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Estudo teórico de efeitos de solvatação do tetraidrofurano sobre um mecanismo modelo de Suzuki-Miyaura / Theoretical study of the effects of tetrahydrofuran's solvation over a Suzuki-Miyaura's model mechanismSilva, Maurício Chagas da 02 March 2011 (has links)
Orientador: Nelson Henrique Morgon / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-18T09:48:03Z (GMT). No. of bitstreams: 1
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Previous issue date: 2011 / Resumo: Utilizando a implementação do método da coordenada geradora discretizada nos orbitais atômicos, conjuntos de bases adaptados ao pseudopotencial de caroço SBKJC (conjuntos GBSMCS) foram desenvolvidos, validados e utilizados no estudo de possíveis efeitos de solvatação do tetraidrofurano sobre um mecanismo modelo de Suzuki-Miyaura. As metodologias de validação adotadas para os conjuntos GBSMCS foram os cálculos teóricos da afinidade por próton de sistemas atômicos e moleculares, iônicos e neutros, das entalpias de liquefação de alguns solventes orgânicos rotineiros e das entalpias de hidratação de 29 compostos orgânicos diversos. Nas etapas de validação, observou-se de uma maneira geral, uma boa relação entre custo e benefício na utilização dos conjuntos de bases GBSMCS, obteveram-se desvios médios por volta de 0 até 20 kJ.mol, nas propriedades estudadas. Com as metodologias propostas neste trabalho e com a utilização dos conjuntos GBSMCS, determinou-se o perfil potencial da reação modelo de Suzuki-Miyaura tanto em fase gasosa como em fase solvatada de tetraidrofurano. Não se observou efeitos significativos nas estruturas dos estados estacionários caracterizados e nem nas DrG para as etapas de adição-oxidativa, transmetalação, eliminação-redutiva e isomerização. Contudo, observou-se que há efeitos consideráveis de solvatação para as espécies individuais. As etapas de adição-oxidativa e de eliminação-redutiva apresentaram-se como sendo etapas exergônicas e a etapa de transmetalação como sendo uma etapa endergônica tanto em fase gasosa como em tetraidrofurano. Abordou-se um mecanismo associativo em todas as etapas principais reacionais, contudo inferiu-se que a etapa de transmetalação tenha possíveis rotas mecanísticas dissociativas iônicas que serão estudadas em trabalhos futuros / Abstract: Using the implementation of the discretized generator coordinate method in atomic orbitals, atomic basis sets adapted to the pseudopotential core SBKJC were developed ( GBSMCS ), validated and used to study possible effects of tetrahydrofuran¿s solvation over a model Suzuki-Miyaura¿s mechanism. The methodologies adopted for the validation of GBSMCS basis sets were the theoretical calculations of proton affinities of atomic and molecular, ionic and neutral, systems, the liquefaction enthalpies of some common organic solvents and the hydration enthalpies of 29 organic compounds. In the validation steps a good relationship was abserved between cost and benefit in the use of GBSMCS basis set, average deviations around 0 to 20 kJ.mol for the properties studied. Applying the methodologies proposed in this research and using the GBSMCS atomic basis sets, the potential profile of the Suzuki- Miyaura¿s model mechanism was determinated in the gas and tetrahydrofuran phases. No significant tetrahydronfuran¿s solvation effects were observed for molecular stationarys state structures, neither for DrG for oxidative- addition, transmetallation, reductive-elimination and isomerization reaction steps. However, some strong solvation effects were observed for individual species. The oxidative-addition and reductive-elimination reaction steps were characterized as exergonic steps, but transmetallation reaction step was presented as an endergonic step, both in the gas and tetrahydrofuran phases. This work approaches an associative mechanism for all main reaction steps; however, we inferred that the transmetallation reaction step could have some ionic pathways and should be studied in future works / Doutorado / Físico-Química / Doutor em Ciências
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Solvatação de alcaloides em fluidos supercriticos por simulação de dinamica molecular / Solvation of alkaloids in supercritical fluids by molecular dynamics simulationsFavero, Frank Wilson 12 July 2006 (has links)
Orientador: Munir Salomão Skaf / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-08T16:04:54Z (GMT). No. of bitstreams: 1
