Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1989. / Vita. / Includes bibliographical references. / by Cheryl Ann Martin. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1962. / Vita. / Includes bibliographical references. / by Gary H. Rasmusson. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. / Includes bibliographical references. / This dissertation describes studies of the feasibility and scope of intramolecular [4+2] cycloadditions of hetarenynes and alkynes as a method for the synthesis of polycyclic benzo[b]-fused five-membered heteroaromatic compounds. Only scattered reports of this transformation existed prior to our work and these were very limited in their scope. The research presented in this thesis demonstrates that the synthesis of benzo[b]-fused five-membered heteroaromatic compounds can be effectively carried out under relatively mild thermal conditions utilizing alkynylpyrroles, -thiophenes, or -furans tethered to alkynes. The hetarenyne cycloaddition substrates are readily prepared in 2-3 steps from commercially available or known 2- or 3-halohetarenes via Sonogashira coupling followed in most cases by a Mitsunobu reaction. In the majority of cases metalation of a terminal alkyne with a Grignard reagent and then reaction with various electrophilic reagents allows for the creation of a library of cycloaddition substrates. The scope of the hetarenyne cycloaddition was explored with respect to four major variables in the cycloaddition substrates: / (cont.) (1) the nature of activating groups attached to the alkynyl 2c component; (2) the composition of the tether connecting the 2n and 4 components; (3) the type of hetarene (i.e., pyrrole, thiophene, or furan); and (4) the position of attachment of the tether to the hetarene. The experimental findings can be summarized as follows: (1) electron-withdrawing and electronegative groups attached to the 2 component accelerate the cycloaddition; (2) electronegative heteroatoms within the tether accelerate the cycloaddition; (3) the order of reactivity of hetarenynes is: alkynyl-(N-Boc)pyrrole - alkynylfuran > alkynylthiophene; and (4) attachment of the tether bearing the 2c component at C-2 of the hetarene leads to a more facile reaction than attachment at C-3. Finally, the cycloaddition of substrates having Lewis basic substituents attached to the 27c component can be effectively promoted by the use of Lewis acids under very mild conditions, leading in most cases to an improved yield. / by Javier Enrique Horta. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1943. / Vita. / Includes bibliographical references (leaf 46). / by Stanley Marple, Jr. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Vita. Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references. / A series of monopyrroletriamine ligands [Arpyr(Ar')2]H3 of the form ArC4H2NHCH2N(CH2CH2NHAr')2 (Ar = 2,4,6-mesityl (Mes), 2,4,6-triisopropylphenyl (TRIP); Ar' = C6F5, 2-tolyl (o-tol), naphthyl, 3,5-(2,4,6-triisopropylphenyl)phenyl (HIPT), 3,5- dimethylphenyl, 3,5-di-tert-butylphenyl were synthesized. [Mespyr(C6F5)2]MoCl, ([Mespyr(C6F5)2]Mo = MesitylC4H2NCH2N(CH2CH2NC6F5)2) was prepared by reaction of [Mespyr(C6F5)2]H3 with MoCl4(THF)2 and base and [Mespyr(3,5-t-Bu)2]MoCl and [Mespyr(3,5- Me)2]MoCl (3,5-t-Bu=3,5-di-tert-butylphenyl, Me = 3,5-dimethylphenyl) were synthesized likewise. All three monochlorides are paramagnetic. [Mespyr(C6F5)2]MoNMe2, [[Mespyr(otol) 2]MoNMe2, [Mespyr(3,5-t-Bu)2]MoNMe2, [Mespyr(3,5-Me)2]MoNMe2 were synthesized by reaction of the ligands with Mo(NMe2)4. The resulting compounds are diamagnetic and range in color from teal blue to emerald green. These low spin monodimethylamide complexes exist in rapid equilibria with their high spin forms. [Mespyr(C6F5)2]MoN and [Mespyr(3,5-t-Bu)2]MoN were synthesized by reaction of their respective monochlorides with NaN3 and are yellow diamagnetic species. Reaction of [Mespyr(3,5-t-Bu)2]MoN with Et3OBF4 leads to {[Mespyr(3,5- t-Bu)2]MoNEt}BF4, also a diamagnetic yellow species. [Mespyr(C6F5)2]MoOTf is synthesized by the reaction of [Mespyr(C6F5)2]MoCl with AgOTf. Reduction of [Mespyr(3,5-t-Bu)2]MoCl with Na under N2 