We have used the first-principle molecular-dynamics method to study the dependence of the sticking property of a C gas-phase atom on C (100) on its initial position. For all the three cases, Cn never penetrates through the dimer layer even when Cn impinges on an opening in the surface. We find Cn becomes bonded with two substrate C atoms and one hydrogen atom with the hydrogen atom moving on the vacuum side.

The application of commercial herbicide restricts weed growth and significantly improves control over crop vitality and yield. Despite their utility in the agriculture sector, herbicides have the potential to contaminate local water sources. To minimize environmental impacts, the development of efficient separation processes to clean-up contaminated water bodies is necessary. However, complex speciation and conformational flexibility in the condensed phase poses a significant challenge. In this work, we investigate structure and speciation of three common organic herbicides (glyphosate, atrazine, and metolachlor) in aqueous solution. We employ the PBE-D3 density functional to perform ab initio molecular dynamics (MD) simulations in the canonical and isothermal-isobaric ensembles. We analyze MD trajectories to understand hydrogen bonding dynamics and lifetime as well as diffusional and vibrational characteristics. To enhance configurational sampling, we conduct metadynamics simulations to obtain the free energies of dissociation and intramolecular proton transfer of glyphosate.

No description available.

Transition metal nitrides (TMNs) refractory ceramic materials are  widely employed as wear-resistant protective coatings in industrial machining as well as diffusion barriers inhibiting migration of metal impurities from the interconnects to the semiconducting region of electronic devices. TiN is the prototype of this class of materials and the most studied among TMNs. However, also for this system, a complete picture of the migration processes occurring at the atomic scale is still lacking. In this work I investigate the stability of Ti vacancy configurations and corresponding migration rates in TiN by means of density functional theory (DFT) calculations and ab-initio molecular dynamics simulations (AIMD). DFT calculations show that Ti vacancies tend to stay isolated because of repulsive interaction which decreases as the inverse of the distance between the vacancies.The equilibrium jump rate of single Ti vacancies in TiN is extrapolated temperature as a function of temperature from the results of non-equilibrium AIMD simulations accelerated by a bias force field according to the color diffusion algorithm. For each force field and, the jump occurrence times are fitted with the two parameters Gamma distribution in order to obtain the non equilibrium jump rate with the corresponding uncertainty. Extrapolated equilibrium values show an Arrhenius-like behavior, with activation energy Ea= (3.78 ± 0.28)eV and attempt frequency A = 4.45 (x3.6±1) x 1014 s-1.

Mechanisms of reactions of the frustrated Lewis pairs (FLPs) with carbon dioxide (CO2) and hydrogen (H2) are studied by using quantum chemical modelling. FLPs are relatively novel chemical systems in which steric effects prevent a Lewis base (LB) from donating its electron pair to a Lewis acid (LA). From the main group of the periodic table, a variety of the electron pair donors and acceptors can create an FLP and the scope of the FLP chemistry is rapidly expanding at present. Representative intermolecular FLPs are phosphines and boranes with bulky electron-donating groups on phosphorus and bulky electron-withdrawing groups on boron – e.g., the tBu3P/B(C6F5)3 pair. The intramolecular FLPs feature linked LB and LA centers in one molecule. Investigations of the FLP reaction mechanisms were carried out using the transition state (TS) and the potential energy surface (PES) calculations plus the Born-Oppenheimer molecular dynamics (BOMD) as an efficient and robust implementation of general ab initio molecular dynamics scheme. In BOMD simulations, quantum and classical mechanics are combined. The electronic structure calculations are fully quantum via the density functional theory (DFT). Molecular motion at finite (non-zero) temperature is explicitly accounted for at non-quantized level via Newton’s equations. Due to recent advancements of computers and algorithms, one can treat fairly large macromolecular systems with BOMD and even include significant portion of the first solvation shell surrounding a large reacting complex in the molecular model. Main results are as follows. It is shown that dynamics is significant for understanding of FLP chemistry. The multiscale nature of motion – i.e., light molecules such as CO2 or H2 versus a pair of heavy LB and LA molecules – affects the evolution of interactions in the reacting complex. Motion which is perpendicular to the reaction coordinate was found to play a role in the transit of the activated complex through the TS-region. Regarding the heterolytic cleavage of H2 by tBu3P/B(C6F5)3 FLP simulated in gas phase and with explicit solvent, it was found that (i) the reaction path includes shallow quasi-minima “imbedded” in the TS-region, and (ii) tBu3P/B(C6F5)3 are almost stationary while proton- and hydride-like fragments of H2 move toward phosphorous and boron respectively. For binding of CO2 by tBu3P/B(C6F5)3 FLP, it was found that (i) the reacting complex can “wander” along the “potential energy wall” that temporarily blocks the path to the product, and (ii) the mechanism can combine the concerted and two-step reaction paths in solution. The discovered two-step binding of CO2 by tBu3P/B(C6F5)3 FLP involves solvent-stabilized phosphorus-carbon interactions (dative bonding). These and other presented results are corroborated and explained using TS and PES calculations. With computations of observable characteristics of reactions, it is pointed out how it could be possible to attain experimental proof of the results. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 6: Accepted.</p><p> </p>

