Дисертації: "Ab initio molecular dynamics. DFT"

1

Rey, Jérôme. "Mechanisms and kinetics of alkenes isomerization and cracking in chabazite zeolite quantified by constrained ab initio molecular dynamics." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSEN049.

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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

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2

Das, S. "Theoretical investigation on structure and reactivity properties of molecule and metal clusters: a conceptual DFT and Ab initio molecular dynamics approach." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2015. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2015.

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3

Failali, Abdelmounaim. "Molecular modeling of organic phases after plutonium extraction." Electronic Thesis or Diss., Université de Lille (2018-2021), 2021. http://www.theses.fr/2021LILUR002.

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Après son séjour au sein d'un réacteur nucléaire, le combustible contient encore une quantité importante de matières valorisables qu’il est intéressant de récupérer, à savoir le plutonium et l'uranium.La récupération et la purification de ces actinides sont réalisées à l'aide d'un procédé hydrométallurgique appelé PUREX (Plutonium Uranium Recovering by Extraction), basé sur les techniques d'extraction liquide-liquide. Ce procédé nécessite l'utilisation d'une molécule spécifique pour extraire Pu et U, le phosphate de tri-n-butyle TBP. Les N, N-dialkylamides (monoamides) sont considérés comme une famille alternative d'agents d'extraction au TBP en raison de leur forte capacité d'extraction des éléments Pu(IV) et U(VI). De plus, ces molécules présentent des caractéristiques intéressantes, telles que la forte dépendance des propriétés d'extraction (coefficient de distribution et sélectivité) à la structure des ligands ainsi qu'aux conditions chimiques. Afin de proposer le meilleur design de molécule d'extraction pour les futures usines de retraitement de combustible, il est crucial de comprendre la relation entre la structure et la capacité d'extraction. Cependant, le caractère radioactif de ces éléments combinés à leur complexité chimique rendent les études expérimentales de ces phases complexes. Par conséquent, la modélisation moléculaire semble être la solution idéale pour obtenir de nouvelles informations à l'échelle moléculaire.Dans la première partie de cette thèse, une étude quantique relativiste scalaire utilisant la théorie fonctionnelle de la densité a été réalisée pour déterminer l'influence de la nature de la chaîne alkyle monoamides sur la stabilité des complexes Pu(IV). Il a été possible de mieux comprendre la forte influence de la structure amide sur l'extraction du plutonium. Pour les deux complexes d’amide-plutonium-nitrate étudiés (complexes de sphères interne et externe), il a été constaté que l'introduction d'un groupe alkyle volumineux du côté carbonyle a un impact majeur sur l'énergie de complexation. L'impact de la polarité de la solution a été également étudié et jugé significatif.Dans le but d'étudier des systèmes plus réalistes, contenant des monoamides avec des longues chaînes alkyles, des actinides et des contre-ions, et d'aller au-delà de l'image statique de géométries optimisées au niveau QM/DFT avec des simulations de dynamique moléculaire classique, nous avons développé des champs de force polarisable pour les molécules de solvant (alcanes et monoamides) ajustés uniquement sur des calculs de chimie quantique.L'approche ab initio retenue pour le paramétrage ainsi que le champ de force résultant et détaillés nous permettent d'obtenir des propriétés macroscopiques comparables aux données expérimentales (thermodynamiques et structurales). L'excellent accord nous permet d'avoir confiance quant à la précision des prédictions réalisées sur les systèmes pures de monoamides. Enfin, les résultats préliminaires de simulations des mélanges monoamides-dodécane (DEHiBA/dodécane et DEHBA/dodécane) sont présentés The nuclear fuel after its dwell time in reactor still bears a substantial amount of recoverable U and Pu. The recovery and purification of these actinides is achieved using a hydro-metallurgical process known as PUREX (Plutonium Uranium Recovering by EXtraction). Based on Liquid-Liquid extraction techniques, this process requires the use of a specific molecule to extract Pu and U, the tri-n-butylphosphate TBP. N,N-dialkylamides (monoamides) are regarded as an alternative family of extractants to TBP, as they are well-known for their strong extraction ability of Pu(IV) and U(VI) elements. In addition to this, they show some interesting features, such as, the strong dependence of the extraction properties (distribution coefficient and selectivity) on the ligands structure as well as chemical conditions. In order to propose the best extracting molecule design for future fuel reprocessing plants, it is crucial to understand the relationship between the structure and the extraction ability. However, the radioactivity of these elements combined with their chemical complexity make the study of these phases experimentally a real challenge. Hence, molecular modeling appears to be the golden solution for getting new insights on this issue.In the first part of this thesis, a relativistic density functional theory study was performed to investigate the influence of the monoamides alkyl chain nature on the relative stability of Pu(IV) complexes. It was possible to reach a better understanding of the strong influence of amide structure on plutonium extraction. For both investigated amide-plutonium-nitrate complexes (inner and outer-sphere complexes), it was found that the introduction of a bulky alkyl group on the carbonyl side has a major impact on the complexation energy. The impact of the polarity of the solution was also investigated and found to be significant.In the second part, within the aim of studying more realistic systems, i.e systems containing long alkyl chains monoamides, heavy elements and other counter ions, and to go beyond the static picture of QM/DFT optimized geometries with molecular dynamics simulations, we have developed a consistent polarizable FF model for the solvent molecules (alkanes, monoamides) based solely on quantum chemical calculations. The chosen ab initio parameterization approach as well as the final force field are presented. Then, the results of molecular dynamics simulations were compared to available experimental macroscopic thermodynamics and structural properties, and show an excellent agreement, making the predictions of properties of pure monoamides reliable. Finally, preliminary MD simulations results for monoamides-dodecane mixtures (DEHiBA/dodecane and DEHBA/dodecane) are presented

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4

Cheik, Njifon Ibrahim. "Modélisation des modifications structurales, électroniques et thermodynamiques induites par les défauts ponctuels dans les oxydes mixtes à base d'actinides (U,Pu)O2." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0356/document.

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(U,Pu)O2 (aussi appelé MOX) est actuellement utilisé comme combustible dans les réacteurs nucléaires à eau pressurisée (REP) avec une teneur massique en Pu d’environ 10 %. Il est également envisagé comme combustible de référence pour les réacteurs à neutrons rapides à caloporteur sodium, avec une teneur massique en Pu d’environ 25 %. En conditions opérationnelles, (U,Pu)O2 est soumis à des réactions de fission qui génèrent une grande quantité de défauts et de produits de fission. Par migration, ces défauts et produits de fission gazeux peuvent s'agréger en nano-cavités, dislocations et bulles de gaz, conduisant à une modification de la microstructure. Une meilleure description du comportement du combustible à l’échelle atomique, notamment des mécanismes élémentaires impliqués dans la diffusion des défauts et des produits de fission, est donc nécessaire pour affiner les modèles utilisés dans les codes de performance des combustibles. Pour l’étude des propriétés de (U,Pu)O2, nous avons effectué des calculs de structure électronique basés sur la méthode DFT+U combinée au contrôle des matrices d’occupation des orbitales corrélées. Des minimisations d’énergie ainsi que la dynamique moléculaire ab initio ont été utilisées. Nous avons étudié dans un premier temps les propriétés du cristal de (U,Pu)O2 pour différentes teneurs en Pu. Nous avons ensuite étudié la stabilité des défauts ponctuels ainsi que les modifications structurales et électroniques induites par ces défauts ponctuels dans (U,Pu)O2 et (U,Ce)O2, matériau utilisé comme simulant de (U,Pu)O2. Enfin, nous avons étudié le piégeage et la solubilité des gaz de fission (Kr, Xe) et de l’hélium dans la matrice de (U,Pu)O2 (U,Pu)O2 (commonly called MOX) is currently used as nuclear fuel in pressurized water reactors with a Pu content of around 10 wt.%, and is envisaged as the reference fuel in Generation IV sodium fast reactors (SFR) with a Pu content of around 25 wt.%. Under operation, (U,Pu)O2 is submitted to fission reactions which generate a large quantity and variety of point defects, as well as fission products. By migrating, point defects and gaseous fission products can aggregate into nano-voids, dislocations and fission gas bubbles, which lead to the modification of the fuel microstructure. Therefore, a better description of the fuel behaviour at the atomic scale, and especially of the elementary mechanisms involved in the diffusion of point defects and fission products, is necessary to refine the models used in the fuel performance codes used to simulate the behaviour of fuels at the macroscopic scale. We use electronic structure calculations based on the DFT+U method combined with the occupation matrix control scheme (OMC) to investigate (U,Pu)O2 properties for various Pu contents. Static energy minimizations and ab initio molecular dynamics were used. We have first determined bulk structural, electronic and thermodynamics properties of (U,Pu)O2. We then studied the stability of point defects in (U,Pu)O2 and (U,Ce)O2, as well as the structural and electronic modifications induced by these point defects, in (U,Pu)O2 and the common experimental surrogate (U,Ce)O2. Finally, the fission gas (Kr and Xe) and helium (He) trapping and solubility in (U,Pu)O2 matrix are investigated

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5

Eklund, Robert. "Computational Analysis of Carbohydrates : Dynamical Properties and Interactions." Doctoral thesis, Stockholm : Department of Organic Chemistry, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-538.

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6

Rasim, Karsten. "Conductivité protonique et structures locales par simulations ab initio d'oxydes utilisés comme électrolyte dans les piles à combustible." Phd thesis, Université de Nantes, 2011. http://tel.archives-ouvertes.fr/tel-00983483.

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Cette thèse porte sur une étude de matériaux oxydes fortement désordonnés de type Brownmillerite et présentant diverses substitutions. Les aspects les plus étudiés sont la conductivité protonique des phases hydratées ainsi que les propriétés structurales des composés anhydres. L'étude repose majoritairement sur des calculs de type DFT (réalisés de manière statique à 0 K et à température élevée en utilisant la dynamique moléculaire ab initio). Elle est complétée de mesures XANES (spectroscopie d'absorption des rayons X) qui ont permi de confirmer certains résultats issus des calculs DFT. Ces approches combinées ont fourni des informations cruciales sur la préférence de coordination chimique de plusieurs substituants, sur la mobilité des protons dans divers composés en fonction de leur contenu cationique ainsi que sur les propriétés vibrationnelles. Le matériau Ba2 In2(1 − x)Ti2xO5+x (BITx) a été le centre d'intérêt de cette thèse, au vu des performances prometteuses dans des piles à combustible de type PC-SOFC. Dans une optique de comparaison et de rationalisation, des composés de formulation voisine Sr2In2(1 − x)Ti 2xO5+x (SITx), Ba2In2(1 − x)Zr2xO5+x (BIZx) et Ba2In2(1 − x)Y2xO5 (BIYx) ont également été étudiés pour préciser le rôle des différents substituants sur le comportement de la conductivité protonique (e.g. les effets de piégeage, la force des liaisons hydrogène, la distinction entre plusieurs arrangements protoniques etc...). Tous ces aspects ont été obtenus grâce à la dynamique moléculaire qui intègre naturellement les effets de température et d'entropie.

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7

Caussé, Maélie. "Étude de quelques propriétés de superhydrures à haute pression et à haute température." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASF041.

