Both bromodeprotonation and bromodesulphonation occur during aqueous bromination of sodium p-methoxybenzenesulphonate, A, and potassium l-methylnaphthalene-4-sulphonate, B. Extensive kinetic studies reported here suggest that bromodesulphonation of A proceeds by a two-step process with Br2 as the brominating species, but do not completely exclude Br+ (or H2OBr+) acting in either a one- or two-step process. For B, the kinetic data can be interpreted by either a one- or two-step process with Br2 as the brominating species. Kinetic sulphur isotope effects have been measured for the bromodesulphonation of A and B and found to vary with bromide-ion concentration, thus strongly supporting the two-step process involving molecular bromine. The kinetic results for the bromodeprotonation of A cannot distinguish between a one- and two-step process involving Br2l the two-step mechanism has been confirmed by the observation of a variation in kinetic hydrogen isotope effect with bromide-ion concentration. / Thesis / Doctor of Philosophy (PhD)

Enzyme dynamics occur on a wide range of length and timescales. This work is focused on understanding enzyme dynamic at the fs-ps timescale as this is the dynamic range at which bonds are typically made and broken during chemical reactions. Our work focuses on enzymes that catalyze hydride transfer between two carbon atoms - a fundamental reaction in biology. Primary kinetic isotope effects and their temperature dependence have implied that fast dynamics of the enzyme are important in facilitating hydride transfer, however these experiments do not measure any such motions directly. We make use of two-dimensional infrared spectroscopy (2D IR), a technique that interrogates the vibrations of molecules to extract dynamic information from the surrounding environment with 100 fs resolution. A model system, formate dehydrogenase (FDH), is an excellent probe of dynamics at the fs-ps timescale. Azide bound to the ternary complex of FDH offers the ability to measure dynamics of an analog structure of the reactive complex using 2D IR, while also studying the reaction directly with and KIE’s and their temperature dependence. By altering various parts of the structure of FDH via mutagenesis and other techniques, we investigate the role of structure and dynamics to determine how fast dynamics of the active site influence the the kinetics of hydride transfer. These experiments are the first means of providing a dynamic interpretation of KIEs and their temperature dependence.

The results of kinetic isotope determination and computational studies on Noyori-type catalytic systems for the hydrogenation of ketones are presented. The catalysts examined include RuH2(NHCMe2CMe2NH2)(R-binap) and RuH(NHCMe2CMe2NH2)(PPh3)2. These complexes are active catalysts for ketone hydrogenation in benzene without addition of an external base. The kinetic isotope effect (KIE) for catalysis by RuH2(NHCMe2CMe2NH2)(R-binap) was determined to be 2.0 ± (0.1). The calculated KIE for the model system RuH(NHCH2CH2NH2)(PH3)2 was 1.3, which is smaller than the experimentally observed value but does not include tunneling effects. The complex OsH(NHCMe2CMe2NH2)(PPh3)2 is known to display autocatalytic behaviour when it catalyzes the hydrogenation of acetophenone in benzene. Pseudo first-order reaction conditions are obtained via addition of the product alcohol at the beginning of each kinetic experiment. The KIE determined using various combinations of deuterium-labeled gas, alcohol and ketone was found to be 1.1 ± (0.2). DFT calculations were used to explore the effect of the alcohol and the KIE. An induction period is observed at the start of the hydrogenation that is attributed to the formation of an alkoxide complex. A novel, diamine-orchestrated hydrogen-bonding network is proposed based on DFT calculations to explain how the alkoxide is converted back to the active catalyst. The tetradentate complexes trans-RuHCl[PPh2(ortho-C6H4)CH2NHCH2)]2 and RuHCl[PPh2(ortho-C6H4)CH2NHCMe2)]2 are known to be catalysts for the hydrogenation of acetophenone and benzonitrile in toluene when activated by KOtBu/KH. DFT studies were performed and a mechanism is proposed. The calculated rate limiting step for acetone hydrogenation was found to be heterolytic splitting of dihydrogen, which agrees well with experiment. The novel outer-sphere sequential hydrogenation of a CN triple bond and then a C=N double bond is proposed. A mechanism is proposed, which is supported by DFT studies, to explain the selectivity observed in the nucleophilic attack of amines or aziridines on palladium -prenyl phosphines complexes. Calculations on based on a palladium complex with two phosphorus donor ligands indicated that the observed selectivity would not be produced. Using two new model intermediates with either THF or aziridine substituted for a phosphine ligand trans to the unhindered side of the prenyl ligand did predict the experimentally observed selectivity.