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Previous issue date: 2006 / Resumo: Foram realizados estudos por Simulações de Dinâmica Molecular em sistemas formados por alcalóides em CO2 supercrítico para determinarmos suas propriedades estruturais e dinâmicas. Os alcalóides estudados foram as xantinas (cafeína, teofilina e teobromina) e os alcalóides indólicos (voacangina e coronaridina), todas substãncias de grande interesse da indústria farmacêutica e/ou de alimentos. Detalhes da estrutura de solvatação em torno do soluto foram obtidos através de mapas de contornos onde a escala de cores representa a densidade local em relação ao valor médio da densidade no "bulk". Os mapas mostraram uma distribuição não homogênea do solvente com concentrações em regiões específica como nos planos dos anéis e nas carbonilas das moléculas. Os resultados dos coeficientes de difusão do solvente puro e do sistema cafeína/CO2 reproduziram muito bem os valores experimentais. É conhecido que a adição de pequenas quantidades de co-solventes polares amplia o poder de solubilização do CO2. Estudamos como a inclusão do co-solvente etanol à mistura afeta as propriedades de estrutura e dinâmicas dos sistemas. Observamos uma ampliação das interações soluto-solventes com a formação de ligações de hidrogênio, uma solvatação preferencial do soluto pelo co-solvente. As dinâmicas dos solutos tornaram-se mais lentas com a inclusão do co-solvente. / Abstract: Molecular Dynamics Simulation of systems formed by alkaloids in supercritical CO2 have been performed in order to determine their structural and dynamic properties. The studied alkaloids are the xanthines (caffeine, theophylline, and theobromine) and indole alkaloids (voacangine and coronaridine), substances of great interest of the pharmaceutical and foods industry. Details of the solvation structure around the solute were obtained by means of density maps representing the local density in relation to the average value of the density in bulk. The maps show an inhomogeneous distribution solvent with concentrations in specific regions such as above end below the planar rings and carbonyl groups of the molecules. The simulations results for the diffusion coefficients of pure solvent and the caffeine/CO2 system reproduce the experimental values very well. It is known that the addition of small amounts of polar co-solvent increases the power of CO2 solubilization. We investigated the effects of co-solvent ethanol to the systems structural and dynamical properties. We observe a magnification of the solute-solvent interactions with the formation of hydrogen bonding and the preferential solvation by the co-solvent. The dynamics of the solute become slower upon addition of the co-solvent. / Doutorado / Físico-Química / Doutor em Ciências
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Da fase gasosa à solução: reatividade e estrutura de ésteres e funções análogas de Si, N, S e espectroscopia de íons solvatados em fase gasosa / From the gas-phase to solution: gas-phase reactivity and structure of Si, N and S esters and their analogs and spectroscopy of gas-phase solvated ions.Thiago Carita Correra 21 March 2013 (has links)
A presente tese tem por objetivo inicial estudar a reatividade de ésteres de Si, N, S e seus análogos em fase gasosa para obter informações detalhadas do mecanismo destas espécies quando submetidas a ataque nucleofílico, sobretudo no que tange a competição entre as vias de substituição nesses centros e no carbono. Esses estudos são realizados experimentalmente através da técnica de espectrometria de massas por transformada de Fourier e ressonância ciclotrônica de íons (FT-ICR) e amparados por cálculos de estrutura eletrônica. Os resultados obtidos indicam que, para o Si, as alcoxissilanas reagem com os nucleófilos através de um aduto pentacoordenado que desloca, preferencialmente, um alcóxido. De forma minoritária, pode ocorrer o deslocamento de outro ligante gerando silóxidos ou carbânions. Neste estudo, foi caracterizada uma reação inédita de troca de Me por F nos silóxidos mediada por NF3. Os estudos dos ésteres de nitrogênio indicam que as reações de eliminação são mais favoráveis que as de substituição e que a substituição no nitrogênio, apesar de ser considerada mais favorável pelos cálculos, não é observada. Esse comportamento foi elucidado através do uso de dinâmica molecular e indica que o complexo de entrada para a via de reação no nitrogênio não é formado devido à repulsão sofrida pelo nucleófilo pelos oxigênios que rodeiam o centro de N. Resultados teóricos semelhantes foram encontrados para os ésteres de enxofre e, em adição aos resultados experimentais disponíveis, indicam que não só a dinâmica de reação