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Ces dix dernières années, une nouvelle chimie de l'hydrogène avec les métaux a été observée sous hautes pressions. Des composés très riches en hydrogène, appelés superhydrures, se forment dans le domaine des 100 GPa. Certaines propriétés remarquables de ces composés ont été mises en évidence comme une supraconductivité BCS à très haute température critique, dans le superhydrure de lanthane (LaH₁₀) avec un sous-réseau en cages d'hydrogène et une supraconductivité à -23° C. Une question très actuelle est de savoir si de tels composés peuvent être stables à pression ambiante et la piste des hydrures ternaires est actuellement explorée. Dans un premier temps, grâce à des calculs de dynamique moléculaire ab initio, nous avons mis en évidence une nouvelle propriété de LaH₁₀ : la superionicité, qui indique une diffusion très rapide des ions hydrures. La superionicité stabilise également LaH₁₀ à très haute température. Cette propriété devrait exister pour d'autres superhydrures. Dans un second temps, nous avons recherché des hydrures ternaires dans le système Y-Fe-H. En comprimant, sous forte pression d'hydrogène dans une presse à enclumes de diamant, le composé de Laves YFe₂, bien connu pour ses capacité de stockage d'hydrogène à pression ambiante, nous avons découvert deux hydrures interstitiels, YFe₂H₆ et YFe₂H₇. Nous avons également démontré une limite à l'incorporation d'hydrogène dans ce type de composés. Ces deux composés ne sont pas stables à pression ambiante. Enfin, à l'aide d'un chauffage laser, nous avons synthétisé l'hydrure ternaire Y₃Fe₄H₂₀ qui a pu être ramené métastable à pression ambiante. La structure et les propriétés de ce superhydrure ont été caractérisées par diffraction X sur monocristal et par calculs ab initio. Une structure inédite pour un hydrure est mise en évidence avec des entités anioniques [FeH₈] reliées entre elles et formant des cages autour des cations d'yttrium. Ce composé est métallique et cette structure pourrait servir de modèle pour trouver un hydrure ternaire supraconducteur stable à pression ambiante Over the past ten years, a new chemistry of hydrogen with metals has been observed under high pressures. Very hydrogen-rich compounds, called superhydrides, form in the 100 GPa range. Remarkable properties of these compounds have been highlighted, such as BCS superconductivity at very high critical temperatures, like LaH₁₀ with a hydrogen cage sublattice and superconductivity at -23 ° C. A current question is whether such compounds can be stable at ambient pressure, and the path of ternary hydrides is currently being explored. Firstly, using ab initio molecular dynamics calculations, we have revealed a new property of LaH₁₀ : superionicity, which indicates very rapid diffusion of hydride ions. This property should exist for other superhydrides. Secondly, we have searched for ternary hydrides in the Y-Fe-H system. By compressing, under high hydrogen pressure in a diamond anvil press, the Laves phase compound YFe₂, well known for its hydrogen storage capacity at ambient pressure, we discovered two interstitial hydrides, YFe₂H₆ and YFe₂H₇. We also demonstrated a limit to hydrogen incorporation in this type of compound. These two compounds are not stable at ambient pressure. Finally, using laser heating, we synthesized the ternary hydride Y₃Fe₄H₂₀, which was brought back metastable at ambient pressure. The structure and properties of this superhydride were characterized by single-crystal X-ray diffraction and ab initio calculations. An unprecedented structure for a hydride is highlighted with [FeH₈] anionic entities linked to each other and forming cages around yttrium cations. This compound is metallic and this structure could serve as a model to find a ternary hydride superconductor stable at ambient pressure

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8

Halbert, Stéphanie. "Étude du comportement dynamique de systèmes catalytiques greffés sur silice." Phd thesis, Université Montpellier II - Sciences et Techniques du Languedoc, 2013. http://tel.archives-ouvertes.fr/tel-01005016.

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Ce mémoire présente une méthodologie théorique pour comprendre l'origine de différence de comportement dynamique de complexes alkylidènes, catalyseurs de type Schrock de la métathèse des oléfines, greffés un support de silice amorphe. Dans un travail antérieur, les différences entre les valeurs de l'anisotropie de déplacement chimique (CSA) obtenues par des mesures de RMN du solide et celles estimées par le calcul pour des systèmes figés avaient conduit à suggérer des régimes dynamiques différents pour ces complexes, certains étant proposés comme immobiles, d'autres comme mobiles. Dans le premier groupe se trouve les complexes du molybdène et dans le second les complexes du tungstène, rhénium et tantale. Dans le cadre de cette thèse, nous nous sommes donc attachés à mettre en place une méthodologie pour déterminer ces CSA et donc la nature de la dynamique de chaque système qui conduit au CSA moyenné. Nous nous sommes d'abord intéressés à des systèmes moléculaires pour révéler des interactions non covalentes entre les complexes et le support silice à partir d'une approche de type petit cluster en utilisant divers niveaux de calculs DFT et modèles moléculaires. Cette modélisation moléculaire de la silice étant insuffisante, nous avons entrepris une modélisation de la surface de silice amorphe par dynamique moléculaire classique dont les caractéristiques ont été comparées aux données expérimentales existantes. Le comportement dynamique de ces systèmes greffés sur silice amorphe a été simulé par dynamique moléculaire ab initio QM/MM, couplant une description quantique du complexe organométallique à une description classique du support. Ces études dynamiques ont conduit à des valeurs de CSA moyennées dans le temps de la dynamique. La comparaison de ces valeurs calculées et des valeurs expérimentales a permis d'apporter des éléments de réponse sur l'origine des différences de comportement dynamique de ces complexes alkylidènes. De façon remarquable des mouvements d'ensemble des espèces greffées par rapport à la surface de silice et des modification de la coordination du métal par l'apparition d'interaction agostique contribuent à moyenner le CSA.

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Eliah, Dawod Ibrahim. "Structural integrity of highly ionized peptides." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-387886.

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In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

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10

Cheik, Njifon Ibrahim. "Modélisation des modifications structurales, électroniques et thermodynamiques induites par les défauts ponctuels dans les oxydes mixtes à base d'actinides (U,Pu)O2." Electronic Thesis or Diss., Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0356.

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(U,Pu)O2 (aussi appelé MOX) est actuellement utilisé comme combustible dans les réacteurs nucléaires à eau pressurisée (REP) avec une teneur massique en Pu d’environ 10 %. Il est également envisagé comme combustible de référence pour les réacteurs à neutrons rapides à caloporteur sodium, avec une teneur massique en Pu d’environ 25 %. En conditions opérationnelles, (U,Pu)O2 est soumis à des réactions de fission qui génèrent une grande quantité de défauts et de produits de fission. Par migration, ces défauts et produits de fission gazeux peuvent s'agréger en nano-cavités, dislocations et bulles de gaz, conduisant à une modification de la microstructure. Une meilleure description du comportement du combustible à l’échelle atomique, notamment des mécanismes élémentaires impliqués dans la diffusion des défauts et des produits de fission, est donc nécessaire pour affiner les modèles utilisés dans les codes de performance des combustibles. Pour l’étude des propriétés de (U,Pu)O2, nous avons effectué des calculs de structure électronique basés sur la méthode DFT+U combinée au contrôle des matrices d’occupation des orbitales corrélées. Des minimisations d’énergie ainsi que la dynamique moléculaire ab initio ont été utilisées. Nous avons étudié dans un premier temps les propriétés du cristal de (U,Pu)O2 pour différentes teneurs en Pu. Nous avons ensuite étudié la stabilité des défauts ponctuels ainsi que les modifications structurales et électroniques induites par ces défauts ponctuels dans (U,Pu)O2 et (U,Ce)O2, matériau utilisé comme simulant de (U,Pu)O2. Enfin, nous avons étudié le piégeage et la solubilité des gaz de fission (Kr, Xe) et de l’hélium dans la matrice de (U,Pu)O2 (U,Pu)O2 (commonly called MOX) is currently used as nuclear fuel in pressurized water reactors with a Pu content of around 10 wt.%, and is envisaged as the reference fuel in Generation IV sodium fast reactors (SFR) with a Pu content of around 25 wt.%. Under operation, (U,Pu)O2 is submitted to fission reactions which generate a large quantity and variety of point defects, as well as fission products. By migrating, point defects and gaseous fission products can aggregate into nano-voids, dislocations and fission gas bubbles, which lead to the modification of the fuel microstructure. Therefore, a better description of the fuel behaviour at the atomic scale, and especially of the elementary mechanisms involved in the diffusion of point defects and fission products, is necessary to refine the models used in the fuel performance codes used to simulate the behaviour of fuels at the macroscopic scale. We use electronic structure calculations based on the DFT+U method combined with the occupation matrix control scheme (OMC) to investigate (U,Pu)O2 properties for various Pu contents. Static energy minimizations and ab initio molecular dynamics were used. We have first determined bulk structural, electronic and thermodynamics properties of (U,Pu)O2. We then studied the stability of point defects in (U,Pu)O2 and (U,Ce)O2, as well as the structural and electronic modifications induced by these point defects, in (U,Pu)O2 and the common experimental surrogate (U,Ce)O2. Finally, the fission gas (Kr and Xe) and helium (He) trapping and solubility in (U,Pu)O2 matrix are investigated

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11

Pezzotti, Simone. "DFT-MD simulations and theoretical SFG spectroscopy to characterize H-Bonded networks at aqueous interfaces : from hydrophobic to hydrophilic environments Structural definition of the BIL and DL: a new universal methodology to rationalize non-linear χ(2)(ω) SFG signals at charged interfaces, including χ(3)(ω) contributions What the Diffuse Layer (DL) Reveals in Non-Linear SFG Spectroscopy 2D H-Bond Network as the Topmost Skin to the Air-Water Interface Combining ab-initio and classical molecular dynamics simulations to unravel the structure of the 2D-HB-network at the air-water interface 2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations Spectroscopic BIL-SFG Invariance Hides the Chaotropic Effect of Protons at the Air-Water Interface Molecular hydrophobicity at a macroscopically hydrophilic surface Graph theory for automatic structural recognition in molecular dynamics simulations DFT-MD of the (110)-Co3O4 cobalt oxide semiconductor in contact with liquid water, preliminary chemical and physical insights into the electrochemical environment". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLE008.

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Améliorer notre connaissance de la structure de l'eau dans l'environnement spécial offert par une interface est essentiel pour la compréhension de nombreux phénomènes naturels et applications technologiques. Pour révéler cette structure interfaciale de l'eau, des techniques capables de fournir des informations microscopiques, de manière sélective, pour cette couche interfaciale (BIL) sont nécessaires. Dans le présent travail de thèse, nous avons donc étudié les interfaces aqueuses au niveau moléculaire, en couplant la modélisation théorique à partir de simulations DFT-MD avec les spectroscopies SFG et THz-IR. En développant de nouveaux protocoles/outils d'investigation associant simulations DFT-MD et spectroscopie SFG, en particulier pour la rationalisation plus complexe des interfaces chargées, nous avons fourni une compréhension globale de l'effet des conditions interfaciales d'hydrophilicité, de pH, de force ionique sur le réseau des liaisons-H formé dans la couche interfaciale BIL, sur ses signatures spectroscopiques et sur son impact sur les propriétés physico-chimiques. Nous avons montré pour la première fois que, dans des conditions suffisamment hydrophobes, l'eau interfaciale crée des réseaux des liaisons-H bidimensionnels, révélé expérimentalement par les spectres THz-IR. Le réseau-2D dicte la dynamique de l'eau interfaciale, le potentiel de surface, l'acidité de surface, la tension superficielle et la thermodynamique d'hydratation des solutés hydrophobes. Cet "ordre horizontal" aux interfaces hydrophobes est opposé à "l'ordre verticale" obtenu aux interfaces hydrophiles. Nous avons aussi révélé comment les ions et les conditions de pH modifient ces arrangements structuraux Improving our knowledge on water H-Bonded networks formed in the special environment offered by an interface is pivotal for our understanding of many natural phenomena and technological applications. To reveal the interfacial water arrangement, techniques able to provide detailed microscopic information selectively for the interfacial layer are required. In the present thesis work, we have hence investigated aqueous interfaces at the molecular level, by coupling theoretical modeling from DFT-MD simulations with SFG & THz-IR spectroscopies. By developing new investigation protocols/tools, coupling DFT-MD simulations and SFG spectroscopy, in particular for the more complex rationalization of charged interfaces, we have provided a global comprehension of the effect of various interfacial conditions (hydrophilicity, pH, ionic strength) on the HB-Network formed in the interfacial layer (BIL), on its spectroscopic signatures and on its impact on physico-chemical properties. We have shown for the first time that, in sufficiently hydrophobic conditions, BIL interfacial water creates special 2-Dimensional HB-Networks, experimentally revealed by one specific THz-IR marker band. Such 2D-network dictates HBs and orientational dynamics of interfacial water, surface potential, surface acidity, water surface tension and thermodynamics of hydration of hydrophobic solutes. Such "horizontal ordering” of water at hydrophobic interfaces is found opposite to the “vertical ordering” of water at hydrophilic interfaces, while coexistence of the two orders leads to disordered interfacial water in intermediate hydrophilic/hydrophobic conditions. Both DFT-MD and SFG further revealed how ions & pH conditions alter these BIL-water orders

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12

Mohamed, Fawzi Roberto. "Advanced methods in Ab-initio molecular dynamics /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16893.

