4-(12-mercaptododecyloxy)phenol (1), 3-(12-mercaptododecyloxy)phenol (2), 4-(12-mercaptododecyl)phenol (3), 4-(12-mercapto-dodecyl)phenol (4), 12-phenyldodecyl-mercaptan (5), 12-phenylundecyoxymercaptan (6), 4-(6-mercapto-hexyl)phenol (7), and 4-(12-mercaptododecyloxy)phenol (8) were synthesized. The thiol products were characterized by NMR, HRMS, and elemental analysis. Self-assembled monolayers (SAMs) on gold substrates were prepared from thiols 1-8, and the resulting monolayer surfaces were analyzed using Reflectance Absorbance Infrared Spectroscopy (RAIRS), contact angle goniometry, ellipsometry, reductive desorption cyclic voltametry, and impedance spectroscopy. Several aromatic C-C vibrational frequencies in the RAIRS spectra, for SAMs of 1-8, reveal a dependence of peak intensity on substitution regiochemistry of the aromatic ring. This result suggests that the orientation of the aromatic ring changes with substitution. Peak intensity, and peak widths of alkyl C-H vibrational features in the RAIRS spectra also reveal a dependence of the environment of the alkyl chain on structure of thiols 1-8. Meta-substitution seems to significantly alter the projection of the terminal -OH group relative to para-substitution. Contact angles were obtained for each SAM surface using water, glycerol, and ethylene glycol. From the contact angle data, Zisman and Fowkes analyses were performed in order to determine surface free energy values and also to determine the dispersive contribution to the surface energy. The energy values obtained from the Zisman plots as well as the dispersive contributions obtained from the Fowkes plots suggest a dependence of surface energy on substitution regiochemistry of the aromatic ring. The results are consistent with the interpretation of the RAIRS spectra as they relate to the effect substitution regiochemistry has on SAM structure and interfacial properties. The results of the reductive desorption measurements performed on each monolayer surface, indicate that changes in substitution regiochemistry do not seem to affect the surface coverage of SAMs 1-8. Desorption potentials however, are affected by the structure of the thiols composing the SAM, which suggests that the lateral stability resulting from interactions of the terminal groups and alkyl chains, is different for each monolayer surface. Specifically SAMs of 12-phenyldodecylmercaptan (5) and SAMs of 4-(12-mercaptododecyloxy)phenol (1) seem to be more stable due to interactions of the terminal aromatic ring in SAMs of (5) and due to an increase in van der Waals interactions in SAMs of (1). Film thicknesses, as determined by ellipsometry, also suggest that meta-substitution of the aromatic ring results in lower thicknesses for SAMs of (4), which is consistent with the interpretation of the structural changes resulting from meta-substitution, suggested by the interpretation of the RAIRS spectrum of SAMs of (4). Thickness measurements also indicate that most of the functionalized SAMs (1-4, 7, 8) react with OTS, which suggests the terminal -OH group is not shielded at the interface and is available for reaction. Following reaction with OTS the RAIRS spectra of the reacted surfaces reveal structural changes to the underlying SAM. Impedance spectroscopic measurements performed on SAMs of 1-8 reveal what seems to be a correlation between the orientation of the aromatic ring and the resistance properties of the SAM. It appears meta-substitution of the ring lowers the monolayers ability to resist electron transfer. These data suggest that meta-substitution of the aromatic ring has a significant impact upon the structure of the resulting monolayer relative to monolayers composed of para-substituted molecules. The data also suggests that there is a correlation between molecular structure and interfacial properties particularly as it relates to surface energy and reactivity. Small atomic changes in the molecules composing the SAM result in measurable differences in macroscopic properties of the interface. It is important to recognize the need for understanding structure-property relationships in self-assembled monolayers particularly if logical design of surfaces is to be achieved and applied towards solving problems associated with corrosion and adhesion of metal surfaces. / Ph. D.

