The parkinsonian inducing drug 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is bioactivated in a reaction catalyzed by the flavoenzyme monoamine oxidase B (MAO-B) to form the corresponding dihydropyridinium (MPDP+) subsequently pyridinium (MPP+) metabolites. As part of our ongoing studies to characterize the structural features responsible for this unexpected biotransformation, we have synthesized and examined the MAO-B substrate properties of a variety of MPTP analogs bearing various heteroaryl groups at the 4-position of the tetrahydropyridinyl ring. The results of these SAR studies indicate that electronic features, steric features and polar interactions can contribute to the substrate activities. Additionally, isotope effects have been examined to investigate the mechanism and stereoselectivity of the MAO-B catalytic pathway. The synthesis and characterization of regio and stereoselectively deuterated MPTP analogs have been achieved. The results indicate that the catalytic step occurs exclusively at the allylic C-6 position and is rate-determining for both good and poor substrates. The two enantiomers of MPTP bearing a deuterium atom at C-6 have been prepared via chiral aminooxazolinyl derivatives and have been characterized by 2H NMR in a chiral liquid crystal matrix. These enantiomers were used to determine the selectivity of the MAO-B catalyzed a C-H bond cleavage reaction leading to the dihydropyridinium metabolite MPDP+. Some of the cyclopropyl analogs of MPTP have also been synthesized as the potential inhibitors. / Ph. D.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Complex polymer systems have multiple distributions with regard to molecular parameters such as molar mass, functionality, chemical composition, molecular architecture and microstructure. These distributions affect the properties of the polymers making it necessary to develop separation methods to be able to correlate structure to property. A single onedimensional chromatographic method is usually not sufficient to separate these complex polymers with respect to all the distributions. Hence, multidimensional liquid chromatography is necessary for the complete analysis of complex polymers using two or more chromatographic techniques before detection. In this work, two novel liquid chromatographic methods were developed to separate complex polymers according to microstructure. Comprehensive two-dimensional liquid chromatography (LC x LC) was carried out to observe the correlation between microstructure and molar mass. The separation according to microstructure was coupled to NMR (LC-NMR) to observe, identify and quantify the different microstructural components during chromatographic elution. The first chromatographic method separated hydrogenated and deuterated polystyrene homopolymers with respect to the isotope effect. For the LC x LC experiments, liquid chromatography at critical conditions (LCCC) was employed as the first dimension separating according to the isotope effect and size exclusion chromatography (SEC) as the second dimension separating according to molar mass. The LC x LC results of the blends showed that there was an improvement in isotopic separation with an increase in molar mass. The LCNMR coupling using both 1H and 2H NMR detection allowed for the identification of low molar mass blend components which were not sufficiently separated by liquid chromatography. The second chromatographic method separated stereoregular poly(methyl methacrylate)s (PMMAs) with respect to tacticity. The LC x LC experiments of stereoregular PMMAs utilised solvent gradient liquid chromatography as the first dimension to separate according to tacticity and size exclusion chromatography (SEC) as the second dimension to separate according to molar mass. The LC x LC results showed a change in the triad composition with elution of the stereoregular PMMAs with a slight influence of molar mass. The LC-NMR coupling allowed the observation of the triad composition during chromatographic elution. / AFRIKAANSE OPSOMMING: Komplekse polimeriese sisteme het meervoudige verspreidings ten opsigte van molekulêre parameters, soos byvoorbeeld, molêre massa, funksionaliteit, chemiese samestelling, molekulêre argitektuur en mikrostruktuur. Hierdie verspreidings beïnvloed die eienskappe