Dissertations / Theses on the topic 'Solvation energies'

Two computer simulation studies were performed; one to help understand the structure-function relationships of prolyl peptides (Part I) and the other to help predict more efficient pharmaceutical drug delivery by molecular modification of small peptides (Part II).

In Part I, the free energy perturbation (FEP) method, using AMBER, was utilized to calculate the Gibbs free energy difference between cis and trans conformers of Ace-Tyr-Pro- NMe and Ace-Asn-Pro-NMe, from which the ratio of cis to trans conformers was obtained. Our simulation generated much lower %cis for both peptides as compared with experimental values and possible problems in our computational schemes are presented. However, our results were encouraging in that they predicted preference of trans conformers for both peptides and higher %cis for Ace-Tyr-Pro-NMe, compared to Ace-Asn-Pro-NMe, which agrees with experimental results.

Part II applied semi empirical (AMS0L) and microscopic simulation (POLARIS) methods to obtain the solvation free energies of a series of phenylalanyl peptides with various degrees of methylation on their backbone nitrogens. It was clearly predicted that as a peptide length increased, so solvation free energy decreased, indicating less favorable permeability through the cell membrane system, in agreement with data in the literature. AMSOL also showed that solvation free energy change upon methylation was variable depending on the position of the substituted backbone nitrogen, which disagrees with the literature. However, non-systematic solvation free energy change of small amines upon methylation was successfully predicted by AMSOL, in good accord with experimental data.

Master of Science

Given the wide and fundamental roles proteins play in cells, as well as their potential medical and industrial applications, a detailed understanding of the relationships between sequence, structure, dynamics, and function is of critical importance. Molecular models are required to solve this problem, as well as models of the associated conformational spaces. One of the most challenging aspects of modeling these vast ensembles is the computer power required to carry out the requisite simulations. Reduced solvent models, and particularly a class referred to as implicit solvent models, have been developed extensively; however, they make many assumptions and approximations that are likely to affect accuracy. Here, several implicit solvent models commonly used for protein modeling are evaluated by comparing the expected changes in free energies of solvation upon folding ΔGsolv derived from micro--ms simulations of fast folding proteins to those given by the implicit solvent models. In the majority of cases, there is a significant and substantial difference between the ΔGsolv values calculated from the two approaches, with the implicit solvent models excessively favouring the folded state over the unfolded state. This could only be remedied by selecting values for the model parameters -- the internal dielectric constant for the polar term and the surface tension coefficient for the apolar term -- that were system specific or physically unrealistic.
Science, Faculty of
Graduate

In this dissertation, different approaches have been employed to address the quest of understanding the formation and growth mechanisms of carbon-containing molecular ions with relevance to astrochemistry. Ion mobility mass spectrometry and DFT computations were used to investigate how a second nitrogen in the pyrimidine ring will affect the formation of a covalent bond between the benzene radical cation and the neutral pyrimidine molecule, after it was shown that a stable covalent adduct can be formed between benzene radical cation and the neutral pyridine. Evidence for the formation of a more stable covalent adduct between the benzene radical cation and the pyrimidine is reported here. The effect of substituents on substituted-benzene cations on their solvation by an HCN solvent was also investigated using ion mobility mass spectrometry and DFT computations were also investigated. We looked at the effect of the presence of electron-withdrawing substituents in fluorobenzene, 1,4 di- fluorobenzene, and benzonitrile on their solvation by up to four HCN ligands, and compared it to previous work done to determine the solvation chemistry of benzene and phenylacetylene by HCN. We report here the observed increase in the binding of the HCN molecule to the aromatic ring as the electronegativity of the substituent increased. We also show in this dissertation, DFT calculations that reveal the formation of both hydrogen-bonded and electrostatic isomers, of similar energies for each addition to the ions respectively. The catalytic activity of the 1st and 2nd row TM ions towards the polymerization of acetylene done using the reflectron time of flight mass spectrometry and DFT calculations is also reported in this dissertation. We explain the variation in the observed trend in C-H/C-C activity of these ions. We also report the formation of carbide complexes by Zr+, Nb+, and Mo+, with the acetylene ligands, and show the thermodynamic considerations that influence the formation of these dehydrogenated ion-ligand complexes. Finally, we show in this dissertation, a novel ionization technique that we employed to generate ions that could be relevant to the interstellar and circumstellar media using the reflectron time of flight mass spectrometry.