Ion implantation of titania nanotubes is a highly versatile approach for tailoring structural and electrical properties. While recently self-organized nanoscale compositional patterning has been reported, the atomistic foundations and impact on electronic structure are not established at this point. To study these aspects, ab initio molecular dynamic simulations based on atomic compositions in C implanted titania nanotubes according to elastic recoil detection analysis are employed. Consistent with experimental data, carbon accumulates in chainlike precipitates, which are favorable for enhancing conductivity, as revealed by density-functional theory electronic ground states calculations are demonstrated.

Water is of essential importance for life on earth, yet the physics concerning its various anomalous properties has not been fully illuminated. This thesis is dedicated to the understanding of liquid water from aspects of microscopic structures, dynamics, electronic structures, X-ray absorption spectra, and proton transfer mechanism. This thesis use the computational simulation techniques including density functional theory (DFT), ab initio molecular dynamics (AIMD), and theoretical models for X-ray absorption spectra (XAS) to investigate the dynamics and electronic structures of liquid water system. The topics investigated in this thesis include a comprehensive evaluation on the simulation of liquid water using the newly developed SCAN meta-GGA functional, a systematic modeling of the liquid-water XAS using advanced ab initio approaches, and an explanation for a long-puzzling question that why hydronium diffuses faster than hydroxide in liquid water. Overall, significant contributions have been made to the understanding of liquid water and ionic solutions in the microscopic level through the aid of ab initio computational modeling. / Physics