van die polimere en dus is dit nodig om skeidingsmetodes te ontwikkel ten einde polimeerstruktuur met polimeereienskappe te kan korreleer. ‘n Enkele een-dimensionele chromatografiese metode is gewoonlik nie voldoende om hierdie komplekse polimere te skei met betrekking tot al die verspreidings nie. Multidimensionele vloeistofchromatografie, met die insluiting van twee of meer chromatografiese tegnieke, is dus nodig om polimere te skei voor waarneming kan plaasvind. Twee nuwe chromatografiese metodes is ontwikkel om komplekse polimere volgens mikrostruktuur te skei. Twee-dimensionele vloeistofchromatografie (LC x LC) is uitgevoer ten einde die korrelasie tussen mikrostruktuur en molêre massa te ondersoek. Daarna is die skeiding wat op mikrostruktuur gebasseer is, gekoppel aan KMR (LC-KMR) om die verskillende mikrostrukturele komponente gedurende chromatografiese eluering waar te neem, te identifiseer en te kwantifiseer. Die eerste chromatografiese metode het die gehidrogeneerde en gedeutereerde polistireen geskei met betrekking tot die isotoopeffek. Hier het die LC x LC skeiding bestaan uit vloeistofchromatografie onder kritiese kondisies (LCCC) as die eerste dimensie, wat skeiding bewerkstellig het gebasseer op die isotoopeffek, en grootte-uitsluitingschromatografie (SEC) as die tweede dimensie, wat skeiding bewerkstellig het gebasseer op die molêre massa. Die LC x LC resultate van die vermengings het ‘n verbetering in isotopiese skeiding met ‘n toename in molêre massa getoon. Deur gebruik te maak van die LC-KMR koppeling, waar beide 1H en 2H KMR waarneming gebruik is, was dit moontlik om die lae-molêre-massakomponente van vermengings wat nie volledig d.m.v. LC geskei kon word nie, te identifiseer. Die tweede chromatografiese metode het stereoreëlmatige polimetielmetakrilate (PMMAs) m.b.t. taktisiteit geskei. Die LC x LC skeiding van stereoreëlmatige PMMAs het bestaan uit oplosmiddel -gradiënt-LC as eerste dimensie om volgens taktisiteit te skei, en SEC as tweede dimensie om volgens molêre massa te skei. Die LC x LC resultate het ‘n molêre massa afhanklikheid van stereoreëlmatige PMMAs op taktisiteit getoon. Die LC-KMR koppeling het dit moontlik gemaak om die triade-samestelling gedurende chromatografiese eluering waar te neem.

A combined experimental and computational study on the reversible ortho-metalation exhibited by the triosmium cluster Os3(CO)10(dppm) (dppm = 1,1-bis(diphenylphosphino)methane is reported. The conversion of nonacarbonyl cluster HOs3(CO)9[-PhP(C6H4)CH2PPh2] to Os3(CO)10(dppm) is independent of added CO and exhibits a significant inverse equilibrium isotope effect (EIE). Reductive coupling of the C-H bond in HOs3(CO)9[-PhP(C6H4)CH2PPh2] leads to the formation of agostic C-H and two distinct aryl-π species prior to the rate-limiting formation of the unsaturated cluster Os3(CO)9(dppm). Heating the unsaturated dimer H2Re2(CO)8 with Cp*Rh(CO)2 (Cp* = 1,2,3,4,5-pentamethylcyclopentadiene) at elevated temperature affords the new trimetallic clusters H2RhRe2Cp*(CO)9 and HRh2ReCp*2(CO)6, and the spiked-triangular cluster HRhRe3Cp*(CO)14. H2Re2(CO)8 reacts with Cp*2Rh2(CO)2 under identical conditions to furnish H2RhRe2Cp*(CO)9 and HRh2ReCp*2(CO)6 as the principal products, in addition to the tetrahedral cluster H2Rh2Re2Cp*2(CO)8. H2RhRe2Cp*(CO)9 undergoes facile fragmentation in the presence of halogenated solvents and the thiols RSH (where R = H, C6H4Me-p) to afford the structurally characterized products Cp*Rh(-Cl)3Re(CO)3, S2Rh3Cp*(CO)4, Cp*Rh(-Cl)(-SC6H4Me-p)2Re(CO)3, and Cp*Rh(-SC6H4Me-p)3Re(CO)3. The new hydrazido-substituted compounds TaCl(NMe2)3[N(TMS)NMe2] (TMS = tetramethylsilyl) and Ta(NMe2)4[N(TMS)NMe2] have been synthesized and their structures established by X-ray crystallography. The latter product represents the first structurally characterized octahedral tantalum(V) complex containing a single hydrazido(I) ligand in an all-nitrogen coordinated environment about the metal center. The fluxional properties of the amido and hydrazido ligands in these new compounds have been established by VT 1H NMR spectroscopy (VT = variable temperature). Preliminary data using Ta(NMe2)4[N(TMS)NMe2] as an ALD (ALD = atomic layer deposition) precursor for the preparation of tantalum nitride and tantalum oxide thin films are presented.