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13

Marzari, Nicola. "Ab-initio molecular dynamics for metallic systems." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285270.

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14

Kochman, Michal. "Ab initio simulations of reactions occurring in molecular crystals." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8906.

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Although the solid state may not usually be thought of as an environment suitable for chemical reactions under mild conditions, a growing number of organic compounds are known to undergo interesting and, in many cases, practically useful chemistry in the molecular crystal phase. Of particular interest are photochemical reactions occurring in molecular crystals, which possess a number of characteristic features that make them attractive to study using the methods of theoretical chemistry. Firstly, molecular packing and steric effects strongly influence the mechanistic course of reactions in the crystal phase, which in some cases enables clean and controllable chemistry, including synthetic reactions as well as reversibly switchable isomerisations accompanied by a change of the macroscopic properties of the crystal, such as shape and colour. Secondly, in part due to their fast (subpicosecond) timescales and relatively low conversion rates (of the order of a few per cent), many of these reactions present challenges to experimental techniques, which computer simulation methods are uniquely positioned to overcome. Finally, these systems lend themselves well to simulation using a hybrid combination of two ab initio electronic structure methods, one of which is used to describe the electronic excitation of a reactive molecule while the other is applied to the surrounding bulk lattice. This thesis describes the computational modelling of two such reactions: the syn-anti photoisomerisation of 7-(2-pyridyl)indole and the reversible cis-enol⇄trans-keto photoisomerisation of N-salicylidene-2-chloroaniline. The solid-state mechanisms and rates of both reactions are computed using the TD-DFT/DFT hybrid method, in the latter case validating a previously postulated reaction mechanism. Furthermore, the thermal (ground-state) tautomerisation reaction in the photochromic and non-photochromic polymorphs of N-salicylidene-2-chloroaniline is investigated through calculations at the DFT level of theory. The results of these calculations indicate that both polymorphs are thermochromic, but tautomeric equilibrium in the non-photochromic polymorph is more sensitive to temperature than in the photochromic polymorph. Additionally, a critical assessment is presented of the accuracy of the various emphab initio methods employed throughout this work.

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15

Creazzo, Fabrizio. "Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field Ionic diffusion and proton transfer in aqueous solutions of alkali metal salts Ionic Diffusion and Proton Transfer in Aqueous Solutions under an Electric Field: State-of-The-Art Ionic diffusion and proton transfer of MgCl2 and CaCl2 aqueous solutions: an ab initio study under electric field DFT-MD of the (110)-Co 3 O 4 cobalt oxide semiconductor in contact with liquid water, preliminary chemical and physical insights into the electrochemical environment Enhanced conductivity of water at the electrified air–water interface: a DFT-MD characterization Ions tune interfacial water structure and modulate hydrophobic interactions at silica surfaces." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASE012.

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Dans cette thèse, des simulations DFT-MD couplées à des techniques inno-vantes de métadynamique, sont appliquées pour acquérir une compréhensionglobale des interfaces aqueuses d'oxyde de cobalt Co3O4 et CoO(OH) dansla catalyse de la réaction d'évolution de l'oxygène (OER), et ainsi éventuellement aider à la conception de nouveaux catalyseurs basés sur des matériaux non précieux, un domaine clé de la recherche scientifique et technologique, particulièrement important pour l'économie de l'hydrogène, pour les technologies vertes dans une période de temps avec une demande toujours plus croissanteen énergie verte. Dans cette thèse, nous révélons étape par étape les mécanismes de l'OER sur les électrocatalyseurs aqueux d'oxyde de cobalt Co3O4 etCoO(OH) via de nouvelles techniques de métadynamique.Jusqu'à présent, la littérature n'a jamais pris en compte les modificationsau niveau atomique de la structure des électrodes ainsi que de l'eau interfaciale dans leur modélisation des processus OER. Ce manque de connaissances représente clairement un obstacle important au développement de catalyseurs améliorés, qui pourrait être surmonté en utilisant des méthodes capables de suivre les caractéristiques catalytiques de l'OER à l'échelle atomique. Pour la première fois, nous montrons combien il est important de prendre en considération la présence de l'environnement aqueux dans la caractérisation structurale des surfaces du catalyseur, c'est-à-dire (110)-Co3O4 et (0001)-CoO(OH) dans ce travail. Une caractérisation détaillée des propriétés chimiques et physiques des interfaces aqueuses est fournie (la structure, la dynamique, la spectroscopie, le champ électrique), pour les surfaces (110)-Co3O4 et (0001)-CoO(OH) en contact avec l'eau liquide.Une étude détaillée de l'OER est présentée non seulement du point de vue descatalyseurs, mais aussi en abordant le rôle de l'environnement de l'eau dans leprocessus catalytique, ce qui n'a pas été fait auparavant dans la littérature. En conséquence, l'OER en phase gazeuse et en phase liquide sont étudiés ici auxinterfaces aqueuses (110)-Co3O4 et (0001)-CoO(OH) en adoptant une nouvelleapproche de métadynamique d'échantillonnage amélioré, capable d'identifieret caractériser les mécanismes de réaction chimique et d'intégrer pleinement lerôle des degrés de liberté du solvant, permettant ainsi de dévoiler des réactivités chimiques d'une complexité remarquable. L'énergétique, la cinétique et la thermodynamique derrière l'OER sont donc trouvées à ces surfaces d'oxyde de cobalt à l'interface avec l'eau In this thesis, DFT-MD simulations, coupled with state-of-the-art metadynamics techniques, are applied to gain a global understanding of Co3O4 and CoO(OH) cobalt oxide aqueous interfaces in catalyzing the oxygen evolution reaction (OER), and hence possibly help in the design of novel catalysts basedon non-precious materials, a current key field of research in science and technology, especially of importance for the hydrogen economy, for green technology in a period of time with an ever more growing demand in green-energy. In this thesis, we step-by-step reveal the OER mechanisms on spinel Co3O4 andCoO(OH) cobalt aqueous electrocatalysts carefully and rationally via novelmetadynamics techniques.Up to now, the literature has never taken into account the atomistic modifications on the electrode structure as well as on the interfacial water into their modeling of OER processes. Such lack of knowledge clearly represents a significant hurdle toward the development of improved catalysts, which couldbe overcome by employing methods able to track the catalytic features of theOER at the atomistic scale. For the first time, we show how important itis to take into consideration the presence of the liquid water environment inthe structural characterization of catalyst surfaces, i.e. for (110)-Co3O4 and(0001)-CoO(OH) in this work. A detailed characterization of chemical andphysical properties of the aqueous interfaces is provided (i.e. structure, dynamics, spectroscopy, electric field), for the (110)-Co3O4 and (0001)-CoO(OH)aqueous surfaces.A study of the OER is presented not only by looking at the catalysts, butalso by addressing the role of the water environment in the catalytic process,not done before in literature. Accordingly, both gas-phase and liquid-phaseOER are here investigated at the (110)-Co3O4 and (0001)-CoO(OH) adoptinga novel enhanced sampling metadynamics approach able to address a widerange of chemical reaction mechanisms and to fully include the role of thesolvent degrees of freedom, allowing to unveil reaction networks of remarkablecomplexity. The energetics, kinetics and thermodynamics behind the OER aretherefore found at these cobalt oxide surfaces

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16

Del, Fré Samuel. "Études théoriques de la photodésorption d'analogues de glaces moléculaires interstellaires : application au monoxyde de carbone." Electronic Thesis or Diss., Université de Lille (2022-....), 2024. http://www.theses.fr/2024ULILR039.

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Des quantités inhabituelles de molécules en phase gazeuse sont détectées dans les régions froides (environ 10 K) du milieu interstellaire (ISM), principalement attribuées à la désorption non thermique de molécules depuis les glaces déposées sur les grains de poussière. En particulier, la désorption induite par les rayons ultraviolets du vide (photodésorption VUV) est considérée comme étant une voie de désorption majoritaire dans les régions de l'ISM dominées par les photons. Les investigations expérimentales ont révélé que dans les glaces pures de monoxyde de carbone (CO), espèce omniprésente dans l'ISM, la photodésorption VUV peut suivre un mécanisme indirect de désorption induite par transition électronique (DIET) pour les photons dont l'énergie est comprise entre 7 et 10 eV. Néanmoins, la compréhension des mécanismes moléculaires sous-jacents reste un sujet de débat scientifique. Dans ce contexte astrochimique, nous présentons une étude théorique combinée utilisant la dynamique moléculaire ab initio (AIMD) basée sur la théorie de la fonctionnelle de la densité (DFT) et des potentiels machine learning (PML) construits avec des réseaux de neurones artificiels (ANN), afin d'étudier la dernière partie du mécanisme DIET dans les glaces amorphes de CO. Ici, une molécule CO hautement excitée vibrationnellement (v = 40) au centre d'un agrégat composé de 50 molécules de CO, initialement optimisé puis thermalisé à 15 K, déclenche, la désorption indirecte de molécules de surface. Nos résultats théoriques révèlent que le processus de désorption consiste en 3 étapes fondamentales qui commence par une attraction mutuelle entre la molécule excitée vibrationnellement et une ou deux molécules voisines, activée par l'étirement de la liaison CO et favorisée par l'effet stérique des molécules environnantes. Cela est suivi par une séquence de transferts d'énergie initiée par une collision, se concluant en la désorption de molécules CO vibrationnellement froides dans 88% des trajectoires AIMD. De plus, les distributions théoriques de l'énergie interne et translationnelle des molécules désorbées concordent remarquablement avec les résultats expérimentaux, ce qui soutient le rôle crucial de la relaxation vibrationnelle dans le processus de désorption. Enfin, les premiers PML construits à partir des simulations AIMD, sont capables d'ajuster avec précision la surface d'énergie potentielle multidimensionnelle du système, permettant de prédire efficacement les énergies des agrégats et les forces atomiques. Les simulations de dynamique moléculaire classique utilisant ces potentiels sont plus de 1800 fois plus rapides que celles basées sur l'AIMD, tout en offrant des précisions similaires à ceux de la DFT Unusual amounts of gas-phase molecules are detected in the cold regions (around 10 K) of the interstellar medium (ISM), primarily attributed to the non-thermal desorption of molecules from ices deposited on dust grains. In particular, vacuum ultraviolet (VUV) photon-induced desorption (photodesorption) is considered a major desorption pathway in photon-dominated regions of the ISM. Experimental investigations have revealed that in pure carbon monoxide (CO) ices, a ubiquitous species in the ISM, VUV photodesorption can follow an indirect mechanism of desorption induced by electronic transitions (DIET) for photons with energy between 7 and 10 eV. Nevertheless, the understanding of the underlying molecular mechanisms remains a topic of scientific debate. In this astrochemical context, we present a combined theoretical study using ab initio molecular dynamics (AIMD) based on density functional theory (DFT) and machine learning potentials (PML) constructed with artificial neural networks (ANN) to study the final part of the DIET mechanism in amorphous CO ices. Here, a highly vibrationally excited CO molecule (v = 40) at the center of an aggregate initially composed of 50 CO molecules, optimized and then thermalized at 15 K, triggers the indirect desorption of surface molecules. Our theoretical results reveal that the desorption process consists of three fundamental steps, beginning with a mutual attraction between the vibrationally excited molecule and one or two neighboring molecules, activated by CO bond stretching and facilitated by the steric effect of surrounding molecules. This is followed by a sequence of energy transfers initiated by a collision, resulting in the desorption of vibrationally cold CO molecules in 88% of the AIMD trajectories. Additionally, the theoretical distributions of the internal and translational energy of desorbed molecules remarkably match experimental results, supporting the crucial role of vibrational relaxation in the desorption process. Finally, the first PML constructed from AIMD simulations accurately fit the multidimensional potential energy surface of the system, allowing efficient prediction of aggregate energies and atomic forces. Classical molecular dynamics simulations using these potentials are over 1800 times faster than those based on AIMD while offering precision comparable to DFT

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17

Sahli, Beat. "Ab initio molecular dynamics simulation of diffusion in silicon /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16888.