The results of kinetic isotope determination and computational studies on Noyori-type catalytic systems for the hydrogenation of ketones are presented. The catalysts examined include RuH2(NHCMe2CMe2NH2)(R-binap) and RuH(NHCMe2CMe2NH2)(PPh3)2. These complexes are active catalysts for ketone hydrogenation in benzene without addition of an external base. The kinetic isotope effect (KIE) for catalysis by RuH2(NHCMe2CMe2NH2)(R-binap) was determined to be 2.0 ± (0.1). The calculated KIE for the model system RuH(NHCH2CH2NH2)(PH3)2 was 1.3, which is smaller than the experimentally observed value but does not include tunneling effects. The complex OsH(NHCMe2CMe2NH2)(PPh3)2 is known to display autocatalytic behaviour when it catalyzes the hydrogenation of acetophenone in benzene. Pseudo first-order reaction conditions are obtained via addition of the product alcohol at the beginning of each kinetic experiment. The KIE determined using various combinations of deuterium-labeled gas, alcohol and ketone was found to be 1.1 ± (0.2). DFT calculations were used to explore the effect of the alcohol and the KIE. An induction period is observed at the start of the hydrogenation that is attributed to the formation of an alkoxide complex. A novel, diamine-orchestrated hydrogen-bonding network is proposed based on DFT calculations to explain how the alkoxide is converted back to the active catalyst. The tetradentate complexes trans-RuHCl[PPh2(ortho-C6H4)CH2NHCH2)]2 and RuHCl[PPh2(ortho-C6H4)CH2NHCMe2)]2 are known to be catalysts for the hydrogenation of acetophenone and benzonitrile in toluene when activated by KOtBu/KH. DFT studies were performed and a mechanism is proposed. The calculated rate limiting step for acetone hydrogenation was found to be heterolytic splitting of dihydrogen, which agrees well with experiment. The novel outer-sphere sequential hydrogenation of a CN triple bond and then a C=N double bond is proposed. A mechanism is proposed, which is supported by DFT studies, to explain the selectivity observed in the nucleophilic attack of amines or aziridines on palladium -prenyl phosphines complexes. Calculations on based on a palladium complex with two phosphorus donor ligands indicated that the observed selectivity would not be produced. Using two new model intermediates with either THF or aziridine substituted for a phosphine ligand trans to the unhindered side of the prenyl ligand did predict the experimentally observed selectivity.

An effiecient stoichiometric amount system has been developed for the synthesis of N-phenylpyridin-2-amine Palladacycle, and then reation with aryl trifluoroborate to 9-(pyridine-2-yl)-9H-carbazoles by C-H bond activation/ C-C bond formation and C-N bond formation. The subsitutent effect of the aryl trifluoroborate with N-phenylpyridin-2-amine Palladacycle intermediate was observed. Mechanistic studies of C-H bond cleavaged, including trapping of reaction intermediates and kinetic isotope effect experiments, are also presented.

