Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012. / "June 2012." Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / Membrane proteins mediate critical functions in biological systems and are important drug targets for a number of diseases. Determining the three-dimensional structure and function of membrane proteins under physologically relevant conditions is a long sought-after goal in structural biology. In pursuit of this objective we have applied Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR) to investigate the structure and function of the 32 kDa human integral membrane protein VDAC, the Voltage Dependent Anion Channel. Our results on VDAC have relied on a number of improvements in NMR methodology described in this thesis. These new methods include '3C-' 3C and 5N- 3C recoupling experiments optimized for measuring long-range homonuclear and heteronuclear restraints at high magnetic field strengths and spinning frequencies. We also describe precise 13C-33C distance measurements used to define a protein hydrophobic core. Novel methods for processing nonuniform sampling are presented as well as optimized sampling schedules for faster data acquisition. This new methodology is extended first from small peptides to a microcrystalline preparation of GB 1, a 56 residue globular protein. Methods are then extended to the much larger membrane protein VDAC. This thesis then presents structural and functional characterization of VDAC in lipid bilayer two-dimensional (2D) crystals. A strategy combining specific isotopic labeling with advanced 3D heteronuclear experiments enabled assignment of a large extent of the primary sequence. Extensive assignments of VDAC in lipid bilayers permitted comparison of VDAC's secondary structure between lipid bilayers and detergent micelles. MAS NMR experiments were paired with temperature dependent 2H NMR and DSC experiments to investigate protein-lipid interactions in the 2D crystals. Functional studies performed on the same samples used for NMR showed proper channel gating. To assess the function of VDAC we characterize its pH dependence as well as a phosphorylation mimetic. / by Matthew T. Eddy. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1989. / Includes bibliographical references (leaves 191-193). / Ph.D.

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Some images on CDROM are in colour. / Includes bibliographical references (leaves 33-34, first group). / A novel, three-coordinate gold(I) dimer, Au2(tfepm)3Cl2 (la, lb), was synthesized and structurally characterized. Four gold(I)-rhodium(I) heterobimetallic complexes, AuIRh'(tBuNC)2(-dppm)2C12 (2), Au'Rh'(tBuNC)2(u-dmpm)2Cl2 (3), Au'Rh'(tBuNC)2(,u-tfepm)2C12 (4), and AuIRh(tBuNC)2(u-tfepma)2Cl2 (5) were synthesized and 2, 3, and 5 were crystallographically characterized. Absorption spectra at room temperature, excitation spectra, emission spectra, and phosphorescence lifetimes of glass-solution and solid state samples at 77 K are reported for 2-5 and interpreted in context of crystallographic structure, electronic structure, and time-dependent density functional theory (TD-DFT) calculations. 2-5 are intensely luminescent at 77 K, with 4 and 5 exhibiting "dual emission." / by Jillian Lee Dempsey. / S.B.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004. / Includes bibliographical references. / In Part I the development of a new method for the construction of oxindoles and benzofuranones bearing quaternary stereocenters is discussed. A planar-chiral PPY derivative catalyzes the O-to-C acyl group migration (Black rearrangement) in a highly efficient and enantioselective manner. The utility of this method is further demonstrated by the formal total synthesis of the natural product aplysin. In Part II reactivity of bisphosphine palladium-complexes is discussed. It is shown that the oxidative addition of bisphosphine palladium-complexes bearing P(t-Bu₂)Me occurs through an SN2-type mechanism. This discovery allows us rationalize the difference in catalytic activity between Pd(P(t-Bu₂)Me)₂ and Pd(P(t-Bu₂)Et)₂ for the cross-coupling of alkyl electrophiles. The reductive elimination of H-X from bisphosphine palladium-hydride complexes is also discussed. The discovery that (P(t-Bu)₃)₂PdHCl undergoes facile reductive elimination in the presence of Cy₂NMe, while (PCy₃)₂PdHCl does not, is explained using X-ray crystal structures. These reactivity patterns may help to explain why Pd(P(t-Bu)₃)₂ is a much better catalyst than Pd(PCy₃)₂ for the Heck coupling of aryl chlorides. Finally, Part III describes preliminary work on a palladium-hydride catalyzed isomerization of allylic alcohols as well as initial attempts to study the mechanism of nickel-catalyzed cross-couplings of secondary alkyl-electrophiles. / by Ivory Derrick Hills. