Functional materials with controllable phase transitions have been widely used in devices for information storage (e.g. hard-disk, CD-ROM, memory) and energy storage (e.g. battery, shape memory alloy). One of the important issues to design such materials is to realize the desirable phase transition processes, in which atomistic simulation can be used for the prediction of materials properties. The accuracy of the prediction is largely dependent on searching the true value of the transition rate, which is determined by the minimum energy barrier between stable states, i.e. the saddle point on a potential energy surface (PES). Although a number of methods that search for saddle points on a PES have been developed, they intend to locate only one saddle point with the maximum energy along the transition path at a time. In addition, they do not consider the input uncertainty associated with the calculation of potential energy. To overcome the limitations, in this dissertation, new saddle point search methods are developed to provide a global view of energy landscape with improved efficiency and robustness. First, a concurrent search algorithm for multiple phase transition pathways is developed. The algorithm is able to search multiple local minima and saddle points simultaneously without prior knowledge of initial and final stable configurations. A new representation of transition paths based on parametric Bézier curves is introduced. A curve subdivision scheme is developed to dynamically locate all the intermediate local minima and saddle points along the transition path. Second, a curve swarm search algorithm is developed to exhaustively locate the local minima and saddle points within a region concurrently. The algorithm is based on the flocking of multiple groups of curves. A collective potential model is built to simulate the communication activities among curves. Third, a hybrid saddle-point search method using stochastic kriging models is developed to improve the efficiency of the search algorithm as well as to incorporate model-form uncertainty and numerical errors associated with density functional theory calculation. These algorithms are demonstrated by predicting the hydrogen diffusion process in FeTiH and body-centered iron Fe8H systems.

Geometry optimization is a fundamental step in the numerical modelling of chemical reactions. Many thermodynamic and kinetic properties are closely related to the structure of the reactant, product, and the transition states connecting them. Different from the reaction and product, which are local minima on the potential energy surface, a transition state is the first-order saddle point with only one negative curvature. Over years, many methods have been devised to tackle the problem. Locating stable structures is relatively easy with a reliable algorithm and high accuracy. One can follow the gradient descent direction to pursuit the local minimum until convergence is reached. But for the transition state, the determination is more challenging as either the up-hill or down-hill direction is allowed in the process. Motivated by the difficulty, many well-designed optimization algorithms are elaborated specifically to stress the problem. The performance of geometry optimization is affected by various aspects: the initial guess structure, the coordinate system representing the molecule, the accuracy of the initial Hessian matrix, the Hessian update schemes, and the step-size control of each iteration. In this thesis, we propose a new geometry optimization algorithm considering all the important components. More specifically, in Chapter 2, a new set of robust dihedral and redundant internal coordinates is introduced to effectively represent the molecular structures, as well as a computational efficient transformation method to generate a guess structure. In Chapter 3 and 5, a sophisticated robust algorithm is presented and tested to solve intricate transition state optimization problems. In Chapter 4, a new algorithm to exploring reaction pathways based on redundant internal coordinates is illustrated with real chemical reactions. Last but not least, in Chapter 6, a systematic test to explore the optimal methods in each procedure is presented. A well-performed combination of optimization methods is drawn for generic optimization purposes. All the methods and algorithms introduced in this thesis is included in our forth-coming open-source Python package named GOpt. It's a general-purpose library that can work in conjunction with major quantum chemistry software including Gaussian. More features are under development and await to be released in the coming update. / Thesis / Doctor of Science (PhD)

Inverse geochemical modelling has been used frequently in groundwater systems between wells along a known flowpath and between precipitation and stream waters in catchments. This research expands the use of inverse geochemical modelling through a reaction path model (RPM) between waters in an alpine catchment to determine the geochemical connections and disconnections within the catchment. The data for this study are from the Green Lake 4 catchment in the Colorado Front Range during the 1996 snowmelt season, which has been divided into discrete time intervals based on snowmelt hydrology. Unique combinations of geochemical connections occur during these time intervals, and they show a dynamic hydrologic system. RPM results show notable disconnections; soil water is not geochemically connected to any other end member. These changes reflect changes in weathering reactions in the catchment that are dependent on the duration and timing of snowmelt. Previously end-member mixture analysis (EMMA) models have been used to discern the water sources in catchments. The combination of RPM and EMMA approaches offers the opportunity to connect the source of water to the internal hydrologic structure of the catchment, to better understand how catchments might respond to changes in climate or atmospheric deposition.

