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. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references. / Chapter 1: Reaction of Mo(NR)(CHR')(OTf)2(dme) (R = 2,6-i-Pr2C6H3 (Ar), 2,6-Me2C6H3 (Ar'), 2,6-Cl2C6H3 (ArCl), 1-adamantyl (Ad); R' = CMe2Ph, CMe3; dme = dimethoxyethane) with the lithium salt of ArCl-nacnac ([2,6-Cl2C6H3NC(Me)]2CH), led to complexes of the type Mo(NR)(CHCMe2R')(OTf)(ArCl-nacnac). Treatment of these compounds with Na{BArF 4} (ArF = 3,5-(CF3)2C6H3) afforded rare examples of cationic imido alkylidene complexes, {Mo(NR)(CHR')(OTf)(ArCl-nacnac)}{BArF 4}. Addition of {HNMe2Ph}{BArF 4} to Mo(NR)(CHR')(L)2 (L = NC4H4 (Pyr), 2,5-Me2NC4H2 (Me2Pyr)) in THF produced {Mo(NR)(CHR')(L)(THF)x}{BArF 4} (x = 2 for Me2Pyr or 3 for Pyr). Addition of alcohol or phenol to {Mo(NAr)(CHCMe2Ph)(Pyr)(THF)3}{BArF 4} produced {Mo(NAr)(CHCMe2Ph)(OR")(THF)x}{BArF 4} (R" = CMe(CF3)2 (x = 2 or 3), Ar (x = 1), Ad (x = 2)). Complexes Mo(NAr)(CHCMe2Ph)(MesPyr)2 (MesPyr = 2- mesitylpyrrolide), Mo(NAd)(CHCMe3)(MesPyr)2, and Mo(NAr)(CHCMe2Ph)(OTf)(BinaphPPh2) (BinaphPPh2 = (R)-2'-(diphenylphosphino)- [1,1'-binaphthalen]-2-oxide) were also generated. The solid-state structures of Mo(NAr)(CHCMe2Ph)(OTf)(ArCl-nacnac), {Mo(NAr)(CHCMe2Ph)(ArClnacnac)}{ BArF 4}, {Mo(NAr)(CHCMe2Ph)(Pyr)(THF)3}{BArF 4}, {Mo(NAr)(CHCMe2Ph)(OCMe(CF3)2)(THF)3}{BArF 4}, {Mo(NAr)(C2H4)(OCMe(CF3)2)(THF)3}{BArF 4}, {Mo(NAr)(CH2CMe2Ph)(OAr)2}{BArF 4}, Mo(NAr)(CHCMe2Ph)(MesPyr)2, and Mo(NAr)(CHCMe2Ph)(OTf)(BinaphPPh2) have been determined by X-ray diffraction. The initial reactivity with simple olefins employing many of these new alkylidenes was explored. Chapter 2: Two diastereomers of the MAP (monoaryloxidepyrrolide) species, W(NAr)(CH2)(Me2Pyr)(OBitetBr2) (OBitetBr2 = (R)-3,3'-dibromo-2'-(tertbutyldimethylsilyloxy)- 5,5',6,6',7,7',8,8'-octahydro-1,1'-binaphthyl-2-olate), were generated through addition of HOBitetBr2 to W(NAr)(CH2)(Me2Pyr)2. The unsubstituted tungstacyclobutane species, W(NAr)(C3H6)(Me2Pyr)(OBitetBr2), was isolated by exposing the methylidene species to ethylene. A variety of NMR experiments were carried out on the methylidene and metallacycle to elucidate the exchange process between these species. Neophylidene W(NR)(CHCMe2Ph)(Me2Pyr)(OTPP) (OTPP = 2,3,5,6-tetraphenylphenoxide), methylidene W(NR)(CH2)(Me2Pyr)(OTPP), and 6 tungstacyclobutane W(NR)(C3H6)(Me2Pyr)(OTPP) were prepared. Treatment of W(NAr)(CH2)(Me2Pyr)(OTPP) with PMe3 yielded yellow W(NAr)(CH2)(Me2Pyr)(OTPP)(PMe3). NMR studies on compounds W(NAr)(C3H6)(Pyr)(OHIPT) (OHIPT = 2,6-bis-(2,4,6-triisopropylphenyl)phenoxide) and Mo(NAr)(C3H6)(Pyr)(OHIPT) were carried out to examine the exchange process between the metallacyclobutane and the methylidene. Compounds W(NAr)(C3H6)(Me2Pyr)(OBitetBr2), W(NAr)(CH2)(Me2Pyr)(OTPP), W(NAr)(CH2)(Me2Pyr)(OTPP)(THF), W(NAr)(CH2)(Me2Pyr)(OTPP)(PMe3), W(NAr)(C3H6)(Me2Pyr)(OTPP), Mo(NAr)(CH2)(Pyr)(OHIPT), Mo(NAd)(CHCMe3)(Pyr)(OHIPT), and W(NAr)(C3H6)(Pyr)(OHIPT) were crystallographically characterized. Chapter 3: Molybdenum and tungsten catalysts of the type M(NR)(CHR')(Pyr)(OR'') were prepared for highly Z-selective homocoupling metathesis of terminal olefins. Substrates screened were: 1-hexene, 1-octene, allylbenzene, allyltrimethylsilane, methyl-9-decenoate, methyl- 10-undecenoate, allylboronic acid pinacol ester, allylbenzylether, allyltosylamide, Nallylaniline, allyloxy(tert-butyl)dimethylsilane, and allylcyclohexane. Homocoupled products were isolated in moderate yields employing <1 mol% catalyst loading and with >90% Z-selectivity. Chapter 4: Exposing Mo(NAr)(C2H4)(MesPyr)2 to two equivalents of HOCH(CF3)2 afforded Mo(NAr)(C2H4)(OCH(CF3)2)2(Et2O). Mo(NAr)(C2H4)(OCH(CF3)2)(Et2O) was shown to isomerize and metathesize olefins such as propene, 1-hexene, and 1-octene at elevated temperatures. Evidence of isomerization and olefin metathesis was also observed with complexes Mo(NAd)(C2H4)(Pyr)(OHIPT) and Mo(NAr)(C2H4)(Me2Pyr)(OAr). / by Annie Jinying Hannah King. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references (p. 219-231). / Picosecond laser ultrasonic techniques for acoustic wave generation and detection were adapted to probe longitudinal and transverse acoustic waves in liquids at gigahertz frequencies. The experimental effort was designed for the study of supercooled liquids whose slower relaxation dynamics extend to gigahertz frequencies at high temperatures and whose faster dynamics are centered uniquely in the gigahertz frequency range. The experimental approach used a unique laser pulse shaping technique and, in the case of shear acoustic waves, a crystallographically canted metal transducer layer, to generate frequency tunable compressional and shear acoustic waves. Either time-domain coherent Brillouin scattering or interferometry was used to detect the waves in or after propagation through a liquid layer. The study of liquid-state gigahertz acoustic behavior required advances in both the experimental methodology and in the theoretical modeling of the results. A particular challenge was posed by the extraordinarily strong damping of gigahertz-frequency acoustic waves in liquids at some temperature ranges. This demanded the design and construction of a liquid sample cell allowing access to a wide range of liquid thicknesses, from less than a nanometer up to several microns. This was achieved by squeezing the liquid between two specially prepared high quality optical substrates held in a non-parallel configuration by a custom-designed sample holder jig. Several metallic layer materials were used for conversion of optical pulse energy into acoustic waves that were launched into the liquid samples, and different probe geometries were developed to enable access to a wide frequency range. The developed spectroscopic strategies were then applied to the study of two liquids, glycerol and tetramethyl tetraphenyl trisiloxane (DC704). Measurements of the density responses of both liquids from 400 K to below their respective glass transition temperatures were carried out. Longitudinal acoustic waves were either monitored via time-domain Brillouin scattering in the liquid or via interferometry after transmission through variably thick liquid layers, granting access to longitudinal acoustic frequencies from 10 GHz up to about 200 GHz. The information obtained on gigahertz frequency liquid relaxation was pieced together with data from several other techniques to create broadband relaxation spectra (from millihertz up to gigahertz), allowing characterization of the complex structural relaxation dynamics over many orders of magnitude and enabling both empirical modeling and testing of the predictions of the mode-coupling theory of supercooled liquids. The requirements for gigahertz shear wave generation and detection, including the properties of the photo-acoustic transducer materials, the sample and experimental geometry, and the detection material choices, are discussed. Results on shear wave propagation in glycerol and DC704 are presented. The technique for shear wave generation and detection is not limited to the study of viscous liquids but can also be applied to liquids like water, from which initial results are presented. / by Christoph Klieber. / Ph.D.

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1885. / MIT copy bound with: Albertite or melan asphalt / Frederick Fox, Jr. -- The action of bromine on the substituted anilides / Henry Martin -- Decomposition of paraffine hydrocarbons by heat / Henry P. Talbot. / Includes bibliographical references (leaves 71-73). / by Charles R. Allen. / B.S.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2015. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / Metal-organic frameworks (MOFs) represent a class of functional coordination polymers with long-range order, great synthetic flexibility, and exceptionally high internal surface area. Although they have been proposed for a myriad of potential applications, many of these require that MOFs be processed as thin films or other nanostructures to reach peak performance. Thus, a general and facile fabrication process is still much desired. In this thesis, I describe cathodic electrodeposition as an alternative approach to MOF crystallization, which is traditionally achieved solvothermally via ligand deprotonation through in-situ formation of base (often by amine release from the decomposition of an amide solvent). In cathodic electrodeposition, electrochemical reduction of probase molecules produces base equivalents to initiate the metal-ligand bond formation and subsequently the self-assembly process. There are three major advantages to this process in the context of producing MOF films: 1) the formation of base can be controlled more precisely, 2) the acid-base reaction is spatially confined close to the electrode surface, and 3) electrodeposition is, by definition, conformal, and therefore lends itself to electrodes of any geometry, as will be shown in Appendix I. Using cathodic electrodeposition, several Zn-BDC (BDC: 1,4-benzenedicarboxylate) MOFs could be formed as polycrystalline coatings on electrodes. In particular, a microporous composite of Zn₄O(BDC)₃ i.e. MOF-5, and Zn metal could be synthesized at room temperature in less than 15 minutes. This work is described in Chapter 2. By modulating the pH at the electrode surface in the presence of an appropriate probase, biphasic or bilayer structures of different polymorphs could also be accessed with a simple change in the applied potential, thereby providing a facile means of making composite films described in Chapter 4. Lastly, systematic studies of the effects of various variables on the electrodeposition process brought unique mechanistic insights to the early stages of MOF crystallization, as described in Chapter 3. Chapters 1 and 5 provide a context for this research within the larger area of MOF film formation, and a preliminary account on the possible sources of the [mu]₄-O²- atom in the iconic MOF-5 structure, respectively. / by Minyuan Miller Li. / Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2015. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / This thesis describes the design and development of new methods to functionalize graphitic materials as well as the synthesis and properties of a new triptycene poly(arylether), triptycene- PEEK (Trp-PEEK) and its derivatives. In chapters 1-3, the development of new methods to functionalize graphitic materials with both small molecule functional groups and polymers and their implementation as functional materials is described. Chapter 4 explores the synthesis, postpolymerization functionalization, and applications of a new poly(arylether), Trp-PEEK. Chapter 1: In this chapter, I describe an attempt to covalently functionalize graphene oxide with ketone derivatives via the Carroll rearrangement, a [3,3]-sigmatropic reaction. Graphene oxide was reacted with 5-acyl derivatives of Meldrum's acid to produce p-ketoester functionalized graphene, and these materials were submitted to multiple reaction conditions to induce the Carroll rearrangement. A 13C labeling study the under the explored reaction conditions the revealed that Carroll product is not predominant. However, it was found that the 20% of the installed functionality was not removed by exposure to strong base, suggesting some rearranged product may have been produced. 