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2003. / Vita. / Includes bibliographical references (leaf 29). / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Photochemical and time-resolved spectroscopic studies of di- and mono-rhodium inorganic complexes were undertaken to elucidate the mechanism of photocatalytic hydrogen generation from hydrohalic acid solutions ... / by David James Krodel. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2003. / Vita. / Includes bibliographical references. / It is now accepted that the structural transition from PrPc to PrPSc is the major event leading to transmissible spongiform encephalopathies. Although the mechanism of this transition remains elusive, glycosylation has been proposed to impede the PrPc to PrPSc conversion. Structural studies on glycoprotein fragments in the Imperiali group has previously shown that N-linked glycosylation can play a major role modulating polypeptide conformation. It has also been shown that glycosylation can alter the thermodynamics of disulfide bond formation, favoring oxidation. To address the role of glycosylation on PrP, we have prepared glycosylated and unglycosylated peptides derived from the 175-195 fragment of the human prion protein. The synthesis of a Fmoc-Asn[chitobiose(TBDMS)5-OH amino acid precursor allowed the preparation of the glycopeptide in high yields. Comparison of the structure, aggregation kinetics, fibril formation capabilities and redox susceptibility of Cys 179 has shown that the N-linked glycan (at Asn 181) significantly reduces the rate of fibrillization by promoting intermolecular disulfide formation via Cys 179. Furthermore, the aggressive fibrillization of a C179S mutant of this fragment highlights the significant role of disulfide stability in retarding the rate of fibril formation. Additionally, a novel method for the temporal control of fibrillization of this peptide was developed using a synthetic photolabile linker and a "fibril inhibitory unit" positioned at the N-terminus of the peptide. This stabilized the fragment as a soluble monomeric species until photoactivation, which triggered the peptide self-assembly. / by Carlos J. Bosques. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Vita. / Includes bibliographical references. / by Lawrence Francis Rozsnyai. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1998. / Includes bibliographical references. / by James D. Harper. / Ph.D.

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1913. / MIT copy bound with: The reaction between ferric salts and thiocyanates in aqueous solution / Leon W. Parsons, Arthur E. Bellis. / Includes bibliographical references. / by Gerould T. Lane. / B.S.

Thesis: Ph. D. in Physical Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 151-164). / Low-dimensional nanostructured semiconductors are promising technologies for next generation optoelectronics. Colloidal quantum dots (QDs) have been applied in many light emitting applications such as ambient lighting downconverters, LEDs, and displays. Proof-of-concept transistors, phototransistors and LEDs have been demonstrated using two dimensional atomically thin transition metal dichalcogenides (TMDs). To realize efficient next generation optoelectronics using these materials it is crucial to understand the dynamics and transport of energy and charge in these materials and hybrid structures built from them. The first Chapter of this thesis briefly motivates the technological importance of QDs and TMDs. The remainder explores exciton dynamics and transport in these low-dimensional semiconductor systems. In Chapter 2, low temperature spectroscopy and time-resolved photoluminescence spectroscopy are used to probe the complex energy landscape seen by excitons in acid-treated MoS₂. We show that deeply trapped "dark" exciton states are responsible for the surprisingly long lifetime of band-edge photoluminescence in acid-treated single-layer MoS₂ . Temperature-dependent transient photoluminescence spectroscopy reveals an exponential tail of long-lived states extending hundreds of meV into the band gap. These subband states, which are characterized by a 4 [mu]s radiative lifetime, quickly capture and store photogenerated excitons before subsequent thermalization up to the band edge where fast radiative recombination occurs. By intentionally saturating these trap states, we are able to measure the "true" 150 ps radiative lifetime of the band-edge exciton at 77 K, which extrapolates to ~600 ps at room temperature. These