This thesis is dedicated to the theoretical study of the methyl cation CH3+ electronic states and, globally, falls within the study of the interstellar clouds molecular synthesis and the chemistry of the hydrocarbons which are present in high-energy plasmas such as in the experimental nuclear fusion reactor ITER. Among the different possible formation reactions, we chose two reactions involved in these fields: the ionization of the methyl radical CH3 ground state and the reactive collisions between simple carbonated or hydrocarbonated (C, CH+ and CH2+) and hydrogen species (H3+, H2 and H, respectively).<p><p>As this cation is characterized by 8 electrons and 4 nuclei, this allowed us to perform high-level ab initio calculations using the CASSCF/MRCI method with the Dunning aug-cc-p(C)VXZ basis sets. These calculations were completed by a study of different methodological effects such as the core-valence electronic correlation, the complete basis set extrapolation and the basis set superposition error.<p><p>We calculated equilibrium geometries (precision within 10^-5 angtröm and 10^-2° and their energies for the methyl radical and cation, studied the potential energy surfaces involved by the Jahn-Teller effect targeting the methyl cation E' states and achieved frequencies calculations. From these values were derived ionization potentials (IP) from the methyl radical ground state towards the methyl cation lowest-lying states (precision within 10^-2 eV). Vibrational corrections and nuclear relaxation effects were taken into account.<p><p>The calculated IPs and frequencies should facilitate the analysis of methyl radical threshold photoelectron spectra leading to the methyl cation lowest-lying states, recorded at the synchrotron facility Soleil by the Dr. Alcaraz group from the Université Paris-Sud.<p><p>Through reaction paths calculations using a quadratic steepest-descent method, we have proposed new reactional pathways enabling the connections between the different dissociation channels correlated to the cation lowest-lying triplet states. The absence of potential barriers in the energy profiles allows us to propose these reactions as sources, in interstellar clouds, of hydrocarbonated molecules whose stability increases with growing size according to the series C -> CH+ -> CH2+ -> CH3+.<p><p>The groups of Pr. Urbain from UCL and Dr. Savin from Columbia University studied the collisions in copropagating beams of C and H3+ leading to the formation of these hydrocarbonated species. The proposed reactional mechanisms are in good agreement with the experimental observations, what permits a better understanding of the chemistry behind these collisional processes of astrochemical interest. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Density functional theory calculations were performed to study the dissociative chemisorption of methane over Pt(111) with the idea of finding the minimum energy path for the reaction and its dependence on surface coverage. Two approaches were used to evaluate this problem; first, we used different sizes of supercells (2x2, 3x3, 4x4) in order to decrease surface coverage in the absence of pre-adsorbed H and CH3 fragments to calculate the energy barriers of dissociation. The second approach uses a 4x4 unit cell and surface coverage is simulated by adding pre-absorbed H and CH3 fragments. Results for both approaches show that in general the height of the dissociation barriers increases as the surface coverage increases, although, the first approach yields slightly lower barriers due to the fact that all repeatable images of the incident molecule are approaching the surface simultaneously. Using the reaction path formulation we were able to compute the potential energy surface for CH4 dissociation. Our results suggest that excitation of the symmetric stretch and bend modes will likely increase the probability for reaction.