led to [Mespyr(3,5-t-Bu)2]MoNNNa(THF)x, several species with varying numbers of THF coordination, x. A single species can be obtained when [Mespyr(3,5-t- Bu)2]MoNNNa(THF)x is reacted with either NBu4Cl or 15-crown-5 ether to yield purple green 4 {[Mespyr(3,5-t-Bu)2]MoNN}NBu4 or [Mespyr(3,5-t-Bu)2]MoNNNa(15-c-5). All the diazenide species are diamagnetic. Oxidation of the diazenide with AgOTf yields [Mespyr(3,5-t- Bu)2]Mo(N2). [Mespyr(3,5-t-Bu)2]Mo(CO) is synthesized by exposure of [Mespyr(3,5-t- Bu)2]Mo(N2) to CO. Reaction of [Mespyr(3,5-t-Bu)2]MoCl with NaBPh4 and NH3 yields {[Mespyr(3,5-t-Bu)2]Mo(NH3)}BPh4. Catalytic runs employing [Mespyr(3,5-t-Bu)2]MoN as the catalyst yielded one equivalent of NH3. A triamidoamine ligand [(HIPTNCH2CH2CH2)3N]3- was synthesized and metalated with MoCl4(THF)2 to produce [(HIPTNCH2CH2CH2)3N]MoCl ([HIPTtrpn]MoCl). Reduction of [HIPTtrpn]MoCl by KC8 under an atmosphere of dinitrogen leads to the green species [HIPTtrpn]MoNNK which can be oxidized by ZnCl2(dioxane) to produce [HIPTtrpn]Mo(N2). Other complexes synthesized include {[HIPTtrpn]Mo(NH3)}+ salts and [HIPTtrpn]Mo(CO). Xray studies were carried out on [HIPTtrpn]MoN and {[HIPTtrpn]Mo(NH3)}BAr'4. This system is not catalytic for the reduction of dinitrogen to ammonia and studies were carried out to elucidate the reasons. Oxidation studies were carried out on [HIPTN3N]Mo(N2) and [HIPTN3N]W(N2) ([HIPTN3N] = [(HIPTNCH2CH2)3N]3-). The rate of conversion of [HIPTN3N]Mo(NH3) to [HIPTN3N]Mo(N2) was studied and found to be increased in the presence of BPh3. [HIPTN3N]Mo(N2) conversion to [HIPTN3N]Mo(CO) was found to be dependent on CO pressure. Protonation studies of [HIPTN3N]Mo(N2) were also carried out. Studies of [HIPTN3N]MoNNH decomposition showed that decomposition is not base-catalyzed. [HIPTN3N]W(CO) was synthesized by exposure of [HIPTN3N]W(N2) to CO. It is a green, paramagnetic compound and its use as a standard (for determining relative concentrations of other compounds in the IR sample) in IR spectroscopic studies appears to be promising. [HIPTN3N]MoCNH2 was synthesized by addition of acid and reducing agent to [HIPTN3N]MoCN and is a yellow, diamagnetic compound. Two triamidophosphine ligands, triHIPTamine and tri-n-Buamine were synthesized. Metalation of Zr(NMe2)4 with these ligands leads to formation of pn3HIPTZrNMe2 and pn3-n- BuZrNMe2, both diamagnetic, pale yellow complexes. / by Jia Min Chin. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004. / Vita. / Includes bibliographical references. / Highly convergent annulation strategies have been developed for the synthesis of azulenes and polycyclic nitrogen heterocycles. Specifically, substituted azulenes have been synthesized via a ring expansion-annulation strategy based on n-halo diazo ketones. The method employs the use of readily available benzenoid starting materials and achieves the synthesis of azulenes substituted on both the five- and seven-membered rings regioselectively. The synthetic utility of the ring expansion annulation products, in particular azulenyl halides and triflates, has been demonstrated by their successful application in transition metal-mediated carbon-carbon bond forming reactions. These reactions have been used to further functionalize the five- and seven-membered rings and also in the synthesis of oligoazulenes and azulenylamino acid derivatives. In addition, polycyclic nitrogen heterocycles have been synthesized via a tandem ring forming strategy. The strategy employs a novel benzannulation reaction of substituted cyclobutenones with ynamides, which are synthesized via the strategy for the N-alkynylation of amides strategy developed in the Danheiser laboratory. The products of these benzannulation reactions, highly-substituted anilines, then participate in ring closing metathesis reactions to form various nitrogen heterocycles. In particular dihydroquinolines, hydrobenzoazepines, and hydrobenzoazocines were synthesized via this tandem ynamide benzannulation ring closing metathesis strategy. / by Aimee Lynn Crombie. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996. / Includes bibliographical references. / by David A. Kocisko. / Ph.D.