5-acyl derivatives of Meldrum's acid were ultimately found to be versatile reagents for the functionalization of graphene oxide with various functional groups, allowing for the synthesis of graphenes with controlled intergallery spacings. Chapter 2: Using a modified version of the Arbuzov reaction, graphene oxide is covalently functionalized with phosphonate functionalities. Due to the oxidizing nature of graphene oxide, the reaction produces a large amount of phosphate salts which organize around the covalently installed phosphonate anchor sites. This results in a graphene material which can be extensively decorated with a controllable amount of phosphate material. The ligand properties of this material were explored by synthesizing a number of metal composites. Graphene phosphate was ultimately found to possess outstanding compressive strength properties, which could be tuned according to the reaction conditions. Portions of this chapter contain work which was assisted by Prof. Stefanie A. Sydlik, who aided in the compression strength testing of graphene phosphate and associated analysis. Additionally, Dr. Joseph Walish fabricated the iron molds used to create the graphene phosphate pellets. Chapter 3: The synthesis of a brine-stable graphene is reported. Using AIBN initiated radical polymerization, random co-polymers containing both aniline and imidazole species were synthesized. These polymers were then covalently attached to the graphene basal plane using diazonium chemistry and converted into imidazolium betaine structures. The resulting composite shows indefinite stability in high-temperature brine solutions, which are particularly relevant for the imaging of oil reservoirs. The work reported in this chapter was performed with equal contributions from both John B. Goods and Dr. Carlos Zuniga. Dr. Jason Cox also provided valuable discussions. Chapter 4: A new poly(aryl ether), triptycene poly(ether ether ketone) (Trp-PEEK) was synthesized and its properties investigated. Incorporation of a triptycene into the PEEK backbone results in a significantly elevated glass transition temperature, and its increased solubility allows for high molecular weight polymer to be synthesized without the use of specialty solvents and high temperatures typically required for PEEK. This polymer is derivatized by both sulfonation and nitration. The sulfonated S-Trp-PEEK can be cast into robust transparent membranes, and shows exceptional performance as a proton conductor in this form. It can also stabilize solutions of singlewalled carbon nanotubes in polar solvents, such as water and methanol. From these solutions, conductive films and foams can be cast. The N0 2-Trp-PEEK derivative can be reduced into its amine form and then reacted with isocyanates to form urea and thiourea derivatives of Trp-PEEK. Thio-Trp-PEEK can be used as a selector in the gas-phase sensing of acetone. Its hydrogen bonding properties can also be exploited to form self-healing viscoelastic materials when blended with poly(THF). The work contained in this chapter regarding sulfonated Trp-PEEK and proton conductivity of those polymers was performed with equal contributions from John B. Goods and Lionel Moh. Lionel Moh also assisted with the characterization of the other polymers covered in this chapter. / by John B. Goods. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996. / Includes bibliographical references (p. 173-179). / by Yongwu Yang. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996. / Includes bibliographical references (p. 38-42). / by Robert Lester Murry. / M.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2002. / Vita. / Includes bibliographical references (p. 279-298). / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Electrostatic interactions play an important role in determining the energetics of association in biomolecular complexes. Previous work has shown that, within a continuum electrostatic model, for any given complex there exists a ligand charge distribution which optimizes the electrostatic binding free energy - the electrostatic complement of the target receptor. This electrostatic affinity optimization procedure was applied to several systems both in order to understand the role of electrostatic interactions in natural systems and as a tool in the design of ligands with improved affinity. Comparison of the natural and optimal charges of several ligands of glutaminyl-tRNA synthetase