Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, February 2008. / Vita. / Includes bibliographical references. / (Trialkylsilyl)vinylketenes ("TAS-vinylketenes") are versatile four-carbon building blocks in a variety of methods for the synthesis of carbocyclic and heterocyclic compounds. This thesis discusses the development of a new benzannulation strategy for the synthesis of phenols based on the reaction of TAS-vinylketenes with lithium ynolates. Studies have shown that the reaction proceeds by formation and electrocyclic ring closure of 3-oxidodienylketene intermediates, followed by an intramolecular 1,3-silyl migration to provide highly substituted 3-siloxy phenols. Further transformations of these products providing efficient access to ortho-benzoquinones and benzofuran, benzoxepine, and benzoxocine ring systems are described. Additionally, unsuccessful attempts to prepare TAS-vinylketenes by the rearrangement of siloxy alkynes and by cross-metathesis are discussed. / by Wesley F. Austin. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Includes bibliographical references. / by Anne Marie LaPointe. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Includes bibliographical references. / by Michael C. Amendola. / M.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Vita. / Includes bibliographical references. / Metal ion homeostasis is critical to the survival of all cells, because requirements for these essential nutrients must be balanced with their toxicity when present at elevated concentrations. Regulation of nickel concentrations in Escherichia coli is achieved via nickel-induced transcriptional repression of the nickel permease complex, NikABCDE, mediated by the NikR metalloregulatory transcription factor. To understand how this takes place at a molecular level, X-ray crystallography was used to determine three- dimensional structures of the NikR. Structures of apo-NikR and Ni⁺²-NikR show an interesting quaternary arrangement of the functional NikR tetramer, consisting of two dimeric Ribbon-Helix-Helix (RHH) DNA-binding domains separated by a tetrameric regulatory domain that binds metal ions (MBD). NikR is the only known metal- responsive member of the RHH family of transcription factors, and the structural relationships between NikR and other RHH proteins are detailed in this thesis. The high- affinity nickel-binding site of NikR is located at the tetramer interface of the MBD, with square-planar coordination by three histidines and a cysteine sidechain. A structure of NikR in complex with a 30 base-pair oligonucleotide containing the nik operator sequence illustrates the dramatic conformational changes associated with DNA binding, shows the nature of the specific and non-specific contacts between NikR and its operator, and reveals a second functionally relevant metal-binding site created at the interface of the RHH domain and MBD. Binding of nickel ions to the high-affinity site of NikR is proposed to increase affinity for the nik operator through a combination of mechanisms. / (cont.) Perhaps the most important of these is by ordering one face of the MBD of NikR, allowing productive interaction with the DNA phosphate backbone in the center of the operator. Additional metal ions further increase the affinity for operator by binding to the site situated at the RHH-MBD domain interface, and perhaps by binding to one of several sites on the surface of NikR identified by soaking crystals in excess Ni⁺². / by Eric R. Schreiter. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2009. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides supplying the dNTPs required for DNA replication and DNA repair. Class I RNRs require two subunits ([alpha] and [beta]) for activity. The [alpha] subunit binds the substrates and the allosteric effectors that govern specificity and turnover. The 32 subunit houses the diferric Y* cofactor required to initiate nucleotide reduction. Human cells possess two type of P subunits of RNR: one ([beta]) is involved in DNA replication and the second (p53[beta]') is required for mitochondrial DNA replication and likely plays some role in DNA repair. Gemcitabine (2',2'-difluoro-2'-deoxycytidine, F2C) is used clinically in a variety of cancer treatments and the phosphorylated F2C targets many enzymes involved in nucleotide metabolism, including RNR. The studies presented here with [1 '-3H]- and [5- 3H]-F 2CDP have established that F2CDP is a sub-stoichiometric mechanism based inhibitor (0.5 equivalents F2CDP/[alpha]) of both the E. coli and the human RNRs in the presence of a reductant. Inactivation is caused by covalent labeling of RNR by the sugar of F2CDP (0.5 equivalents/[alpha]) and is accompanied by the release of 0.5 equivalent cytosine/[alpha]. Studies using size exclusion chromatography reveal that in the E. coli RNR, an u212 tight complex is generated subsequent to enzyme inactivation by F2CDP, while in the human RNR, an [alpha]6[beta]6 or [alpha]6[beta]'6 tight complex is generated. The second part of this thesis focuses on the Sml inhibition mechanism in S. cerevisiae. Smll is a 12 kDa small protein RNR inhibitor. / (cont.) It regulates RNR activity by binding directly to a to repress RNR activity. The binding of Smll to a has been proposed to block the reduction of the active site disulfide formed concomitantly with dNTP production, leaving a in the oxidized form. A fluorescence titration method was employed to measure the Kd of Smll with different forms of c. Our data suggest that Smll binds to a by a mechanism that involves its C-terminal helix (likely the hydrophobic face) and a region of a that includes W688. The kinetics studies suggest that Smll behaves as an uncompetitive inhibitor relative to the substrate, and binds to the oxidized form of [alpha] in preference to the reduced form. / by Jun Wang. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 249-265). / Coherent control has been at the heart of the study of physical chemistry. Great advancement has been achieved in the past few decades in coherent control of classical systems by using spatially and temporally shaped electromagnetic waves. In this dissertation, we extend the concept of coherent control to a purely quantum mechanical collective system, namely, microcavity exciton-polariton Bose-Einstein condensates. Microcavity exciton-polaritons, hereafter simply polaritons, are bosonic quasiparticles formed in a resonant semiconductor microcavity by coupling the excitonic polarizabilities in quantum wells to the transverse mode of the confined optical field in the cavity. The light-matter dual nature allows direct control of polaritons through either their excitonic or photonic components. By utilizing the fact that polariton-exciton and polariton-polariton interactions are repulsive, all-optical control of polaritons was realized. By shaping the intensity fronts of the optical beam incident on a microcavity, the potential landscape felt by polaritons can be easily tailored. This is the key ingredient of this dissertation work. The light-matter dual nature endows polaritons a very small effective mass that is one hundred million times less than that of a hydrogen atom, leading to the observation of quantum phenomena such as condensation, superfluidity and quantized vortices at temperatures ranging from tens of Kelvin up to room temperatures. However, debates persist over whether the observed phenomena can be related to Bose- Einstein condensation because polaritons are not in thermal equilibrium. By applying all-optical trapping to a high-quality microcavity structure, polaritons at both spatial and thermal equilibrium were achieved across a broad range of densities and bath temperatures, as evidenced by the observed equilibrium Bose-Einstein distributions. A phase diagram for Bose-Einstein condensation of polaritons was produced for the first time, which agrees with the predictions of basic quantum gas theory. The thermalization behavior depends crucially on the interactions