] 95 GHz) are now available commercially but to date very few spectrometers operating at higher frequencies have been described. The spectrometer developed in the Francis Bitter Magnet Laboratory operates at a microwave (MW) frequency of 139.5 GHz corresponding to [approximately] 5 T magnetic field. The applications presented in this thesis illustrate the potential of high frequency, time domain EPR spectroscopy at 139.5 GHz in obtaining structural and mechanistic insights of several paramagnetic systems. Well resolved EPR spectra observed at 139.5 GHz of the stable tyrosine radical in ribonucleotide reductase (RNR) revealed the existence of a hydrogen bond in RNR from yeast, chapter 1. The bond length and orientation were determined from the nuclear frequencies of the proton, detected by orientation selective electron nuclear double resonance (ENDOR). / (cont.) The advantage of the time domain detection scheme is demonstrated in chapters 4, 5 and 6. A stimulated echo sequence is used to separate different organic radicals associated with the reduction chemistry and inhibition mechanisms of RNR. Using the dispersion in relaxation rates at high temperature ([approximately] 60 K) it is possible to filter the multi component spectrum. The assignment of new radicals is possible at high field, 5 T, due to the high resolution in g anisotropy. The findings support earlier proposals for the mechanism of nucleotide reduction and inhibition of this very important enzyme. To study photoexcited triplet molecules a light source was coupled to the high frequency spectrometer and the pulsed mode detection scheme was used to acquire EPR spectra. The new technique is demonstrated on several model systems. In addition to the basic advantages described above, high frequency EPR opens new frontiers for high spin systems, S >[or equal to] 1, with large spin-spin interaction. Because of the inverse field dependency of the zero field splitting, such systems may be totally EPR-silent at normal EPR frequencies. However their EPR spectra are accessible at high frequencies due to the reduction of linewidth. The Mn(II), S = 5/2, in superoxide dismutase (SOD) is a good example for such system. / by Galit Bar. / Ph.D.