Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate beta-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.

Despite comprehensive studies addressing the chemical kinetics of butanol isomers, relevant uncertainties associated with the emissions of relevant pollutants persists. Also, a lack of chemistry knowledge of processes designed to produce biofuels limits their implementation at industrial scales. Therefore, the first objective of this thesis was to use cutting-edge kinetic theories to calculate rate constants of propen-2-ol, 1-pronenol, and vinyl alcohol keto-enol tautomerizations, which account for the production of the harmful carbonyl species. The second objective was to use the predictive capabilities of dynamic theories to reveal new chemistry of syngas oxy-combustion in supercritical CO2 and complexities of the zeolite dealumination, two processes involved in coal and biomass conversion. Rate constants computations considered transition state theory with variational effects, tunneling correction, and multistructural torsional anharmonicity. The study also included pressure effects by using and improving the system-specific quantum Rice-Ramsperger-Kassel/modified strong collision model. The atomistic simulations used ReaxFF force fields in hydrogen/oxygen/carbon monoxide/ carbon dioxide mixtures to represent the syngas system and an MFI zeolite with different water loading to model the dealumination. The results show that the studied assisted tautomerizations have much lower energy barriers than the unimolecular process. However, the “catalytic” effect is efficient only if the partner molecule is at high concentrations. Pressure effects are pronounced in the chemically activated tautomerizations, and the improved algorithm to compute pressure-dependent rate constants overcomes the initial difficulties associated with its application to C3 or larger molecules at temperatures above 800-1000 K. Reactive molecular dynamics simulations revealed the role of CO2 as an initiator in the syngas oxy-combustion and a new step involving the formation of formic acid. Those simulations for the zeolite dealumination process also showed that proton transfer, framework flexibility, and aluminum dislodging mediated by silicon reactions are complex dynamic phenomena determining the process. These aspects complement the dealumination theory uncovered so far and establish new paths in the study of water-zeolite interactions. Overall, the rate constants computed in this work reduce relevant uncertainties in the chemical kinetic mechanisms of alcohol oxidation, and the molecular dynamics simulations broaden the chemical knowledge of processes aimed at the utilization of alternative energy resources.

This thesis describes a computational investigation of the mutagenicity of 5-bromouracil (BrU). In Chapter 1, three models of spontaneous and BrU-induced base mispairing (rare tautomer, wobble pair, and ion) are reviewed. Chapter 2 presents the computational techniques used: electronic structure methods (Hartree–Fock-based and density functional theory) and molecular dynamics. Chapter 3 presents optimisations of the keto and enol tautomers of BrU and uracil (U) in water clusters. The enol tautomer of BrU is found to be more stable than that of U. Chapter 4 is a molecular dynamics study of the keto-enol tautomerism of BrU and U in a periodic water box. The pKₐ of BrU at N3 is found to be lower than that of U. Chapter 5 is a study of stacked base dimers containing BrU, U, or thymine (T) stacking with natural bases. Some structures were taken from the Protein Data Bank, while others were generated using an in-house methodology. BrU is found to stack more strongly than T in vacuo, but solvation and thermal effects nullify this difference. Chapter 6 discusses the significance of the results in Chapters 3–5 in terms of BrU-induced mutagenesis. Appendices A and B–D provide supplementary material to Chapters 2 and 5, respectively. Appendix E is an investigation of the “base flipping” pathway of 2-aminopurine (2AP). Both 2AP/N and A/N dinucleosides (N = thymine or guanine) are found to adopt a wide range of energy-minimum conformations – not only stacked and “flipped”, but also intermediate – and the stacked are not the most favourable by free energy. Appendix F is a list of publications and papers in preparation. One publication concerns BrU stacking. The other is a conformational study of the dipeptide tyrosine-glycine: the theoretical results are shown to be consistent with experiment (R2PI spectra) if thermal effects are taken into account.

The work presented in this thesis has broadly established a few findings about the structure¬hyperpolarizability relation in molecular compounds: First, by measuring βHRS of an organic keto-enol tautomer, benzoylacetanilide in a binary solvent, I have shown that the first hyperpolarizability can be manipulated favourably by changing the composition of the solvent or by altering the pH of the solution. BA which exists in the pure keto form in water and as a keto-enol tautomer in ethanol, co-exists in equilibrium with the keto and enol forms at pH 11 in aqueous solution. The β value of the anion form is 709 x 10¬30 esu , whereas that of the enol is 232 x 10-30 esu and of the keto is 88 x 10-30 esu. There is an enhancement of β by ~ 8 times for the anion and ~3 times for the enol compared to the keto form. This opens up the possibility of finding large nonlinearities in organic molecules by simply ionizing it. Second, in organometallic complexes of divalent Ru, the first hyperpolarizability could be manipulated by altering the valence state of the metal center by oxidation or reduction or by introducing highly polarisable halogen atoms as substitutions in ligands attached to the metal center. The enhancement of first hyperpolarizability was observed in mononuclear [RuII(acac)2(CH3CN)2] complex by 1.7 times when the metal center was oxidized from RuII to RuIII. As it is already known that the complexes like [(acac)2Ru-bptz-Ru(acac)2] produce stable mixed valent compound, the enhancement of β by ~1.6 times is appearing because of that species only. Exploring Large Nonlinearity in Tautomers In this thesis I have taken a linear ketone for studying the effect of structure on β via the enol and anion formation mediated by solvent and pH of the medium. In the present study the proton transfer in BA took place in the ground state of the ketone and the enol or anion are produced in the ground states. The proton transfer reaction (tautomerism) can also happen in the excited state as well in some molecules where there is a substantial barrier to the proton transfer reaction in the ground state. In such systems, once the ketone is excited using ultraviolet light the barrier to proton transfer in the medium is overcome and a proton transfer in the excited state takes place and the enol is produced. Since such a system will be at higher energy, it will be interesting to do a two-laser experiment where the excited state hyperpolarizability is measured in a time resolved manner and the β value is determined in the excited state. Building Molecular Nonlinearity in Step-by-Step Electron Transfer In this thesis, I have dealt with a binuclear complex of Ru(II) which in one-step electrochemical oxidation produced a mixed valence compound which had substantially higher β value compared to the unoxidized complex. In this way it is possible to build a multicentered complex and see if sequential one-electron transfer and subsequent oxidation/reduction of the metal centers produce a mixed-valent metal compound with large molecular nonlinearity. The indication from the present study is that such a scheme should double the β value in each one-electron transfer step. Also the linker group/moiety between the successive metal centers will play an important role in dictating the efficiency of electron transfer. If the metal d-electrons in a multinuclear complex are linked through a π-conjugation, one would expect manifold enhancement of β. Such metal arrays can also be designed in 2 or 3 dimensions. The dimensionality of the multinuclear metal complexes can easily be changed by supramolecular design and synthesis strategy. Such metal networks may or may not generate large β molecules since electronic polarization in such systems may not be superimposable in a coherent fashion and may not add in a positive sense. All these remain to be tested and explored in the future.

