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In this thesis, quantum chemistry, in particular the B3LYP density functional method, is used to investigate a number of methyl transfer enzymes. Quantum chemical methodology is today a very important tool in the elucidation of properties and reaction mechanisms of enzyme active sites. The enzymes considered in this thesis are the S-adenosyl L-methionine-dependent enzymes - glycine N-methyltransferase, guanidinoacetate methyltransferase, phenylethanolamine N-methyltransferase, and histone lysine methyltransferase. In addition, the reaction mechanism of the DNA repairing enzyme O6-methylguanine methyltransferase is studied. Active site models of varying sizes were designed and stationary points along the reaction paths were optimized and characterized. Potential energy surfaces for the reactions were calculated and the feasibility of the suggested reaction mechanisms was able to be judged. By systematically increasing the size of the models, deeper insight into the details of the reactions was obtained, the roles of the various active site residues could be analyzed, and, very importantly, the adopted modeling strategy was evaluated. / QC 20100927

Cumene hydroperoxide (CHP), a type of organic peroxide, is widely used in the chemical industry for diverse applications. However, it decomposes and undergoes highly exothermic runaway reactions under high temperature because of its unstable peroxide functional group. The risk of runaway reaction is intensified by the fact that operation temperature of CHP is close to its onset temperature in many cases. To ensure safe handling of CHP in the chemical industry, a lot of research has been done on it including theoretical research at the microscopic level and experimental research at the macroscopic level. However, the unstable radicals in the CHP decomposition reactions make it difficult to study its reaction pathway, and therefore lead to incomplete understanding of the reaction mechanism. The slow progress in theoretical research hinders the application of the theoretical prediction in experimental research. For experimental research, the lack of integration of operational parameters into the reactivity evaluation limits its application in industrial process. In this thesis, a systematic methodology is proposed to evaluate the reactivity hazards of CHP. This methodology is a combination of theoretical research using computational quantum chemistry method and experimental research using RSSTTM. The theoretical research determined the dominant reaction pathway of CHP decomposition reaction through the study of thermodynamic and kinetic stability, which was applied to the analysis of experimental results. The experimental research investigated the effect of CHP concentration on runaway reactions by analyzing the important parameters including temperature, pressure, self-heat rate and pressure rate. This methodology could also be applied to other organic peroxides or other reactive chemicals. The results of theoretical research on reaction mechanism show that there is a dominant reaction pathway, which consumes most of the CHP in decomposition reaction. This conclusion agrees with the experimental results that 40 wt% is a critical point for almost all important parameters of runaway reactions. In the high concentration range above 40 wt%, some unknown reaction pathways are involved in decomposition of CHP because of lack of cumene. The shift of reaction mechanism causes the change of the effect of concentration on runaway reactions.

Many reaction mechanisms have been developed over the past few decades to predict flame characteristics. A detailed reaction mechanism can predict flame characteristics well, but at a high computational cost. The reason for reducing reaction mechanisms is to reduce the computational time needed to simulate a problem. The focus of this work is on the validity of reduced methane-air combustion mechanisms, particularly pertaining to satisfying the entropy inequality. While much of this work involves a two-step reaction mechanism developed by Dr. Charles Westbrook and Dr. Frederick Dryer, some consideration is given to the four-step and three-step mechanisms of Dr. Norbert Peters. These mechanisms are used to simulate the Flame A experiment from Sandia National Laboratories. The two-step mechanism of Westbrook and Dryer is found to generate results that violate the entropy inequality. Modifications are made to the two-step mechanism simulation in an effort to reduce these violations. Two new mechanisms, Mech 1 and Mech 2, are developed from the original two-step reaction mechanism by modifying the empirical data constants in the Arrhenius reaction form. The reaction exponents are set to the stoichiometric coefficients of the reaction, and the concentrations computed from a one-dimensional flame simulation are matched by changing the Arrhenius parameters. The new mechanisms match experimental data more closely than the original two-step mechanism and result in a significant reduction in entropy inequality violations. The solution from Mech 1 had only 9 cells that violated the entropy inequality, while the original two-step mechanism of Westbrook and Dryer had 22,016 cells that violated the entropy inequality. The solution from Mech 2 did not have entropy inequality violations. The method used herein for developing the new mechanisms can be applied to more complex reaction mechanisms.

