Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / This thesis describes the development and application of chemical methodologies for the use of 2-pyridyl and other aryl and heteroaryl organometallic nucleophiles. Aiming for a practical and effective alternative to 2-pyridylboron reagents, a solid 2-pyridylzinc compound was prepared and is described in Chapter 1. Chapter 2 details a new approach to the synthesis of sulfonamides using aryl and heteroaryl organozine nucleophiles. Chapter 3 describes ongoing collaborative efforts to discover new malaria therapeutics where the synthetic method developed in Chapter 2 facilitated access to targeted compounds. Chapter 1. The Synthesis of a Solid, Air-Stable 2-Pyridylzine Reagent and its Use in Negishi Cross-Coupling Reactions. As an alternative to unstable or unreliable 2-pyridylboron reagents, a solid, air-stable 2- pyridylzinc reagent was developed. Using 1,4-dioxane as an additive enabled a 2-pyridylzinc concentrate as a free-flowing solid that was not deliquescent. The reagent can be manipulated in air and is a competent nucleophile in Negishi cross-coupling reactions. The reagent can also be stored in paraffin wax capsules for significant added stability. Chapter 2. Synthesis of Heteroaryl Sulfonamides from Organozinc Reagents and 2,4,6- Trichlorophenyl Chlorosulfate. A method for the preparation of aryl and heteroaryl sulfonamides using 2,4,6-trichlorophenyl chlorosulfate (TCPC) is described. The reaction of 2-pyridylzinc reagents with TCPC resulted in 2,4,6-trichlorophenyl (TCP) pyridine-2-sulfonates, and the parent pyridine-2-sulfonate was shown to react with amines. Less electron-rich aryl- and heteroarylzinc reagents reacted with TCPC to afford sulfonyl chlorides that were converted in situ to sulfonamides. Chapter 3. Structure-Activity Relationship Studies on Selective Inhibitors of Plasmodium Falciparum Growth. Two classes of compounds that selectively inhibit P. Falciparum were identified by the Lindquist Lab at MIT through the MLPCN compound library and high-throughput screening facilities at the Broad Institute. Using the sulfonamide synthesis methodology described in Chapter 2 and other approaches, analogs of these compounds were prepared and tested using a yeast assay in collaboration with the Lindquist lab at MIT and a P. falciparum assay in collaboration with the Wirth lab at the Harvard T.H. Chan School of Public Health. / by James Robert Colombe. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2007. / Vita. / Includes bibliographical references. / Iminoacetonitriles participate as reactive dienophiles in intermolecular and intramolecular Diels-Alder cycloadditions leading to quinolizidines, indolizidines, and piperidines. The resultant a-amino nitrile cycloadducts are versatile synthetic intermediates which can be further elaborated by stereoselective alkylation, reduction, reductive cyclization, and Bruylants reactions. The first part of this thesis describes the full details of our studies on the synthesis of iminoacetonitriles, the scope of their Diels-Alder reactions, and the synthetic elaboration of the a-amino nitrile cycloadducts to provide access to a variety of substituted quinolizidine and indolizidine derivatives. The second part of this thesis reports on the total synthesis of quinolizidine (-)-217A and our efforts directed toward the total synthesis of indolizidine (-)-235B'. / by Kevin M. Maloney. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1997. / Includes bibliographical references. / by Edcon Chang. / Ph.D.