exerce um papel importante nesses sistemas, como também sugerem uma compensação entre o caráter dinâmico e a termoquímica destes sistemas. Para nucleófilos fracos que não são favoráveis do ponto de vista termoquímico, a formação do complexo de entrada não é impedida pela repulsão, dado que esses nucleófilos não costumam ter centros nucleofílicos com carga muito localizada. O oposto ocorre com nucleófilos fortes, que procederiam pelo caminho de substituição no S por uma via praticamente sem barreira, mas não o fazem já que a repulsão do nucleófilo é muito intensa. Em uma segunda etapa a solvatação dos íons F-, Br- e I- foram estudadas na fase gasosa a partir da espectroscopia dissociação no infravermelho. A partir da formação por uma fonte de eletrospray de agregados altamente solvatados, foi possível determinar o efeito dos íons na organização das moléculas de solvente, determinar a mudança da solvatação interna para solvatação de superfície e determinar o número de hidratação em fase gasosa para os íons Br- e F-. Além disso, tanto os resultados experimentais quanto teóricos mostram que a natureza do íon influencia a primeira camada de solvatação e que a carga formal tem um efeito predominante em longo alcance, podendo organizar até centenas de moléculas de solventes. Por fim, realizamos a adaptação do sistema de aquisição do FT-ICR do laboratório. Isso não só confere um sistema atualizado ao nosso instrumento, como possibilita que novos experimentos, como a espectroscopia de íons, possam ser realizados no nosso grupo de pesquisa. / This thesis comprises the study of the reactivity of gas-phase ions in the gas-phase and the structural modifications observed for gas-phase ions as a function of progressive solvation by spectroscopic techniques. In the first part, we describe the gas-phase reactivity of Si, N, and S esters and their analogs towards simple nucleophiles and a detailed analysis of the competition between different reaction channels namely substitution vs. elimination. These studies were carried out by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and supported by theoretical calculations. Our results suggest that alkoxysilanes react with nucleophiles via a pentacoordinated adduct that results in alkoxide displacement as the major reaction channel. The displacement of other ligands can also occur to yield siloxides or carbanions. As part of these studies, we also report a Me/F exchange reaction in siloxide ions mediated by NF3. Results obtained for the nitrogen esters show elimination-type reactions to be the most favorable pathway followed by nucleophilic displacement. No displacement was observed at the nitrogen center in spite of the fact that calculations predict this channel to be the most favorable pathway. This behavior was further explored by ab initio molecular dynamics calculations that show that the entrance complex for the nitrogen pathway is avoided because of the strong electrostatic repulsion exerted by the oxygen atoms as the nucleophile approaches the N center. Similar theoretical results were obtained for the sulfur esters. Comparison of these calculations with the experimental results also suggests that the reaction dynamics play an important role in these systems. Furthermore, we propose that a combination of thermochemical and dynamic balance hinders substitution at the heteroatom. For strong nucleophiles that could undergo substitution at the S center via a barrierless pathway, the reaction is hindered by the strong repulsion experienced by these nucleophiles. In the second part, we study the structure of gas-phase solvated F-, Br- and I- by infrared dissociation spectroscopy. The highly solvated clusters were generated by electrospray ionization and their structures probed to gather information regarding the short and long-range effect of these ions on the solvation network. Solvation parameters such as the number of water molecules needed for a switch from internal to surface solvation and the hydration numbers for F- and Br- were determined. Theoretical and experimental results show that the solvation pattern of the first solvation shell for these ions depends on the nature of the ion while the ion charge prevails in determining the long-range pattern. This pattern effect is shown to prevail up to hundreds of solvent molecules. Finally, a new data acquisition and control system is described for our FT-ICR spectrometer. This system not only updates the original instrument but it also brings in new capabilities to the spectrometer such as the ability to carry out gas-phase ion dissociation spectroscopy.