Laboratory microcosm experiments were conducted to assess the potential for biostimulation and bioaugmentation as source reduction measures in support of a monitored natural attenuation remedial strategy at Naval Amphibious Base (NAB) Little Creek. Previous work with laboratory microcosms conducted under simulated natural (unamended) conditions has demonstrated that indigenous dehalorespirators were capable of partial dechlorination of tetrachloroethene (PCE) to cis-dichloroethene (cis-DCE). This study attempts to achieve complete reductive dechlorination with amendments to static microcosms to test the hypotheses that nutrient-limited or microorganism-limited conditions exist in aquifer sediments obtained from the site. The enhanced bioremediation experiments were comprised of nutrient-amended microcosms receiving additions of electron donors, mineral medium, or anaerobic digester supernatant, and dechlorinating culture-amended microcosms were inoculated with a culture capable of transforming PCE to ethene. Reductive dechlorination in the nutrient-amended microcosms proceeded to cis-DCE over a 260-day study period, at slightly higher rates than in experiments conducted with aquifer sediments from the same location under natural conditions. Inoculation of aquifer sediments with a small amount of dechlorinating culture initiated rapid transformation of PCE to vinyl chloride (VC) by day 18 of the study. Zero-order rates of PCE dechlorination in unamended, propionate-, formate-, mineral medium-, digester supernatant-, and dechlorinating culture-amended microcosms were 0.24, 0.750, 1.30, 0.339, 0.177, and 1.75 µM/day, respectively. The results of this study suggest that an engineered biostimulation approach alone may not be as beneficial for PCE source reduction at NAB Little Creek, than bioaugmentation with competent dehalorespirators, along with the inclusion of supplemental nutrients which would be available to stimulate dechlorination activity of both indigenous and introduced microorganisms. / Master of Science

The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. Moreover, surface sediments were relatively oxidized, as indicated by the prevalence of aerobic bacteria such as beta- Proteobacteria, alpha-Proteobacteria, Sphingobacteria, and Nitrospira in 16S rRNA sediment clone libraries. On the other hand, several reductive dechlorinators were detected in sediments, including Dehalococcoides, Desulfitobacterium spp. which suggested that reductive dechlorination might be possible in sediments under certain biogeochemical conditions. Considerable amounts of PCBs were transformed by reductive dechlorination (80% in 177 days by pattern N) when sediments were maintained under anaerobic conditions, amended with nutrients and organic carbon, and incubated at 25 ºC in lab microcosms. Analysis of 16S rRNA clone libraries from these treatments revealed that Bacteroidetes, Chloroflexi and Firmicutes were enriched and Proteobacteria were depleted compared to clone libraries from treatment without organic amendments. Reductive dechlorination was decreased in sediments incubated at 10 and 40 ºC, and was not affected by FeSO4 amendments compared to unamended sediments incubated at 25 ºC. Transformations of PCB-153 were investigated in sediments under anaerobic, aerobic and sequential anaerobic and aerobic conditions. Transformations were only observed in treatments with an anaerobic phase, which occurred by reductive dechlorination by pattern N. Neither PCB-153 nor dechlorination products PCB-99 or PCB-47 were transformed under aerobic conditions. Analysis of 16S rRNA clone libraries revealed that Bacteoridetes, Chloroflexi, and Firmicutes were enriched under anaerobic conditions and Proteobacteria were enriched under aerobic conditions. Results from this study revealed that natural attenuation and biostimulation were not effective at removing PCBs from Ohio River sediments. Hence, other remediation methods will need to be employed to decrease PCB levels in this ecosystem.

