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The timescale of chemical reactions in solid-state systems greatly exceeds what may be modeled by direct integration of Newton's equation of motion. This limitation spawned the development of many different methods such as (adaptive) kinetic Monte Carlo (A)KMC, (harmonic) transition state theory (H)TST, parallel replica dynamics (PRD), hyperdynamics (HD), and temperature accelerated dynamics. The focus of this thesis was to (1) implement many of these methods in a single open-source software package (2) develop standard benchmarks to compare their accuracy and computational cost and (3) develop new long timescale methods. The lack of a open-source package that implements long timescale methods makes it difficult to directly evaluate the quality of different approaches. It also impedes the development of new techniques. Due to these concerns we developed Eon, a program that implements several long timescale methods including PRD, HD, and AKMC as well as global optimization algorithms basin hopping, and minima hopping. Standard benchmarks to evaluate the performance of local geometry optimization; global optimization; and single-ended and double-ended saddle point searches were created. Using Eon and several other well known programs, the accuracy and performance of different algorithms was compared. Important to this work is a website where anyone may download the code to repeat any of the numerical experiments. A new method for long timescale simulations is also introduced: molecular dynamics saddle search adaptive kinetic Monte Carlo (AKMC-MDSS). AKMC-MDSS improves upon AKMC by using short high-temperature MD trajectories to locate the important low-temperature reaction mechanisms of interest. Most importantly, the use of MD enables the development of a proper stopping criterion for the AKMC simulation that ensures that the relevant reaction mechanisms at the low temperature have been found. Important to the simulation of any material is knowledge of the experimental structure. Extended x-ray absorption fine structure (EXAFS) is a technique often used to determine local atomic structure. We propose a technique to quantitatively measure the accuracy of the commonly used fitting models. This technique reveals that the fitting models interpreted nanoparticles as being significantly more ordered and of much shorter bond length than they really are. / text

In the technologically driven information age, the consumption of power is as vital to daily life as food and shelter. The generation of that power comes from a variety of sources of which coal is the predominant provider of electrical energy. Coal combustion is a well-known technology and the United States possesses the most abundant coal deposits on Earth, however, the drawback accompanying this process is the significant emissions which are released during combustion. Over the years, much effort has gone into reducing the emissions of majority constituent elements CO2, CO, NOx, SOx, etc. but it is only in the last decade or so that much attention has been given to the trace metals present within coal. Most of the work into examining these trace metals has been upon Hg and how it speciates within the flue gas in order to determine the most effective means of removal. In this study, the trace metals arsenic (As) and selenium (Se) will be investigated in a similar manner to evaluate the speciation of these elements. While previous experimental work has been performed in this area, it has been limited to thermodynamic studies which determine the speciation after equilibrium has been reached, this ignores the fact the residence times within the flue are often only several minutes during which time rapid quenching is taking place. This study takes a different approach by examining the speciation using computational chemistry which affords the advantage of being able to perform a kinetic study which is more useful in creating a flue gas model. Using ab initio the properties of various As and Se species can be evaluated compared to existing experimental data for validation. After which, a number of reactions may be selected and the structure of the transition state for each identified. Once the properties of the transition structure are known, the appropriate kinetic model, be it Transition State Theory, RRKM Theory, etc. can be applied and the rate constant determined. It is by the determination of these rate constants that the kinetic model of the flue gas can be improved and a more accurate depiction of the speciation of these race metals created.

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.

In the design of novel materials, tunable properties are parameters such as composition or structure that may be adjusted in order to enhance a desired chemical or material property. Trends in tunable properties can be accurately predicted using computational and combinatorial chemistry tools in order to optimize a desired property. I present a study of tunable properties in materials and employ a variety of algorithms that ranges from simple screening to machine learning. In the case of tuning a nanocomposite membrane for olefin/paraffin separations, I demonstrate a rational design approach based on statistical modeling followed by ab initio modeling of the interaction of olefins with various nanoparticles. My simplified model of gases diffusing on a heterogeneous lattice identifies the conditions necessary for optimal selectivity of olefins over paraffins. The ab initio modeling is then applied to identify realistic nanomaterials that will produce such conditions. The second case, [alpha]-Fe₂O₃, commonly known as hematite, is potential solar cell material. I demonstrate the use of a screened search through chemical compound space in order to identify doped hematite-based materials with an ideal band gap for maximum solar absorption. The electronic structure of hematite is poorly treated by standard density functional theory and requires the application of Hartree-Fock exchange in order to reproduce the experimental band gap. Using this approach, several potential solar cell materials are identified based on the behavior of the dopants within the overall hematite structure. The final aspect of this work is a new method for identifying low-energy chemical processes in condensed phase materials. The gap between timescales that are attainable with standard molecular dynamics and the processes that evolve on a human timescale presents a challenge for modeling the behavior of materials. This problem is particularly severe in the case of condensed phase systems where the reaction mechanisms may be highly complicated or completely unknown. I demonstrate the use of support vector machines, a machine-learning technique, to create transition state theory dividing surfaces without a priori information about the reaction coordinate. This method can be applied to modeling the stability of novel materials. / text