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No. of bitstreams: 1 raphaeldasilvaalvin.pdf: 3200596 bytes, checksum: 01129a5b7d70b7b3e44dd871c5c77b1d (MD5) Previous issue date: 2009-02-19 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os organofosforados encontram aplicações na indústria, nas áreas de corantes, vernizes, couro artificial, isolantes elétricos, impermeabilizantes, plásticos, aditivos de petróleo e dissolventes; também são usados na medicina no tratamento de doenças, como o glaucoma; no uso doméstico e na agricultura encontram aplicabilidade como inseticidas e pesticidas. Além dessas várias utilidades civis, os organofosforados são utilizados, também, como armas químicas de destruição em massa, e possuem estrutura similar àquelas dos compostos utilizados como inseticidas e pesticidas. No caso do VX, um organofosforado utilizado como arma química, a quebra da ligação P­S é essencial na sua degradação química. Embora muitas reações químicas possam ser empregadas para decompor agentes químicos de guerra, somente algumas podem ser utilizadas na prática em uma neutralização, porque estas reações precisam ser simples e os reagentes empregados devem ser estáveis, baratos e de baixa massa molecular. No entanto, muitas das reações que podem ser úteis para a neutralização do agente neurotóxico VX ainda seguem em discussão em recentes pesquisas, mas na maioria delas se limita alguns sucessos a hidrólise catalisada. Nesta dissertação foram estudados processos de hidrólise catalisada do agente VX por MgO(001) por meio de cálculos ab initio. Foi utilizado o programa PWscf ­ Plane­Waves Self Consistent Field. O PWscf utiliza a Teoria do Funcional da Densidade, a partir de um conjunto de base de autofunções dado por ondas planas e pseudopotenciais. Entre outros atributos, este código é capaz de calcular a energia do estado fundamental dos orbitais de Kohn­Sham para um elétron, além de forças atômicas em diferentes condições de tensão, otimização estrutural e estado de transição. A molécula de VX foi substituída por uma molécula menor, chamada de p­VX, em que foram substituídos alguns radicais do VX por grupos metila. Isto foi feito para diminuir o tamanho da molécula, que reduzirá o custo computacional, mas sem afetar substancialmente a química do problema, o estudo da quebra da ligação P­S. O mecanismo de hidrólise proposto esta relacionado com a quebra heterolítica da ligação P­S, com a conseqüente formação de íons intermediários R­P+ e R'­S­, estes, por sua vez, estabilizados por quimissorção na superfície de MgO(001). Em conjunto com essa reação, acontece a dissociação de moléculas de água para a formação dos íons H+ e HO­, cujos íons também são estabilizados na superfície de MgO(001). O passo final é a recombinação desses íons, para gerar os produtos de hidrólise R­POH e R'­SH, seguida pelo processo de dessorção destas moléculas da superfície do catalisador. Para a reação global de hidrólise da molécula de p­VX, a variação da energia interna foi calculada em ­5,66kcal/mol. Foram determinadas as estruturas dos íons R­P+ e R'­S­ estabilizados sobre a superfície de MgO(001), com uma energia de formação calculada em ­0,20kcal/mol, indicando que os intermediários teriam boa estabilidade sobre a superfície se comparados com a molécula de p­VX original. Na quimissorção dissociativa de moléculas de água sobre a superfície de MgO(001), verificou­se que os íons formados somente ficam estabilizados se estiverem a uma distância mínima de 4,70Å. Qualquer distância abaixo desta levará a formação da molécula de água novamente. No processo envolvendo duas moléculas de água, apenas uma delas se dissocia, enquanto a outra estabiliza os íons formados via ligação de hidrogênio. A molécula não dissociada também interage com um sítio superficial de magnésio. Este resultado foi comprovado pelos cálculos de diferença de densidade de carga eletrônica do sistema, determinação do caminho de reação, onde este obteve uma barreira energética calculada em 5,55kcal/mol para a reação direta e em 7,53kcal/mol para a reação inversa, e pela dissociação parcial utilizando um trímero de moléculas de água, com energia calculada em ­5,40kcal/mol. Os resultados permitem concluir que o mecanismo proposto para a hidrólise catalisada do agente neurotóxico VX pelo MgO é possível. Os modelos construídos podem ser