A highly diastereoselective nickel-catalysed reductive aldol cyclisation is described. Using Ni(acac)2 as a precatalyst and diethylzinc as a stoichiometric reductant, various α,β-unsaturated carbonyl compounds tethered through an amide or ester linkage to a ketone electrophile underwent efficient cyclisation to afford β-hydroxylactams and β-hydroxylactones respectively. The scope of this process is broad with variation in the α,β-unsaturated carbonyl component, ketone and, where applicable, the nitrogen protecting group all tolerated. A series of experiments, including deuterium-labelling studies, were carried out in an attempt to gain insight into the possible reaction mechanisms that might be operative. II. Development of Novel Methodologies for the Silylation and Stannylation of Base-Sensitive Cyclopropenes Two distinct approaches to the synthesis of silyl- and stannylcyclopropenes are described. Using substoichiometric quantities of Cu(acac)2 and 1,2-bis(diphenylphosphino)ethane in combination with (trifluoromethyl)trimethylsilane, a diverse range of 1,3,3-trisubstituted cyclopropenes underwent direct silylation to afford the corresponding 1-silylcyclopropenes in good to excellent yield. Attempts to adapt these conditions to synthesise the corresponding stannylcyclopropenes proved unsuccessful. However, by employing (pentafluoroethyl)tributylstannane and stoichiometric potassium fluoride, it was possible to access 1-stannylcyclopropenes in comparable yields. It was also demonstrated that both the stannyl- and silylcyclopropene derivatives synthesised using these methodologies were able to serve as precursors for a variety of novel molecules that might otherwise be difficult to access using alternative methods.

D-Arginine dehydrogenase (DADH) catalyzes the oxidation of D-arginine to imino arginine using FAD as the cofactor. The enzyme is part of a recently discovered two-enzyme complex from Pseudomonas aeruginosa involved in arginine utilization. Function of the enzyme within the organism is unknown. Work on this enzyme has been undertaken to understand the structure as well as its reaction mechanism so as to eventually assign a function to the enzyme within the physiological context. In the reductive half-reaction 2 e- and 1 H+ are transferred from the amino acid substrate to FAD cofactor. In the oxidative half-reaction the reducing equivalents from the FAD cofactor are passed to an electron acceptor that is yet to be discovered. The enzyme has been established to have no reactivity with O2. Choline oxidase (CHO) from Arthrobacter globiformis is a well characterized member of Glucose-Methanol-Choline Superfamily that reacts with molecular O2. It catalyzes the oxidation of choline to glycine betaine mediated by betaine aldehyde intermediate using FAD as the cofactor and O2 as the oxidant to regenerate oxidized FAD for further reaction. Glycine betaine, the product of the reaction is an important osmolyte that regulates nutrients for plants under stressful conditions. Therefore it is of commercial interest to genetically engineer crops that do not typically possess competent pathways for glycine betaine synthesis. In this dissertation molecular details concerning the reductive half-eaction of DADH and oxidative half-reaction of CHO have been studied using a combination of steady state kinetics, rapid kinetics, pH, multiple substrates, mutagenesis, substrate deuterium and solvent isotope effects, viscosity effects or computational approaches. In DADH, the oxidation of amino acid substrate by FAD has been shown to most likely proceed via hydride transfer mechanism in the reductive half-reaction with Glu87, Tyr53, Tyr249 and His48 emerging as key players in substrate binding, catalysis or for up keeping the integrity of the FAD cofactor. In CHO, the oxidative half-reaction proceeds without stabilization of any reaction intermediates with H atom from reduced FAD and H+ from solvent or solvent exchangeable site occurring in the same kinetic step.

