Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2017. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / 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 and the basic anilide ligand moiety of this Cs-symmetric phosphorus compound. Finally, Chapter 4 extends the study of distorted phosphorus compounds to [sigma]⁴ -phosphorus molecules. Iminophosphoranes bearing constrained ligand platforms are synthesized and their distortion-induced B-H, B-O and Si-H bond activation reactivity are presented. This research provides insight into the influence of molecular symmetry on the reactivity of [sigma]³- and [sigma]⁴-phosphorus compounds and represents an initial step toward the discovery of new chemistry in other distorted phosphorus molecules. / by Yi-Chun Lin. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, June 2004. / Vita. / Includes bibliographical references. / Class II major histocompatibility complex (MHC) proteins bind peptides and present them at the cell surface for interaction with CD4+ T cells as part of the system by which the immune system surveys the body for signs of infection. Peptide binding is known to induce conformational changes in class II MHC proteins on the basis of a variety of hydrodynamic and spectroscopic approaches, but the changes have not been clearly localized within the overall class II MHC structure. Local structural changes were mapped for HLA-DR1, a common human class II MHC variant, using a series of monoclonal antibodies which recognize the beta subunit and are specific for the empty conformation. Additional structural information was obtained using side chain-specific chemical modification and identification of modified residues by in-gel tryptic digestion and mass spectrometric peptide mapping. Together, the chemical modification studies and the mapping results illuminate aspects of the structure of the empty forms and the nature of the peptide-induced conformational change. Empty class II MHC proteins have been observed on the surface of immature dendritic cells in both humans and mice. Immature DC also secrete a protease activity that is capable of generating antigenic peptides from whole antigen. The protease activity secreted by dendritic cells is characterized and the role of empty MHC proteins in dendritic cell antigen presentation is discussed. / by Gregory J. Carven. / Ph.D.

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1873. / MIT copy bound with: Artificial stone & stone brick / L. F. Wood. / by Ellen H. Swallow. / B.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Includes bibliographical references. / Nuclear magnetic resonance (NMR) spectroscopy is unique in the content of structural as well as dynamic information that it can provide at atomic resolution. The aim of this PhD-thesis was to contribute to the understanding of biochemical processes by means of NMR-spectroscopic techniques, targeting specific problems as well as contributing to the general understanding and providing new, widely applicable methods. The main focus was on the structural as well as dynamic study of ribonucleic acids (RNA). A new structural NMR method was developed aimed at the determination of the glycosidic torsion angle [chi] in RNA, which defines the relative orientation of the nucleobases in respect to the ribose moiety (Duchardt et al., 2004). [Chi] was derived from the angle dependence of carbon-hydrogen dipole-dipole, nitrogen chemical shift anisotropy cross-correlated relaxation rates (gamma-rates). Method development comprised the design of a novel NMR experiment, the [gamma](HCN), as well as the introduction of [gamma] versus [chi] parameterization curves. The novel method provides an accuracy of around 10 degrees or better, comparable to the precision of conventional angle determination techniques. In contrast to conventional methods, the [gamma](HCN) is sensitive to molecular size and will therefore proof beneficial in the investigation of larger RNAs by NMR Apart from this methodological contribution to RNA structure determination, the dynamic properties of the abundant YNMG RNA tetraloop motif (with Y=C or U; N= any base; M=C or A) were studied in a residue specific manner by means of ¹³C NMR relaxation measurements. The dynamics of the extraordinarily stable cUUCGg motif were compared to the less stable uCACGg hairpin, which forms the stem-loop D (SLD) in the regulatory 5'-cloverleaf of coxsackievirus 3B. / (cont.) Measurements were carried out at 25⁰C, at which both motifs are stable, as well as at close to the melting point of SLD (43⁰0). Ribose and base moiety specific amplitudes and time-scales of motion were extracted from R₁, R₁-[rho] and the heteronuclear nOe of C₆ and C₁. in pyrimidines and C₈ and C₁. in purines by application of the model-free formalism (Lipari and Szabo, 1982). The application of the model-free formalism to C₁, and C₆ which possess an additional adjacent carbon spin, was examined for the uniformly isotope labeled RNA hairpins investigated in this study. In addition, the relaxation data analysis was optimized for the ¹³C chemical shift anisotropy based on chemical shift tensors available to date (Stueber and Grant, 2002;Fiala et al., 2000). While at room temperature, the dynamics closely follow the structural features of both hairpins, residues in the loop closing as well as in the adjacent base-pair exhibit highly increased flexibility at temperatures close to the melting point of SLD. In contrast, loop dynamics remain unperturbed. In SLD, the residues close to the loop are conserved among the family of rhino- and enteroviruses, indicating a sequence based mechanism of decoupling loop structure and stability in order to adjust to the twofold requirement of a defined structure for protein recognition and low stability to ensure efficient melting within the genomic transcription process. In addition to investigations on RNA, structural studies were also conducted on the [zeta]-chain of the T-cell receptor (TCR) in order to contribute to the elucidation of the early events in T-cell activation. According to earlier studies (Aivazian and Stem, 2000), the extracellular encounter of the T-cell receptor with an antigen is transmitted into the T-cell via a lipid induced structural transition of the TCR [zeta]-chain cytoplasmic domain. / by Elke Duchardt. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Nonlinear terahertz (THz) spectroscopy is a rapidly developing field, which is concerned with driving and observing nonlinear material responses in the THz range of the electromagnetic spectrum. In this thesis, I present several advances in nonlinear THz spectroscopy that expand the range of systems in which responses may be driven, the types of responses that may be initiated, and the way in which these responses may be observed. Sufficiently strong THz pulses are generated using the tilted-pulse-front technique, and are collected, focused, and detected using a THz spectrometer specifically designed for maximum peak THz electric field strength and maximum flexibility, allowing for a wide range of experimental geometries to be implemented. Further enhancement in the peak THz electric field strength is obtained through the use of metamaterial structures, which concentrate free-space THz fields in their antenna gaps. Impact ionization was observed in high-resistivity silicon, a material in which no nonlinear THz response had been previously seen, using metamaterial structures to enhance free space THz electric fields. Using three-dimensional metamaterial structures, the THz magnetic field is shown to also be capable of driving ionization processes both in high-resistivity silicon as well as air. Using metamaterial structures with open gaps, the THz electric field is shown to induce breakdown in air at both high and low pressures due to field ionization processes involving the gold metamaterial antennas. Furthermore, THz-driven electromigration of the gold metamaterial antennas is observed. Probing of THz-driven structural changes in both vanadium dioxide and perovskite ferroelectrics is demonstrated using femtosecond Xray pulses from the LCLS facility at the SLAC National Accelerator Laboratory. Finally, ongoing results involving energetic materials, stimulated Raman measurements, and Stark effect measurements are discussed. This work, coupled with the ongoing expansion of nonlinear THz techniques and potential applications demonstrates the continued development of nonlinear THz spectroscopy into a robust and valuable method for investigating fundamental processes in a multitude of systems. / by Nathaniel Curran Brandt. / Ph. D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1987. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Bibliography: leaves 68-71. / by Susan E. Drozda. / M.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1985. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Vita. / Includes bibliographical references. / by Alan Edmund Walts. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2002. / Vita. / Includes bibliographical references. / The human disease leishmaniasis afflicts over 20 million people worldwide, and is caused by unicellular protozoan parasites. Cell surface carbohydrates are implicated in immune recognition of the parasite by host macrophages. The synthesis of a unique tetrasaccharide found on the parasite cell surface lipophosphoglycan is described. The synthetic material was used to create two novel immungens that are currently being evaluated in an animal model. New methods were also developed for an automated solid-phase synthesis that took a fraction of the time required for the solution-phase synthesis. Malaria kills over 2 million people per year, and is caused by protozoan parasites of the genus Plasmodium. Much of the morbidity and mortality associated with malaria is thought to be due to a toxin released in the host following red blood cell rupture. A glycosylphosphatidylinositol (GPI) anchor of parasite origin was recently identified, and had the properties of a toxin. The synthesis of a modified version of the malarial GPI both in solution and on solid-phase in an automated fashion is described. The synthetic material was attached to a carrier protein and used to immunize mice, who were substantially protected against all aspects of a subsequent challenge by malarial parasites. A new capping protocol for automated solid-phase synthesis is described. A novel fluorous silyl triflate was used to tag deletion sequences that could then be separated from the desired sequence by filtration through fluorous reverse-phase silica gel. Two trisaccharide sequences were synthesized both with and without fluorous capping to demonstrate the effectiveness of the capping protocol. / by Michael Charles Hewitt. / Ph.D.

Massachusetts Institute of Technology. Dept. of Chemistry. Thesis. 1965. Ph.D. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996. / Includes bibliographical references (leaves 86-97). / by Charles R. Wescott. / Ph.D.