Hydrogen isotope separation systems using palladium (Pd) are currently being designed for both reactor designs with the aim of separating and purifying the reactor exhaust products which contain valuable unspent hydrogen isotopes. Hydrogen isotope exchange in Pd offers an efficient, ambient condition process that can produce pure isotopic species in a process far simpler and less costly than the current state of the art cryogenic distillation processes. The method is applicable whether separating hydrogen (protium), deuterium or tritium and any combination of these. If practical fusion devices are ever to be realised it is essential to produce an economical and efficient fuel cycle capable of separating and purifying hydrogen isotopes. Hydrogen isotope exchange in Pd is also of interest to the waste separation and purification industries, in particular those using hydrogen separation membranes which used Pd and Pd-alloy membranes. Understanding hydrogen isotope exchange, with particular regard to the formation of the intermediate (and often unwanted) hydrogen deuteride (HD), will aid significantly in future designs of hydrogen isotope separation systems. Novel hydrogen isotope exchange experiments involving hydrogen and deuterium at a number of temperatures (208 K, 293 K and 373 K) and pressures (1.3 bar – 8 bar) not yet explored are presented in this thesis. The experiments were carried out on a unique piece of laboratory apparatus provided to and further developed at the University of Bath. Alongside experimentation, a novel comprehensive multidimensional multi-physics model has been created to analyse the experimental data obtained using the new apparatus and elucidate the kinetics and mechanisms of the reactions occurring between hydrogen isotopic species and Pd during hydrogen isotope exchange based on Langmuir-Hinshelwood surface reaction mechanism. The surface reaction rates, kinetic rate constants and heat effects have been examined in detail, and in tandem, for the first time.

The relationship between protein structure, motions, and catalytic activity is an evolving perspective in enzymology. An interactive approach, where experimental and theoretical studies examine the same catalytic mechanism, is instrumental in addressing this issue. We combine various techniques, including steady state and pre-steady state kinetics, temperature dependence of kinetic isotope effects (KIEs), site-directed mutagenesis, X-ray crystallography, and quantum mechanics/molecular mechanics (QM/MM) calculations, to study the catalytic mechanisms of thymidylate synthase (TSase). Since TSase catalyzes the last step of the sole intracellular de novo synthesis of thymidylate (i.e. the DNA base T), it is a common target for antibiotic and anticancer drugs. The proposed catalytic mechanism for TSase comprises a series of bond cleavages and formations including activation of two C-H bonds: a rate-limiting C-H→C hydride transfer and a faster C-H→O proton transfer. This provides an excellent model system to examine the structural and dynamic effects of the enzyme on different C-H cleavage steps in the same catalyzed reaction. Our experiments found that the KIE on the hydride transfer is temperature independent while the KIE on the proton transfer is temperature dependent, implying the protein environment is better organized for H-tunneling in the former. Our QM/MM calculations revealed that the hydride transfer has a transition state (TS) that is invariable with temperature while the proton transfer has multiple subsets of TS structures, which corroborates with our experimental results. The calculations also suggest that collective protein motions rearrange the network of H-bonds to accompany structural changes in the ligands during and between chemical transformations. These computational results not only illustrate functionalities of specific protein residues that reconcile many previous experimental observations, but also provide guidance for future experiments to verify the proposed mechanisms. In addition, we conducted experiments to examine the importance of long-range interactions in TSase-catalyzed reaction, using both kinetic and structural analysis. Those experiments found that a remote mutation affects the hydride transfer by disrupting concerted protein motions, and Mg2+ binds to the surface of TSase and affects the hydride transfer at the interior active site. Both our experiments and computations have exposed interesting features of ecTSase that can potentially provide new targets for antibiotic drugs targeting DNA biosynthesis. The relationship between protein structure, motions, and catalytic activity learned from this project may have general implications to the question of how enzymes work.