Les réactions d’oxydation d’hydrocarbures en phase liquide (aussi appelées auto-oxydation) jouent un rôle essentiel dans un grand nombre de procédés de l’industrie pétrochimique car elles assurent la conversion du pétrole en composés chimiques organiques valorisables. Elles régissent également la stabilité à l’oxydation des carburants (vieillissement) et des produits chimiques dérivés du pétrole. Ces réactions d’oxydation en phase liquide relèvent de mécanismes radicalaires en chaîne impliquant des milliers d’espèces et de réactions élémentaires. La modélisation cinétique de tels systèmes reste actuellement un défi car elle nécessite de disposer de données thermodynamiques et cinétiques précises, qui sont rares dans la littérature. Le logiciel EXGAS, développé au LRGP, permet de générer automatiquement des modèles cinétiques détaillés pour des réactions d’oxydation d’hydrocarbures en phase gazeuse. Qu’il s’agisse d’une phase gazeuse ou liquide, les réactions élémentaires mises en jeu sont de même nature et la méthodologie de génération du mécanisme est la même. Pour passer d’un mécanisme en phase gaz à un mécanisme en phase liquide il convient d’adapter les valeurs des constantes d’équilibre et de vitesse (appelées constantes thermocinétiques) des réactions du mécanisme. L’objectif de cette thèse est de proposer une méthode pour corriger les constantes thermocinétiques de la phase gaz pour qu’elles deviennent applicables à la phase liquide. Cette correction fait intervenir une grandeur appelée énergie de GIBBS de solvatation molaire partielle. Une analyse de la définition précise de cette quantité nous a permis de montrer qu’elle s’exprime simplement en fonction d’un coefficient de fugacité et d’une densité molaire. Nous avons ensuite relié cette grandeur à des quantités thermodynamiques mesurables (coefficients d’activité, constantes de HENRY …) et nous nous sommes appuyés sur toutes les données qu’il nous a été possible de trouver dans la littérature pour créer la banque de données expérimentales d’énergies de GIBBS de solvatation molaires partielles la plus complète (intitulée CompSol). Cette banque de données a ensuite servi à valider l’utilisation de l’équation d’état UMR-PRU pour prédire ces énergies. Les bases d’une équation d’état de type SAFT, au paramétrage original, développé dans le cadre de cette thèse, ont été posées. Notre objectif était de simplifier l’estimation des paramètres corps purs de cette équation d’état en proposant une méthode de paramétrage ne nécessitant aucune procédure d’optimisation, claire et reproductible, à partir de données très facilement accessibles dans la littérature. Cette équation a été utilisée pour estimer les énergies de GIBBS de solvatation molaires des corps purs et les énergies de GIBBS de solvatation molaires partielles de systèmes {soluté+solvant}. Enfin, ces méthodes d’estimation des énergies de GIBBS de solvatation molaires partielles ont été combinées au logiciel EXGAS afin de modéliser l’oxydation du n-butane en phase liquide
Liquid phase oxidation of hydrocarbons (also called autoxidation) is central to a large number of processes in the petrochemical industry as it plays a key role in the conversion of petroleum feedstock into valuable organic chemicals. This phenomenon is also crucial in oxidation-stability studies of fuels and its derivatives (aging). These liquid-phase oxidation reactions entail radical mechanisms involving more than thousands of compounds and elementary reactions. Kinetic modelling of these kinds of reactions remains a significant challenge because it requires thermodynamic and kinetic parameters, which are not abundant in literature. The EXGAS software, developed at LRGP, is able to generate these kinds of models but only for oxidation reactions taking place in a gaseous phase. It is assumed that the nature of elementary reactions in the liquid and gaseous phases is the same. The unique need to transfer a kinetic mechanism from a gas phase to a liquid phase is to update kinetic rate constant values and equilibrium constant values (called thermokinetic constants) of mechanism reactions. Therefore, in the framework of this PhD thesis, a new method aimed at applying a correction term to thermokinetic constants of gaseous phases is proposed in order to obtain constants usable to describe liquid-phase mechanisms. This correction involves a quantity called partial molar solvation GIBBS energy. An analysis of the precise definition of this property led us to conclude that it can be simply expressed as a function of fugacity coefficients and liquid molar density. As a result, this property could also be expressed with respect to measurable thermodynamic quantities as activity coefficients or HENRY’s law constants. By combining all the experimental data related to these measurable properties that can be found in the literature, it was possible to develop a comprehensive databank of partial molar solvation GIBBS energies (called the CompSol database). This database was used to validate the use of the UMR-PRU equation of state to predict solvation quantities. Moreover, the bases of a new parameterization for SAFT-type equations of state were laid. It consists in estimating pure-component parameters of SAFT-like equation using a very simple, reproducible and transparent path for non-associating pure components. This equation was used to calculate partial molar GIBBS energy of solvation of pure and mixed solutes. Last, equations of state were combined with EXGAS software to model the oxidation of n-butane in the liquid phase