among polaritons. By changing the underlying excitonic/photonic fractions in polaritons, the interaction strength of polaritons can be varied, leading to control between nonequilibrium and equilibrium behavior of the polariton gas. The interactions also play a crucial role in polaritonic device operations. However, an accurate measurement of the polariton-polariton interaction strength has been not possible because of the difficulty in separating polaritons and excitons that are created by the same optical excitation. After propagating to the center of a sufficiently large optically induced annular trap, polaritons were separated from the incoherent populations of free carriers and hot excitons. The polariton interaction strength was then extracted from energies measured as a function of the polariton density. The measured interaction strength was about two orders of magnitude larger than previous theoretical estimates, putting polaritons squarely into the strongly interacting regime. Optical control can also be utilized to directly manipulate polariton condensates. By tailoring the size and pumping intensity of the optical trap, polariton condensates can be switched among different high-order modes and the homogeneous condensate mode. The redistribution of spatial densities is accompanied by a superlinear increase in the emission intensity as a function of excitation power, implying that polariton condensates in this geometry could be exploited as a multistate switch. The parameters for reproducible switching between the high-order states in the optical trap have been measured experimentally, giving us a phase diagram for the mode switching. It will serve well to calibrate the implementation of an exciton-polaritonic multistate switch. / by Yongbao Sun. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2002. / Includes bibliographical references. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Single molecule spectroscopy has progressed substantially in the past ten years and the accompanying progress in the optical study of single semiconductor nanocrystals has opened a new dimension in our understanding of the photophysical properties of these quantum-confined materials. In this thesis, I describe experimental advances that investigate and manipulate optical dynamics--blinking and spectral diffusion--in single CdSe and CdTe nanocrystals caused by complex interactions of electric fields and charge migration between a nanocrystal and its nearby environment. With the aid of a simple yet powerful fluorescence far-field microscope, we examine the blinking phenomenon using statistical analysis to determine a temperature-independent physical mechanism (charge tunneling) that is universal to every nanocrystal. Furthermore, we uncover a strong correlation between the blinking and spectral diffusion processes. This correlation proves to be critical in connecting the power-law statistics observed from blinking in isolated nanocrystals with the binary spectral shifts in surface plasmon coupled nanocrystals. Moreover, we identify charged nanocrystal emission signatures and create charged nanocrystals on command. This level of control, whether to turn the nanocrystals off or to eliminate the blinking behavior, also improves the prospects for nanocrystal device applications. Finally, we explore the impact of external magnetic fields on single nanocrystal optical properties and reveal behavior that is dependent on nanocrystal orientations relative to the applied field. In addition, we observe evidence of zero-field splitting in a subset of nanocrystals. This corroborates theoretical models that propose paramagnetic interactions as an explanation for the fundamental physics of CdSe nanocrystal emission. / by Kentaro Shimizu. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. / Includes bibliographical references. / W(NAr)(CH-t-Bu)(CH2-t-Bu)2 (Ar = 2,6-i-Pr2C6H3) was synthesized in four steps starting from WCI6. The reaction of W(NAr)(CH-t-Bu)(CH2-t-Bu)2 with various alcohols (1-AdamantylOH, t-BuOH, ArOH, (CF3)2CHOH, (CF3)2MeCOH, CF3Me2COH, (CF3)3COH, C6F5OH) in hydrocarbon solvents gave either W(NAr)(CH-t-Bu)(CH2-t-Bu)(OR) or W(NAr)(CH2-t-Bu)3(OR) depending on the pKa of the alcohol used. W(NAr)(CH2-t-Bu)3(OR) appears to be formed when the alcohol has a relatively low pKa. W(NAr)(CH2-t-Bu)3(OR) evolves neopentane gas to give W(NAr)(CH-t-Bu)(CH2-t-Bu)(OR). The reaction between W(NAr)(CH2-t-Bu)3CI and LiOR similarly afforded W(NAr)(CH-t-Bu)(CH2-t-Bu)(OR). W(NAr)(CH-t-Bu)(CH2-t-Bu)(OR) complexes were found to be active catalysts for various metathesis reactions, with the reactivity varied in the order of OAr - OC(CF3)3 > OCMe(CF3)2 > OCMe2CF3 > OCMe3. Conversion was sometimes limited by the tendency of tungsten to form stable metallacyclobutane in the presence of ethylene, and the bimolecular decomposition of intermediate alkylidenes to yield dimeric species that contain W(IV)/W(IV) double bonds. / (cont.) Chapter 2 Tungsten imido alkylidene complexes were found to undergo bimolecular reaction to give dimers that contain W(IV)/W(IV) double bonds and no bridging ligands. A modest number of W=W species of two general types were obtained and structurally characterized. One type is [W(NR)(CH2-t-Bu)(OR')]2 (NR = N-2,6-Me2C6H3, N-2,6-iPr2C6H3; OR' = OC6F5, OCH(CF3)2) which was found to exist in both heterochiral and homochiral isomeric forms. The other type is [W(NR)(OR')2]2 (NR = N-2,6-Me2C6H3 or N-2,6-iPr2C6H3; OR' = OCMe2CF3, OCMe(CF3)2) which has a virtual C2h symmetry. To the best of our knowledge, these dimers are the first examples of compounds that contain unbridged W(IV)/W(IV) double bonds despite the presence of ligands that would typically be expected to bridge such bonds. These compounds are characterized by W-W distance of 2.4-2.5 A, trans orientation of imido ligands, and -90° angle between the imido ligands and the W=W bond vector. A related unbridged molybdenum dimer, {Mo(NAd)[OCMe(CF3)2]2}2 (NAd = N-l-adamantyl) (Mo=Mo = 2.422 A). was also isolated and crystallographically characterized. Remarkably, a compound with the same stoichiometry was recovered from a sealed NMR tube reaction between Mo(NAd)(CHCMe2Ph)[OCMe(CF3)2]2 and bistrifluoromethylnorbornadiene, / (cont.) and was shown in an X-ray study to be the alternative imidobridged isomer in which a single Mo-Mo bond is present (2.609 A). Conversion of unbridged M=M species to their imido-bridged isomer is yet to be observed. Chapter 3 Reaction of [W(NAr')(OCMe2CF3)2]2 (Ar' = 2,6-Me2C6H3) with carbon tetrachloride gave [W(OCMe2CF3)2CI]2(QL-NAr')2, the structure of which was determined by X-ray diffraction studies. Reaction of [W(NAr')(OCMe2CF3)2]2 with iodine gave mixture of products, two of which were identified to be W(NAr)(OCMe2CF3)31 and W(OCMe2CF3)313. Reaction of [W(NAr')(OCMe2CF3)2]2 with PMe3 gave a stable mono-adduct. Reaction of [W(NAr')(OCMe2CF3)2]2 with CH3CN gave a mixture of two products, both with empirical formula "W(NAr')(OCMe2CF3)2(CH3CN)". The minor product was found by X-ray diffraction studies to be [(CF3)Me2CO]2W(g-NAr')(g-N(Me)C=C(Me)N=)W(NAr')(OCMe2CF3)2, resulting from reductive coupling of two acetonitrile ligands. Reaction of [W(NAr')(OCMe2CF3)2]2 with MeC-CMe gave a mono-adduct, the structure of which shows MeC-CMe bridging the two metal centers in approximately perpendicular manner. / (cont.) Reaction of [W(NAr')(OCMe2CF3)]2 with CO resulted in the formation of W(NAr')2(OCMe2CF3)2 along with other yet unidentified products of the reaction [W(NAr')(OCMe2CF3)2]2 was found to slowly catalyze the ring opening metathesis polymerization of norbomene. However, no alkylidene species was observed by 'H NMR, as only a relatively small amount (<2%) of the dimer species was believed to be "activated" by the olefin. Addition of ethylene to [W(NAr')(OCMeCF3)2]2 gave what is essentially a ditungstacyclobutane complex that contains a bridging alkoxide and a "semi-bridging" ethylene. Upon heating, the ethylene adduct was transformed