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

This thesis describes a method for calculating lake evaporation as a proportion of water inputs (E/I) for large surface water bodies, using stable isotope ratios of oxygen (18O/16O) and hydrogen (2H/1H) in water. Evaporation as a proportion of inflow (E/I) is calculated for each Laurentian Great Lake using a new dataset of 516 analyses of δ18O and δ2H in waters sampled from 75 offshore stations during spring and summer of 2007. This work builds on previous approaches by accounting for lake effects on the overlying atmosphere and assuming conservation of both mass and isotopes (18O and 2H) to better constrain evaporation outputs. Results show that E/I ratios are greatest for headwater Lakes Superior and Michigan and lowest for Lakes Erie and Ontario, controlled largely by the magnitude of hydrologic inputs from upstream chain lakes. For Lake Superior, stable isotopes incorporate evaporation over the past century, providing long-term insights to the lake’s hydrology that may be compared to potential changes under a future – expectedly warmer – climate. Uncertainties in isotopically derived E/I are comparable to conventional energy and mass balance uncertainties. Isotope-derived E/I values are lower than conventional energy and mass balance estimates for Lakes Superior and Michigan. The difference between conventional and isotope estimates may be explained by moisture recycling effects. The isotope-based estimates include only evaporated moisture that is also advected from the lake surface, thereby discounting moisture that evaporates and subsequently reprecipitates on the lake surface downwind as recycled precipitation. This shows an advantage of applying an isotope approach in conjunction with conventional evaporation estimates to quantify both moisture recycling and net losses by evaporation. Depth profiles of 18O/16O and 2H/1H in the Great Lakes show a lack of isotopic stratification in summer months despite an established thermocline. These results are indicative of very low over-lake evaporation during warm summer months, with the bulk of evaporation occurring during the fall and winter. This seasonality in evaporation losses is supported by energy balance studies. For Lakes Michigan and Huron, the isotope mass balance approach provides a new perspective into water exchange and evaporation from these lakes. This isotope investigation shows that Lake Michigan and Lake Huron waters are distinct, despite sharing a common lake level. This finding advocates for the separate consideration of Lake Michigan and Lake Huron in future hydrologic studies.

La nutrition azotée des bactéries et des plantes est actuellement un sujet de grande importance, notamment pour comprendre comment améliorer les voies métaboliques aboutissant à l’assimilation de l’azote et à plus grande échelle, optimiser des apports d’engrais et augmenter le rendement des cultures. Dans ce contexte, la réaction d’amidation catalysée par la glutamine synthétase (GS), qui fixe l’ammonium (NH₄)⁺ en glutamine, est cruciale car elle est à la fois le point d’entrée de l’azote dans les végétaux, et une étape-clef du recyclage de l’azote (en particulier, NH₄⁺ photorespiratoire). Dans cette étude, nous nous sommes intéressés à la cinétique enzymatique et au mécanisme chimique de la GS. Des systèmes analytiques (HPLC, RMN , GC-MS) ont  été optimisés pour permettre la mesure de l’activité enzymatique in vitro et pour réaliser des analyses par spectrométrie de masse à ratio isotopique. Avec ces techniques, nous avons pu regarder précisément les effets isotopiques ¹²C/¹³C, ¹⁴N/¹⁵N et H₂O/D₂O (solvant) lors de la catalyse, en utilisant la GS d’E. coli et d’Arabidopsis thaliana (GS1,2). Nos résultats montrent qu’il n’y a pas d’effet isotopique ¹²C/¹³C, mais qu’il y a un fractionnement ¹⁴N/¹⁵N de »16‰. En outre, il y a un effet inverse du solvant (réaction 1.5 à 2 fois plus rapide dans D₂O).  Cela suggère que la création de la liaison C----N (amidation) est partiellement limitante (engagement catalytique de »14% seulement) et que le réseau de ponts hydrogènes dans le site actif est crucial pour déterminer la vitesse de la réaction. L’apparition d’effets ¹⁴N/¹⁵N inverses dans certaines circonstances et les effets drastiques causés par une substitution du cofacteur métallique (Mg²⁺) suggèrent en outre que l’étape d’amidation peut être réversible et que la coordination par un métal joue un rôle très important pour stabiliser les intermédiaires de la réaction, en interaction avec le solvant. Ainsi, dans son solvant naturel qu’est H₂O, la GS réalise une réaction ‘chimiquement difficile’ (barrière énergétique élevée de l’amidation) rendue possible par le clivage de l’ATP et son caractère exergonique. / Nitrogen nutrition in bacteria and plants is currently an important topic, in particular to identify key points for metabolic improvements in N assimilation and more generally, to optimize fertilization and crop yield. In such a context, the amidation reaction catalyzed by glutamine synthetase (GS), which fixes ammonium (NH₄)⁺ into glutamine, is of crucial importance since it both represents the N entry in plants and the main step of N recycling (such as photorespiratory (NH₄)⁺. Here, we examined GS kinetics and chemical mechanism. Analytical methods (HPLC, NMR, GC-MS) have been set up so as to measure in vitro activities and isotopic abundance by isotope ratio mass spectrometry. These gave access to isotope effects (¹²C/¹³C, ¹⁴N/¹⁵N et H₂O/D₂O – solvent) during catalysis, with the GS from either E. coli or A. thaliana (GS1,2). Our results show that there no ¹²C/¹³C isotope effect but there is significant ¹⁴N/¹⁵N isotope fractionation of ca. 16‰. In addition, there is an inverse solvent isotope effect (reaction 1.5 to 2 times faster in D₂O). This suggests that forming the C----N bond (amidation) is partially rate-limiting (catalytic commitment of ca. 14% only) and the H-bond network in the active site is of substantial importance for the reaction rate. The occurrence of inverse ¹⁴N/¹⁵N isotope effects under certain circumstances as well as the drastic impact of changing the metal cofactor (Mg²⁺)) indicate that the amidation step can be reversible and that the coordination by the metal plays a key role in stabilizing reaction intermediates, by interfacing the solvent. In other words, in its natural solvent H₂O, the GS catalyses an intrinsically ‘difficult’ reaction (high energy barrier of amidation) made possible by both ATP cleavage and its exergonic nature.