Thesis: Ph. D. in Biological Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Ribonucleotide reductases (RNRs) catalyze nucleotide reduction via complex radical chemistry, providing deoxynucleotides for DNA synthesis in all domains of life. The focus of this thesis is the class III RNR, found in anaerobic bacteria and archaea, which uses an O₂-sensitive glycyl radical cofactor (G*). The class III RNRs studied to date couple nucleotide reduction to the oxidation of formate to CO₂. We started by studying the Escherichia coli class III RNR (NrdD1), and found that reaction with CTP (substrate) and ATP (effector) in the absence of formate leads to loss of G* concomitant with stoichiometric formation of a new radical species and a "trapped" cytidine derivative, proposed to be 3'-keto-deoxycytidine. Addition of formate results in the recovery of G* and reduction of the cytidine derivative to dCTP. The new radical was identified by 9.5 and 140 GHz EPR spectroscopy to be a cysteine-methionine thiosulfuranyl radical [RSSR2]*. Analogies with the disulfide anion radical proposed in the class I and II RNRs provide further evidence for the involvement of thiyl radicals in the reductive half reaction of all RNRs. A subsequent bioinformatics investigation led to the identification of a second subtype of class III RNR (NrdD2) with distinct active-site residues suggesting that, like the class I and 1I RNRs, reducing equivalents for nucleotide reduction are provided by a redoxin, which are ubiquitous proteins found in all organisms, instead of formate, a metabolite produced by some but not all organisms. The Neisseria bacilliformis NrdD2 was cloned and expressed, and found to catalyze nucleotide reduction using the thioredoxin / thioredoxin reductase / NADPH system. An activesite model based on a crystal structure of the homologous Thermotoga maritima enzyme showed conserved residues appropriately positioned to carry out chemistry. Phylogenetic studies suggest that NrdD2 is present in bacteria and archaea that carry out diverse types of anaerobic metabolism. The bioinformatics study also uncovered a third subtype of class III RNR (NrdD3) present in certain methanogenic archaea. The presence of a redoxin (NrdH) in the operon suggested redoxin-dependent chemistry like NrdD2. However, its distribution among the different types of methanogens suggested that reducing equivalents might come from reduced ferredoxin (Fdx) generated in methanogenesis, rather than from NADPH. The Methanosarcina barkeri class III RNR was cloned and expressed, and found to catalyze nucleotide reduction using a system involving Fdx, NrdH and a [4Fe4S] protein ferredoxin:thioredoxin reductase. The diversity of reducing equivalents used for anaerobic ribonucleotide reduction reflects the diversity of electron carriers used in anaerobic energy metabolism. / by Yifeng Wei. / Ph. D. in Biological Chemistry

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Vita. / Includes bibliographical references (p. 129-145). / Trace species play a major role in many physical and chemical processes in the atmosphere. Improving our understanding of the impact of each species requires a combination of laboratory exper- imentation, field measurements, and modeling. The results presented here focus on spectroscopic and kinetic laboratory measurements and photochemical box modeling. Laboratory experiments were conducted using IntraCavity Laser Absorption Spectroscopy (ICLAS), a high-resolution, high sensitivity spectroscopic method that had been used primarily for static cell measurements in the Steinfeld Laboratory at MIT. Several modifications and improvements have been made to expand its versatility. Firstly, a discharge flow tube was coupled with the ICLA Spectrometer, and the formation kinetics of nitrosyl hydride, HNO, were measured as a means to test the system. Secondly, a novel edge-tuner was introduced as a means to expand the spectral range of the ICLA Spectrometer. An experiment for the detection of the hydroperoxyl radical employing the edge-tuner in the ICLA Spectrometer is discussed and proposed. The results from the laboratory measurements are followed by the presentation of a near-explicit kinetic box model designed to improve our understanding of the oxidative capacity of the urban troposphere in the Mexico City Metropolitan Area (MCMA). The box model was constructed using the Master Chemical Mechanism and was constrained using a large dataset of field measurements collected during the 2003 MCMA field campaign. / (cont.) The modeling is focused on the hydroxy and hydroperoxyl radicals (OH and HO₂), with an emphasis on the role of volatile organic compounds (VOCs) in the formation of both species. / by Philip M. Sheehy. / Ph.D.