The objective of this Ph.D. study is to explore an important and fertile research topic on the methods for synthesis of nanomaterials by homogeneous nonaqueous solution phase reaction. Research in this work focuses on synthesizing several kinds of nanomaterials in different environments and structure, including spherical nanoparticles, nanowires and core-shell structure composites We first synthesized metallic nanomaterials in this system, such as ~10 nm Fe nanoparticles, ~6 nm Au nanoparticles, and ~100 nm Bi nanoparticles, this system are the preparation for the following studies. Secondly, we synthesized bimetallic nanomaterials in this system, such as Fe50Co50 alloy and Bi doped with Mn. For FeCo alloy, after annealing at 500 °C, a pure phase of Fe50Co50 was obtained. And we first synthesized the nanowires of bismuth doped with manganese. By studying intermediates at different temperatures during the growth process of nanowires, the evolution of the crystallization of metallic products and the mechanism of the formation of the nanowires are investigated. Thirdly, we synthesized core-shell structure nanocomposites, including either gold as the shell or polymer as the shell. Au-coated magnetic Fe nanoparticles have been successfully synthesized by partial replacement reaction in a polar aprotic solvent with about 11 nm core of Fe and about 2.5 nm shell of Au. HRTEM images show clear core-shell structure with different crystal lattices from Fe and Au. SQUID magnetometry reveals that particle magnetic properties are not significantly affected by the overlayer of a moderately thick Au shell. The Aucoated particles exhibit a surface plasmon resonance peak that red-shifts from 520 to 680 nm. And Poly (Vinyl Pyrolidone) (PVP) coated iron nanoparticles also have been successfully synthesized in a polar aprotic solvent, which shows the welldefined core-shell structures. In this approach, Poly (Vinyl Pyrolidone) (PVP) was employed as the coating polymer directly coated on metallic core (iron) nanoparticles. In this work, a combination of TEM (transmission electron microscopy), EDS (Energy disperse X-ray spectroscopy), XRD (X-ray powder diffractometry), ICP (inductively-coupled plasma spectrometer), TGA (Thermogravimetric analysis), UV-visible absorption spectroscopy, IR (infrared) spectroscopy and SQUID magnetometry (Superconducting Quantum Interference Device) were employed to characterize the morphology, structure, composition and magnetic properties of the products. In summary, this Ph.D. study successfully and systematically synthesized several kinds of nanocomposites in a system. The synthetic procedure is simple, economic and easily scaled-up for further applications. And many techniques were employed to characterize the products.

Reductive functionalization of methyl ligands by 3d metal catalysts and two possible side reactions has been studied. Selective oxidation of methane, which is the primary component of natural gas, to methanol (a more easily transportable liquid) using organometallic catalysis, has become more important due to the abundance of domestic natural gas. In this regard, reductive functionalization (RF) of methyl ligands in [M(diimine)2(CH3)(Cl)] (M: VII (d3) through CuII (d9)) complexes, has been studied computationally using density functional techniques. A SN2 mechanism for the nucleophilic attack of hydroxide on the metal-methyl bond, resulting in the formation of methanol, was studied. Similar highly exergonic pathways with very low energy SN2 barriers were observed for the proposed RF mechanism for all complexes studied. To modulate RF pathways closer to thermoneutral for catalytic purposes, a future challenge, paradoxically, requires finding a way to strengthen the metal-methyl bond. Furthermore, DFT calculations suggest that for 3d metals, ligand properties will be of greater importance than metal identity in isolating suitable catalysts for alkane hydroxylation in which reductive functionalization is used to form the C—O bond. Two possible competitive reactions for RF of metal-methyl complexes were studied to understand the factors that lower the selectivity of C—O bond forming reactions. One of them was deprotonation of the methyl group, which leads to formation of a methylene complex and water. The other side reaction was metal-methyl bond dissociation, which was assessed by calculating the bond dissociation free energies of M3d—CH3 bonds. Deprotonation was found to be competitive kinetically for most of the 1st row transition metal-methyl complexes (except for CrII, MnII and CuII), but less favorable thermodynamically as compared to reductive functionalization for all of the studied 1st row transition metal complexes. Metal-carbon bond dissociation was found to be less favorable than the RF reactions for most 3d transition metal complexes studied. The first dinitrogen dicopper (I) complex has been characterized using computational and experimental methods. Low temperature reaction of the tris(pyrazolyl)borate copper(II) hydroxide {iPr2TpCu}2(µ-OH)2 with triphenylsilane under a dinitrogen atmosphere gives the µ -N2 complex, {iPr2TpCu}2(µ -N2). X-ray crystallography reveals an only slightly activated N2 ligand (N-N: 1.111(6) Å) that bridges between two iPr2TpCuI fragments. While DFT studies of mono- and dinuclear copper dinitrogen complexes suggest a weak µ-backbonding between the d10 CuI centers and the N2 ligand, they reveal a degree of cooperativity in the dinuclear Cu-N2-Cu interaction.

