Theoretical study of chloroperoxidase catalyzed chlorination of beta-cyclopentanedione and role of water in the chlorination mechanism

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 β-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.

Mangrove tannins in aquatic ecosystems: Their fate and possible influence on dissolved organic carbon and nitrogen cycling

We describe the fate of mangrove leaf tannins in aquatic ecosystems and their possible influence on dissolved organic nitrogen (DON) cycling. Tannins were extracted and purified from senescent yellow leaves of the red mangrove (Rhizophora mangle) and used for a series of model experiments to investigate their physical and chemical reactivity in natural environments. Physical processes investigated included aggregation, adsorption to organic matter-rich sediments, and co-aggregation with DON in natural waters. Chemical reactions included structural change, which was determined by excitation–emission matrix fluorescence spectra, and the release of proteins from tannin–protein complexes under solar-simulated light exposure. A large portion of tannins can be physically eliminated from aquatic environments by precipitation in saline water and also by binding to sediments. A portion of DON in natural water can coprecipitate with tannins, indicating that mangrove swamps can influence DON cycling in estuarine environments. The chemical reactivity of tannins in natural waters was also very high, with a half-life of less than 1 d. Proteins were released gradually from tannin–protein complexes incubated under light conditions but not under dark conditions, indicating a potentially buffering role of tannin– protein complexes on DON recycling in mangrove estuaries. Although tannins are not detected at a significant level in natural waters, they play an important ecological role by preserving nitrogen and buffering its cycling in estuarine ecosystems through the prevention of rapid DON export/loss from mangrove fringe areas and/or from rapid microbial mineralization.

Development of an enhanced hydro-geochemical model to address mercury-speciation fate and transport in aquatic environments

An awareness of mercury (Hg) contamination in various aquatic environments around the world has increased over the past decade, mostly due to its ability to concentrate in the biota. Because the presence and distribution of Hg in aquatic systems depend on many factors (e.g., pe, pH, salinity, temperature, organic and inorganic ligands, sorbents, etc.), it is crucial to understand its fate and transport in the presence of complexing constituents and natural sorbents, under those different factors. An improved understanding of the subject will support the selection of monitoring, remediation, and restoration technologies. The coupling of equilibrium chemical reactions with transport processes in the model PHREEQC offers an advantage in simulating and predicting the fate and transport of aqueous chemical species of interest. Thus, a great variety of reactive transport problems could be addressed in aquatic systems with boundary conditions of specific interest. Nevertheless, PHREEQC lacks a comprehensive thermodynamic database for Hg. Therefore, in order to use PHREEQC to address the fate and transport of Hg in aquatic environments, it is necessary to expand its thermodynamic database, confirm it and then evaluate it in applications where potential exists for its calibration and continued validation. The objectives of this study were twofold: 1) to develop, expand, and confirm the Hg database of the hydrogeochemical PHREEQC to enhance its capability to simulate the fate of Hg species in the presence of complexing constituents and natural sorbents under different conditions of pH, redox, salinity and temperature; and 2) to apply and evaluate the new database in flow and transport scenarios, at two field test beds: Oak Ridge Reservation, Oak Ridge, TN and Everglades National Park, FL, where Hg is present and is of much concern. Overall, this research enhanced the capability of the PHREEQC model to simulate the coupling of the Hg reactions in transport conditions. It also demonstrated its usefulness when applied to field situations.

Ab initio quantum chemical studies on neutral-radical reactions of ethynyl (C2H) and cyano (CN) with unsaturated hydrocarbons

An Ab Initio/RRKM study of the reaction mechanism and product branching ratios of neutral-radical ethynyl (C2H) and cyano (CN) radical species with unsaturated hydrocarbons is performed. The reactions studied apply to cold conditions such as planetary atmospheres including Titan, the Interstellar Medium (ISM), icy bodies and molecular clouds. The reactions of C2H and CN additions to gaseous unsaturated hydrocarbons are an active area of study. NASA's Cassini/Huygens mission found a high concentration of C2H and CN from photolysis of ethyne (C2H2) and hydrogen cyanide (HCN), respectively, in the organic haze layers of the atmosphere of Titan. The reactions involved in the atmospheric chemistry of Titan lead to a vast array of larger, more complex intermediates and products and may also serve as a chemical model of Earth's primordial atmospheric conditions. The C2H and CN additions are rapid and exothermic, and often occur barrierlessly to various carbon sites of unsaturated hydrocarbons. The reaction mechanism is proposed on the basis of the resulting potential energy surface (PES) that includes all the possible intermediates and transition states that can occur, and all the products that lie on the surface. The B3LYP/6-311g(d,p) level of theory is employed to determine optimized electronic structures, moments of inertia, vibrational frequencies, and zero-point energy. They are followed by single point higher-level CCSD(T)/cc-vtz calculations, including extrapolations to complete basis sets (CBS) of the reactants and products. A microcanonical RRKM study predicts single-collision (zero-pressure limit) rate constants of all reaction paths on the potential energy surface, which is then used to compute the branching ratios of the products that result. These theoretical calculations are conducted either jointly or in parallel to experimental work to elucidate the chemical composition of Titan's atmosphere, the ISM, and cold celestial bodies.<.