Master of Science / Department of Chemical Engineering / Keith Hohn / The study will utilize a probabilistic reaction modeling method for ring-opening reactions of epoxide. In particular, to elucidate the reaction mechanism by the methods presented, focus will be placed on the nucleophillic attack of ethylene oxide by ammonia and its anion. This focus was chosen because of the potential to gain significant advantage in computational intensity required to model the epoxy-amino macromolecular curing reactions and resulting thermochemical and physical properties of the cured resin. The method employed utilizes the combinatorial probability that 1. Two molecules will approach a transition state with sufficient energy to drive reaction 2. Any reaction will occur for a given penetration into the potential energy surface. The concept of a transition state is relaxed to allow a dynamic probability that any reaction will proceed given a position on the intrinsic reaction coordinate (IRC) rather than searching for a specific transition state of theoretical reaction probability. 3. The reaction that occurs yields a desired stable or semi-stable molecular complex This study will focus on identifying possible stable and semi-stable products and corresponding rate constants. The technique developed here is novel in that it provides an unsupervised method to identify all structures corresponding to minima on the potential energy surface. The technique provides a pragmatic and efficient approach to sample a molecular system for different reaction mechanisms and provides a relative energy requirement to achieve these mechanisms with no presupposition of the mechanism, product, or transition state. It is possible from this data to derive rate constants for a reacting system, however, the rate constant derived for the EO/NH2 molecular system yielded significantly understated reaction probabilities and therefore rate constants.

This study was to prepare nanoscale MgO using the homogeneous precipitation process and to investigate its destructive adsorption with dye wastewater of reactive black-5 and reactive blue-19. In addition, UV-vis Spectrophotometer, Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF/MS) and Gas Chromatograph/Mass Spectrometer (GC/MS) were used to analyze the intermediates resulting from destructive adsorption. Based on the results obtained, the destructive adsorption mechanisms for the treatment of dye wasterwater by nanoscale MgO were proposed in this study. In this work, the optimal operating conditions for nanoscale MgO synthesis were determined to be the following: (1) a chemical reaction time of 7 hr, (2) reaction temperature of 125¢J, (3) molar ratio of 9 for urea/MgCl2¡D6H2O, (4) water addition of 250 mL, (5) mixing intensity of 90 strokes per min, (6) calcination at 450¢J for 4 hr, (7) reflux time of 24 hr, (8) freeze-drying method, (9) two stage calcinations. Using these operating conditions one is able to prepare 2-D nanoscale MgO of hexagonal platelets with a thickness of 20-30 nm and BET surface area of 120-125 m2/g. The adsorption model of nanoscale MgO for RB-5 and RB-19 was fitted to the Langmuir equation and their adsorption capacity were 196.08 mg/g and 163.93 mg/g, respectively. Both of them were fitted to the pseudo-second-order kinetic model equation. The optimal operating conditions of nanoscale MgO for destructive adsorption of both dyes were determined to be the following: (1) an initial dye concentration of 1000 mg/L, (2) a nanoscale MgO dose of 15 g/L, (3) a vigorous mixing of 30 min, (4) no need of system pH adjustment. Under such conditions, chemical oxygen demand (COD) and American Dye Manufacturers Institute (ADMI) of RB-5 and RB-19 were lower than the textile effluent standards. According to the UV-vis spectrophotometer scanning results, the color removal of nanoscale MgO for RB-5 and RB-19 was good. At the same time, the absorbance of their second maximal peaks was decreased and some peaks were observed. Therefore, it proved that the model dyes were destroyed. Experimental results have shown that nanoscale MgO has a better performance of destructive adsorption on RB-5 than that of RB-19. This might be ascribed to the following reasons: (1) a greater molecular weight, (2) a longer molecule structure, (3) more sulfate ethyl sulfone groups for RB-5, and (4) a hard to be destroyed structure of anthraquinone for RB-19. The destructive adsorption of dye wastewater by nanoscale MgO presumably took place mainly on the surface active sites of nanoscale MgO, including anion/cation vacancies, superoxide anion, edge, corner, isolated OH, lattice bound OH and assiocited-OH groups. According to the results of MALDI-TOF/MS and GC/MS analysis, the relevant reaction mechanism for RB-5 could be divided into three stages: (1) adsorption and water-soluble groups exfoliation stage, (2) chromophor decomposition and decolorization stage, and (3) further degradation stage for light-color intermediates. On the other hand, the relevant reaction mechanism for RB-19 might involve only the adsorption and auxochrome exfoliation stage and chromophor decomposition and decolorization stage.