<p>This thesis concerns the study of reaction mechanisms by means of kinetic isotope effects (KIEs). Studies of the nucleophilic bimolecular substitution (S_N2) reaction had the dual purpose of improving our fundamental understanding of molecular reactivity and assessing the ability of kinetic isotope effects to serve as mechanistic tools. The transition state of the S_N2 reaction between a cyanide ion and ethyl chloride in tetrahydrofuran was found to be reactant like and only slightly tighter than has been found previously for the same reaction in dimethyl sulphoxide. One conclusion was that the transition-state structure in this reaction was predicted fairly well by the theoretical calculations, even without solvent modelling. The S_N2 reactions between cyanide ions and <i>para</i>-substituted benzyl chlorides were found to have reactant-like transition states, of which the C_α-Cl bond was most influenced by the <i>para</i>-substitution. Theoretical calculations indicated that the chlorine KIEs could be used as probes of the substituent effect on the C_α-Cl bond if bond fission was not too advanced in the transition state. Furthermore, the nucleophile carbon ¹¹C/¹⁴C KIEs were determined for the reactions between cyanide ions and various ethyl substrates in dimethyl sulphoxide.</p><p>Precision conductometry was employed to estimate the aggregation status of tetrabutylammonium cyanide in tetrahydrofuran and in dimethyl sulphoxide, which is of interest as tetrabutylammonium cyanide is frequently used as the nucleophilic reagent in mechanistic investigations and synthetic reactions. The tendency for ion-pair formation was found to be very slight, significant, and very strong in dimethyl sulphoxide, water, and tetrahydrofuran, respectively. </p><p>The nitrogen kinetic isotope effect on monoamine oxidase B catalysed deamination of benzylamine was determined in an attempt to obtain conclusive evidence regarding the mechanism of the oxidation. Monoamine oxidase is an important drug target in connection with the treatment of, for example, depression and Parkinson’s disease, and knowledge on how the enzyme effects catalysis would facilitate the design of highly selective and efficient inhibitors.</p>

This thesis concerns the study of reaction mechanisms by means of kinetic isotope effects (KIEs). Studies of the nucleophilic bimolecular substitution (SN2) reaction had the dual purpose of improving our fundamental understanding of molecular reactivity and assessing the ability of kinetic isotope effects to serve as mechanistic tools. The transition state of the SN2 reaction between a cyanide ion and ethyl chloride in tetrahydrofuran was found to be reactant like and only slightly tighter than has been found previously for the same reaction in dimethyl sulphoxide. One conclusion was that the transition-state structure in this reaction was predicted fairly well by the theoretical calculations, even without solvent modelling. The SN2 reactions between cyanide ions and para-substituted benzyl chlorides were found to have reactant-like transition states, of which the Cα-Cl bond was most influenced by the para-substitution. Theoretical calculations indicated that the chlorine KIEs could be used as probes of the substituent effect on the Cα-Cl bond if bond fission was not too advanced in the transition state. Furthermore, the nucleophile carbon 11C/14C KIEs were determined for the reactions between cyanide ions and various ethyl substrates in dimethyl sulphoxide. Precision conductometry was employed to estimate the aggregation status of tetrabutylammonium cyanide in tetrahydrofuran and in dimethyl sulphoxide, which is of interest as tetrabutylammonium cyanide is frequently used as the nucleophilic reagent in mechanistic investigations and synthetic reactions. The tendency for ion-pair formation was found to be very slight, significant, and very strong in dimethyl sulphoxide, water, and tetrahydrofuran, respectively. The nitrogen kinetic isotope effect on monoamine oxidase B catalysed deamination of benzylamine was determined in an attempt to obtain conclusive evidence regarding the mechanism of the oxidation. Monoamine oxidase is an important drug target in connection with the treatment of, for example, depression and Parkinson’s disease, and knowledge on how the enzyme effects catalysis would facilitate the design of highly selective and efficient inhibitors.