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18

Sahli, Beat. "Ab initio molecular dynamics simulation of diffusion in silicon /." Konstanz : Hartung-Gorre, 2007. http://www.loc.gov/catdir/toc/fy0804/2007481782.html.

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19

Watson, Stuart. "Structural relaxation at defects by Ab initio molecular dynamics." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320648.

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20

Walker, Brent Graham. "Ab initio molecular dynamics studies of liquid metal surfaces." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615985.

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21

Laino, Teodoro. "Multigrid QM/MM approaches in ab initio molecular dynamics." Doctoral thesis, Scuola Normale Superiore, 2006. http://hdl.handle.net/11384/85799.

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22

Au, Yat-yin. "Ab initio calculations : an extension of Sankey's method /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21482706.

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23

Luo, Ye. "Ab initio molecular dynamics of water by quantum Monte Carlo." Doctoral thesis, SISSA, 2014. http://hdl.handle.net/20.500.11767/3896.

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The chapter 2, we deal with the challenge b). It focuses on the variational Monte Carlo (VMC) and the wavefunction optimization methods based on VMC. The performance of different methods are displayed through the op- timization of the Jastrow factor in our test case Beryllium dimer and the efficiency is improving surprisingly during the evolution of these methods. In chapter 3, we focus on the challenge a). It describes the wavefunc- tion ansatz used by our simulation. In this thesis, we introduce the atomic hybrid orbitals which significantly increase the compactness of our wavefunc- tion without hurting accuracy. This chapter also explain how to optimize the determinant in a way that the number of variational parameters scales only linearly with the system size. This further helps the efficiency of the wavefunction optimization. In chapters 4 and 5, the issue c) is explained in detail. In chapter 4, a second order Langevin dynamics (SLD) scheme is devised particularly for QMC and this thesis improves this scheme by developing a better integration method. Here, we also highlight the remarkable power of the force covari- ance matrix which can be defined only in QMC and is capable of accelerating the slow modes of a dynamics. In chapter 5, this SLD for QMC is validated through intensive benchmarking on the calculation of the vibrational frequen- cies of water and other small molecules. It is shown that many systematic biases in our MD scheme and QMC evaluation can be controlled so that we are confident to push forward this ab initio molecular dynamics for applica- tions on large systems. Finally in chapter 6, we perform the simulation of liquid water with all the preparation done in the previous chapters. The results are encouraging since we’ve closed the discrepancy of the peak positions of RDFs between experi- ments and ab initio simulations. The power of QMC is also demonstrated by the fact that the shapes of our RDFs are much less structured than previous DFT-based ab initio simulations even if the two water molecule interaction is dealt with the same level of accuracy as the DFT/BLYP calculation. In this chapter, we have also studied the features of hydrogen bonds in our simulation of liquid water. All our results indicate that it is important to consider the quantum nature of the ions for a faithful description of liquid water. This will be left for future studies, possible in principle even within the QMC approach.

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24

Li, Hongfei. "Density functional simulations of defect behavior in oxides for applications in MOSFET and resistive memory." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274924.

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Defects in the functional oxides play an important role in electronic devices like metal oxide semiconductor field effect transistors (MOSFETs) and resistive random-access memories (ReRAMs). The continuous scaling of CMOS has brought the Si MOSFET to its physical technology limit and the replacement of Si channel with Ge channel is required. However, the performance of Ge MOSFETs suffers from Ge/oxide interface quality and reliability problems, which originates from the charge traps and defect states in the oxide or at the Ge/oxide interface. The sub-oxide layers composed of GeII states at the Ge/GeO2 interface seems unavoidable with normal passivation methods like hydrogen treatment, which has poor electrical properties and is related to the reliability problem. On the other hand, ReRAM works by formation and rupture of O vacancy conducting filaments, while how this process happens in atomic scale remains unclear. In this thesis, density functional theory is applied to investigate the defect behaviours in oxides to address existing issues in these electronic devices. In chapter 3, the amorphous atomic structure of doped GeO2 and Ge/GeO2 interface networks are investigated to explain the improved MOSFET reliability observed in experiments. The reliability improvement has been attributed to the passivation of valence alternation pair (VAP) type O deficiency defects by doped rare earth metals. In chapter 4, the oxidation mechanism of GeO2 is investigated by transition state simulation of the intrinsic defect diffusion in the network. It is proposed that GeO2 is oxidized from the Ge substrate through lattice O interstitial diffusion, which is different from SiO2 which is oxidized by O2 molecule diffusion. This new mechanism fully explains the strange isotope tracer experimental results in the literature. In chapter 5, the Fermi level pinning effect is explored for metal semiconductor electrical contacts in Ge MOSFETs. It is found that germanides show much weaker Fermi level pinning than normal metal on top of Ge, which is well explained by the interfacial dangling bond states. These results are important to tune Schottky barrier heights (SBHs) for n-type contacts on Ge for use on Ge high mobility substrates in future CMOS devices. In chapter 6, we investigate the surface and subsurface O vacancy defects in three kinds of stable TiO2 surfaces. The low formation energy under O poor conditions and the +2 charge state being the most stable O vacancy are beneficial to the formation and rupture of conducting filament in ReRAM, which makes TiO2 a good candidate for ReRAM materials. In chapter 7, we investigate hydrogen behaviour in amorphous ZnO. It is found that hydrogen exists as hydrogen pairs trapped at oxygen vacancies and forms Zn-H bonds. This is different from that in c-ZnO, where H acts as shallow donors. The O vacancy/2H complex defect has got defect states in the lower gap region, which is proposed to be the origin of the negative bias light induced stress instability.

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25

區逸賢 and Yat-yin Au. "Ab initio calculations: an extension of Sankey's method." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31222195.

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26

Silaghi, Marius-Christian. "Ab initio Molecular Modelling of the Dealumination and Desilication Mechanisms of Relevant Zeolite Frameworks." Thesis, Lyon, École normale supérieure, 2014. http://www.theses.fr/2014ENSL0930/document.

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Les zéolites, aluminosilicates cristallisés microporeux, sont largement utilisés en raffinage, en pétrochimie et en conversion de la biomasse. En raison du faible diamètre des micropores, limitations diffusionnelles et effets de confinement peuvent favoriser la formation de sous-Produits non désirés. L'introduction de mésopores par désalumination et/ou désilication ("zéolites hiérarchisées") peut diminuer ces phénomènes. Cependant, les mécanismes ces réactions restent méconnus à l'échelle moléculaire. Par calculs quantiques périodiques, au niveau de la théorie de la fonctionnelle de la densité (DFT) et selon une approche hybride QM/QM, nous avons pu mettre en évidence l'importance de l'attaque de la molécule d'eau sur l'atome d'aluminium, qui se fait en anti par rapport au site acide de Brønsted. Des structures d'Al penta ou tetra coordinées ont aussi été suggérées expérimentalement comme précurseurs de la désalumination. Malgré une forte hétérogénéité structurale des sites T, l'élucidation des chemins réactionnels et les énergies d’activation des étapes d’hydrolyse des liaisons Al-O (70-100 kJ/mol) dans les systèmes zéolitiques investigués (MOR, FAU, MFI, CHA) nous a permis d'établir des corrélations du type Brønsted-Evans-Polanyi. Ces corrélations permettent d'estimer et prédire des énergies d'activation par le biais de la thermodynamique, donne ainsi une prédiction aisée des sites T sensibles à la désalumination. Un autre facteur clé pour la compréhension de la désalumination est l'effet de confinement sur l'espèce aluminique extra-Réseau générée (EFAL), exercé par les cavités. Finalement nous avons pu montrer que le chemin réactionnel de désalumination et désilication, consécutif ou simultané, , est thermodynamiquement plus favorable qu'une simple désalumination ce qui est en accord avec les propositions mécanistiques de la littérature sur la genèse de mésopores par démétallation Zeolites are crystalline microporous aluminosilicates widely used in refining, petrochemistry and biomass conversion. However, diffusion limitation and confinement effect can promote the formation of undesired products. The introduction of mesopores by dealumination and/or desilication ("hierarchical zeolites") is a possible solution widely used experimentally. Nevertheless, the mechanisms of these demetallation reactions are poorly described at the molecular scale. We determine the mechanisms of the formation of extraframework Al species (EFAL) for zeotypes MOR, FAU, MFI and CHA occurring during the dealumination process, possibly associated with desilication. First-Principles periodic density functional theory (DFT) and hybrid QM/QM calculations have been employed in order to analyze full reaction paths leading to extraframework species and to quantify the activation energies of the determining steps. It has been demonstrated that the initiation of an Al-O(H) bond break takes place via water adsorption on the Al atom in anti-Position to the Brønsted acid site, via a penta- or tetra-Coordinated Al species. Such species are shown to be at the initiation of the Al dislodgement from the zeolitic framework. Despite a strong structural heterogeneity of T sites, we determined Brønsted-Evans-Polanyi (BEP) relationships for the entire dealumination pathway. Moreover, it is shown that not only the initiation and propagation mechanisms are primordial for the understanding of an Al extraction, but also the confinement effect on EFAL species within the zeolites cavities. Finally, from the energy profile of combined dealumination/desilication pathways, we show that it is thermodynamically favoured to extract extraframework Si species (EFSI) in the course of dealumination

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27

Li, Ming, and 李銘. "Some AB initio studies of positron annihilation in semiconductors." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B31238919.

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28

Li, Ming. "Some AB initio studies of positron annihilation in semiconductors /." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20128496.

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29

Spura, Thomas [Verfasser]. "Ab initio path integral molecular dynamics : theory and applications / Thomas Spura." Paderborn : Universitätsbibliothek, 2015. http://d-nb.info/1078666504/34.

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30

Blumberger, Jochen. "Ab-initio molecular dynamics simulation of redox reactions in aqueous solution." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616223.

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31

Tocci, G. "Realistic modelling of water/solid interfaces from ab initio molecular dynamics." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1457448/.

