This thesis describes the use of kinetic isotope effects, linear free energy relationships and stereochamical studies to distinguish between different mechanistic alternatives and to obtain information about transition state structure. In the first part fluorine and deuterium kinetic isotope effects were determined for the base promoted HF elimination from 4-fluoro-4-(4’-nitrophenyl)butane-2-on. During this work a new method for the determination of fluorine kinetic isotope effects was developed. The results from the study demonstrates that the reaction proceeds via an E1cBip mechanism. In the second part the transition state structure for the SN2 reaction between ethyl chloride and cyanide ion in DMSO was studied. Kinetic isotope effects for six different positions in the reacting system, both in cyanide and ethyl chloride, were determined. The experimental isotope effects were then compared with the theoretically predicted isotope effects. The third part describes the use of Hammett type free-energy relationships and stereochemical evidence to study the mechanism of the copper catalysed alkene aziridination. The results from the study support a model that involves the simultaneous presence of two different copper nitrene intermediates. One which reacts non-stereospecifically via a radical intermediate and one which reacts stereospecifically via a concerted mechanism. In the fourth part a mechanistic study of the Ru(aminoalcohol) catalysed transfer hydrogenation of acetophenone in isopropanol is described. Kinetic isotope effects were determined for both proton and hydride transfer. The observation of significant primary deuterium kinetic isotope effects for both proton and hydride transfer support a mechanism where the proton and hydride are transferred simultaneously in a concerted mechanism.

Nitronate monooxygenase (E.C. 1.13.11.16), formerly known as 2-nitropropane dioxygenase (EC 1.13.11.32), is a flavin dependent enzyme that catalyzes the oxidation of nitronates to their corresponding carbonyl compounds and nitrite. Despite the fact that the enzyme was first isolated from Neurospora crassa 60 years ago, the biochemical and physiological properties of nitronate monooxygenase have remained largely elusive. This dissertation will present the work that established both the catalytic mechanism and physiological role of the fungal enzyme. The biological and biochemical properties of propionate-3-nitronate, the recently discovered physiological substrate for nitronate monooxygenase, will be extensively reviewed. The nitronate is produced by a variety of variety leguminous plants and fungi and is a potent and irreversible inhibitor of succinate dehydrogenase. Nitronate monooxygenase allows N. crassa to overcome the toxicity of propionate-3-nitronate as demonstrated by in vivo studies of the yeast, which showed that the wild-type can grow in the presence of the toxin whereas a knock out mutant that lacks the gene encoding for the enzyme could not. In addition to establishing the physiological role of nitronate monooxygenase, the work presented here demonstrates that the catalytic mechanism of the enzyme involves the formation of an anionic flavosemiquinone intermediate. This intermediate is stabilized by the protonated form of an active site histidine residue (His-196) that acts as an electrostatic catalyst for the reaction as demonstrated by pH studies of the reductive half reaction of the enzyme. Histidine 196 also serves as the catalytic base for the reaction of the enzyme with nitroethane as substrate as revealed through mutagenesis studies in which the residue was replaced with an asparagine. The kinetic implications of branching of reaction intermediates in enzymatic catalysis are also demonstrated through studies of the kinetic isotope effects of nitronate monooxygenase with 1,1-[2H2]-nitroethane as substrate. Finally the use of competitive inhibitors as a probe of enzyme structure will be presented through a study of the inhibition of nitronate monooxygenase with mono-valent inorganic ions. The dissertation will close with unpublished work on the enzyme and concluding remarks concerning the biochemistry and physiology of nitronate monooxygenase.