into a new species that contains an ethyl group as a consequence of activation of an ortho methyl group in the NAr' ligand. Chapter 4 The reaction between H2[F3N2NMe] [F3N2NMe = (3,4,5-F3C6H2NCH2CH2)2NMe] and TaCl5 in the presence of triethylamine in dichloromethane yielded [F3N2NMe]TaCI3, which was used as a precursor compound for the synthesis of various organotantalum complexes. The trimethyl species [F3NNMe]TaMe3 was obtained from the reaction between [F3N2NMe]TaCI3 and methylmagnesium chloride. Treatment of [F3N2NMe]TaCI3 with trimethylsilylmethylmagnesium chloride afforded [F3NNMe]Ta(CHSiMe3)(CH2SiMe3). / (cont.) The monoalkyl complex, [F3N2NMe]Ta(CH2-t-Bu)CI2 was obtained from the reaction between [F3N2NMe]TaCI3 and t-BuCH2MgCl. Further alkylation of [F3N2NMe]TaCI3 with methylmagnesium chloride gave [F3N2NMe]Ta(CH-t-Bu)(CH3). By extending the reaction time in the synthesis of [F3N2NMe]Ta(CH2-t-Bu)C12, [F3N2NMe]Ta(CH-t-Bu)(CH,-t-Bu) could be isolated, albeit in low yield. The reaction between [F3N2NMe]TaCl3 and ethylmagnesium chloride gave the olefin complex, [F3N2NMe]Ta(r2-CH2CH2)(CH2CH3). The alkyl/alkylidene complexes [F3N2NMe]Ta(CHSiMe3)(CH2SiMe3), [F3N2NMe]Ta(CH-t-Bu)(CH3) and [F3N2NMe]Ta(CH-t-Bu)(CH2-t-Bu) have relatively upfield alkylidene H, resonances (0 - 6 ppm) and uniformly low IJCH values. [F3N2NMe]Ta(CHSiMe3)(CH2SiMe3) and [F3N2NMe]Ta(l 2-CH2CH2)(CH2CH3) were crystallographically characterized. The niobium complexes, [F3N2NMe]NbCI3 and [F3N2NMe]NbMe3, were similarly prepared. Tantalum complexes of the triamidoamine ligand [(3,5-CI2C6H3NCH2CH2)3N]3- were synthesized. [(3,5-CI2C6H3NCH2CH2)3N]TaCI2 was obtained from the reaction between H3[(3,5-CI2C6H3NCH2CH2)3N] and TaC15 in the presence of triethylamine. / (cont.) Treatment of [(3,5-Cl2C6H3NCH2CH2)3N]TaCI2 with methylmagnesium chloride gave [(3,5-Cl2C6H3NCH2CH2)3N]TaMe2, the structure of which was determined by X-ray diffraction studies. Ethylene and acetylene complexes, [(3,5-Cl2C6H3NCH2CH2)3N]Ta(tj2-CH2CH,) and [(3,5-CI2C6H3NCH2CH2)3N]Ta(q2-HCCH), were obtained when [(3,5-CI2C6H3NCH2CH2)3N]TaCI2 was reacted with ethylmagnesium chloride and vinyl magnesium chloride, respectively. / by Lourdes Pia H. Lopez. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. / Includes bibliographical references. / The dinitrogen reduction capability of a series of new triamidoamine based molybdenum compounds has been studied. The synthesis of a number of different triamidoamine ligands, and their resulting molybdenum compounds, is described. While symmetric variants containing electron-withdrawing hexaisopropyl terphenyl substituents can successfully catalyze dinitrogen reduction to ammonia, only the most bulky unsymmetric "hybrid" compounds can facilitate this reaction. Further study of these systems reveals a different pathway for catalyst failure than had previously been observed. It was discovered that, at least for the smaller ligands, a base-catalyzed hydrogenase reaction occurs at a rate much faster than that of ammonia formation. The Mo(IV) diazenido (LMoN2H) compound undergoes net H. loss, forming the Mo(III) dinitrogen (LMoN2) species with concomitant release of H2. Examination of the "parent" system has also revealed previously unknown intricacies of the dinitrogen reduction reaction. By developing a means to measure H2 formation, we are now able to fully quantify the reducing equivalents added to our system. / (cont.) This supports our belief that only NH3 and H2 are formed during catalysis. In addition, control experiments demonstrate that the proton source typically utilized for catalytic study, [2,6-lutidinium][BAr4'], can be reductively coupled under catalytic conditions. Therefore an acid that avoids this coupling reaction ([2,4,6-collidinium][BAr4']) is now utilized during most catalytic experiments. / by Walter Warren Weare. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1997. / Vita. / Includes bibliographical references (leaves 288-294). / by Shane William Krska. / Ph.D.