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Water/solid interfaces are of utmost importance to a number of technological processes. Theoretical studies, based on ab initio approaches are suitable to unveil processes occurring at water/solid interfaces and can therefore be instrumental to delineate guidelines to improve the efficiency of these processes. In this thesis we study several systems of current interest using ab initio methods based on density functional theory (DFT). By going often beyond the use of standard DFT methods and approximations we have provided insights into processes occurring at water/solid interfaces under ambient conditions and in non stoichiometric conditions. Specifically, we will investigate the interactions between water and ZnO, an important metal-oxide especially used in industry to produce methanol. One of the most mportant results of this study is that proton hopping is dramatically enhanced under wet conditions compared to ideal ultra-high vacuum conditions. Also, we will compute the friction between liquid water in contact with 2-D layered materials, and delineate the guidelines on how to alter the friction coe cient in membranes used for desalination or osmotic power harvesting. Finally, in collaboration with Geoff Thornton's group we have investigated the role of defects on the surface chemistry of the rutile TiO2(110), which is the model oxide surface used in photocatalysis applications. On the whole, in this work we have used ab initio methods to reduce the gap between the ultra-high vacuum-style studies of adsorption on perfect defect-free surfaces and the complex behaviour of liquid/solid interfaces under technologically relevant conditions.

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32

Pires, Marcelo da Silva. "Dinâmica molecular e cálculos ab initio em moléculas, nanocones de carbono e agregados de água." reponame:Repositório Institucional da UFC, 2009. http://www.repositorio.ufc.br/handle/riufc/12928.

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PIRES, Marcelo da Silva. Dinâmica molecular e cálculos ab initio em moléculas, nanocones de carbono e agregados de água. 2009. 95 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2009. Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-06-23T20:42:04Z No. of bitstreams: 1 2009_dis_mspires.pdf: 6865198 bytes, checksum: 5e8a1e933acef9d9453a7b24155a31de (MD5) Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-06-23T21:05:27Z (GMT) No. of bitstreams: 1 2009_dis_mspires.pdf: 6865198 bytes, checksum: 5e8a1e933acef9d9453a7b24155a31de (MD5) Made available in DSpace on 2015-06-23T21:05:27Z (GMT). No. of bitstreams: 1 2009_dis_mspires.pdf: 6865198 bytes, checksum: 5e8a1e933acef9d9453a7b24155a31de (MD5) Previous issue date: 2009 A presente dissertação insere-se no escopo da Nanociência e da Nanotecnologia, que têm como objeto de estudo são sistemas (nanoestruturas, nanopartículas, nanoagregados, etc.) com dimensões características no intervalo 1{100 nm (1nm = 10ºA). Nela sao investigadas: (a) propriedades estruturais de nanocestas moleculares de carbono e sua interação com o aminoácido L-alanina; (b) a interação entre nanocones de carbono anin- hados; e (c) a transição estrutural dependente da temperatura de agregados de água. Os nanosistemas foram estudados através de Dinâmica Molecular, que permite o estudo de sistemas com cerca até milhões de átomos, e da Teoria do Funcional da Densidade, que permite a obtenção das propriedades do estado fundamental de sistemas com até centenas de ¶atomos. No estudo das nanocestas de carbono C20-coranuleno, C30-hemifulereno, C35- hemifulereno e C36-triacenaftotrifenileno, obteve-se que as mesmas s~ao est¶aveis a temper- aturas elevadas, e demonstrou-se a capacidade das mesmas de servirem como armadilhas para o amino¶acido L-alanina, como efeito da mistura dos orbitais ¼ e ¾ nestas estruturas produzida pela curvatura. Nanocones de carbono s~ao estruturas c^onicas de carbono ob- servadas durante o processo de s¶³ntese de nanotubos de carbono, existindo com ^angulos de abertura 19:2 ±, 38:9 ±, 60:0 ±, 83:6 ±, e 112:9 ±. Experimentalmente estes nanocones encontram-se, em geral, aninhados. Para pares de nanocones de carbono aninhados, obteve-se a depend^encia do potencial de intera»c~ao entre os mesmos com o ^angulo ddas pontas e o n¶umero de ¶atomos de carbono. Finalmente, obteve-se que a intera»c~ao entre mol¶eculas de ¶agua atrav¶es de liga»c~oes de hidrog^enio d¶a origem a agregados estáveis de água: dímeros , trímeros, tetrâmeros, pentâmeros, hexâmeros, etc. quando formados por duas, três, quatro, cinco e seis moléculas de água, respectivamente. Para estes agregados, foi obtido o potencial de interação entre duas camadas empilhadas, e demonstrou-se uma surpreendente transição de fase de dois trímeros empilhados para um hexâmero, de quatro trímeros empilhados para dois hexâmeros, e também de três tetrâmeros empilhados para dois hexâmeros. As pesquisas realizadas enquadram-se na temática de atuação do In- stituto de NanoBioEstruturas & Simulação NanoBioMolecular [NANO(BIO)SIMES], um dos Institutos Nacionais de Ciência e Tecnologia financiados pelo CNPq a partir do início de 2009, que visa desenvolver atividades de pesquisa e formação de recursos humanos de alto nível em nanobioestruturas e simulação nanobiomolecular.

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33

Altschäffel, Jan [Verfasser]. "Ab initio molecular dynamics simulations of molecular scattering from metal(111) surfaces / Jan Altschäffel." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://nbn-resolving.de/urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-58F1-5-3.

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34

Gambino, Davide. "Titanium vacancy diffusion in TiN via non-equilibrium ab initio molecular dynamics." Thesis, Linköpings universitet, Teoretisk Fysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-129555.

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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.

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35

More, Joshua N. "Algorithms and computer code for ab initio path integral molecular dynamics simulations." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:b8ca7471-21e3-4240-95b1-8775e5d6c08f.

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This thesis presents i-PI, a new path integral molecular dynamics code designed to capture nuclear quantum effects in ab initio electronic structure calculations of condensed phase systems. This software has an implementation of estimators used to calculate a wide range of static and dynamical properties and of state-of-the-art techniques used to increase the computational efficiency of path integral simulations. i-PI has been designed in a highly modular fashion, to ensure that it is as simple as possible to develop and implement new algorithms to keep up with the research frontier, and so that users can take maximum advantage of the numerous electronic structure programs which are freely available without needing to rewrite large amounts of code. Among the functionality of the i-PI code is a novel integrator for constant pressure dynamics, which is used to investigate the properties of liquid water at 750 K and 10 GPa, and efficient estimators for the calculation of single particle momentum distri- butions, which are used to study the properties of solid and liquid ammonia. These show respectively that i-PI can be used to make predictions about systems which are both difficult to study experimentally and highly non-classical in nature, and that it can illustrate the relative advantages and disadvantages of different theoretical methods and their ability to reproduce experimental data.

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36

Pires, Marcelo da Silva. "DinÃmica molecular e cÃlculos ab initio em molÃculas, nanocones de carbono e agregados de Ãgua." Universidade Federal do CearÃ, 2009. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=3655.

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Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico A presente dissertaÃÃo insere-se no escopo da NanociÃncia e da Nanotecnologia, que tÃm como objeto de estudo sÃo sistemas (nanoestruturas, nanopartÃculas, nanoagregados, etc.) com dimensÃes caracterÃsticas no intervalo 1{100 nm (1nm = 10ÂA). Nela sao investigadas: (a) propriedades estruturais de nanocestas moleculares de carbono e sua interaÃÃo com o aminoÃcido L-alanina; (b) a interaÃÃo entre nanocones de carbono anin- hados; e (c) a transiÃÃo estrutural dependente da temperatura de agregados de Ãgua. Os nanosistemas foram estudados atravÃs de DinÃmica Molecular, que permite o estudo de sistemas com cerca atÃ milhÃes de Ãtomos, e da Teoria do Funcional da Densidade, que permite a obtenÃÃo das propriedades do estado fundamental de sistemas com atÃ centenas de Âatomos. No estudo das nanocestas de carbono C20-coranuleno, C30-hemifulereno, C35- hemifulereno e C36-triacenaftotrifenileno, obteve-se que as mesmas s~ao estÂaveis a temper- aturas elevadas, e demonstrou-se a capacidade das mesmas de servirem como armadilhas para o aminoÂacido L-alanina, como efeito da mistura dos orbitais Â e Â nestas estruturas produzida pela curvatura. Nanocones de carbono s~ao estruturas c^onicas de carbono ob- servadas durante o processo de sÂÂntese de nanotubos de carbono, existindo com ^angulos de abertura 19:2 Â, 38:9 Â, 60:0 Â, 83:6 Â, e 112:9 Â. Experimentalmente estes nanocones encontram-se, em geral, aninhados. Para pares de nanocones de carbono aninhados, obteve-se a depend^encia do potencial de interaÂc~ao entre os mesmos com o ^angulo ddas pontas e o nÂumero de Âatomos de carbono. Finalmente, obteve-se que a interaÂc~ao entre molÂeculas de Âagua atravÂes de ligaÂc~oes de hidrog^enio dÂa origem a agregados estÃveis de Ãgua: dÃmeros , trÃmeros, tetrÃmeros, pentÃmeros, hexÃmeros, etc. quando formados por duas, trÃs, quatro, cinco e seis molÃculas de Ãgua, respectivamente. Para estes agregados, foi obtido o potencial de interaÃÃo entre duas camadas empilhadas, e demonstrou-se uma surpreendente transiÃÃo de fase de dois trÃmeros empilhados para um hexÃmero, de quatro trÃmeros empilhados para dois hexÃmeros, e tambÃm de trÃs tetrÃmeros empilhados para dois hexÃmeros. As pesquisas realizadas enquadram-se na temÃtica de atuaÃÃo do In- stituto de NanoBioEstruturas & SimulaÃÃo NanoBioMolecular [NANO(BIO)SIMES], um dos Institutos Nacionais de CiÃncia e Tecnologia financiados pelo CNPq a partir do inÃcio de 2009, que visa desenvolver atividades de pesquisa e formaÃÃo de recursos humanos de alto nÃvel em nanobioestruturas e simulaÃÃo nanobiomolecular.

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37

Cassone, Giuseppe. "Ab initio molecular dynamics simulations of H-bonded systems under an electric field." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066061/document.

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Malgré le mécanisme de base du transport protonique (PT) dans l'eau ait été proposé en 1806, à ce jour il n'existe pas de théorie complète qui décrive la protolyse. Ce phénomène est à la base du fonctionnement des batteries à hydrogène et de nombreux processus biologiques. Grâce à la technique de dynamique moléculaire Car-Parrinello (CPMD) et à l'aide de l'application d'un champ electrique (EF), une partie de cette thèse a été consacrée à l'étude du PT dans deux phase de la glace: la phase Ih et sa contrepartie ferroélectrique, la glace XI. Certains mécanismes ont été révélés: le rôle joué par les oxygènes lorsque se produit le PT et la contribution du (dés)ordre afin d'assister ce processus [1,2]. Le phénomène du PT est aussi à la base de nombreaux convertisseurs d'énergie constitués par le méthanol tels que le Direct Methanol Fuel Cells et les membranes Nafion. Afin de révéler la nature intime du PT dans le méthanol liquide, une série de simulations CPMD ont été menées sous l'effet d'un EF extérieur. De cette façon il a été possible de comparer le rôle joué par les liasons hydrogène afin d'assister le PT [3]. De plus, quand les intensités du champ sont plus élevées que celles qui donnent lieu au PT, certaines réactions chimiques ont été observées dans le même échantillon "numérique" du méthanol. En exploitant des paramètres typique de la "Théorie de la fonctionnelle de la densité conceptuelle", il a été possible de clarifier les conditions qui donnent lieu à ces réactions chimiques. Enfin, afin de quantifier la contribution du EF à la formation de méthane et de formaldéhyde dans le système, des simulations de métadynamique en conjonction à ceux ab initio ont été menées Although the basic mechanism of the proton transfer (PT) phenomenon in water has been envisaged in 1806, nowadays does not exist a detailed theoretical framework that envelop the protolysis process. This phenomenon is at the base of the operation of hydrogen batteries, as well as of many biological processes. Via the Car-Parrinello Molecular Dynamics (CPMD) technique and by means of the application of an electric field (EF), part of this thesis has been devoted to the detailed study of PT in two ice phases: ice Ih and its ferroelectric counterpart, ice XI. Several previously unknown mechanisms have been shown. As an example, the role played by the oxygens when a PT occurs and the contribution due to (dis)order in assisting this process [1,2]. The PT phenomenon is also at the base of the functioning of some methanol-based energy converters such as Nafion membranes. To the aim of disclosing the intimate nature of PT in liquid methanol, a series of CPMD simulations have been carried out by applying an external EF; the role played by the H-bond network have been also compared with the similar PT mechanism in water [3]. At field strengths higher than those leading to PT, several chemical reactions have been observed in this sample. By exploiting the conceptual Density Functional Theory framework, it has been possible to clarify the circumstances under which a given chemical reaction occurs. Moreover, in order to disclose the role played by the EF in assisting chemical reactions, the mechanism leading to the formation of formaldehyde and methane in the sample has been studied with metadynamics approaches in conjuction with the ab initio ones

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38

Koči, Love. "Studies of Material Properties using Ab Initio and Classical Molecular Dynamics." Doctoral thesis, Uppsala universitet, Kondenserade materiens teori (Fysik IV), 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8626.