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Analise conformacional por ressonância magnética nuclear e cálculos teóricos em anéis de cinco membros : 2-Halociclopentanonas / Nuclear magnetic resonance and theoretical investigation on the conformational analysis of five-membered ring systems : 2-HalocyclopentanonesMartins, Carina Rabelo 28 February 2005 (has links)
Orientador: Roberto Rittner Neto / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-04T16:43:04Z (GMT). No. of bitstreams: 1
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Previous issue date: 2005 / Resumo: Este trabalho apresenta estudos sobre o isomerismo conformacional das 2-halociclopentanonas (halo= cloro e bromo) utilizando a constante de acoplamento JHH, cálculos teóricos e a teoria de solvatação. Foi realizada a otimização das geometrias e das energias dos confôrmeros mais estáveis na forma C2 (meia cadeira) dos diferentes compostos, utilizando o programa Gaussian 98, sendo que a conformação mais estável obtida no vácuo foi a pseudo-axial para todos os compostos estudados. Os dados experimentais de JHH dos derivados clorado e bromado, juntamente com o resultado da otimização das geometrias e das energias nos níveis B3LYP e MP2 foram tratados computacionalmente pelos programas Models e BESTFIT, o que permitiu a análise do equilíbrio conformacional destes compostos em diferentes solventes. Os dados obtidos apontam para uma estabilização do confôrmero pseudo-equatorial (de maior momento de dipolo) de acordo com o aumento da polaridade do solvente, conforme o esperado. Estes resultados foram comparados aos resultados obtidos pela análise dos espectros de infravermelho, cujos resultados também mostram a estabilização do confôrmero pseudo-equatorial com o aumento da polaridade do meio. / Abstract: The present work reports an NMR metthod using the variation of the JHH coupling constants with the solvents, togethr with theoretical calculations and solvation theory for the conformational analysis of 2-halocyclopentanones (halo = chlorine and bromine). The results trom Ab initio calculations, performed with GAUSSIAN 98 program using DFT/B3LYP and MP2, showed that the theories for the chlorine and bromine-derivatives. The pseudo-axial half-chair (C2) form is stable, in vapour phase, for both compounds. The H NMR spectra were obtained in solvents of various polarities. The essential parameters for the solvation energy calculations were obtained through MODELS program using the optimized geometries trom Gaussian. The best values of intrinsic coupling constants tor each conformer and the experimental energy difference, in the vapour, phase were obtained through BESTFIT program, using the experimental coupling constants and data from theoretical calculations. These gave that the pseudo-equatorial conformer is stabilized with the increase in the solvent polarity. The results were complemented with data from infrared spectroscopy, which are in complete agreement with theoretical data. / Mestrado / Quimica Organica / Mestre em Química
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Étude du comportement de l’uranium et de l’iode dans le mélange de fluorures fondus LiF-ThF₄ à 650 °C / Study of uranium and iodine behavior in the molten fluorides LiF-ThF₄ at 650 ° CDurán-Klie, Gabriela 25 September 2017 (has links)
Le Réacteur Nucléaire à sel fondu à spectre rapide (Molten Salt Fast Reactor, MSFR) est un concept innovant de quatrième génération développé par le CNRS depuis 2004 et actuellement étudié dans le cadre du projet européen SAMOFAR de H2020. Le MSFR fonctionne avec un combustible nucléaire liquide constitué d’un mélange de sels fluorures LiF-ThF₄-(UF₄/UF₃) (77,5-20-2,5) mol% fondus à haute température (700-900°C). Ce réacteur est particulièrement intéressant pour le cycle de combustible du thorium (²³²Th-²³³U). Ce concept propose un retraitement intégré du combustible nucléaire basé sur des méthodes pyrochimiques afin d’extraire la matière fissile et de séparer les actinides des produits de fission.Un schéma de traitement du sel combustible, proposé lors d’un précédent projet européen (EVOL, FP7), est basé sur les propriétés redox et acido-basiques des éléments produits par les réactions de fission et de capture ayant lieu dans le cœur du réacteur. La base d’évaluation de ce schéma a été dans un premier temps thermodynamique. Une validation expérimentale est actuellement en cours qui consiste à étudier le comportement chimique et électrochimique du sel fondu et des éléments qui y sont solubilisés. Les études précédentes sur les réacteurs sels fondus ne peuvent être utilisées que partiellement pour ce concept car la composition du sel du MSFR définie par le projet européen EVOL est différente en nature et composition des sels proposés