Thesis: Ph. D. in Biological Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2018. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / In response to an invading pathogen, the host organism initiates an immune response to fight infection. One component of the response involves metal-sequestering proteins that starve pathogens of essential metal nutrients. Humans release calprotectin (CP), a heterooligomer of S100A8 and S100A9, from neutrophils and epithelial cells to prevent microbes from accessing manganese, iron, nickel, and zinc. CP also binds Ca(II) ions, which increases the transition-metal affinity and antimicrobial activity of CP. In addition, Ca(II) causes the S100A8/S100A9 CP heterodimer to form a S100A82/S100A9₂ tetramer. When this dissertation research began, it was known that CP inhibited bacterial growth by sequestering transition metals, and that CP could transmit a proinflammatory signal; however, little was known about the fate of CP after release. The focus of this work was to better understand how the extracellular space may affect CP on biophysical and biochemical levels. Our approach was to study the molecular-level consequences of Ca(II) binding and tetramerization. We found that the heterotetramer exhibited significant resistance to enzymatic proteolysis compared to the heterodimer. Using NMR spectroscopy, we observed that the dynamics of CP change significantly upon Ca(II) binding small, yet notable, alterations in secondary structure. Finally, we discovered that methionine oxidation of CP inhibited Ca(II)-induced tetramerization, resulting in accelerated proteolysis. Taken together, our studies provided new insights into how CP survives the harsh conditions of the extracellular space, and a mechanism for clearing CP from the extracellular space. / by Jules Rabie Stephan. / Ph. D. in Biological Chemistry

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The intracellular delivery of therapeutic biomolecules such as oligonucleotides and proteins remains a key challenge today. Protective antigen, a naturally evolved protein translocase derived from Bacillus anthracis, has shown promise as a platform of protein delivery due to its ability to form a transmembrane pore that allows the cargo to have cytosolic access. We and others have used the LFN/PA system to deliver a wide variety of natural and non-natural peptides and proteins. Despite the significant progress made with the LFN/PA delivery platform, some aspects including cargo selection and targeting still remain limited. In the first part of the thesis, we greatly expand the application of the platform by demonstration of efficient delivery of peptide nucleic acids (PNAs), an oligonucleotide analog. Using this technology, we successfully exploited a cancer- specific gene dependency by the intracellular delivery of an anti-sense PNA in a receptor-dependent manner. In addition to exploiting new types of cargo for delivery, we developed a new strategy to target the LFN/PA system to specific cell types. In the second part of the thesis, we chemically conjugated a full-length immunoglobulin G (IgG) to a mutant PA (mPA). Significantly, we took advantage of the fact that PA activation is protease-dependent and created highly specific delivery vehicles that can only be activated by the concurrent presence of two entities on the cell surface. We showed a protein toxin delivered by these IgG-mPA variants effectively inhibited cell growth in different cancer cell lines and exhibited a significantly increased therapeutic window over previously reported PA variants both in vitro and in vivo. In the last part of the thesis, we explored the possibility of simplifying the LFN/PA system by directly ligating protein cargos to PA. In the absence of LFN, the chemically created single-component system significantly increased the amount of delivered cargo. Moreover, the single-component system combined with a short N-terminal polylysine tag further improved the delivery efficiency by more than 100-fold. Our findings raise the prospect of a simpler PA-mediated delivery platform.. / by Zeyu (Mike) Lu. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2003. / Vita. / Includes bibliographical references (p. 297-309). / In this thesis, the chemistry of sulfur oxides on transition metals is studied extensively via first-principles density functional theory (DFT) computations, focusing on the chemical reactivity and selectivity in sulfur poisoning chemical processes that address environmental concerns. The systematic approach we establish can be extended to general computational studies of small gas-phase molecules interacting with extended surfaces or finite-size clusters. The thesis starts with a theoretical presentation of modem quantum many-body theory that brings together mean-field theory, DFT, and Green's function quantum Monte Carlo theory. The essence of chemical reactivity theory in the framework of DFT is emphasized. The thesis continues with an extensive survey of the current status of sulfur oxide chemistry and an overall presentation of our computational approaches towards a detailed understanding of chemical reactivity and selectivity. The basic guidelines in chemical reactivity are systematically constructed by computed comprehensive thermodynamic data of surface S, O, SO, SO2, SO3, and S04 species as a function of coverage at low and intermediate temperatures. Under these basic guidelines, experimentally measured surface spectra are interpreted, contradictory experimental observations are resolved, and applicable experimental measurements are suggested for confirming computational predictions. Moreover, the chemical reactivity study is supplemented by our chemical kinetics study focusing on the catalytic oxidation of SO2 under oxygen rich conditions. This is the key process that hampers the implementation of the next-generation automotive catalytic converter. The revealed Langmuir-Hinshelwood mechanism demonstrates the essential catalytic performance of the Pt(1 11) surface. / (cont.) The thesis closes with a chemical selectivity analysis of the effects of catalyst particle size on chemisorption of gas-phase adatoms. In summary, the presentation of the chemistry of sulfur-containing molecules in this work is aimed at a scientific understanding of the strong poisoning effects in heterogeneous catalysis. However, the chemistry of sulfur-containing molecules has many more fundamental implications, such as in designing novel re-conjugated conducting devices for quantum computers. The underlying hybrid bonding flexibility of sulfur allows it to simultaneously bind to heavy transition metal atoms (such as Pt, Cu, or Au) and first-row atoms (such as oxygen atoms or carbon atoms in organic molecules). / by Xi Lin. / Ph.D.