modificados para testes de novos catalisadores com estrutura tipo MgO, via adição de defeitos ou dopantes à superfície da estrutura cristalina, visando a elaboração de catalisadores mais eficientes para a reação de hidrólise com o mesmo mecanismo. / The organophosphates are used in industry, in the fields of dyes, varnishes, artificial leather, electrical insulation, waterproofing, plastics, oil additives and solvents, are also used in medicine to treat diseases such as glaucoma, in the household and in agriculture are applied as insecticides and pesticides. Besides these various civilian facilities, the organophosphates are used as well as chemical weapons of mass destruction, and have similar structure to those of compounds used as insecticides and pesticides. In the case of VX, an organophosphate used as a chemical weapon, the fall in P­S binding is essential in its chemical degradation. Although many chemical reactions can be used to decompose the chemical agents of war, only some can be used in practice in a breakthrough, because these reactions need to be simple and the reagents used should be stable, inexpensive and low molecular weight. However, many of the reactions that may be useful for the neutralization of the neurotoxic VX agent still follow under discussion in recent polls, but most of them are confined to some successes catalyzed hydrolysis. In this dissertation we studied processes of the VX agent catalyzed hydrolysis by MgO (001) by means of ab initio calculations. We used the program PWscf ­ Plane Waves Self­Consistent Field. The PWscf using the Density Functional Theory from a set of basic autofunction given by plane waves and pseudopotentials. Among other attributes, this code is able to calculate the energy of the ground state of the Kohn­Sham orbital for an electron, and atomic force under different conditions of stress, structural optimization and transition state. The VX molecule was replaced by a smaller molecule, called a p­VX, which replaced some of the radicals VX for methyl groups. This was done to reduce the size of the molecule, which reduces the computational cost, but not substantially affect the chemistry of the problem, the study of breaking the link P­S. The proposed mechanism of hydrolysis is related to the breaking of the link heterolytic P­S, with the consequent formation of intermediate ion R­P+ and R'­S­, they, in turn, stabilized by quimissorption the MgO(0010 surface. Together with this reaction, is the dissociation of water molecules to the formation of ions H+ and HO­, whose ions are stabilized on the MgO(001) surface. The final step is the recombination of these ions, to generate products of hydrolysis and R­POH and R'­SH, followed by the process of desorption of molecules from the surface of the catalyst. For the overall reaction of hydrolysis of the molecule p­VX, the variation of internal energy was calculated to be ­5.66 kcal/mol. Were determined the structures of ion R­P+ and R'­S­ stabilized on the MgO(001) surface, with an formation energy calculated at ­0.20 kcal/mol, indicating that the middlemen have good stability on the surface is compared with the p­VX molecule original. In dissociative quimissorption of water molecules on the MgO(001) surface, it was found that the ions formed are stable only if a minimum distance of 4.70 Å. Any distance below this will lead to formation of the water molecule again. In the process involving two water molecules, only one is dissociated, while the other ions stabilizes by the hydrogen bonding formed. The non­dissociated molecule also interacts with a surface site of magnesium. This result was confirmed by the calculations of load density difference of the system, determining the reaction path, where he obtained a energy barrier calculated at 5.55 kcal/mol for the direct reaction and 7.53 kcal/mol for the reverse reaction and by partial decoupling using a trimer of water molecules, with energy calculated at ­5.40 kcal/mol. The results show that the proposed mechanism for the catalyzed hydrolysis of the neurotoxic agent VX by MgO is possible. The models constructed can be modified for testing of new catalysts with MgO type structure, via addition of doping or defects on the surface of the crystal structure, to the development of more efficient catalysts for the hydrolysis reaction with the same mechanism.