Thesis advisor: James P. Morken / This dissertation details the development, application and study of new palladium-catalyzed carbon-carbon bond forming strategies that generate synthetically useful enantioenriched small molecules. Controlled by a bidentate phosphine ligand, these transformations are thought to operate through a unique 3,3'-reductive elimination that leads to high regio- and stereoselectivity. Specifically, Chapter 1 introduces background on prior work that led to the first allyl-allyl coupling to deliver branched 1,5-dienes, and presents new computational studies on the origins of regioselectivity with mono- and bidentate ligands. Building on these studies, Chapter 2 describes the development of a diastereoselective allyl-allyl coupling of substituted allylboron reagents with allylic chloride electrophiles. To extend the scope of allyl-allyl coupling, Chapter 3 details further reaction optimization and mechanistic studies that have allowed for increasingly congested bond formations. In Chapter 4, a related allyl-propargyl coupling to give enantioenriched 1,5-enynes through stereospecific reactions and kinetic resolution is presented. These developments are accompanied by laboratory and computational data that provide a deeper understanding of reaction mechanisms and the origins of regio- and stereoselectivity. / Thesis (PhD) — Boston College, 2014. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis advisor: James P. Morken / The catalytic allylation of aldehydes, ketones, and imines is a very useful reaction for the formation of a new carbon-carbon bond in synthetic organic chemistry. There have been several successful reports of catalytic asymmetric reactions that use aldehydes as the substrate. However, there have been very few successful examples with ketones. Herein, a nickel-catalyzed allylation of dienones with the pinacol ester of allylboronic acid is presented. Based on 3,3’-reductive elimination, the relationship between the dienone structure and 1,2- and 1,6-regioselectvity has been studied. The development of a catalyzed asymmetric 1,2 allylation of dienones is also presented. / Thesis (MS) — Boston College, 2008. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Novel biocatalysts for the enantioselective reduction of imines and reductive amination of a broad range of carbonyl compounds have been developed. Unlike other imine reductases (IREDs), the IRED from Amycolaptosis orientalis (AoIRED) features an aprotic "catalytic" residue Asn171 and as such became an interesting candidate for detailed mechanistic, specificity and stereoselectivity studies. AoIRED has been shown to be an efficient catalyst for the enantioselective reduction of imines and iminium ions to yield the corresponding chiral amines in high conversions and good to excellent enantioselectivity. The enzyme exhibits unusual stereoselective properties, displaying a selectivity switch for structurally similar substrates and in certain cases for the same substrate depending on the age of the enzyme. Mutagenesis studies have highlighted important residues that may play key roles in the substrate specificity and stereoselectivity of the enzyme. The reductive aminase from Aspergillus oryzae (AspRedAm) is a multifunctional catalyst that efficiently catalyses i) the reductive coupling of carbonyl compounds and amine nucleophiles, ii) the enantioselective reduction of prochiral cyclic and preformed imines or iii) the oxidative deamination of amines towards kinetic resolution of racemic amines. Detailed kinetic studies have led to the construction of a kinetic model/mechanism and based on structure guided investigation of conserved active site residues, a putative catalytic mechanism has been proposed. It has also been possible to engineer wild-type AspRedAm for improved stereoselectivity as well as to invert the enzyme's enantioselectivity towards a range of substrates. Using AspRedAm as a catalyst, efficient systems have been developed that allow the kinetic resolution of several racemic amines. This thesis has been organised into separate chapters each addressing a specific theme. Chapter 1 gives an overview of recent advances in the field of amine biocatalysis with emphasis on biocatalytic imine reduction and reductive amination; it also outlines the objectives of this project. Chapter 2 describes methods and materials used in these studies while Chapters 3-7 present and discuss results from different projects that constitute the work in this thesis. Initial discovery and characterisation studies of IREDs are described in Chapter 3. Chapter 4 describes detailed characterisation of AoIRED with particular emphasis on stereoselectivity and synthetic applicability while Chapter 5 presents and discusses results from the study of the reductive aminase (AspRedAm) from Aspergillus oryzae. Chapters 6 and 7 respectively describe the engineering of AoIRED and AspRedAm, and the application of AspRedAm in kinetic resolution of racemic amines. The results from these chapters have been summarised and discussed in Chapter 8 and recommendations for future directions in this field have been offered.