from E. coli, an enzyme with a strong natural requirement for specificity, shows remarkable similarity in many areas, suggesting that the optimization of electrostatic interactions played a role in the evolution of this system. The optimization procedure was also applied to the design of improvements to two inhibitors of HIV-1 viral-cell membrane fusion. Two tryptophan residues that are part of a D-peptide inhibitor were identified as contributing most significantly to binding, and a novel computational screening procedure based on the optimization methodology was developed to screen a library of tryptophan derivatives at both positions. Additionally, the optimization methodology was used to predict four mutations to standard amino acids at three positions on 5-Helix, a protein inhibitor of membrane fusion. All mutations were computed to improve the affinity of the inhibitor, with a five hundred-fold improvement calculated for one triple mutant. / (cont.) In the complex of b-lactamase inhibitor protein with TEM1 b-lactamase, a novel type of electrostatic interaction was identified, with surface exposed charged groups on the periphery of the binding interface projecting significant energetic effects through as much as 10 A of solvent. Finally, a large number of ab initio methods for determining partial atomic charges on small molecules were evaluated in terms of their ability to reproduce experimental values in continuum electrostatic calculations, with several preferred methods identified. / by David Francis Green. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Ribonucleotide reductases (RNRs) catalyze the reduction of nucleotides to deoxynucleotides in all organisms. The class Ia and lb RNRs comprise two subunits: a2 contains the site of nucleotide reduction, and p2 contains an essential stable tyrosyl radical (Y·), generated by oxidation of a dinuclear metal cluster. The diferric-Y (Fe" 2-Y·) cofactor of the class Ia RNRs self-assembles by reaction of Fe"2-NrdB with 02 and a reducing equivalent. Whether the class Ib RNRs utilize a diiron or dimanganese cofactor in vivo has been controversial. To determine the physiological metallocofactor of the Escherichia coli class lb RNR, we recombinantly express and purify a2 (NrdE) and p2 (NrdF) and show that NrdF self-assembles an active Fe 12- Y· cofactor using Fe" and 02. We also present the first purification of NrdI, a protein of unknown function conserved in class lb RNR systems. We show that NrdI is a flavodoxin-like protein with unusual redox properties. Although Mnr 2-NrdF does not react with 02, in the presence of reduced NrdI (Nrdlhq) and 02, it assembles an active dimanganese(III)-Y· (Mn 12- Y·) cofactor. Biochemical evidence indicates that Nrdlhq binds tightly to NrdF and reacts with 02 to provide an oxidant that channels to the metal site in NrdF to assemble the Mn"12-Ycofactor, a model supported by crystal structures of a Mn"2-NrdF*NrdI complex. NrdF purified from its endogenous levels in an iron-limited E. coli strain contains the Mn" 2 -Y· cofactor, establishing its physiological relevance. Rapid kinetics studies of Mn"'12 -Y· cofactor assembly in Bacillus subtilis NrdF support a mechanism in which NrdIhg rapidly reduces 02 to 02- and the 02'- channels to and reacts with Mn"2-NrdF to form a Mn" Mnv intermediate, which oxidizes tyrosine to Y·. Finally, we also demonstrate that E. coli NrdF, when incubated anaerobically with Mn" and Fe" and then exposed to H202 , forms an active Y·-containing metallocofactor that we suggest is Fe"Mn'l-Y·. These results raise the issues of how a single active site can generate a stable, active Ye using three different metal cofactors and oxidants in vitro, and therefore how metallation of NrdF with manganese is controlled in vivo. / by Joseph Alfred Cotruvo, Jr.. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1994. / Includes bibliographical references (leaves 152-161). / by Jeffrey H. Tidwell. / Ph.D.