jusqu’à présent pour ce type de réacteurs. Or, les coefficients de diffusion et d’activité dépendent des propriétés physico-chimiques du sel fondu (en particulier de la solvatation) et nous avons, lors d’études précédentes, montré que les propriétés de solvatation des sels fondus dépendent fortement de leur nature et de leur composition.Les objectifs de ce travail de thèse sont l’étude du mélange fondu LiF-ThF₄ et du comportement électrochimique de l’uranium et de l’iode dans ce mélange.L’étude électrochimique du comportement de l’uranium a montré la stabilité de deux espèces solubles (UF₄ et UF₃) de cet élément dans le milieu fondu et la possibilité de le réduire à l’état métallique. Ce point est d’importance car la co-existence de ces deux composés permettra de contrôler le potentiel du sel combustible dans le cœur du réacteur et de limiter les réactions de corrosion avec les matériaux de structure. Les coefficients d’activité de U(IV) et de U(III) ont été déterminés. Les valeurs obtenues montrent que la solvatation de l’uranium au degré d’oxydation (IV) par les ions fluorure est beaucoup plus importante que celle de l’uranium au degré (III), ce qui est en accord avec des observations ultérieures dans d’autres sels fluorures. Notre choix pour l’étude des produits de fission dans le sel combustible s’est porté sur l’iode. Dans le cœur du réacteur, la forme stable de l’iode est la forme halogénure soluble I- et dans le schéma général de traitement du sel combustible, il est prévu d’extraire l’iode par une étape de fluoration qui permet de produire le gaz I₂. Cette étude a montré la contribution d’une réaction chimique à l’oxydation des ions iodures en iode gazeux. Cette réaction chimique d’oxydo-réduction correspond à l’oxydation des ions iodures par l’oxygène. Cette réaction n’est expliquée que par l’existence d’un oxyfluorure de thorium soluble ThOF₂. Une efficacité d’extraction de I₂ (g) supérieure à 95 % a été obtenue par électrolyse à potentiel contrôlé. Ces électrolyses, qui simulent la fluoration, permettent de valider l’étape d’extraction de l’iode dans le schéma de traitement.Ce travail de recherche a permis d’acquérir une meilleure connaissance de la stabilité du sel et du comportement chimique et électrochimique de différents composés (U et I) dans le sel. / The Molten Salt Fast Reactor (MSFR) is an innovative concept of GEN IV developed by the CNRS since 2004. It is currently studied in the framework of the European project SAMOFAR of H2020. The MSFR operates with a liquid nuclear fuel consisting of a mixture of fluoride salts LiF-ThF₄- (UF₄ / UF₃) (77.5-20-2.5) mol% melted at high temperature (700-900° C). This reactor is particularly advantageous for the thorium fuel cycle (²³²Th-²³³U). This concept proposes an integrated reprocessing of the nuclear fuel based on pyrochemical methods in order to extract the fissile material and to separate the actinides from the fission products.A scheme for the treatment of the fuel salt, proposed in a previous European project (EVOL, FP7), is based on the redox and acido-basic properties of the elements produced by the fission and capture reactions occurring in the reactor core. The baseline for this scheme was initially thermodynamic. Experimental validation is currently under way to study the chemical and electrochemical behavior of the molten salt and the elements solubilized therein. Previous studies on molten salt reactors can only be partially used for this concept because the composition of the MSFR salt defined by the European EVOL project is different from the composition of the salts proposed up to now for this type of reactor. However, the diffusion and activity coefficients depend on the physicochemical properties of the molten salt (in particular solvation) and in previous studies we have shown that the solvation properties of molten salts are strongly dependent on their nature and their composition.The objectives of this thesis are the electrochemical characterization of the molten mixture LiF-ThF₄ and the study of the electrochemical behavior of uranium and iodine.The electrochemical study of the behavior of uranium shows the stability of two soluble species (UF₄ and UF₃) of this element in the molten medium and the possibility of its reduction to the metallic state. This point is important because the co-existence of these two compounds will make possible to control the potential of the fuel salt in the core of the reactor in order to limit the corrosion reactions with the structural materials. The activity coefficients of U (IV) and U (III) were determined. The values obtained show that the solvation of uranium to the degree of oxidation (IV) by fluoride ions is much greater than that of uranium to degree (III), which is in agreement with subsequent