Abstract Ammonia (NH3) is one of valuable chemicals which is commonly used in manufacturing the fertilizer, synthetic fiber, synthetic plastics, and dynamites, and is used in the factories such as papermaking, textile mill, camera and electrical. NH3 is also a typical pollutant which is found to be emitted from industrial processes, agriculture areas and livestock farm. It causes burn damage due to the corrosion and has a long-term impact on human bronchus. This study was to investigate the performance and kinetics in oxidation of ammonia by using a method of selective catalytic oxidation (denoted by SCO) over a series catalysts of Cu/Ce . The major parameters were performed at the following conditions: initial concentration NH3 of influent in ranging from 500 ppm to 1000 ppm, temperatures ranging from 150¢J to 500¢J, oxygen content in inlet stream in ranging from 4¢Hto 20¢Hand humidity in ranging from 1¢Hto 20¢H(or an absolute humidity of 607 ppm-12136 ppm). In the first stage experiments, the purpose was to select a best catalyst, which had the great activity and highest selectivity on nitrogen. The catalysts used in this work were prepared into three types in the following: Cu/La/Ce (molar ratio: 8/1/1, 7/1/2, 7/2/1, 6/1/3, 6/2/2 and 6/3/1), Cu/La (molar ratio: 6/4, 7/3, 8/2 and 9/1) and Cu/Ce (molar ratio: 6/4, 7/3, 8/2 and 9/1); total numbers of catalysts were 14. Test results showed the molar ratio 6:4 of Cu/Ce catalyst was found to have the best activity and selectivity to convert NH3 in this work. The second stage experiments were carried to investigate the effect of parameters on conversion of NH3 over a Cu/Ce catalyst of molar ratio 6:4. The conversion of NH3 in process of SCO increased with operation conditions such as the going up of temperature, and the increasing both of oxygen content and of residence time. The lower conversion of NH3 was achieved by an increasing on initial concentration of NH3, space velocity and humidity. The third stage experiments were conducted to investigate the effect of operation period on deactivation of NH3 over the above catalyst. At constant initial concentration of NH3, oxygen content and space velocity for 30 hr continuously, we found Cu/Ce catalyst had an excellent stability in conversion of NH3. Further tests by XRD, SEM and EA were determined. The kinetics of SCO over a Cu/Ce catalyst of molar ratio 6:4 in oxidation of NH3, using differential method, was found that a pseudo-first order reaction could be described by Mars-Van Krevelend model. An equation of destruction efficiency in terms of NH3 was obtained, and a good fitting was got between the predicted and the experimental values.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22454号 / 工博第4715号 / 新制||工||1736(附属図書館) / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 松原 誠二郎, 教授 杉野目 道紀, 教授 中尾 佳亮 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Becke's three-parameter hybrid density functional method in conjunction with Lee-Yang-Parr's correlation functional (B3LYP) was used to investigate the pyrolysis mechanisms of indole yielding benzyl cyanide and o- and m- tolunitriles. All equilibrium and transition state structures of the proposed reaction channels were fully optimized by B3LYP using the 6-31G** basis set. Single point energies were evaluated by B3LYP with the 6-311 + + G(2d,2p) basis set. Two hydrogen migration tautomers of indole, seemingly playing no important roles in the pyrolysis due to destruction of aromaticity of the benzene ring, were predicted to be easily accessible under the experimental conditions and may be important intermediates in the reactions. Two other transition states suggested to play important roles in the experimental study were not found and may not exist. Instead stepwise processes via hydrogen migration tautomers arriving at the same products are shown likely to be responsible for the observed products. IR spectral features of three hydrogen-migration tautomers are predicted to help future experimental identification.