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18448号 / 理博第4008号 / 新制||理||1578(附属図書館) / 31326 / 京都大学大学院理学研究科化学専攻 / (主査)教授 林 重彦, 教授 寺嶋 正秀, 教授 松本 吉泰 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Many chemical reactions can be described as the crossing of an energetic barrier. This process is mediated by an invariant object in phase space. One can construct a normally hyperbolic invariant manifold (NHIM) of the reactive dynamical system which is an invariant sphere that can be considered as the geometric representation of the transition state itself. The NHIM has invariant cylinders (reaction channels) attached to it. This invariant geometric structure survives as long as the invariant sphere is normally hyperbolic. We applied this theory to the hydrogen exchange reaction in three degrees of freedom in order to figure out the reason of the transition state theory (TST) failure. Energies high above the reaction threshold, the dynamics within the transition state becomes partially chaotic. We have found that the invariant sphere first ceases to be normally hyperbolic at fairly low energies. Surprisingly normal hyperbolicity is then restored and the invariant sphere remains normally hyperbolic even at very high energies. This observation shows two different energy values for the breakdown of the TST and the breakdown of the NHIM. This leads to seek another phase space object that is related to the breakdown of the TST. Using theory of the dividing surface including reactive islands (RIs), we can investigate such an object. We found out that the first nonreactive trajectory has been found at the same energy values for both collinear and full systems, and coincides with the first bifurcation of periodic orbit dividing surface (PODS) at the collinear configuration. The bifurcation creates the unstable periodic orbit (UPO). Indeed, the new PODS (UPO) is the reason for the TST failure. The manifolds (stable and centre-stable) of the UPO clarify these expectations by intersecting the dividing surface at the boundary of the reactive island (on the collinear and the three (full) systems, respectively).