observations in other fluoride salts.Our choice for the study of fission products in the fuel salt has focused on iodine. In the core of the reactor, the stable form of the iodine is the soluble halide form I- and in the general scheme of treatment of the fuel salt, it is planned to extract iodine by a fluorination step in order to produce the gaseous compound I₂. The electrochemical study shows the contribution of a chemical reaction to the electrochemical oxidation of iodide ions in gaseous iodine. This redox chemical reaction corresponds to the oxidation of the iodide ions by oxygen. This reaction is explained for the existence of a soluble thorium oxifluoride ThOF₂. Extraction efficiencies of I₂ (g) greater than 95% were obtained by electrolysis at controlled potential. These electrolysis, which simulate fluorination process, make it possible to validate the method for the extraction of the iodine in the reprocessing scheme.This research has led to a better understanding of salt stability and of the chemical and electrochemical behavior of several compounds (U and I) in the molten salt.
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Modeling Nonlocality in Quantum SystemsJames A. Charles (5929571) 16 January 2020 (has links)
<div>The widely accepted Non-equilibrium Greens functions (NEGF) method and the Self-Consistent Born Approximation, to include scattering, is employed. Due to the large matrix sizes typically needed when solving Greens functions, an efficient recursive algorithm is typically utilized. However, the current state of the art of this so-called recursive Greens function algorithm only allows the inclusion of local scattering or non-locality within a limited range. Most scattering mechanisms are Coulombic and are therefore non-local. Recently, we have developed an addition to the recursive Greens function algorithm that can handle arbitrary non-locality. Validation and performance will be assessed for nanowires.</div><div><br></div><div>The second half of this work discusses the modeling of an active ingredient in a liquid environment. The state of the art is outlined with options for different modeling approaches - mainly the implicit and the explicit solvation model. Extensions of the explicit model to include an open, quantum environment is the main work of the second half. First results for an extension of the commonly used molecular dynamics with thermodynamic integration are also presented.</div>
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Studies Based on Statistical Mechanics for Mechanism of Multidrug Efflux of AcrA/AcrB/TolC / AcrA/AcrB/TolCの多剤排出機構に関する統計力学的研究Mishima, Hirokazu 23 March 2015 (has links)
京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第19092号 / エネ博第316号 / 新制||エネ||64(附属図書館) / 32043 / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 木下 正弘, 教授 森井 孝, 教授 片平 正人 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DFAM
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Effect of Chiral Solvent and Pressure on the Dynamic Screw-Sense Induction to Poly(quinoxaline-2,3-diyl)s / ポリ(キノキサリン-2,3-ジイル)の動的らせん構造の誘起におけるキラル溶媒と圧力の効果Takeda, Ryohei 25 September 2017 (has links)
京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20714号 / 工博第4411号 / 新制||工||1685(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 杉野目 道紀, 教授 村上 正浩, 教授 松田 建児 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM
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Integral Equation Theories of Diffusion and Solvation for Molecular Liquids / 分子性液体における拡散と溶媒和の積分方程式理論Kasahara, Kento 26 March 2018 (has links)
京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21123号 / 工博第4487号 / 新制||工||1697(附属図書館) / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 佐藤 啓文, 教授 関 修平, 教授 山本 量一 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM
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The Phosphate Vibration as a Sensor for Ion-Pair Formation Studied by Nonlinear Time-Resolved Vibrational SpectroscopySchauss, Jakob 24 August 2022 (has links)
Die Struktur und Dynamik von Biomolekülen wird durch ein komplexes Wechselspiel mit Ionen und Wassermolekülen der Hydratationshülle beeinflusst. Die Wechselwirkungen sind kaum verstanden, zum Teil weil es an experimentellen molekularen Sonden mangelt. Lokale Schwingungen des RNA-Rückgrats bieten solch nicht-invasive Sonden, empfindlich gegenüber den ersten Schichten der RNA-Solvatationshülle. Die Empfindlichkeit rührt von elektrischen Feldern auf der biomolekularen Oberfläche. Diese Dissertation nutzt die Sensitivität aus, um mit Femtosekunden-2D-IR-Spektroskopie der asymmetrischen Phosphatstreckschwingung die Rolle positiv geladener Ionen, insbesondere Magnesium, Mg2+, zu untersuchen, die negativ geladene Phosphatgruppen des Rückgrats kompensieren.