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No. of bitstreams: 1 vivianedasilvavaiss.pdf: 3626163 bytes, checksum: 3a5c810252b870e4922ae7564819b604 (MD5) Previous issue date: 2011-01-27 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os hidróxidos lamelares, dentre os quais se incluem os compostos tipo brucita e os hidróxidos duplos lamelares (HDL), apresentam inúmeras aplicações devido às suas propriedades, tais como: alta estabilidade térmica, capacidade de troca iônica, porosidade e elevada área específica, eletroquímicas, fotoquímicas e outras. A capacidade de adsorção e troca iônica apresentada por estes compostos faz com que estes materiais sejam amplamente utilizados na remoção de espécies aniônicas e contaminantes. Assim, por exemplo, tais materiais podem ser usados na remoção do excesso de fluoreto de água potável, pois fluoreto em excesso pode causar fluorose esquelética ou dental, e na desativação de agentes neurotóxicos, organofosforados que atacam o sistema nervoso. O presente trabalho, apresenta um estudo detalhado dos mecanismos de reação de H2O, HF e sarin com hidróxidos lamelares. Para tanto, foram utilizados cálculos ab initio baseados na Teoria do Funcional da Densidade com condições de contorno e o método CI-NEB (Climbing Image-Nudging Elastic Band) para calcular o caminho de reação e a barreira energética de cada reação envolvida nos processos. A reação de HF foi baseada num mecanismo proposto composto por quatro reações elementares: a adsorção de HF sobre a superfície dos hidróxidos, a dissociação do HF adsorvido, a dessorção da molécula de água formada na reação de dissociação e a formação do composto M(OH)2−xFx. Os resultados mostram que a formação do composto M(OH)2−xFx é espontânea. Este resultado está de acordo com trabalhos experimentais, que prevêem como estável o composto formado pela substituição de OH- por F- em hidróxidos lamelares. Foram analisadas duas propostas para a formação de hidroxila sobre a superfície de hidróxidos lamelares. Na primeira uma hidroxila da própria lamela do hidróxido migra para a superfície e na segunda uma molécula de água se dissocia sobre a superfície do hidróxido, formando uma molécula de água e hidroxila adsorvidas na superfície, sendo esta última proposta mais favorável segundo os cálculos realizados. Os trabalhos anteriores foram etapas necessárias para o objetivo central da tese: estudar a desativação do agente neurotóxico sarin. No processo de desativação do sarin foram estudados intermediários formados pela dissociação e quimissorção do agente sobre a superfície da brucita. Com base nos resultados dos três processos estudados pôde-se verificar que a reação de desativação do agente sarin utilizando a brucita é termodinamicamente mais estável do que a reação de hidrólise. Além disso, verificou-se que a água pode participar do processo de desativação como um catalisador. Tal estudo está no âmbito do Programa Pró-Defesa do ministério da Defesa em conjunto com a CAPES. / Layered hydroxides, including brucite-like compounds and layered double hydroxides (LDHs), present numerous applications due to their properties such as: high thermal stability, ion exchange capacity, porosity and high surface area, electrochemistry, photochemistry and others. The capacity of adsorption and ion exchange presented by these materials make them to be widely used in the removal of anionic species and contaminants. Thus, for example, such materials can be used in the removal of excess fluoride from drinking water, because fluoride in excess can cause dental or skeletal fluorosis, and degradation of nerve agents, like organophosphates that attack the nervous system. This work presents a detailed study of the reactions H2O, HF and sarin with layered hydroxides. Therefore, were used ab initio calculations based on Density Functional Theory (DFT) with periodic boundary conditions and the CI-NEB method (Climbing Image – nudging Elastic band) to calculate the reaction path and the energetic barrier for each reaction involved in the process. The reaction of HF was based on a proposed mechanism consisting of four elementary steps: the adsorption of HF on the surface of hydroxides, the dissociation of adsorbed HF, the desorption of water molecule formed in the dissociation reaction and the formation of the compound M(OH)2−xFx. The results show that the formation of the compound M(OH)2−xFx is spontaneous. This result agrees with experimental works, that predicts as stable the compound formed by replacing OH- by F- in layered hydroxides. Two proposals were analyzed for the formation of hydroxyl on the surface of layered hydroxides. In the first proposal a hydroxyl of the hydroxide lamella migrates to the surface and in the second proposal a water molecule dissociates on the surface of the hydroxides, forming a water molecule and hydroxyl adsorbed on the surface; the latter proposal is more favorable according to the calculations performed. The previous studies were necessary steps for the central goal of the thesis: to study the deactivation of the nerve agent sarin. In the deactivation process of the nerve agent sarin intermediates formed by dissociation and chemisorption of the agent on the surface of brucite were studied. Based on the results of the three cases studied it could be checked that the deactivation reaction of the agent sarin using brucite is thermodynamically more stable than the hydrolysis reaction. Moreover, it appears that water can participate in the deactivation process as a catalyst. This study has happened into the ambit of the Pro-Defense program of the Defense Menistry in conjunction with the CAPES.

No description available.

<p>In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.