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. Leaf 68 blank. / Includes bibliographical references. / Chapter 1. Microwave-assisted, palladium-catalyzed C-N bond-forming reactions with aryl/heteroaryl nonaflates/halides and amines using the soluble amine bases DBU (1,8-diazabicyclo[5.4.0]undec-7-ene) or MTBD (7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene) and a catalyst system consisting of Pd2dba3 and ligands (XantPhos, 2-dicylcohexylphosphino-2',4',6'-triisopropyl-1,1 '-biphenyl (XPhos) and 2-di-tert-butylphosphino-2',4',6'-triisopropyl-1, '-biphenyl) resulted in good to excellent yields of arylamines in short reaction times. Chapter 2. Using a catalyst comprised of the bulky, electron-rich monophosphine ligand di-tert-Butyl XPhos (2-di-tert-butylphosphino-2',4',6'-triisopropyl-1,1'-biphenyl) and Pd2dba3 with sodium tert-butoxide as the base, amino heterocycles were coupled successfully with aryl/heteroaryl halides in moderate to excellent yields. / by Rachel E. Tundel. / S.B.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, February 2008. / Vita. / Includes bibliographical references. / Inside the cell, ribonucleotide reductases (RNRs) are responsible for the conversion of nucleotides to 2'-deoxynucleotides, an essential step in DNA biosynthesis and repair. The E. coli RNR is the best studied RNR to date and consists of two protein subunits, a2 and P2. a2 is the site of nucleotide reduction and 02 contains a diiron tyrosyl radical (Y122*) cofactor. Each turnover requires radical propagation from the Y122* in 32 to the active site of a2 over 35 A. The mechanism of this unprecedented, long-range radical propagation step is poorly understood. Based on structural studies, a pathway of aromatic residues has been proposed to participate in this process. Site-directed mutants of these residues have been uninformative. In an effort to understand radical propagation, we have employed expressed protein ligation and suppressor tRNA/aminoacyl-tRNA synthetase (RS) methodologies to site-specifically insert unnatural tyrosine analogues into 12 and a2, at residues believed to be involved. On the basis of results with the radical traps 3,4-dihydroxyphenylalanine (DOPA) and 3-aminotyrosine (NH2Y), which we have incorporated into 32 and a2, respectively, and a series of fluorotyrosines (FnYs, n=2, 3, 4), which we have established as probes for proton-coupled electron transfer reactions and incorporated into 12, we propose a mechanism for radical transfer in RNR. We show that binding of substrate and effector are essential for control and gating of radical propagation. We further demonstrate that three Ys, 12-Y356, a2-Y731 and a2-Y730, are redox-active and participate in hole propagation. The NH2Y. observed with NH2Y-a2s likely constitutes the first observation of a transiently oxidized intermediate during active radical propagation. In 12, Y356 participates in radical transfer by an orthogonal proton-coupled electron transfer mechanism, where long-range electron transfer is coupled to short-range, off-pathway proton transfer. / (cont) Within a2, Y731 and Y730o participate by a hydrogen atom transfer mechanism where the proton and electron originate from and arrive at the same moiety. We also establish the positions of these three Ys in the a2/32 complex and present direct evidence for the reversible nature of radical propagation. / by Mohammad R. Seyedsayamdost. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Vita. / Includes bibliographical references (leaves 68-69). / Precatalyst species present in a solution of Pd₂(dba)₃ and Xantphos were identified as Pd(Xantphos)(dba) and Pd(Xantphos)₂ by use of ³¹p NMR and independent syntheses. Pd(Xantphos)₂ was found to form at high ligand concentrations. To determine whether the formation of this species affected reaction rates, reaction calorimetry was used to explore the rate of the palladium-catalyzed coupling of 4-t-butylbromobenzene and morpholine using the ligand Xantphos at varying palladium to ligand ratios. It was found that catalyst activity is dramatically dependent on the concentration of ligand relative to palladium, due to formation of Pd(Xantphos)₂. Two plausible hypotheses for the low activity of Pd(Xantphos)₂ as a precatalyst are (1) a slow rate of dissociation of a ligand from the bis-ligated species, and (2) the high degree of insolubility of Pd(Xantphos)₂. Magnetization transfer experiments were used to probe the rate of dissociation of ligand for the bis-ligated species, and reaction calorimetry experiments were performed using the more soluble t-butylXantphos in comparison to Xantphos to determine whether the insolubility of' Pd(Xantphos)₂ causes it to have relatively low activity. It was found that solubility is not the main cause for the low activity of Pd(Xantphos)₂, and evidence was given to support the hypothesis that low activity results from the slow dissociation of a ligand from the bis-ligated species. / by Liane M. Klingensmith. / S.M.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The immune system distinguishes self from non-self to combat pathogenic incursions. Evasion tactics deployed by viruses, microbes, or malignant cells may impede an adequate response. In such cases, therapeutic interventions aid in the elimination of pathogens and the restoration of physiological homeostasis. A major road block in the development of such therapies is the reliance on imperfect detection methods to identify site(s) of infection, or to monitor immune cell recruitment to sites of infection or inflammation in vivo. The goal of this thesis is overcome at least some of these limitations by utilizing novel tools that have been developed and refined in the laboratory to facilitate in vitro and in vivo characterization of specific immune subsets. We then track their recruitment to sites of active immune responses, such as infection or tumor progression