experiments reveal the dominant role of dark exciton states in acid-treated MoS₂ , and suggest that excitons spend > 95% of their lifetime at room temperature in trap states below the band edge. We hypothesize that these states are associated with native structural defects, which are not introduced by the superacid treatment; rather, the superacid treatment dramatically reduces nonradiative recombination through these states, extending the exciton lifetime and increasing the likelihood of eventual radiative recombination. In the second half of Chapter 2, we study exciton diffusive transport in MoS₂ using time-resolved diffusion imaging. We also probe exciton-exciton dynamics and elucidate the role that exciton traps play in both exciton transport and dynamics. Atomically thin semiconductors such as monolayer MoS₂ and WS₂ exhibit nonlinear exciton-exciton annihilation at notably low excitation densities (below ~10 excitons/pm 2 in MoS₂ ). We show that the density threshold at which annihilation occurs can be tuned by two orders of magnitude by varying the refractive index of the underlying supporting substrate. Using spatially-resolved transient photoluminescence spectroscopy in conjunction with numerical simulations, we find that this behavior arises from screening interactions between trapped and mobile exciton pairs. We measure the effective exciton diffusion coefficient in superacid-treated MoS₂ to be D = 0.06 ± 0.01 cm²/s, corresponding to a diffusion length of LD = 350 nm for an exciton lifetime of [tau] = 20 ns. Exciton-exciton annihilation limits the overall efficiency of 2D semiconductor devices operating at high exciton densities. The ability to tune these interactions via the dielectric environment is an important step toward more efficient optoelectronic technologies featuring atomically thin materials. In Chapter 3 we investigate coupled QD/TMD hybrid structures. In the first half of Chapter 3, we investigate dipole-dipole coupling in the regime that the QD and TMD exhibit weak electronic coupling by engineering the interface to be insulating. We report highly efficient F6rster resonant energy transfer from cadmium selenide (CdSe) quantum dots to monolayer and few-layer molybdenum disulfide (MoS₂). The quenching of the donor quantum dot photoluminescence increases as the MoS 2 flake thickness decreases with the highest efficiency (> 95%) observed for monolayer MoS₂. This counterintuitive result (that deviates from the predictions of F6rster theory) arises from reduced dielectric screening in thin layer semiconductors having unusually large permittivity and a strong in-plane transition dipole moment, as found in MoS₂ In the second half of Chapter 3, we investigate QD/TMD hybrid structures in the strongly coupled regime. We demonstrate tunable electronic coupling between CdSe QDs and monolayer WS₂ using variable length alkanethiol ligands on the QD surface. Using femtosecond time-resolved second harmonic generation (SHG) microscopy, we show that electron transfer from photoexcited CdSe QDs to single-layer WS 2 occurs on ultrafast (10 fs - 1 ps) timescales. Moreover, charge transfer excites coherent acoustic phonons in the donor QDs, which modulate the SHG response of the underlying WS₂ layer on picosecond timescales. These results reveal surprisingly strong electronic coupling at the QD/TMD interface and demonstrate the usefulness of time-resolved SHG for exploring ultrafast electronic-vibrational dynamics in TMD heterostructures. In Chapter 4, we improve the sensitivity of traditional SHG spectroscopy by adding an additional field. We demonstrate the dramatic enhancement of weak second-order nonlinear optical signals via stimulated sum and difference frequency generation. We present a conceptual framework to quantitatively describe the interaction and show that the process is highly sensitive to the relative optical phase of the stimulating field. To emphasize the utility of the technique, we demonstrate stimulated enhancement of second harmonic generation (SHG) from bovine collagen-I fibrils. Using a stimulating pulse fluence of only 3 nJ=cm² , we obtain an SHG enhancement > 10⁴ relative to the spontaneous signal. We discuss the conceptual differences between optical heterodyning of SHG signals and our presented "stimulation" framework. In the second half of Chapter 4, we use the additional field to resolve the SHG signal phase revealing the sign and magnitude of the sample nonlinear susceptibility. We perform phase-resolved SHG imaging of polycrystalline MoS₂ flakes and determine the absolute grain orientations using the phase information. / by Aaron J. Goodman. / Ph. D. in Physical Chemistry