Esta tese tem como objetivo o tratamento quantitativo do desvio de frequência vibracional em líquidos iônicos sob pressão. O estudo dos líquidos iônicos tetrafluoroborato de 1-butil-3- metilimidazólio, 1-hexil-3-metilimidazólio e 1-octil-3-metilimidazólio em alta pressão foram feitos a partir de uma abordagem conjunta entre simulação, espectroscopia e teoria de líquidos. As equações de estado desses sistemas obtidas a partir de dados na faixa de MPa são necessárias na análise de dados espectroscópicos obtidos na região de GPa. Torna-se necessário obter então os dados de densidade desses sistemas para a região de pressão maiores, e uma metodologia para selecionar entre diferentes equações de estado propostas na literatura que extrapolam de forma muito diversa na região de GPa. Duas propostas para validar tais Equações de Estado, e obter os dados de densidade em alta pressão são propostas. A primeira trata de comparar as extrapolações com os dados de Dinâmica Molecular clássica. Isso gera um problema em si pois o próprio campo de força usado nas simulações não foi parametrizado para a região de GPa. No entanto, uma boa concordância da forma da curva obtida via simulação e uma das equações de estado indica que o modelo de Domanska poderia ser considerado superior aos demais. Tal fato é comprovado pela segunda estratégia, em que as diferentes equações de estado são utilizadas para analisar os dados de desvio de frequência do modo de estiramento totalmente simétrico do ânion tetrafluoroborato de forma quantitativa utilizando o modelo de Schweizer e Chandler. A equação de Domanska fornece uma componente atrativa do desvio de frequência com o melhor ajuste linear, como prediz o modelo de Schweizer e Chandler. Além disso, os dados de desvio de frequência dos três sistemas formam uma curva única quando plotados em função da densidade reduzida dos líquidos, e o ajuste geral ao modelo teórico é o melhor dentre todas as equações de estado testadas. Simulações por Dinâmica Molecular ab initio do líquido iônico tetrafluoroborato de 1-butil-3-metilimidazólio sob pressão mostraram que esta metodologia consegue reproduzir quantitativamente o desvio de frequência experimental, mas os espectros vibracionais Raman apresentam uma banda muito ativa que não é observada experimentalmente. / The aim of this thesis is the quantitative treatment of the vibrational frequency shifts of ionic liquids under pressure. The study of the ionic liquids 1-butyl-3-methylimidazolium, 1-hexyl-3- methylimidazolium and 1-octyl-3-methylimidazolium tetrafluoroborate under high pressure were made under a simultaneous approach of simulation, spectroscopy and liquid theories. The equations of state of such systems are obtained with data in the MPa range and are necessary in the analysis of spectroscopic data obtained in the GPa range. It becomes necessary to obtain the density data in a larger pressure range, and to develop a methodology that selects through equations of state proposed in literature that extrapolate very differently in the GPa range. Two proposals to validate such equations of state, and obtain high pressure density data, are made. The first one consists in comparing the extrapolations with classic Molecular Dynamics results. This becomes a problem because the force field is not parametrized for this region. However, a good agreement between the simulation curve and the equation of Domanska are obtained which implicates that this equation could be considered better to describe this system under pressure. This finding is in agreement with the second strategy, in which the different equations of state are used to analyze quantitatively the frequency shift data of the totally symmetric stretching mode of the tetrafluoroborate anion using the Schweizer and Chandler model. The equation of Domanska provides a better linear fit of the attractive frequency shift component, as predicted by the model of Schweizer and Chandler. Moreover, the frequency shift data for the three systems colapse in a master curve when they are plotted versus the reduced density, and the overall fit to the model is the best through all equations of state tested. Ab initio molecular dynamics simulations of the 1- butyl-3-methylimidazolium tetrafluoroborate under pressure were made and show that this methodology is accurate to describe quantitatively describe the experimental frequency shift, but the Raman spectrum presents an intense band which is not observed experimentally.

Les catalyseurs d’hydrocraquage et d’hydroisomérization sont bifonctionnels, avec une fonction hydro-déshydrogénante et une fonction acide, une zéolithe protonée, pour isomériser et craquer les alcènes. Par dynamique moléculaire ab initio avancée, et avec prise en compte explicite des effets thermiques (300 – 500 K), nous avons étudié les mécanismes d’isomérisation et de craquage d’alcènes C7 dans la zéolithe chabazite dans le but d’obtenir des constantes de vitesse fiables et d’interpréter la distribution des produits.Par la méthode blue moon, nous avons établi les premiers profils d’énergie libre d’isomérisations d’alcènes C7, avec des carbocations intermédiaires (et des états de transition cyclopropanes protonés, PCP), reliant des isomères di- à tri- et mono- à di-branchés (Sections III et IV). Nos simulations démontrent que les effets dynamiques et l’échantillonnage correct des rotamères jouent un rôle crucial sur la stabilité des intermédiaires et des états de transition. Ces effets ne pouvaient pas être décrits par les précédentes études de DFT statiques. Les barrières bien plus basses pour l’isomérisation de type A sont ainsi retrouvées, et expliquées par un état de transition mou, alors que l’état de transition de l’isomérisation de type B est contraint, à cause de la formation d’un edge PCP. L’étude des réactions de craquage avec les mêmes méthodes (Section V) éclaircit le rôle des cations secondaires. Pour la première fois, nous identifions les états de transitions des β-scissions. Nous déduisons de cette analyse des constantes de vitesse ab initio qui pourront être utilisées dans un modèle cinétique pour prédire l’activité et la sélectivité du catalyseur. / Hydrocracking and hydroisomerization catalysts are bifunctional, with a hydro-dehydrogenation function and an acidic function, typically an acid zeolite, to isomerize and crack alkenes. With advanced ab initio molecular dynamics approach, and explicit simulation of the effects of temperature (300 – 500 K), we investigate the mechanisms of isomerization and cracking reactions of C7 alkenes within the chabazite zeolite in order to provide reliable rate constants and explain the observed products distribution. By blue moon sampling, we established for the first time, the free energy profiles for the isomerization of C7 alkenes in zeolites, with carbenium ions as intermediates (and protonated cyclopropane (PCP) as transition states), connecting di- to tri-branched, and mono- to di-branched alkene isomers (Sections III and IV). We demonstrate that the dynamic effects with the correct sampling of rotational conformers play an important role to quantify the stability of the key intermediates and transition states. These effects could not be captured by previous static DFT simulations. The much lower barriers for type A isomerization mechanisms are thus recovered, and assigned to a loose transition state, while the transition state of type B isomerization is tighter, due to the formation of an edge PCP. The study of cracking reactions (Section V) with the same methods, unravel the role of secondary cations. For the first time, we identify the structures of transition states involved in the β-scission mechanisms. From this analysis, we deduce the ab initio- rate constants that could be used in future kinetic modeling to predict activity and selectivity of the catalyst.