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In this thesis, material properties have been examined under extreme conditions in computer-based calculations. The research on iron (Fe), nickel (Ni), and ferropericlase (Mg1-xFexO) are not only important for our understanding of the Earth, but also for an improved knowledge of these materials per se. An embedded-atom model for Fe demonstrated to reproduce properties such as structure factors, densities and diffusion constants, and was employed to evaluate temperature gradients at Earth core conditions. A similar interaction together with a two-temperature method was applied for the analysis of shock-induced melting of Ni. For Mg1-xFexO, the magnetic transition pressure was shown to increase with iron content. Furthermore, the C44 softening with pressure and iron composition supports the experimentally observed phase transition for Mg0.8Fe0.2O at 35 GPa. The properties of high density helium (He) is of great interest as the gas is one of the most abundant elements in the solar system. Furthermore, He and neon (Ne) are often used as pressure media in diamond anvil cells. The melting of He showed a possible fcc-bcc-liquid transition starting at T=340 K, P=22 GPa with a Buckingham potential, whereas the bcc phase was not seen with the Aziz form. For Ne, Monte Carlo calculations at ambient pressure showed very accurate results when extrapolating the melting temperatures to an infinite cluster limit. At high pressure, a one-phase ab initio melting curve showed a match with one-phase L-J potential results, which could imply a correspondence between ab initio/classical one-phase/two-phase calculations. In the search for hard materials, ab initio calculations for four TiO2 phases were compared. Just as imposed by experiment, the cotunnite phase was found to be very hard. The anomalous elastic behavior of the superconducting group-V metals V, Nb, Ta was found to be related to shrinking nesting vectors and the electronic topological transition (ETT).

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39

Cassone, Giuseppe. "Ab initio molecular dynamics simulations of H-bonded systems under an electric field." Electronic Thesis or Diss., Paris 6, 2016. http://www.theses.fr/2016PA066061.

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Анотація:

Malgré le mécanisme de base du transport protonique (PT) dans l'eau ait été proposé en 1806, à ce jour il n'existe pas de théorie complète qui décrive la protolyse. Ce phénomène est à la base du fonctionnement des batteries à hydrogène et de nombreux processus biologiques. Grâce à la technique de dynamique moléculaire Car-Parrinello (CPMD) et à l'aide de l'application d'un champ electrique (EF), une partie de cette thèse a été consacrée à l'étude du PT dans deux phase de la glace: la phase Ih et sa contrepartie ferroélectrique, la glace XI. Certains mécanismes ont été révélés: le rôle joué par les oxygènes lorsque se produit le PT et la contribution du (dés)ordre afin d'assister ce processus [1,2]. Le phénomène du PT est aussi à la base de nombreaux convertisseurs d'énergie constitués par le méthanol tels que le Direct Methanol Fuel Cells et les membranes Nafion. Afin de révéler la nature intime du PT dans le méthanol liquide, une série de simulations CPMD ont été menées sous l'effet d'un EF extérieur. De cette façon il a été possible de comparer le rôle joué par les liasons hydrogène afin d'assister le PT [3]. De plus, quand les intensités du champ sont plus élevées que celles qui donnent lieu au PT, certaines réactions chimiques ont été observées dans le même échantillon "numérique" du méthanol. En exploitant des paramètres typique de la "Théorie de la fonctionnelle de la densité conceptuelle", il a été possible de clarifier les conditions qui donnent lieu à ces réactions chimiques. Enfin, afin de quantifier la contribution du EF à la formation de méthane et de formaldéhyde dans le système, des simulations de métadynamique en conjonction à ceux ab initio ont été menées Although the basic mechanism of the proton transfer (PT) phenomenon in water has been envisaged in 1806, nowadays does not exist a detailed theoretical framework that envelop the protolysis process. This phenomenon is at the base of the operation of hydrogen batteries, as well as of many biological processes. Via the Car-Parrinello Molecular Dynamics (CPMD) technique and by means of the application of an electric field (EF), part of this thesis has been devoted to the detailed study of PT in two ice phases: ice Ih and its ferroelectric counterpart, ice XI. Several previously unknown mechanisms have been shown. As an example, the role played by the oxygens when a PT occurs and the contribution due to (dis)order in assisting this process [1,2]. The PT phenomenon is also at the base of the functioning of some methanol-based energy converters such as Nafion membranes. To the aim of disclosing the intimate nature of PT in liquid methanol, a series of CPMD simulations have been carried out by applying an external EF; the role played by the H-bond network have been also compared with the similar PT mechanism in water [3]. At field strengths higher than those leading to PT, several chemical reactions have been observed in this sample. By exploiting the conceptual Density Functional Theory framework, it has been possible to clarify the circumstances under which a given chemical reaction occurs. Moreover, in order to disclose the role played by the EF in assisting chemical reactions, the mechanism leading to the formation of formaldehyde and methane in the sample has been studied with metadynamics approaches in conjuction with the ab initio ones

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40

Ardèvol, Grau Albert. "Study of molecular mechanisms in glycoside hydrocases and transferases by ab initio molecular dinyamics." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/83945.

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Carbohydrates had historically been associated to two biological functions: energy storage and structural support. However, in the last decades, new complex structures of oligosaccharides have been found to play vital roles in many biological processes, such as signal transduction, immune response, cell differentiation and cancer development, among others. Advances in the functional understanding of carbohydrate-protein interactions represented a breakthrough in the field of glycobiology and glycochemistry, opening a new branch of potential therapeutic targets (carbohydrate acting enzymes), glycomimetic drugs and biomarkers. The bottleneck in the field of glycochemistry is the synthesis of complex saccharides; hence many efforts have been devoted to the development of novel enzymatic strategies for carbohydrate synthesis. Glycoside transferases (GT) and glycoside hydrolases (GH) are the enzymes that catalyze the formation and the cleavage of the glycosidic linkage respectively. They are used in complex oligosaccharides synthesis, and recently they have been engineered to produce enzymes with particular substrate specificities or even activities. In spite of these advances, the understanding of the molecular mechanisms of enzymatic carbohydrate synthesis and degradation is far from complete. Structural studies have shown that the puckering of the sugar ring at the cleavage point must change during catalysis. Knowing the conformational catalytic itinerary has an impact in the design of GHs inhibitors. However, these itineraries are not known for all families of GHs. On the other hand, the saccharide puckering is not an issue in GTs, but the reaction mechanism is not known. In fact, the glycosidic bond formation in GTs remains one of the most intriguing and unanswered questions in the field of glycobiology. The coming of age of powerful theoretical methods such as quantum mechanics / molecular mechanics (QM/MM) and ab initio molecular dynamics (AIMD) has enabled the elucidation of complex reactive processes in proteins and enzymes. In particular, the modeling of the Michaelis complex and the reaction mechanisms of GHs highlighted the interplay between electronic and structural changes that preactivate the substrate for catalysis. Some of these changes can already be anticipated by analyzing the conformational energy landscape of the substrate. Part of the research of this Thesis complements previous studies of our group by analyzing the factors that govern substrate distortion in GHs. In this respect, it extends the use of conformational free energy landscapes of simple sugars to predict the conformation of the substrate in Michalis complexes. Additionally, the molecular mechanism of retaining glycoside transferases is elucidated. This Thesis is organized as follows: Chapter I contains an introduction of the enzymes studied (GHs and GTs) and presents the main objectives of this work. The theoretical methods used are detailed in Chapter II. Chapters III to V are focused on enzyme-substrate interactions affecting the conformation of the substrate in GHs. Concretely; in Chapter III we test how mutation of the acid/base catalytic residue, the use of a substrate-like thio-analogue inhibitor or fluorometric aglycons affects the distortion of the substrate. In Chapter IV we study the influence of the enzyme-substrate interactions through the 2-OH, in particular the effect of the commonly used 2-deoxy-2-fluoro substitution. The conformational itinerary of this inhibitor during catalysis is modeled in Chapter V. In Chapter VI, the conformational flexibility of β-D-mannopyranose and α-L-fucopyranose molecules is investigated. The topologies of their corresponding conformational free energy landscapes are related with the observed crystallographic structures of β-mannosidases and α-fucosidases, and the predictive potential of such calculations is discussed. Chapter VII focuses on trehalose 6-phosphate synthase (a family 20 retaining GT that belongs to fold type B). The mechanism of glycosidic bond formation in this enzyme is elucidated. Finally, in Chapter VI, the main conclusions of this work are summarized.

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41

Sulpizi, Marialore. "Ab initio studies of targets for pharmaceutical intervention." Doctoral thesis, SISSA, 2001. http://hdl.handle.net/20.500.11767/4280.

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In this thesis we further explore the capability of first principle methods to provide insights on drug/target interactions in different contexts. In the first part of this work, we address the issue whether OFT methods can be used as a potential tool for drug-screening. First principle calculations are particularly interesting for screening the energetics of drug/target interactions, as they do not involve the painstaking procedure of developing each set of new parameters for each novel drug. In this context, we use ab initio_ methods as a novel tool to determine a scoring function in a series of prodrug I target (herpes simplex type 1 thyimidine kinase) complexes for gene-therapy based anticancer approaches. This work, accompanied by experimental data provided by Prof. Folkers' Lab (ETH, Zurich) provides a new, very simple, ab initiobased approach to the construction of scoring functions for drug-screening. In the second part of the thesis we investigate the capability of OFT to describe non trivial interactions which are encountered in several inhibitor/enzyme complexes of pharmaceutical interest. Clearly, the description of these non-trivial phenomena might require the use of electronic structure methods. Here we present an example of cation-n interaction found in the human immunodeficiency virus reverse transcriptase (HIV-1 RT), one of the major targets for anti-AIDS therapy(Furman et al., 2000)). Furthermore, we provide a description of the hydroxyl-n interactions in the active site of μ-glutathione S-transferase(Xiao et al., 1996) (μ-GST), whose differential expression has been implicated in the development of cancers as well as their resistance to chemotherapeutic drugs ((Mccallum et al., 2000) and reference therein). Finally we present a classic problem treated by quantum-chemical methods: the simulation of an enzymatic reaction. We focus on a class of cysteine proteases, the caspases. These enzymes are extremely important targets for pharmaceutical intervention in therapies against Alzheimer's and other neurodegenerative processes, yet very few inhibitors have been so far designed. Since an important class of inhibitors is the given by the transition state analogs, it is of importance to fully understand the · enzymatic reaction, that is the hydrolysis of peptides. Because of the crucial importance of temperature and environment(Karplus, 2000; Glennon and Warshel, 1998; Varnai and Warshel, 2000; Villa et al., 2000) effects for enzymatic catalysis, we use here a hybrid Car-Parrinello Molecular dynamics I Molecular mechanics approach recently developed in the Lab of Prof. U. Roethlisberger (Laio et al., 2001 ). This technique allows to evaluate the intermolecular interactions at the active site from electronic structure calculations as the simulation proceeds(Car and Parrinello, 1985). Steric and electrostatic effects of the protein scaffold on the quantum region are included using classical MD approach on the rest of the system. The free energy of the process is calculated using a thermodynamic integration approach(Ciccotti et al., 1989; Carloni et al., 2000; Piana et al., 2001). This thesis is organized as follows. The first chapter provides a description of the used computational techniques. The following chapter describes the systems investigated here and summarizes our findings. The subsequent three chapters are devoted to a - detailed description of my thesis work. In a final chapter we draw some conclusions and provide a perspective for possible future applications, which could follow this work.