The [2,3]-sigmatropic rearrangement is a pericyclic reaction of great synthetic utility to organic chemists. Within the scope of this reaction exist some cases in which the product corresponding to a [1,2] rearrangement is formed, despite the fact this is a forbidden process. Generally this is explained by a radical dissociation-recombination pathway; however, studies into the failure of transition state theory and the necessity to incorporate dynamic effects into mechanistic theory lead us to believe such products may arise from these phenomena. In particular, the possibility that many of these products result from an “unsymmetrical bifurcating surface” in the potential energy landscape is intriguing. To investigate this possibility, the Sommelet-Hauser rearrangement of N-allyl-N,N-dimethylglycine methyl ester was explored. The combined use of experimental and theoretically predicted kinetic isotope effects (KIEs) has been previously shown to deliver great mechanistic insight into reactions. The combination of these techniques, however, has found little employ in studying [2,3] rearrangements. This combination was used to study this reaction, using the Singleton method for determining small heavy-atom isotope effects. Resulting experimental KIEs suggest the reaction proceeds by an asynchronous, concerted, early transition state, and is relatively exothermic. This agrees with previous studies and Hammond’s postulate. Predicted theoretical KIEs are in good agreement with experimental KIEs, and the associated transition structure confirms the results suggested by experiment. Interestingly, as calculations proceed from gas phase to solvent models, the activation barrier of the reaction increases, while its exothermicity decreases. The energy difference determined between the lowest and second lowest energy transition structures decreases to 0.81 kcal/mol in the PCM model, so we cannot exclude the contribution of this transition structure to the reaction. However, qualitative results from the associated KIEs and energetics are consistent with the lowest energy transition structure. This reaction does not seem to afford the [1,2] product, and most likely dynamic effects are insignificant in determining product distribution. However, the study has validated, with respect to this body of reactions, both the use of the Singleton method for KIE determination and the combination of these experimental and theoretical techniques.

Underlying all applications of sulfur isotope analyses is our understanding of isotope systematics. This dissertation tests some fundamental assumptions and assertions, drawn from equilibrium theory and a diverse body of empirical work on biochemical kinetics, as applied to the multiple sulfur isotope systematics of microbial sulfate reduction. I take a reductionist approach, both in the questions addressed and experimental approaches employed. This allows for a mechanistic, physically consistent interpretation of geological and biological sulfur isotope records. The goal of my work here is to allow interpreters a more biologically, chemically and physically parsimonious framework to decipher the signals coded in modern and ancient sulfur isotope records. / Earth and Planetary Sciences

No description available.

L’effet isotopique cinétique (KIE) est un outil puissant pour obtenir un aperçu sur le mécanisme d'une grande variété réactions. Nous avons observé différentes mesures de l’effet isotopique cinétique primaire du 13C pour la formation des α-, et β-mannopyranosides et des α- et β-glucopyranosides, en partant du sulfoxyde de glycosyle protégé par le groupement 4,6-O-benzylidène, par la spectroscopie RMN à ultrahaut champ (13C à 200 MHz et 1H à 800 MHz). Nous avons aussi calculé les KIE pour ces réactions en collaboration avec le Prof. Pratt à l'Université d'Ottawa. Les valeurs expérimentale et calculée (B3LYP / 6-31G (d, p) avec un modèle de continuum polarisable) sont en bon accord sauf pour l’α-mannopyranoside. Trois cas (-mannopyanoside,  et -glucopyranosides) parmi les quatre ont montré un caractère “SN2-like“, mais la formation de l'-mannopyranoside suggère fortement un mécanisme dissociatif (SN1). Une telle différence de mécanisme nécessite une authentification par des mesures cinétiques. Nous avons ensuite porté notre attention sur le développement d'une réaction intramoléculaire, comme horloge intramoléculaire, afin d’évaluer la cinétique relative des réactions de glycosylation. La formation des produits tricycliques fournit une grande évidence de l'existence d'un ion mannosyloxocarbénium comme un intermédiaire transitoire. Les réactions de compétition avec de l'isopropanol et du méthallyltriméthylsilane sont interprétées comme indiquant que la β-O-mannosylation passe par un mécanisme associatif (SN2-like), tandis que l’α-O-mannosylation et le β-C-mannosylation sont dissociative (SN1-like). Ceci est en plein accord avec nos résultats expérimentaux sur l’effet isotopique cinétique. Cette approche de la détermination de la cinétique relative des réactions de glycosylation est une méthode directe et est potentiellement applicable à une large variété de donneurs de glycosyle. / Kinetic isotopic effects (KIEs) are powerful tools to obtain insight into the mechanism of a great range of reactions. We demonstrated differing primary 13C kinetic isotope effect (KIE) measurements for the formation of α-, β-mannopyranosides and α-, β-glucopyranosides from the 4,6-O-benzylidene protected mannosyl and glucosyl sulfoxides by NMR (13C at 200 MHz and 1H at 800 MHz). We have also calculated the KIEs in collaboration with the Pratt group at the University of Ottawa for these reactions. Experimental and calculated (B3LYP/ 6-31G (d,p) values with a polarizable continuum model) were in good agreement, except for the -mannopyranoside. Three of (-mannpyanoside and the -, -glupyranosides) four cases showed a SN2-like character. The formation of the -mannopyranoside on the other hand suggests a strongly dissociative mechanism (SN1). Such a difference in mechanism necessarily demands authentication by kinetic measurements. We turned then our attention to the development of an intramolecular clock reaction with which to probe the relative kinetics of glycosylation reactions and to the formation of the tricyclic products that provides strong evidence for the existence of a mannosyl oxocarbenium ion as a transient intermediate. Competition reactions with isopropanol and trimethylmethallylsilane are interpreted as indicating β-O-mannosylation to proceed via an associative SN2-like mechanism, whereas α-O-mannosylation and β-C-mannosylation are dissociative and SN1-like. This is in full agreement with our experimental KIE results. This approach to the determination of relative kinetics of glycosylation reactions, is straightforward and is potentially applicable to a broad range of glycosyl donors.