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2017-04-24T14:13:26Z No. of bitstreams: 1 2012 - Ana Carolina Bello de Souza.pdf: 1911170 bytes, checksum: 62c70571aeb2100b8313dc1ef44eac2b (MD5) / Made available in DSpace on 2017-04-24T14:13:26Z (GMT). No. of bitstreams: 1 2012 - Ana Carolina Bello de Souza.pdf: 1911170 bytes, checksum: 62c70571aeb2100b8313dc1ef44eac2b (MD5) Previous issue date: 2012-10-03 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / In this work, the theoretical study of the gas-phase bimolecular nucleophilic substitution reaction, CH3Cl + OH- CH3OH + Cl-, is introduced, aiming the description of the potential energy surface, the calculation of rate constants and the investigation of the effect of increasing the side chain (changing the CH3 radical in the reaction cited above by the radicals ethyl, n-propyl, i-propyl, n-butyl, s-butyl e t-butyl). The theoretical calculations have been first performed at the MP2/6-31+G(d) level for the geometry optimizations and vibrational frequencies calculations. Single point calculations at the CCSD(T)/6-31+G(d) level have also been performed in order to improve the total energies for the stationary points. However, the relative energies of these stationary points at both MP2 and CCSD(T) level shown close results, so that the single point calculations at the CCSD(T) level have not been proved strictly necessary and have therefore not been performed for all the points along the potential energy surface. The minimum energy path has been described by the intrinsic reaction coordinate method, calculated at the MP2/6-31+G(d) by performing sequential geometry optimizations starting from the saddle point. The calculated enthalpy difference at 298K for the reaction has been determined as -49.5 kcal/mol, in good agreement with the literature value: -50.5 kcal/mol. The calculated rate constant has been obtained as 1.41 x 10-9 cm3.molecule-1.s-1, at 298,15K, in excellent agreement with the experimental data: 1.3 ? 1.6 x 10-9 cm3.molecule-1.s-1.Moreover, the rate constants show non-Arrhenius behavior, decreasing as the temperature increases, which is consistent with the experimental expectation. In this way, the performance of the variational transition state theory for this reaction can be considered satisfactory. By increasing the side chain of the reactant, other reaction channels have been observed: the bimolecular elimination E2 channel and the attack of the nucleophile from the same plane of the exit group (the front-SN2).For these reactions of the alkyl chlorides on n carbon atoms (1 < n ? 4), the B3LYP/6-31+G(d,p) level has been adopted for geometry optimizations and vibrational frequencies. Then, single point calculations at the CCSD(T)/6-31+G(d,p)//B3LYP/6- 31+G(d,p) level have been performed. A comparison of the reaction channels, back- SN2 and E2, shows that the E2 channel is kinetically favored, whereas the SN2 products are thermodynamically more stable. As expected, high values for the potential height have been observed for the front-SN2, being these channels disfavored in all cases. In general, the energy of the saddle points in respect to the isolated reactants slightly depend upon the size of the side chain. / Este trabalho trata do estudo te?rico das rea??es de substitui??o nucleof?lica de segunda ordem, CH3Cl + OH- CH3OH + Cl-, em fase gasosa, visando estudar a superf?cie de energia potencial, obter as constantes de velocidade e ainda verificando o efeito do aumento da cadeia lateral (trocando o radical CH3 na rea??o descrita acima por radicais etil, n-propil, i-propil, n-butil, s-butil e t-butil). Primeiramente, c?lculos te?ricos para otimiza??es de geometria e frequ?ncia foram realizados em n?vel MP2/6-31+G(d) para a rea??o CH3Cl + OH- CH3OH + Cl- e, em seguida, c?lculos single-point em n?vel CCSD(T)/6-31+G(d) foram realizados para corrigir os valores da energia eletr?nica dos pontos estacion?rios obtidos no caminho de rea??o. Entretanto, os valores obtidos para as energias relativas em n?veis MP2 e CCSD(T) foram muito pr?ximos, n?o sendo estritamente necess?rio refinar,atrav?s de c?lculos single-point em n?vel CCSD(T)/6- 31+G(d),os valores de energia de todos os pontos obtidos na superf?cie de energia potencial. O caminho de rea??o menor energia foi descrito pela coordenada de rea??o intr?nseca, calculada por otimiza??es de geometrias de uma sequ?ncia de configura??es ao redor do ponto de sela em n?vel MP2/6-31+G(d). A diferen?a de entalpia a 298K calculada para a rea??o foi de -49,5 kcal/mol, em bom acordo com o dado da literatura, -50,5 kcal/mol. A constante de velocidade da rea??o obtida foi de 1,41 x 10-9 cm3.mol?cula-1.s-1, a 298,15K, em excelente acordo com o dado experimental: 1,3 ? 1,6 x 10-9 cm3.mol?cula-1.s-1. Al?m disso, as constantes de velocidade globais apresentam comportamento n?o-Arrhenius, diminuindo conforme a temperatura aumenta, em um perfil consistente com a observa??o experimental. Dessa forma, a aplica??o da teoria de estado de transi??o se mostra satisfat?ria para essa rea??o. A partir do aumento da cadeia lateral, outros canais de rea??o foram observados, em prov?vel competi??o ? substitui??o nucleof?lica de ordem 2: a elimina??o de segunda ordem, E2. O ataque do nucle?filo pela frente da cadeia tamb?m foi obtido e investigado. Para as rea??es dos cloretos de alquila com cadeia lateral de n carbonos (1 < n ? 4), o n?vel B3LYP/6- 31+G(d,p) foi adotado para c?lculos de otimiza??es e frequ?ncias. Posteriormente, c?lculos em n?vel CCSD(T)/6-31+G(d,p)//B3LYP/6-31+G(d,p) foram realizados. Comparando os canais de rea??o de substitui??o nucleof?lica back e de elimina??o, o canal cineticamente favorecido foi o de elimina??o, por?m os produtos termodinamicamente mais est?veis s?o os de substitui??o nucleof?lica. Como esperado, observa-se uma barreira de potencial muito alta para as rea??es substitui??o pela frente, sendo esses canais desfavorecidos em todos os casos.Em geral, a diferen?a de energia dos pontos de sela em rela??o aos reagentes isolados mostra pequena depend?ncia com o aumento da cadeia lateral linear

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