No description available.

In dieser Arbeit wird die Synthese neuartiger 5-monosubstituierter Barbituratfarbstoffe mit elektronenziehenden Substituenten in 5-Position beschrieben. Durch diese Funktionalisierung entstehen schaltbare Farbstoffe mit einer farblosen Ketoform und einer farbigen Enolform. Die Einflüsse verschieden stark elektronenziehender Substituenten sowie unterschiedlich großer konjugierter π-Systeme auf die Keto-Enol-Tautomerie wurden untersucht. Dies erfolgt einerseits mittels Röntgeneinkristallstrukturanalysen der Festkörper und andererseits mit solvatochromen Untersuchungen in Lösung. Durch die Keto-Enol-Tautomerie der Barbituratfarbstoffe wird die Wasserstoffbrücken¬bindungssequenz beim Übergang zwischen Keto- und Enol-Form verändert. Es wurde gezeigt, dass durch Zugabe von Rezeptoren mit komplementärer Wasserstoffbrückenbindungssequenz zur Enol-Form das tautomere Gleichgewicht der Barbitursäuren hin zur Enol-Form verschoben werden kann. Um hierzu verlässliche Aussagen zu erhalten wurden vergleichende Experimente mit N,N´-dialkylierten Barbituratfarbstoffen durchgeführt. Aufgrund der Synthesestrategie der Barbituratfarbstoffe, welche ausgehend von Barbituratanionen über nukleophile aromatische Substitutionsreaktionen hergestellt wurden, war es zweckmäßig die Nukleophilieparameter der Barbituratanionen zu ermitteln. Dazu wurde der Ansatz von Mayr gewählt und die Nukleophilie von vier Barbituratanionen bestimmt. Weiterhin konnte in dieser Arbeit die Charakterisierung von ionischen Flüssigkeiten nach der 4-Parameter-Gleichung von Catalán umgesetzt werden. Dabei gelang es erstmal für eine vielzahl verschiedener ionischer Flüssigkeiten die Polarisierbarkeit und Dipolarität getrennt voneinander mit Hilfe zweier solvatochromer Farbstoffe zu ermitteln.

In dieser Arbeit wird die Synthese neuartiger 5-monosubstituierter Barbituratfarbstoffe mit elektronenziehenden Substituenten in 5-Position beschrieben. Durch diese Funktionalisierung entstehen schaltbare Farbstoffe mit einer farblosen Ketoform und einer farbigen Enolform. Die Einflüsse verschieden stark elektronenziehender Substituenten sowie unterschiedlich großer konjugierter π-Systeme auf die Keto-Enol-Tautomerie wurden untersucht. Dies erfolgt einerseits mittels Röntgeneinkristallstrukturanalysen der Festkörper und andererseits mit solvatochromen Untersuchungen in Lösung. Durch die Keto-Enol-Tautomerie der Barbituratfarbstoffe wird die Wasserstoffbrücken¬bindungssequenz beim Übergang zwischen Keto- und Enol-Form verändert. Es wurde gezeigt, dass durch Zugabe von Rezeptoren mit komplementärer Wasserstoffbrückenbindungssequenz zur Enol-Form das tautomere Gleichgewicht der Barbitursäuren hin zur Enol-Form verschoben werden kann. Um hierzu verlässliche Aussagen zu erhalten wurden vergleichende Experimente mit N,N´-dialkylierten Barbituratfarbstoffen durchgeführt. Aufgrund der Synthesestrategie der Barbituratfarbstoffe, welche ausgehend von Barbituratanionen über nukleophile aromatische Substitutionsreaktionen hergestellt wurden, war es zweckmäßig die Nukleophilieparameter der Barbituratanionen zu ermitteln. Dazu wurde der Ansatz von Mayr gewählt und die Nukleophilie von vier Barbituratanionen bestimmt. Weiterhin konnte in dieser Arbeit die Charakterisierung von ionischen Flüssigkeiten nach der 4-Parameter-Gleichung von Catalán umgesetzt werden. Dabei gelang es erstmal für eine vielzahl verschiedener ionischer Flüssigkeiten die Polarisierbarkeit und Dipolarität getrennt voneinander mit Hilfe zweier solvatochromer Farbstoffe zu ermitteln.