sites. These tools consist of two components: one that confers specificity for immune cells and the other offers a site for labeling in a controlled manner. Single-domain antibodies (VHHs) from camelids are amongst the smallest (15 KDa) proteins that can recognize a diverse set of targets with excellent specificity. Chemoenzymatic labeling of molecules using sortase allows site-specific attachment of a single label of interest to the target protein containing the sortase recognition sequence LPXTG. VHHs specific for immune cell determinants labeled with sortase technology facilitate non-invasive and efficient monitoring of cells that infiltrate immunological niches in vivo in a manner not possible until now. This thesis presents the development of novel methods to allow in vitro and in vivo detection and imaging of specific immune subsets and their recruitment to sites of an active immune response. This thesis aims to (1) use DNA oligomers as a scaffold to push the limits of fluorescence labelling yield (2) create small and efficient biosensors for the rapid capture of specific lymphocyte subsets from peripheral blood samples using VHHs and graphene oxide nanosheets (3) develop radioisotope-labeled VHHs to track immune cell subsets to elucidate the roles of innate and adaptive immune components in the course of infection. Chapter 1 describes a new method for protein labeling via site-specific modification of proteins using a DNA scaffold. To avoid self-quenching of multiple fluorophores localized in close proximity, Holliday junctions were used to label proteins site-specifically with fluorophores. Holliday junctions enable the introduction of multiple fluorophores with reasonably precise spacing to improve fluorescence yield for both single domain and full-sized antibodies, without deleterious effects on antigen binding. Chapter 2 presents a biosensor generated for characterization of leukocytes from whole blood using a graphene oxide surface coated with single domain antibody fragments. This format allows quick and efficient capture of distinct white blood cell subpopulations from small samples of whole blood in a format that does not require any specialized equipment such as cell sorters or microfluidic devices. Chapter 3 documents a non-invasive immune-PET imaging method for tracing CD8+ T cells in the course of influenza A infection to better elucidate their protective mechanism(s) and immunopathological effects. / by Zeyang Li. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / Chapter 2 investigates the mechanism of the temperature-controlled polymerization of 3- methyl-3-phenylcyclopropene (MPCP) by Mo(NAr)(CHCMe 2Ph)(Pyr)(OTPP) (Ar = 2,6- diisopropylphenyl, Pyr = pyrrolide, OTPP = 2,3,5,6-tetraphenylphenoxide). Cissyndiotactic poly(MPCP) is obtained at -78 °C, while atactic poly(MPCP) is obtained at ambient temperature. The syn initiator (syn refers to the isomer in which the substituent on the alkylidene points towards the imido ligand and anti where the substituent points away) reacts with MPCP to form an anti first-insertion product at low temperatures, which continues to propagate to give cis,syndiotactic polymer. At higher temperatures, the anti alkylidenes that form initially upon reaction with MPCP rotate thermally to syn alkylidenes on a similar timescale as polymer propagation, giving rise to an irregular polymer structure. In this system cis,syndiotactic polymer is obtained through propagation of anti alkylidene species. Chapters 3 - 5 detail the synthesis and reactivity of compounds containing a 2,6- dimesitylphenylimido (NAr*) ligand in order to provide a better understanding of the role of steric hindrance in olefin metathesis catalysts. A new synthetic route to imido alkylidene complexes of Mo and W, which proceeds through mixed-imido compounds containing both NAr* and NtBu ligands, was developed to incorporate the NAr* ligand. Alkylidene formation is accomplished by the addition of 3 equivalents of pyridine*HCl to Mo(NAr*)(NBu)(CH 2CMe2Ph)2 or the addition of 1 equivalent of pyridine followed by 3 equivalents of HCl solution to W(NAr*)(N'Bu)(CH 2CMe2Ph)2 to provide M(NAr*)(CHCMe 2Ph)Cl 2(py) (py = pyridine). Monoalkoxide monochloride, bispyrrolide, and monoalkoxide monopyrrolide (MAP) compounds are isolated upon substitution of the chloride ligands. Reaction of W MAP complexes (W(NAr*)(CHCMe 2Ph)(Me2Pyr)(OR)) with ethylene allows for the isolation of unsubstituted metallacycle complexes W(N Ar*)(C 3H6)(Me 2Pyr)(OR) (R = CMe(CF 3)2, 2,6-Me2C6H3, and SiPh 3). By application of vacuum to solutions of unsubstituted metallacyclebutane species, methylidene complexes W(NAr*)(CH 2)(Me2Pyr)(OR) (R = tBu, 2,6-Me2C6H3, and SiPh 3) are isolated. Addition of one equivalent of 2,3- dicarbomethoxynorbornadiene to methylidene species allows for the observation of firstinsertion products by NMR spectroscopy. Investigations of NAr* MAP compounds as catalysts for olefin metathesis reactions show that they are active catalysts, but not E or Z selective for ring-opening metathesis polymerization the homocoupling of 1-octene or 1,3-dienes. Methylidene species W(NAr*)(CH 2)(Me2Pyr)(OR) (R = 2,6-Me 2C6H3 or SiPh3) catalyze the ring-opening metathesis or substituted norbornenes and norbornadienes with ethylene. / by Laura Claire Heidkamp Gerber. / Ph.D.