EPR spectroscopy and isotopic substitution were used to gain increased knowledge about the proton-coupled electron transfer (PCET) mechanism for the reduction of the tyrosine D radical (YD*) in photosystem II. pL dependence (where pL is either pH or pD) of both the rate constant and kinetic isotope effect (KIE) was examined for YD* reduction. Second, the manner in which protons are transferred during the rate-limiting step for YD* reduction at alkaline pL was determined. Finally, high field electron paramagnetic resonance (EPR) spectroscopy was used to study the effect of pH on the environment surrounding both the tyrosine D radical and the tyrosine Z radical (YZ*). At alkaline pL, it was determined that the proton and electron are both transferred in the rate-limiting step of YD* reduction. At acidic pL, the proton transfer occurs first followed by electron transfer. Proton inventory experiments indicate that there is more than one proton donation pathway available to YD* during PCET reduction at alkaline pL. Additionally, the proton inventory experiments indicate that at least one of those pathways is multiproton. High field EPR experiments indicate that both YD* and YZ* are hydrogen bonded to neutral species. The EPR gx component for YD* is invariant with respect to pH. Analysis of the EPR gx component for Yz* indicates that its environment becomes more electropositive as the pH is increased. This is most likely due to changes in the hydrogen bond strength

<p> The existence of significant and consistent fractionation of sulfur isotopes in natural coexisting sulfide mineral pairs is demonstrated. Such fractionations are shown to depend exclusively on the mineralogy of the assemblage and temperature of equilibration, consistent with a process of fractionation during equilibrium exchange of sulfur isotopes between the sulfide phases . The fractionation of sulfur isotopes between galena, sphalerite and pyrite has been determined experimentally over the temperature range 300-725°C . The fractionation for each mineral pair is shown to vary as T^(-2) so that three isotope geothermometer s have been calibrated. Experi mental results are applied to natural sulfide assemblages to determine the temperature of equilibration and extent to which isotopic equilibriurn has b een attained. </p> / Thesis / Doctor of Philosophy (PhD)

Formaldehyde is a chemical used widely in the manufacture of building materials. A remarkable example is represented by the Lucite two-step Alpha technology for the large scale production of methyl methacrylate (MMA), the essential building block of all acrylic-based products. Esters and ketones are important intermediates in the manufacture of acrylate esters therefore α-hydroxymethylenation of carbonyl compounds using formaldehyde as a one carbon alkylating agent and subsequent dehydration to the corresponding methylenated derivatives has been explored in the current work. We report a novel catalytic approach for the synthesis of methyl methacrylate (MMA) via one-pot α-methylenation of methyl propanoate (a chemical intermediate of the ALPHA process) with formaldehyde, generated in situ by Ru-catalysed dehydrogenation of methanol. Elucidation of the mechanism involved in the catalytic dehydrogenation of methanol along with the collateral alcohol decarbonylation reaction was gained through a combined experimental and DFT study. The development of an alternative process where anhydrous formaldehyde is produced in situ would provide a simplification over the current second step of the ALPHA technology where the formaldehyde is initially produced as formalin, subsequently dehydrated to afford anhydrous formaldehyde in order to ensure high selectivity to MMA. As an alternative approach, ketones, in particular 3-pentanone and 2-butanone, were targeted as potential substrates in order to overcome some of the problems related to competing reactions that occur at the ester group. Hydroxymethylenation, followed by dehydration and Baeyer-Villager oxidation, possibly catalysed by enzymes to reverse the normal selectivity, leads to the formation of acrylate esters. The catalytic reaction is enabled by a gold carbene hydroxide complex in such a way that the substrate undergoes C-H activation and the nascent metal alkyl acts as a nucleophile towards the electrophilic formaldehyde, supplied in the form of alcoform* (solution of paraformaldehyde in methanol).