Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1988. / Includes bibliographical references. / by Jotham Wadsworth Coe. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1999. / Includes bibliographical references. / by Jack S. Liang. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. / Vita. / Includes bibliographical references. / Metal-catalyzed nucleophilic substitution reactions of aryl halides have become one of the most valuable and useful classes of reactions developed in the last 30 years. Foremost among these processes are the classes of palladium- and copper-catalyzed reactions, which employ heteroatom-based nucleophiles. Herein, newly designed catalyst systems are presented for the palladium- and/or copper-catalyzed nucleophilic substitution reactions of aryl halides with a variety of nucleophiles, including (benz)imidazoles, oxindoles, 2-, 3- and 4-hydroxypyridines, anilines, and aliphatic, benzylic, allylic and propargylic alcohols. In many cases, catalyst optimization and ligand structure are discussed and evaluated. Where applicable, the palladiumand copper-based catalyst systems are contrasted to demonstrate the complementary relationships between the employment of these two metals. Chapter One Chapter Two Chapter Three Chapter Four Chapter Five. Palladium- and Copper-catalyzed Reactions of Imidazoles and Benzimidazoles with Aryl Halides. Orthogonal Selectivity in Copper- and Palladium-catalyzed Reactions of Aryl Halides with Oxindoles. Copper-catalyzed Reactions of Hydroxypyridines and Related Compounds with Aryl Halides. Pyrrole-2-carboxylic Acid as a Ligand for the Copper-catalyzed Reactions of Primary Anilines with Aryl Halides. An Improved Copper-based Catalyst System for the Reactions of Aryl Halides with Aliphatic Alcohols. / y Ryan A. Altman. / Ph.D.

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1939. / MIT copy bound with: Reactions of β-ionone / by Ida Rovno [1939] / Includes bibliographical references (leaf [28]). / by Maynard E. Smith. / B.S.

Thesis: S.M., Massachusetts Institute of Technology, Department of Chemistry, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 27-28). / Hydrogels formed from synthetic polypeptides generated by ring opening polymerization (ROP) of a-amino acid N-carboxyanhydrides (NCAs) present a robust material for modeling the interaction between extracellular matrix (ECM) properties and cellular phenomena. The unique properties of the polypeptide backbone allow it to fold into secondary structures and the ability to modify the side chain presents the opportunity to display chemical functionalities that dictate cellular signaling. The ability to induce cells to form tissue is a chemical and engineering challenge due to the fact that cells need physical support in the form of a 3D scaffold with both chemical and mechanical signals. The Hammond group previously reported the combination of synthetic polypeptides with modified side chains available for click chemistry at quantitative grafting efficiencies. Herein, new schemes for hydrolytically stable versions of the polymer system with click functionality are introduced. Additionally, a new random copolymer, poly(y-propargyl-L-glutamate-co-[gamma]-allyl-L-glutamate) (PPALG) is presented that exploits both the azide-alkyne and thiol-ene click reactions to allow orthogonal side chain modification to increase chemical complexity and ultimately allow a library of "designer" gel systems to be generated. / by Mackenzie Marie Martin. / S.M.

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Chapter 1. Palladium-Catalyzed Fluorination of Cyclic Vinyl Triflates: Dramatic Effect of TESCF₃ as an Additive A method for the synthesis of cyclic vinyl fluorides with high levels of regiochemical fidelity has been achieved by Pd-catalysis employing a new biarylphosphine ligand and TESCF₃ as a crucial additive. Five, six, and seven-membered vinyl triflate substrates, as well as a few acyclic substrates undergo the transformation successfully. The intriguing "TESCF₃ effect" provided a new tool for addressing the problem of the formation of regioisomers in Pd-catalyzed fluorination reactions. Chapter 2. Mechanistic Studies on Pd-Catalyzed Fluorination of Cyclic Vinyl Triflates: Evidence for in situ Ligand Modification by TESC₃ as an additive. A detailed mechanistic hypothesis for the Pd-catalyzed fluorination of cyclic vinyl triflates, and the unusual effect of TESCF₃ as an additive has been developed by combined experimental and computational studies. The preference of conducting [beta]-hydrogen elimination rather than reductive elimination from the trans-LPd(vinyl)F complex, which is generated predominantly due to the trans-effect, caused the poor regioselectivity of the fluorination reaction under TESCF₃-free conditions. An in situ ligand modification by trifluoromethyl anion, leading to the generation of the cis-LPd(vinyl)F complex which prefers reductive elimination rather than Phydrogen elimination, is proposed to be responsible for the improved regioselectivity of the fluorination reaction when TESCF₃ was used as an additive. Chapter 3. CuH-Catalyzed Enantioselective Alkylation of Indoles with Ligand-Controlled Regiodivergence A method for the enantioselective synthesis of either NI- and C3-chiral indoles by CuH-catalysis, depending on the choice of ligand, was developed. In contrast to conventional indole functionalization in which indoles are used as nucleophiles, hydroxyindole derivatives are employed as electrophiles in this method. DFT calculations indicated that the extent to which the Cu-P bonds of the alkylcopper intermediate distort, determines the regioselectivity of the reaction. / by Yuxuan Ye. / Ph. D. in Organic Chemistry