State of the art conductivity equipment has been used to measure deuterium isotope effects on the molar conductivity of strong electrolytes in the temperature range of 298 K to 598 K as a means of exploring solvation effects under hydrothermal conditions. Individual ionic contributions were determined by extrapolation of published transference number data to elevated temperature. The temperature dependence of the Walden product ratio indicates that there is little difference in the transport of ions between light and heavy water . Excess conductivity observed in hydrogen and deuterium compounds arising from proton hopping in hydrogen-bonded networks has been determined in the temperature range of 318 K to 598 K for the first time

In der vorliegenden Diplomarbeit wurden sekundäre Isotopeneffekte auf NMR-chemische Verschiebungen mit ab-initio quantenchemischen Methoden bestimmt. Um die zu erwartenden Fehler verschiedener Methoden abschätzen zu können, wurden die sekundären Isotopeneffekte von Fluor(2-2H1)ethan auf HF, MP2 und CCSD(T)-Niveau mit tripel- und quadrupel-Zeta Basissätzen berechnet. Anhand der Ergebnisse dieser Rechnungen lässt sich zeigen, dass gauche und antiperiplanare Konformere bereits mithilfe von sekundären Isotopenverschiebungen unterschieden werden können, die auf HF/tz2p-Niveau berechnet wurden. Weiterhin wurde untersucht, ob es eine Abhängingkeit des Isotopeneffektes von den Diederwinkeln zwischen Deuterium- und Fluorsubstituenten gibt. Die sekundären Isotopeneffekte auf 19F-NMR-chemische Verschiebungen von exo- und endo-2-Fluornorbornanen mit Deuterium Substituenten in den endo-3, exo-3, syn-7 oder anti-7 Positionen wurden auf HF/tz2p-Niveau berechnet. Es wird gezeigt, dass die berechneten Isotopeneffekte an 2-Fluornorbornanen eine Identifizierung der verschiedenen Stereoisomere erlauben. / In the present Diploma thesis secondary isotope effects on NMR chemical shieldings were determined using ab-initio quantum chemical methods. In order to estimate errors of various methods, secondary isotope effects on fluoro(2-2H1)ethane were calculated at the HF, MP2 and CCSD(T) level of theory using triple- and quadruple zeta basis sets. On the basis of these calculations it can be shown that gauche and antiperiplanar conformers can already be distinguished by their secondary isotope shifts calculated at the HF/tz2p level of theory. Furthermore it was investigated, whether a dependency of the isotope effects on dihedral angles between the deuterium and the fluorine substituent exists. The secondary isotope effects on 19F chemical shifts of exo- and endo-2-fluoronorbornanes with deuterium subsituents in the endo-3, exo-3, syn-7 or anti-7 positions were calculated at the HF/tz2p level. It is shown that the calculated isotope effects of 2-fluoronorbornanes allow to identify various stereoisomers.

In der vorliegenden Diplomarbeit wurden sekundäre Isotopeneffekte auf NMR-chemische Verschiebungen mit ab-initio quantenchemischen Methoden bestimmt. Um die zu erwartenden Fehler verschiedener Methoden abschätzen zu können, wurden die sekundären Isotopeneffekte von Fluor(2-2H1)ethan auf HF, MP2 und CCSD(T)-Niveau mit tripel- und quadrupel-Zeta Basissätzen berechnet. Anhand der Ergebnisse dieser Rechnungen lässt sich zeigen, dass gauche und antiperiplanare Konformere bereits mithilfe von sekundären Isotopenverschiebungen unterschieden werden können, die auf HF/tz2p-Niveau berechnet wurden. Weiterhin wurde untersucht, ob es eine Abhängingkeit des Isotopeneffektes von den Diederwinkeln zwischen Deuterium- und Fluorsubstituenten gibt. Die sekundären Isotopeneffekte auf 19F-NMR-chemische Verschiebungen von exo- und endo-2-Fluornorbornanen mit Deuterium Substituenten in den endo-3, exo-3, syn-7 oder anti-7 Positionen wurden auf HF/tz2p-Niveau berechnet. Es wird gezeigt, dass die berechneten Isotopeneffekte an 2-Fluornorbornanen eine Identifizierung der verschiedenen Stereoisomere erlauben. / In the present Diploma thesis secondary isotope effects on NMR chemical shieldings were determined using ab-initio quantum chemical methods. In order to estimate errors of various methods, secondary isotope effects on fluoro(2-2H1)ethane were calculated at the HF, MP2 and CCSD(T) level of theory using triple- and quadruple zeta basis sets. On the basis of these calculations it can be shown that gauche and antiperiplanar conformers can already be distinguished by their secondary isotope shifts calculated at the HF/tz2p level of theory. Furthermore it was investigated, whether a dependency of the isotope effects on dihedral angles between the deuterium and the fluorine substituent exists. The secondary isotope effects on 19F chemical shifts of exo- and endo-2-fluoronorbornanes with deuterium subsituents in the endo-3, exo-3, syn-7 or anti-7 positions were calculated at the HF/tz2p level. It is shown that the calculated isotope effects of 2-fluoronorbornanes allow to identify various stereoisomers.

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).