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B (a human PTP) to the conserved tryptophan residue and their effects on catalytic rate and chemical reaction were studied. The results of these studies are presented in this thesis.

Mechanistic studies of electrochemical proton coupled electron transfer (PCET) have attracted attention for many decades due to their importance in many fields ranging from electrocatalysis to biology. However, mechanistic research is confined to only a few groups, and challenges in this field can be found in both theory and experiment. The contributions to mechanistic studies of electrochemical PCET reaction in this thesis can be categorized under the following two headings: 1) mechanistic studies of an aminobenzoquinone modified monolayer system with multiple electron/proton transfer reaction; 2) studies that attempt to develop the relationship between thermochemical data and electrochemical PCET mechanism. An aminobenzoquinone modified monolayer showing nearly ideal electrochemical behavior and high stability was successfully prepared and used as a model system for the mechanistic study of electrochemical multiple electron/proton transfer. This model system has been proposed to undergo a 2e3H transfer at low pH electrolyte and a 2e2H transfer at high pH electrolyte. Two non-destructive electrochemical techniques (cyclic voltammetry and chronocoulmetry) have been applied for the measurement of apparent standard rate constant as a function of pH. Both pH dependent apparent formal potential and pH dependent apparent standard rate constant have been used to determine the charge transfer mechanism of this monolayer system. Under the assumption of an operative PCET mechanism (i.e. electron transfer step is the rate determining step), a theoretical description of this system has been developed based on the refinement and extension of previous models. By combining this extended theoretical model with pH dependent apparent formal potential and apparent standard rate constant, charge transfer pathways have been determined and shown to be consistent with the observed pH dependent electrochemical response, in addition, the determined pathways in this aminobenzoquinone modified monolayer are similar to previous reported pathways for benzoquinone freely dissolved in aqueous buffered electrolyte. A series of analytical expressions built in this thesis demonstrate that the parameters that differentiate stepwise mechanisms from concerted mechanisms can be classified into two aspects: thermodynamic parameters, namely acid dissociation constants, standard formal potentials; and kinetic parameters, namely standard rate constants, standard transfer coefficients. Although attempts to understand the relation between controlling parameters and electrochemical PCET mechanism (stepwise versus concerted) has been reported previously by some groups, there are still lots of unresolved aspects requiring further investigation. In this thesis, an important conclusion has been drawn which is that for the stepwise mechanism, an apparent experimentally observable kinetic isotope effect (KIE) can be induced by solvent isotope induced variation of acid dissociation constants, which contradicts previous understanding. Additionally, for the first time, values of apparent KIE, which were measured for the aminobenzoquinone modified monolayer system with stepwise PCET mechanism, were successfully explained by variation in acid dissociation constants, not by variation in standard rate constants. Based on theoretical prediction, a nitroxyl radical modified bilayer showing one electron one proton transfer reaction has been prepared in an effort to afford experimental verification. After applying similar analytical procedures as those for the aminobenzoquinone modified monolayer system, this bilayer system has been shown to follow the concerted 1e1H transfer pathway in high pH electrolytes. These latter contributions provide evidence that further development in this field will eventually lead to a comprehensive theory that can use known thermochemical variables to fully predict PCET mechanism.