La théorie de la fonctionnelle de la densité classique est utilisée pour étudier la solvatation de solutés quelconques dans le solvant eau. Une forme approchée de la fonctionnelle d'excès pour l'eau est proposée. Cette fonctionnelle nécessite l'utilisation de fonctions de corrélation du solvant pur. Celles-ci peuvent être calculées par simulations numériques, dynamique moléculaire ou Monte Carlo ou obtenues expérimentalement. La minimisation de cette fonctionnelle donne accès à l'énergie libre de solvatation ainsi qu'à la densité d'équilibre du solvant. Différentes corrections de cette fonctionnelle approchée sont proposées. Une correction permet de renforcer l'ordre tétraédrique du solvant eau autour des solutés chargés, une autre permet de reproduire le comportement hydrophobe à longue distance de solutés apolaires. Pour réaliser la minimisation numérique de la fonctionnelle, la théorie a été implémentée sur une double grille tridimensionnelle pour les coordonnées angulaires et spatiales, dans un code de minimisation fonctionnelle écrit en Fortran moderne, mdft. Ce programme a été utilisé pour étudier la solvatation en milieu aqueux de petits solutés atomiques neutres et chargés et de petites molécules polaires et apolaires ainsi que de solutés plus complexes, une argile hydrophobe et une petite protéine. Dans chacun des cas la théorie de la fonctionnelle de la densité classique permet d'obtenir des résultats similaires à ceux théoriquement exacts obtenus par dynamique moléculaire, avec des temps de calculs inférieurs d'au moins trois ordres de grandeurs.

Dans la cellule des organismes vivants, le solvant (l'eau) joue un rôle très important dans la stabilisation des structures tridimensionnelles des macromolécules biologiques et lors de leurs interactions. Les méthodes théoriques de simulations de modélisation moléculaire permettent de compléter les informations partielles sur l'hydratation des biomolécules obtenues par les méthodes expérimentales. Nous avons développé un nouveau modèle de solvatation semi-implicite pour représenter le solvant en modélisation moléculaire. Ce modèle décrit le solvant comme des particules microscopiques dont les propriétés diélectriques découlent des lois macroscopiques de l'électrostatique. Nous obtenons ainsi à l'équilibre électrostatique un fluide de particules de Lennard-Jones non polaires, polarisables par le champ électrique créé par le soluté. Ce modèle a l'intérêt de prendre en compte la structure moléculaire du solvant tout en calculant efficacement l'énergie libre électrostatique de solvatation du système. De plus, il est d'un faible coût numérique comparé aux méthodes explicites. Après avoir implémenté notre modèle dans un programme de dynamique moléculaire et l'avoir paramétré de façon simple, nous l'avons appliqué à plusieurs peptides, protéines et acides nucléiques (ADN et ARN de transfert). Les trajectoires de ces simulations sont stables sur une à deux nanosecondes, et les structures obtenues sont tout à fait en accord avec les méthodes expérimentales et les méthodes théoriques de solvatation explicites. Notre modèle permet également de retrouver les sites préférentiels d'hydratation des molécules étudiées identifiés expérimentalement ou théoriquement, malgré l'absence de liaisons hydrogène dans notre solvant. De plus, nous observons de bonnes corrélations entre les énergies libres électrostatiques de solvatation calculées avec notre modèle et celles calculées avec les méthodes de résolution de l'équation de Poisson-Boltzmann, et ces résultats paraissent très encourageants.