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. / Includes bibliographical references . / Chapter one has a brief discussion of polythiophene and the important factors to consider with polythiophene synthesis and characterization. In chapter two, a variety of polythiophene derivatives that incorporated 2,2'-biphenyl units into the polymer main chain were synthesized. The potential utility of the 2,2'-biphenyl unit as a scaffold to facilitate the t-n interactions between thiophene oligomers was explored. The linkage of the thiophene to the biphenyl was varied between the a- or O-positions to assess how this variable affected the overall properties of the resulting polymers. The n-linked thiophene monomers produced highly cross-linked polymers and the electroactivity of these polymers depended on the length of the thiophene fragment in the corresponding monomer. The a-linked thiophene monomers produced segmented linear conjugated polymers and the polymers' segmentation dominated the resulting electroactivity. A model study demonstrated that through-space interactions between the oligothiopene fragments of the 2,2'-biphenyl monomers did occur. In chapter three, a synthetic scheme was developed to generate 2,2'-biphenyl monomers with long alkyl chains from which soluble polymers could be generated. / (cont.) The synthetic scheme was also utilized to produce a monomer that could be electrochemically cross-linked in a controlled fashion. In chapter four, a variety of polythiophene derivatives that incorporated azaferrocenes complexes into the main polymer chain were synthesized. These polymers were then used to ascertain the effect of a n-bound metal on the main chain of a conducting polymer. The oxidation of the metal centers in the polymer produced a significant change in the conductivity of the polymer film. Changing the length and oxidation potential of the polythiophene section of the monomer appeared to alter the charge delocalization of the polymers. In chapter five, a series of polythiophene derivatives containing cyclobutadiene cobalt cyclopentadiene complexes in the main polymer chain were synthesized. The viability of the electropolymerization of the complexes was determined by the relative position of organic section's oxidation potential versus the oxidation of the metal centers. The metal coordinated cyclobutadiene ring of the complex appeared to have a modest charge transport ability. / by Paul D. Byrne. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. / Includes bibliographical references (p. 207-230). / This thesis presents the development and application of several computational techniques to aid in the design and analysis of small molecules and peptides that bind to protein targets. First, an inverse small-molecule design algorithm is presented that can explore the space of ligands compatible with binding to a target protein using fast combinatorial search methods. The inverse design method was applied to design inhibitors of HIV-1 protease that should be less likely to induce resistance mutations because they fit inside a consensus substrate envelope. Fifteen designed inhibitors were chemically synthesized, and four of the tightest binding compounds to the wild-type protease exhibited broad specificity against a panel of drug resistance mutant proteases in experimental tests. Inverse protein design methods and charge optimization were also applied to improve the binding affinity of a substrate peptide for an inactivated mutant of HIV-1 protease, in an effort to learn more about the thermodynamics and mechanisms of peptide binding. A single mutant peptide calculated to have improved binding electrostatics exhibited greater than 10-fold improved affinity experimentally. / (cont.) The second half of this thesis presents an accurate method for evaluating the electrostatic component of solvation and binding in molecular systems, based on curved boundary-element method solutions of the linearized Poisson-Boltzmann equation. Using the presented FFTSVD matrix compression algorithm and other techniques, a full linearized Poisson-Boltzmann equation solver is described that is capable of solving multi-region problems in molecular continuum electrostatics to high precision. / Michael Darren Altman. / Ph.D.

Thesis: S.M., Massachusetts Institute of Technology, Department of Chemistry, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Metal organic frameworks (MOFs) are a relatively new class of crystalline, porous materials at the interface of organic and inorganic chemistry that have been applied in gas absorption and storage systems, thin-film devices, and heterogeneous catalysts. While numerous examples of size-exclusive catalysis have been reported, to our knowledge no reports of size-selective oligomerization catalysis have been reported to date. Herein, chemically stable Zr based MOFs, namely UiO-67 and PCN-777, are investigated as possible candidates to promote size-selective oligomerization catalysis. Using acylated propylene-glycol methyl ethers as model substrates, the mass transport properties of these materials was investigated. Unfortunately, slow mass transport of solvated substrates through pores assumed to be sufficiently large for facile diffusion may prevent MOFs from serving as suitable scaffolds. Indeed, pore apertures large enough for quick diffusion rates may require pore volumes too large to allow reasonable size-selectivity. / by Ryan D. Palmer. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Includes bibliographical references. / by Christopher Alan Wiloughby. / Ph.D.