Un procédé de synthèse de dépôts nanostructurés de céramiques à bases d’aluminium au sein de composites carbone/carbone (C/C) est développé. Il consiste à synthétiser à partir de précurseurs dissout en solution aqueuse des nano-particules de morphologies variées. La maîtrise du procédé se déroule en deux étapes. Dans un premier temps une étude sur substrat plan permet de saisir les points clés du procédé, puis l’adaptation de la synthèse au sein d’un échantillon massif permet le changement d’échelle à des échantillons fibreux. Quatre gammes d’éprouvettes de matériaux densifiés sont ainsi élaborées. La caractérisation des matériaux permet de prouver la bonne cohésion de ceux-ci et de mesurer plusieurs propriétés mécaniques et structurales.En complément plusieurs interfaces carbone|alumine ou nitrure d’aluminium sont simulées par une approche de dynamique moléculaire ab initio. La méthode choisie pour générer les modèles consiste à simuler la trempe d’un carbone amorphe à haute température sur une surface céramique immobile, puis de relaxer les contraintes.Des disparités sur l’organisation structurale des nano-structures et en particulier sur l’orientation des plans de graphène générés vis-à-vis de la surface sont observées en fonction des modèles. Lorsque les plans sont plutôt perpendiculaires à la surface, l’interface est constituée de nombreuses liaisons fortes et le comportement en simulation de traction est bon, tandis que des plans parallèles entrainent une interface et un comportement faible.Enfin, la caractérisation HRTEM de certains matériaux élaborés permet d’identifier expérimentalement des interfaces semblables à celles obtenus par les modèles. / A hydrothermal-like process to introduce nano-structured alumina and aluminum nitride in carbon/carbon (C/C) composites is developped. Starting from dissolved reactants in an aqueous media,nanoparticules with various morphology are synthesised. The understanding and control of the processis completed in two steps. In the former the study on simplewafer type substrat allows to identifythe key parameters of the process. During the latter a scaling up of the process is done to allow thesynthesis in situ of C/C composites. The microstructural and some mechanical characterization ofthe four ranges of material produced is achieved.In addition several carbon|alumina and carbon|aluminumnitride are simulated using an ab initiomolecular dynamic approach. The methdology to generate the models consists in sumulating theliquid quench of a high temperature amorphous carbon inbetween fixed ceramic surface, then torelease the constrains. Depending on the system, different organisations of the nano-carbons withinthe surfaces are identified : when the graphene sheets are pependicular to the surface, the modelshows an important number of strong bonds and the simulation traction behavior is good, whereaswhen they are parallel to the surface it leads to weak interface and mechanical behavior.Finally HRMET charasterization of some of the materials produced allows to identify experimentalinterfaces alike to those obtained during themolecular dynamic simulations.