Erste Experimente an Dimethylphosphat, zusammen mit theoretischen Berechnungen, zeigen eine Blauverschiebung der Phosphatmode aufgrund der Bildung von Kontaktionenpaaren. Kurze Abstände zwischen Mg2+ und der Phosphatgruppe führen zu repulsiven Austauschwechselwirkungen, die die Potentialfläche der Schwingung stören.
Bei Doppelstrang-RNA zeigt sich eine starke Abhängigkeit der Phosphatschwingung von lokalen Wasserstrukturen. Frequenzverschiebungen durch den Starkeffekt führen zu drei Schwingungsbanden, die unterschiedliche lokale Geometrien widerspiegeln. Elektrische Felder von solvatisierenden Wassermolekülen beeinflussen dabei das Bindungspotential.
Abschließend erlaubt es die Blauverschiebung der Phosphatmode, die Bildung von Mg2+/Phosphat Kontaktionenpaaren in Transfer-RNA quantitativ zu verfolgen. Es wird gezeigt, dass diese die Tertiärstruktur der tRNA stabilisieren, indem sie die Coulombabstoßung zwischen negativ geladenen Phosphatgruppen kompensieren, besonders in kompakten Regionen.
Die Dissertation demonstriert das Potential zeitaufgelöster Schwingungsspektroskopie, kombiniert mit theoretischen Beschreibungen auf molekularer Ebene, um die komplexen Interaktionen biomolekularer Solvatationsumgebungen zu erforschen. / The structure and dynamics of biomolecules are influenced by a complex interplay with ions and water molecules in the local hydration shell. The underlying interactions are poorly understood, partly because of a lack of experimental probes that can access the molecular scale. Local vibrations of the RNA backbone provide non-invasive probes sensitive to the first hydration layers of the RNA solvation shell via the imposed electric field on the biomolecular surface. This thesis exploits this sensitivity in femtosecond 2D-IR spectroscopy experiments on the asymmetric phosphate stretch vibration to investigate the role of positively charged ions, particularly the magnesium cation Mg2+, in counteracting the negatively charged phosphate backbone.
Initial experiments with the model system dimethyl phosphate in combination with theoretical calculations report a frequency blue-shift due to the formation of contact ion pairs. Short distances between Mg2+ and phosphate lead to exchange repulsion interactions that perturb the vibrational potential energy surface.
In double helical RNA, a strong dependence of the phosphate mode on the local hydration structure of the phosphate group is found. Three distinct vibrational peaks reflect different hydration geometries as a result of vibrational Stark shifts. Responsible for the frequency shifts are electric fields from solvating water molecules.
Ultimately, the blue-shift of the phosphate mode allows to quantitatively follow the formation of Mg2+-phosphate contact pairs in transfer RNA systems. It is shown that these configurations stabilize the tertiary structure of tRNA molecules by efficiently compensating the Coulomb repulsion from negatively charged phosphate groups, particularly in highly congested regions.
The thesis demonstrates the potential of time-resolved vibrational spectroscopy combined with theoretical descriptions on the molecular level to probe the complex interactions of biomolecular solvation environments.
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