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42

Suter, James Lewis. "Ab initio molecular dynamics investigation of 2:1 smectite clay systems and atomic charges." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615007.

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43

Amorim, Edgard Pacheco Moreira. "Propriedades mecânicas e eletrônicas de nanofios de cobre e ouro." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/277683.

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Orientador: Edison Zacarias da Silva Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin Made available in DSpace on 2018-08-16T08:28:05Z (GMT). No. of bitstreams: 1 Amorim_EdgardPachecoMoreira_D.pdf: 19996179 bytes, checksum: a823584c3d800f79a9801386e5274f1f (MD5) Previous issue date: 2010 Resumo: A necessidade de ampliar a capacidade de processamento computacional produziu um intenso esforço científico e tecnológico para produzir circuitos eletrônicos cada vez menores. Recentemente, resultados experimentais e teóricos estabeleceram que nanofios de cobre e ouro sob tensão evoluem para cadeias atômicas, o menor condutor possível. Neste trabalho, utilizando dinâmica molecular tight-binding observamos a evolução dinâmica de nanofios de cobre sob tensão nas direções cristalográficas [100], [110] e [111] elongando-os até a ruptura. As estruturas obtidas antes da ruptura foram usadas para iniciar os cálculos de primeiros-princípios baseado na teoria do funcional da densidade nas aproximações de densidade local e gradiente generalizado (LDA e GGA) até observamos novamente a ruptura. O nanofio elongado na direção [111] foi dopado com impurezas de H, B, C, N, O, S e N2 e elongado para verificarmos como as impurezas afetam suas propriedades estruturais e eletrônicas. Constatamos um efeito mecanoquímico devido a inserção de N e N2 que formam ligações p-d estáveis e muito fortes, causando o rearranjo das pontas adicionando mais átomos a cadeia atômica linear, sugerindo que nanofios unidimensionais maiores poderiam ser obtidos se produzidos em atmosferas nitrogenadas. Observamos as diferenças e similaridades na evolução dinâmica de nanofios de cobre e ouro elongados na direção [111]. Em ambos os metais, o primeiro rearranjo significativo ocorre devido a um átomo do interior do nanofio que vai para sua superfície. Objetivando compreender melhor este efeito, consideramos suas configurações ocas ou de camada única. Comparamos as forças calculadas suportadas pelos nanofios e mostramos que os nanofios de parede única podem suportar forças maiores antes do seu primeiro rearranjo estrutural em ambos os metais comparados aos nanofios originais. Investigamos também a dependência das forças máximas sustentadas pelos nanofios de parede única com respeito ao diâmetro. Nossos resultados sugerem que nanofios de cobre suportam mais tensão uniaxial do que os de ouro além de evoluir para cadeias atômicas lineares menores, indicando uma menor maleabilidade do cobre comparado ao ouro, como observado no sólido macroscópico. Experimentos mostraram que nanofios de ouro formados ao longo da direção [110] reconstroem sob tensão como estruturas helicoidais. Através de sua evolução dinâmica, nossos cálculos mostram que estes nanofios intrinsecamente tornam-se helicoidais devido aos planos (111) compactos que formam um ângulo com a direção de elongação mantendo o registro do seu arranjo angular inicial, além da tendência dos átomos do interior migrarem para sua superfície reconstruindo-a como {111} que é a superfície de mais baixa energia livre. Estes nanofios evoluem sob tensão formando cadeias atômicas lineares mais longas do que nanofios elongados em outras direções porque suas pontas são menos simétricas. Na configuração próxima a ruptura, estudamos a estrutura eletrônica de átomos de diferentes coordenações com cálculos ab-initio na aproximação GGA. Consideramos também outros nanofios [110] de diferentes diâmetros e comprimentos, mostrando que também evoluem para estruturas helicoidais. Discutimos porque este comportamento é observado em nanofios de ouro e inexiste no cobre embora sejam metais isoeletrônicos Abstract: The search to increase the computational processing capability produced intense scientic and technological efforts to make electronic circuits smaller. Recently, experimental and theoretical results established that copper and gold nanowires under tension evolve to atomic chains, the smallest conductors possible. In this work, using tight-binding molecular dynamics, we observing the dynamical evolution of copper nanowires under tension along [100], [110] and [111] crystallographic directions until their rupture. The structures obtained before the rupture were used to start first-principles calculations based on the density functional theory in the local density and generalized gradient approximations (LDA and GGA) until we observed their rupture again. The nanowire elongated in the [111] direction was doped with H, B, C, N, O, S and N2 and it was pulled to verify how the impurities affect its structural and electronic properties. We found a mechanochemical effect due to the insertion of N and N2 which form stable and very strong p-d bonds, causing the rearrangement of tips, adding more atoms to the linear atomic chain, suggesting that larger one-dimensional nanowires could be obtained if produced in nitrogen atmospheres. We observe the differences and similarities in the dynamical evolution of copper and gold nanowires elongated along [111] direction. In both metals, the first signicant arrangement occurs due to one atom from inside the nanowire which goes to the surface. To achieve a better understanding about this effect, we considered their hollow configurations or single wall nanowires. We compare the calculated sustained forces by the nanowires and we show that single wall nanowires can support larger forces before their first structural rearrangement in both metals compared to the original nanowires. We also investigate the dependence of maximum sustained forces by the single wall nanowires with their diameters. Our results suggest that copper nanowires support more uniaxial tension than the gold ones besides to evolve to smaller linear atomic chains, suggesting a smaller malleability of copper when compared with gold, as observed in bulk. Experiments showed that gold nanowires formed along the [110] direction reconstruct under tension as helicoidal structures. Through the dynamical evolution, our calculations show that these nanowires become helicoidal due to the (111) compact planes which form at an angle with the elongation direction keeping registry of their initial angular arrangement, besides the tendency of inside atoms going to their surface reconstructing as {111} surface which is the lower free energy surface. These nanowires evolve under tension forming longer linear atomic chains than the nanowires pulled along other directions because their tips are less symmetrical. In a configuration close the rupture, we studied the electronic structure of distinct coordination atoms with ab-initio calculations in GGA approximation. We also considered other [110] nanowires with different diameters and lengths showing that they also evolve to helicoidal structures and we discuss why this behavior is observed in gold nanowires and nonexistent in cooper, even so these metal are isoelectronics Doutorado Física da Matéria Condensada Doutor em Ciências

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44

Rojas-Cervellera, Víctor. "Ab initio molecular dynamics study of thiolate-protected gold clusters and their interaction with biomolecules." Doctoral thesis, Universitat Politècnica de Catalunya, 2015. http://hdl.handle.net/10803/317382.

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Thiolate monolayer-protected gold clusters (AuMPCs) are being used in various biological and biomedical applications due to their unique physical and chemical properties. The fact that gold-sulphur bonds are very stable enables the binding of biomolecules in the surface of gold clusters through a cysteine, an amino acid that contains a thiol group (SH). Specific AuMPCs-peptide conjugates can cross the blood-brain barrier without altering its integrity, opening the door for the treatment of pathologies related to the central nervous system, such as Alzheimer or Parkinson. Moreover, AuMPCs represent an alternative to the traditional fluorescence-based biosensors, due to their optical properties and its ability to bind specific antigens when certain AuMPCs-antibody conjugates are used. Several synthetic approaches based on the reduction of gold salts have been proposed to synthesize AuMPCs. In 1951 Turkevich and co-workers used sodium citrate for the reduction of chloroauric acid. In 2002 a novel synthetic method was proposed, named solvated metal atom dispersion method. In this method, neutral gold atoms were mixed with alkanethiols, resulting in the formation of AuMPCs, and molecular hydrogen was detected. This finding, together with the first crystallization and X-ray structure determination of Au102(SR)44 by Jadzinsky et.al., triggered a debate in the field, since the protons that were initially present in alkanethiols were not found in the AuMPC structure. One of the main goals of the present Thesis is to elucidate where the alkanethiol hydrogens go during the formation of the AuMPC. To this aim, ab initio metadynamics have been used to unravel the molecular mechanism of the formation of AuMPCs departing from neutral gold clusters and alkanethiols (Chapter III). Key to the usage of AuMPCs as biosensors is the better knowledge of their optical properties. The HOMO-LUMO gap, is a physical parameter related with optical properties. Density Functional Theory (DFT) is extensively used to obtain a theoretical value of the HOMO-LUMO gap, although it is known to severely underestimate it with respect to the experimental values. Nevertheless, recent computational studies using DFT have reported values of the HOMO-LUMO gap of AuMPCs in a very close agreement with the experimental ones. However, a simplified model of the real system was used, raising the question whether the agreement between the theoretical and the experimental values is fortuitous due to a compensation of errors. Our goal is to obtain HOMO-LUMO gap values using the whole experimental systems, i.e. peptides as the protecting ligands of the gold core and water as solvent (Chapter IV) to demonstrate that only a realistic model, and not only the use of appropriate DFT functionals, can lead to values comparable to the experimental ones. In a first step for the understanding of the reactivity of AuMPCs towards proteins, in Chapter V we modelled the binding of AuMPC towards an antibody. This process, known as ligand exchange reaction, is used to label proteins with gold clusters, as reducing agents cannot be used when certain biomolecules are present. Our results show that the neighbouring amino acids of the cysteine that should bind to the gold cluster play an essential role in the reaction. Finally, we focus on the study of the mechanism of the enzymatic reaction of a glycoprotein, a-1,3-glycosyltransferase. In recent years, our group has investigated the mechanism of one family of glycosyltransferases (GTs), providing its catalytic itinerary. In this thesis we extend this study to another family of GTs to elucidate whether or not a common molecular mechanism operates for GTs. This study represents one step towards the modelling of the more complex glycosyltransferases immobilized by gold nanoparticles, a promising technique for the development of automated glycosynthesis. The theoretical methods used along this thesis are detailed in Chapter II. Los clústeres de oro protegidos por tiolatos (AuMPCs) se utilizan en varias aplicaciones biológicas y biomédicas debido a sus propiedades físicas y químicas. El hecho de que el enlace oro-azufre sea muy estable permite la unión de biomoléculas en la superficie de los clústeres de oro a través de una cisteína, un aminoácido que contiene un grupo tiol (SH). Sistemas específicos AuMPC-péptido pueden atravesar la barrera hematoencefálica sin alterar su integridad, pudiéndose utilizar para tratar patologías relacionadas con el sistema nervioso central, como el Alzheimer o el Parkinson. Además, los AuMPCs representan una alternativa a los biosensores tradicionales debido a sus propiedades ópticas y su especificidad ante ciertos antígenos cuando se escoge el sistema AuMPC-péptido adecuado. Métodos basados en la reducción de sales de oro han sido propuestos para sintetizar AuMPCs. En 1951 Turkevich y colaboradores usaron citrato sódico para la reducción de ácido cloroáurico. En 2002 un nuevo método sintético fue propuesto, denominado método de dispersión de átomos metálicos solvatados. En este método, átomos de oro neutros se mezclan con alcanotioles, resultando en la formación de AuMPCs e hidrógeno molecular. Este hecho, junto con la primera cristalización y determinación estructural de Au102(SR)44 llevada a cabo por Jadzinsky y colaboradores, desencadenó un gran debate en el campo, ya que los protones que inicialmente estaban presentes en los alcanotioles no se encontraron en la estructura cristalográfica. Uno de los objetivos de esta tesis es encontrar cómo los átomos de hidrógeno forman H2 durante la formación de AuMPCs. Con este fin, se utiliza metadinámica ab initio para descifrar el mecanismo molecular de la formación de AuMPCs partiendo de clústeres de oro neutros y alcanotioles (capítulo III). Clave para el uso de AuMPCs como biosensores es el conocimiento de sus propiedades ópticas. La energía HOMO-LUMO está relacionada con estas propiedades ópticas. La teoría del funcional de la densidad (DFT) ha sido muy utilizada para obtener valores teóricos de la energía HOMO-LUMO, aunque es sabido que subestima este valor con respecto al obtenido experimentalmente. Aún así, estudios computacionales recientes han seguido utilizando DFT para calcular valores de la energía HOMO-LUMO de AuMPCs, y sorprendentemente los valores obtenidos están de acuerdo con los resultados experimentales. Sin embargo, los sistemas estudiados siempre han sido modelos simplificados de los sistemas reales, originando la pregunta de si la coincidencia es fortuita debido a una compensación de errores. Nuestro objetivo es obtener valores de la energía HOMO-LUMO para sistemas utilizados experimentalmente, es decir, péptidos como ligandos y agua como disolvente (capítulo IV) para demostrar que únicamente un modelo realista y no sólo el uso de funcionales DFT adecuados puede dar resultados comparables con los experimentales. Como primer paso para entender la reactividad de AuMPCs frente a proteínas (capítulo V), se ha modelizado la unión de un AuMPC y un anticuerpo. Este proceso, conocido como reacción de intercambio de ligandos, se utiliza para marcar proteínas con clústeres de oro. Nuestros resultados muestran que los aminoácidos del entorno de la cisteína que debe unirse al clúster de oro juegan un papel esencial en la reacción. Finalmente nos centramos en el mecanismo enzimático de una glicoproteína, la a-1,3-glicosiltransferasa. Recientemente nuestro grupo ha investigado el mecanismo de una familia de glicosiltransferasas (GTs), obteniendo su itinerario catalítico. En esta tesis hemos extendido dicho estudio a otra familia de GTs para averiguar si existe un mecanismo común para todas las GTs. Este estudio representa un primer paso para la modelización de sistemas más complejos de GTs inmovilizadas por AuMPCs, una técnica prometedora para el desarrollo de glicosíntesis automatizada. Los métodos teóricos utilizados en la tesis se describen en el capítulo II.