Ab Initio Quantum Chemical Studies on Neutral-Radical Reactions of Ethynyl (C2H) and Cyano (CN) with Unsaturated Hydrocarbons

An Ab Initio/RRKM study of the reaction mechanism and product branching ratios of neutral-radical ethynyl (C2H) and cyano (CN) radical species with unsaturated hydrocarbons is performed. The reactions studied apply to cold conditions such as planetary atmospheres including Titan, the Interstellar Medium (ISM), icy bodies and molecular clouds. The reactions of C2H and CN additions to gaseous unsaturated hydrocarbons are an active area of study. NASA’s Cassini/Huygens mission found a high concentration of C2H and CN from photolysis of ethyne (C2H2) and hydrogen cyanide (HCN), respectively, in the organic haze layers of the atmosphere of Titan. The reactions involved in the atmospheric chemistry of Titan lead to a vast array of larger, more complex intermediates and products and may also serve as a chemical model of Earth’s primordial atmospheric conditions. The C2H and CN additions are rapid and exothermic, and often occur barrierlessly to various carbon sites of unsaturated hydrocarbons. The reaction mechanism is proposed on the basis of the resulting potential energy surface (PES) that includes all the possible intermediates and transition states that can occur, and all the products that lie on the surface. The B3LYP/6-311g(d,p) level of theory is employed to determine optimized electronic structures, moments of inertia, vibrational frequencies, and zero-point energy. They are followed by single point higher-level CCSD(T)/cc-vtz calculations, including extrapolations to complete basis sets (CBS) of the reactants and products. A microcanonical RRKM study predicts single-collision (zero-pressure limit) rate constants of all reaction paths on the potential energy surface, which is then used to compute the branching ratios of the products that result. These theoretical calculations are conducted either jointly or in parallel to experimental work to elucidate the chemical composition of Titan’s atmosphere, the ISM, and cold celestial bodies.

Chemical characterization of soil organic matter in an oligotrophic, subtropical, freshwater wetland system: Sources, diagenesis and preservation

Freshwater wetland soils of the Everglades were studied in order to assess present environmental conditions and paleo-environmental changes using organic geochemistry techniques. Organic matter in dominant vegetation, peat and marl soils was characterized by geochemical means. Samples were selected along nutrient and hydrology gradients with the objective to determine the historical sources of organic matter as well as the extent of its preservation. Effective molecular proxies were developed to differentiate the relative input of organic matter from different biological sources to wetland soils. Thus historical vegetation shifts and hydroperiods were reconstructed using those proxies. The data show good correlations with historical water management practices starting at the turn of the century and during the mid 1900's. Overall, significant shortening of hydroperiods during this period was observed. The soil organic matter (SOM) preservation was assessed through elemental analysis and molecular characterizations of bulk 13C stable isotopes, solid state 13C NMR spectroscopy, UV-Vis spectroscopy, and tetramethyl ammonium hydroxide (TMAH) thermochemolysis-GC/MS. The relationship of the environmental conditions and degradation status of the soil organic matter (SOM) among the sites suggested that both high nutrient levels and long hydroperiod favor organic matter degradation in the soils. This is probably the result of an increase in the microbial activity in the soils which have higher nutrient levels, while longer hydroperiods may enhance physical/chemical degradation processes. The most significant transformations of biomass litter in this environment are controlled by very early physical/chemical processes and once the OM is incorporated into surface soils, the diagenetic change, even over extended periods of time is comparatively minimal, and SOM is relatively well preserved regardless of hydroperiod or nutrient levels. SOM accumulated in peat soils is more prone to continued degradation than the SOM in the marl soils. The latter is presumably stabilized early on through direct air exposure (oxidation) and thus, it is more refractory to further diagenetic transformations such as humification and aromatization reactions.

Quantum transition state theory and solving a first order master equation for complex reactions numerically

The field of chemical kinetics is an exciting and active field. The prevailing theories make a number of simplifying assumptions that do not always hold in actual cases. Another current problem concerns a development of efficient numerical algorithms for solving the master equations that arise in the description of complex reactions. The objective of the present work is to furnish a completely general and exact theory of reaction rates, in a form reminiscent of transition state theory, valid for all fluid phases and also to develop a computer program that can solve complex reactions by finding the concentrations of all participating substances as a function of time. To do so, the full quantum scattering theory is used for deriving the exact rate law, and then the resulting cumulative reaction probability is put into several equivalent forms that take into account all relativistic effects if applicable, including one that is strongly reminiscent of transition state theory, but includes corrections from scattering theory. Then two programs, one for solving complex reactions, the other for solving first order linear kinetic master equations to solve them, have been developed and tested for simple applications.