The hydroboration of simple alkenes with BH3 preferentially occurs in an anti- Markovnikov fashion. The standard explanation for this preference, reproduced in all general organic chemistry textbooks, is that the selectivity arises from a greater stability for the anti-Markovnikov transition state. This explanation presupposes the applicability of the transition-state theory model for reactivity and selectivity. This dissertation explores the applicability of transition state theory to selectivity in hydroborations and finds that in some cases transition state theory fails to accurately account for observations. Experimental results for the hydroboration of propene-d6 and styrene-d8 with excess BH3 was analyzed by 2H-NMR to determine the percentage of the Markovnikov product for the BH3-mediated reaction. The experimental selectivities were then compared with predictions based on very high-level calculations using transition state theory. It was observed that the regioselectivity of the hydroboration of these alkenes is lower than can be accounted for by transition state theory. The regioselectivity discrepancy was explored through dynamic trajectory analysis. It is proposed here that the observed regioselectivity is that of a “hot” reaction, resulting from an exothermic association of alkene with borane to form an intermediate complex. This complex then overcomes low-energy barriers to form anti-Markovnikov and Markovnikov products faster than excess energy is lost to solvent. This hypothesis was explored for the hydroboration of internal disubstituted and trisubstituted alkenes. The applicability of transition state theory and the role of dynamics in determining the selectivity was gauged by determining product ratios in the presence of large excesses of borane and by considering the energetics of the calculated hydroboration reaction path. In all cases the enthalpic barriers for the rate-limiting association step and the formation of products from the intermediate π -complex were small. Isotope effects were determined experimentally and were found to be too small for the conventional mechanism to be the predominate pathway. When the hydroboration reaction of propene with BH2Cl or BHCl2 was explored through a series of experimental and theoretical studies, we observed that the regioselectivity was lower than that predicted from transition state theory. However, the calculated pathways indicated that energy barriers for product formation were too large for this reaction to be considered a “hot” reaction. The regioselectivity discrepancy was attributed to the chloroboranes undergoing equilibration with selective reaction of the most highly reactive forms of the borane.

Abstract The reactivity and bonding of allyl groups (C3H5) on a Ag(111) surface have been investigated under ultrahigh vacuum conditions by temperature-programmed reaction/desorption (TPR/D) and reflection-adsorption infrared spectroscopy (RAIRS). The atomically clean surface was achieved by Ar+ sputtering and verified by AES. The surface crystallinity was assured by LEED. Surface -bound allyl groups were generated by dissociative adsorption of allyl halides. Our study shows that the C-X (X= I or Cl) bond can be ruptured below 200K to render adsorbed allyl species. Upon further heating, three gas-phase products were detected at ~280 K, 295 K and 320 K in the TPR/D spectra, which are attributed to 1,5-hexadiene, allene, and propene, respectively. These results suggest that allyl undergoes

Spinosyn A is a particularly interesting natural product due to its structural complexity and potent insecticidal activity. The biosynthetic pathway of spinosyn A is interesting as it has two unusual features, the SpnF-catalyzed (4+2) cycloaddition and the SpnL-catalyzed cyclization to produce the perhydro-as-indacene core. The work described in this dissertation focuses on elucidating the mechanisms of the SpnF- and SpnL-catalyzed reactions. SpnF has attracted significant interest as a possible Diels-Alderase. To explain how SpnF catalyzes the formation of cyclohexene ring, three plausible mechanisms have been proposed, the Diels-Alder reaction mechanism, the ionic rearrangement mechanism, and the biradical rearrangement mechanism. Kinetic isotope effect studies were performed using four deuterium-labeled mechanistic probes, specially the C4-D, C7-D, C11-D, and C12-D analogs. Currently, the ionic rearrangement mechanism can be excluded, based on the results using the C4-D and C7-D analogs. In addition, how SpnF accelerates the reaction was studied to assess the contribution of an entropic x preorganization compared to enthalpic transition state stabilization. To measure the relative rate enhancements due to structural perturbations, three mechanistic probes were synthesized, the linear analog, the C13-14 Unc analog, and the C2-3 Unc analog. Unfortunately, the linear analog and C13-14 Unc analog didn’t show any turnover activity under either non-enzymatic or enzymatic conditions. Thus, no conclusion could be drawn from incubation with these substrate analogs. Mechanistic studies of SpnL-catalyzed cyclization were devoted to differentiating between the Rauhut-Currier type mechanism and the Michael addition mechanism. Biochemical studies using the C13-F analog as a mechanism-based inhibitor showed the formation of a covalent adduct with SpnL, which is consistent with the Rauhut-Currier type mechanism. Additional experimental data obtained from isotope trace experiments and kinetic isotope effect studies using C12-D analog supports the Rauhut-Currier type mechanism. Biochemical studies concerning the role of SAM in SpnF and SpnL showed that SAM is required for the activity of SpnL, and were inconclusive for SpnF. SpnL mutant studies showed that Cys60 and Glu96 may be important for the catalysis of SpnL. Chemoenzymatic total synthesis of spinosyn A was completed by chemical etherification of 17-pseudoaglycone and D-forosamine. / text