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45

Dsouza, Raison [Verfasser], and Martin [Akademischer Betreuer] Eckstein. "Revealing key modes in photoprocesses using Ab Initio molecular dynamics / Raison Dsouza ; Betreuer: Martin Eckstein." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2019. http://d-nb.info/1197801200/34.

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46

Adriaanse, Christopher John. "Computation of adiabatic and vertical ionisation energies of aqueous anions using ab initio molecular dynamics." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609155.

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47

Kecik, Deniz. "Ab Initio Design Of Novel Magnesium Alloys For Hydrogen Storage." Master's thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/12609722/index.pdf.

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A candidate hydrogen storing material should have high storage capacity and fast dehydrogenation kinetics. On this basis, magnesium hydride (MgH2) is an outstanding compound with 7.66 wt % storage capacity, despite its slow dehydriding kinetics and high desorption temperature. Therefore in this study, bulk and surface alloys of Mg with improved hydrogen desorption characteristics were investigated. In this respect, formation energies of alloyed bulk MgH2 as well as the adsorption energies on alloyed magnesium (Mg) and MgH2 surface structures were calculated by total energy pseudopotential methods. Furthermore, the effect of substitutionally placed dopants on the dissociation of hydrogen molecule (H2) at the surface of Mg was studied via Molecular Dynamics (MD). The results displayed that 31 out of 32 selected dopants contributed to the decrease in formation energy of MgH2 within a range of ~ 37 kJ/mol-H2 where only Sr did not exhibit any such effect. The most favorable elements in this respect came out to be P, K, Tl, Si, Sn, Ag, Pb, Au, Na, v Mo, Ge and In. Afterwards, a systematical study within adsorption characteristics of hydrogen on alloyed Mg surfaces (via dynamic calculations) as well as calculations regarding adsorption energies of the impurity elements were performed. Accordingly, Mo and Ni yielded lower adsorption energies -9.2626 and -5.2995 eV for substitutionally alloyed surfaces, respectively. MD simulations presented that Co is found to have a splitting effect on H2 in 50 fs, where the first hydrogen atom is immediately adsorbed on Mg substrate. Finally, charge density distributions were realized to verify the distinguished effects of most 3d and 4d transition metals in terms of their catalyzer effects.

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48

Iglesias, Fernández Javier. "Elucidating catalytic mechanisms of glycoside hydrolases and transferases by means of ab initio molecular dynamics simulations." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/283551.

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Carbohydrates play a central role in transport and storage of energy and as molecular building blocks. Additionally, glycoconjugates, specifically glycoproteins and glycolipids, are important components of cell surfaces and the extracellular environment that mediate cellular and molecular interactions. Defects in glycosylation are associated with human diseases while the ability of glycans to modulate immune responses leads to them playing a critical role in susceptibility and resistance to pathogens. This huge amount of glycan structures requires the existence of a diverse group of degrading and remodelling enzymes: glycoside hydrolases (GHs) and glycoside transferases (GTs). GHs and GTs are highly specific enzymes responsible of the hydrolysis (GHs) and formation (GTs) of glycosidic bonds in carbohydrates. They are responsible for the modification of polysaccharides and glycoconjugates involved in numerous biological processes such as pathogenesis mechanisms, cell-cell recognition and polysaccharide degradation for biofuel processing. Knowledge of their enzymatic mechanism at a molecular level is crucial to understand how carbohydrates are assembled/degraded in organisms, as well as in developing new drugs. The detailed characterization of the transition state of the chemical reaction in which they participate, for instance, is key for the development of TS-analog inhibitors, which are known to be very efficient. In recent years, our group has investigated the implications of the conformational changes on the substrate during catalysis in several GHs and has related these changes with the conformations that can be sampled by a single sugar unit (e.g. glucose). This was analyzed by adapting sugar puckering coordinates as collective variables in ab initio metadynamics simulations. These studies are having a significant impact not only in the theoretical community but also in biochemistry and biophysics, because of the possibility to predict substrate catalytic itineraries for GHs. In this thesis, we extend these analyses to other sugar molecules to verify the proposed catalytic itineraries and also to GH inhibitors and sugar oxocarbenium ions to gain insights into transition state mimicry. Unlike GHs, known to operate by means of a double displacement mechanism, the reaction mechanism of retaining GTs is controversial. Both a two-step mechanism (by analogy to retaining glycoside hydrolases) and a one-step mechanism have been proposed and studied by means of quantum mechanics / molecular mechanics (QM/MM) simulations. Here, we applied this methodology to elucidate the catalytic mechanism of an engineered glycoside hydrolase and a glycoside transferase, giving support for a front-face single displacement mechanism. Los azúcares presentan una gran variabilidad estructural que es aprovechada por los diferentes organismos para realizar una multitud de procesos biológicos, que incluyen el almacenamiento de energía, el reconocimiento y la señalización celular. Las glicosil hidrolasas y glicosil transferasas son las enzimas responsables de la hidrólisis y síntesis, respectivamente, de estos biopolímeros y por lo tanto están presentes en una gran variedad de procesos celulares. Las técnicas de modelado molecular permiten analizar estos procesos biológicos, como por ejemplo la reacción de formación de un enlace entre azúcares, a un nivel atomístico. De esta forma, se pueden describir los cambios conformacionales que se producen en el sustrato al unirse a la enzima, identificar el estado de transición de la reacción química y determinar otros aspectos fundamentales de la catálisis enzimática.

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49

Lukinov, Tymofiy. "Computer simulation of materialsunder extreme conditions." Doctoral thesis, KTH, Kondenserade materiens teori, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-188146.

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Extreme conditions allow us to reveal unusual material properties. At the same time an experimental approach is di-cult under such conditions. Capabilities of a theoretical approach based on simplied models are limited. This explainsa wide application of computer simulations at extreme conditions. My thesis is concerned with computer simulations undersuch a conditions. I address such problems as melting, solidsolid phase transitions, shockwave impact on material properties and chemical reactions under extreme conditions. We addressed these problems to facilitate simulations of phase transitions to provide some interpretation of experimental data andexplain enigmatic phenomena in interior of the Earth. QC 20160615

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50

Walbrühl, Martin. "Diffusion in the liquid Co binder of cemented carbides: Ab initio molecular dynamics and DICTRA simulations." Thesis, KTH, Materialvetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-140880.

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A fundamental quantum mechanical modelling approach is used for calculating liquid diffusion parameters in cemented carbides. Up to now, no detailed description of diffusion for alloying elements in a liquid Co matrix is available. Neither are experimental measurements found in the literature for the self- or impurity diffusion in the liquid Co system. State of the art application is the description of gradient formation in cemented carbide systems using DICTRA. In this work it is assumed that diffusion during sintering of cemented carbides takes place mainly in the liquid Co binder phase. With this assumption one can calculate the diffusion coefficient for different alloying elements like W, Ti, N and C in a liquid Co matrix phase. The mean square displacement (MSD) of the diffusing atoms is used to obtain the diffusion coefficients which could be simulated by Ab initio Molecular Dynamics (AIMD). By fitting the computed temperature dependence with the Arrhenius relation one can determine the frequency factor and the activation energy which allows to give a quantitative description of the diffusion. Three methods will be used for validating the data from this work. Available estimated literature values based on calculations (scaling laws, a modified Sutherland equation and classical molecular dynamics) will be used to compare the results in a first instance. The general agreement for diffusion in liquid metals will be done by comparison with experimental data for the liquid Fe system. In a last step, the diffusion values obtained by this work will be used to create a kinetic database for DICTRA. The gradient simulations will be compared with experimentally measured gradients. The AIMD simulations are performed for binary diffusion systems to investigate the diffusion between the liquid Co matrix and one type of alloying element. In a second approach the diffusion for a multicomponent systems with Co, W, Ti and C has been performed. The results from the present AIMD simulations could be shown to be in good agreement with the literature. Only two DICTRA simulations could be performed within the timeframe of this work. Both are predicting a ~3 times bigger gradient zone whereas the initial choice of the labyrinth factor λ = f could be identified as a possible source of disagreement. A labyrinth factor of λ = f2 with the calculated mobility values from the AIMD calculations should give improved results. Although the results from those simulations are not available to this date. The two approaches of the diffusion simulations in the binary and multicomponent system are giving matching results. The non-metallic elements C and N are diffusing two times faster than the fastest metallic element Co. The diffusivity of Ti is slightly lower than Co and W could be identified as the element with the slowest diffusion within the liquid Co matrix. Further investigations of the liquid structure could indicate the tendency to form bonds between C and W and between C and Ti. This gives slowed down diffusion of C in the multicomponent system compared to the diffusion in the binary Co-C system.

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Дисертації з теми "Ab initio molecular dynamics. DFT"

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