Formaldehyde emissions from non-structural wood composites are regulated and the regulation target is urea-formaldehyde (UF) resin. UF resins are hydrolytically unstable and constantly emit formaldehyde as a function of temperature and relative humidity. When heated, wood also generates formaldehyde, but this was of little concern until 2010 when formaldehyde regulations became much more demanding. This regulation motivated the industry to account for all formaldehyde sources, synthetic as from resin, and biogenic as from wood. This effort represents first steps towards quantifying biogenic and synthetic contributions to formaldehyde emissions in non-structural wood composites. It is possible to distinguish the 13C/12C isotope ratio of UF resins from the isotope ratio of plant biomass. Conditions during and after composite hot-pressing promote reactions that generate formaldehyde from wood and UF resin, and the kinetic isotope effect continuously lowers the product isotope ratios as a function of yield. If such isotope fractionation did not occur, it would be a simple matter to quantify contributions of wood and UF resin to formaldehyde emissions using static isotope ratios. Isotope fractionation, therefore, complicates the requirements for distinguishing biogenic and synthetic formaldehyde in wood composite emissions. Those requirements are 1) establish the reference carbon isotope ratios in wood and in UF resin (just the formaldehyde portion of UF), and 2) estimate the kinetic isotope effects in formaldehyde generation by wood and cured UF resin. The latter requirement fixes a range for the respective isotope ratios; the numerical ranges enable a simple model of the average isotope ratio for a mixture of biogenic and synthetic formaldehyde in wood composite emissions. Finally, the measured isotope ratio of captured emissions would be compared to the model. This work did not achieve all aspects of the requirements mentioned, but a solid foundation was established for future completion of the ultimate goals. In reference to requirement 1, the carbon isotope ratio of experimental Pinus taeda wood was accurately measured (including some isolated fractions) using isotope ratio mass spectroscopy (IRMS). IRMS of UF resin first requires removal of urea carbons- UF resin was subjected to acid hydrolysis and capture of the resin formaldehyde into aqueous ammonium hydroxide. This provided a nearly quantitative conversion (negligible isotope fractionation) of resin formaldehyde into hexamine for IRMS. Using this hexamine method, the formaldehyde carbon isotope ratios of two industrial UF resins were accurately measured, demonstrating basic feasibility for the project goal. Estimating the kinetic isotope effect (Requirement 2) required creation of a thermochemical reactor, where wood or cured UF resin was heated under N2 flow such that the emitted formaldehyde was easily captured. In this case, conversion of captured formaldehyde into hexamine was abandoned in favor of silica gel cartridges loaded with sodium bisulfite. Isolation and IRMS of the formaldehyde-bisulfite adduct were effective and considered easily transferable to industrial settings. This system was employed to measure fractionation in cured resin as a function of relative humidity, and in Pinus taeda wood as a function of relative humidity, temperature, and time. More information about isotope fractionation is required; but most notable was the fractionation behavior in wood where evidence was found for multiple formaldehyde generating reactions. Overall, this work established feasibility for the goals and laid the foundation for future efforts. / Master of Science / Home-interior products like cabinetry are often produced with wood composites adhesively bonded with urea-formaldehyde (UF) resin. UF resins are low cost and highly effective, but their chemical nature results in formaldehyde emission from the composite. High emissions are avoided, and the federal government has regulated and steadily reduced allowable emissions since 1985. The industry continuously improved UF technologies to meet regulations, as in 2010 when the most demanding regulations were implemented. At that time, many people were unaware that wood also generates formaldehyde; this occurs at very low levels but heating during composite manufacture causes a temporary burst of natural formaldehyde. Some wood types produce unusually high formaldehyde levels, making regulation compliance more difficult. This situation, and the desire to raise public awareness, created a major industrial goal: determine how much formaldehyde emission originates from the resin and how much originates from the wood. These formaldehyde sources can be distinguished by measuring the carbon isotope ratio, 13C/12C. This ratio changes and varies due to the kinetic isotope effect. Slight differences in 13C and 12C reactivity reveal the source as either petrochemical (synthetic formaldehyde) or plant-based (biogenic formaldehyde). This work demonstrates that achieving the industry goal is entirely feasible, and it provides the analytical foundation. The technical strategy is: 1) establish reference isotope ratios in wood and in UF resin, and 2) from the corresponding wood composite, capture formaldehyde emissions, measure the isotope ratio, and simply calculate the percentage contributions from the reference sources. However, a complication exists. When the reference sources generate formaldehyde, the respective isotope ratios change systematically in a process called isotope fractionation (another term for the kinetic isotope effect). Consequently, this effort developed methods to measure fractionation when cured UF resin and wood separately generate formaldehyde, with greater emphasis on wood. Isotope fractionation in wood revealed multiple fractionation mechanisms. This complexity presents intriguing possibilities for new perspectives on formaldehyde emission from wood and cured UF resin. In summary, this work demonstrated how source contributions to formaldehyde emissions can be determined; it established effective methods required to refine and perfect the approach, and it revealed that isotope fractionation could serve as an entirely novel tool in the materials science of wood composites.

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.