O método de equalização da eletronegatividade (Electronegativity Equalization Method, EEM), fundamentado em teoria do funcional da densidade eletrônica, foi combinado à aproximação de Born generalizada para moléculas (Generalized Born, GB), e denominado GBEEM (Dias et al., 2002). Os momentos de dipolo permanente no vácuo e em meio condensado (constante dielétrica ~ 80), e distribuições de cargas atômicas, mostraram boa concordância com modelo SM5.4 baseado em cargas CM1 em nível PM3 (12 moléculas, correspondendo a 29 cargas atômicas). Este resultado é interessante devido à simplicidade inerente do GBEEM e seu baixo custo computacional. Uma nova parametrização das durezas e eletronegatividades foi feita com o objetivo de melhorar a distribuição de cargas atômicas em moléculas isoladas em relação ao modelo CM1. Um conjunto de 250 estruturas/cargas PM3/CM1 de moléculas neutras pertencentes a 13 funções orgânicas foi utilizado como alvo na parametrização, utilizando uma metodologia Algoritmo Genético/Simplex de pesquisa de mínimos (Menegon et al., 2002). Boa concordância entre os modelos foi obtida. A validação da parametrização e do EEM foi efetuada usando moléculas bifuncionais (tetrapeptídeo e trisacarídeo) mostrando também boa concordância e robustez. Entretanto, a análise do momento de dipolo permanente das 250 moléculas mostrou uma séria limitação do EEM, e portanto do GBEEM, apesar da boa concordância entre as cargas EEM e CM1. O EEM superestimou os momentos de dipolo. Tal fato pode decorrer de vários fatores, dentre os quais, o truncamento da expansão nas cargas atômicas e ausência de tratamento explícito de interação de troca (exchange). Foi sugerida uma aproximação que restringe a transferência de carga entre grupos na molécula que contornou a limitação do método na predição de momentos de dipolo no vácuo e meio condensado (Shimizu et al., 2004). Com base nos recentes resultados, foi desenvolvido um modelo de solvatação baseado no GBEEM e no modelo de Floris-Tomasi. A calibração foi feita com um conjunto de 62 moléculas neutras (13 grupos funcionais) tendo como alvo as energias livres de hidratação experimentais. Os resultados apresentaram um desvio médio absoluto de 0,71 kcal/mol em relação aos valores experimentais.
The electronegativity equalization method (EEM), founded on density functional theory (DFT), has been combined to the generalized Born approximation (GB) for molecules, and called GBEEM (Dias et al., 2002). The permanent dipole moment in vacuum and condensed phase (dieletric constant ~ 80), and atomic charges distributions, have shown good agreement with SM5.4 solvation model based on CM1 charges at PM3 level (12 molecules, corresponding to 29 atomic charges). This result is interesting due the simplicity of GBEEM and its low computational cost. A new parameterization of the hardness and electronegativities was done with the aim to improve the atomic charges distribution on isolated molecules in comparison to CM1 model. The training set with 250 PM3/CM1 structures/charges of neutral molecules in 13 different organic functions was employed as target in the parameterization. A new optimization approach composed of Genetic and Simplex algorithms was used to fit parameters (Menegon et al., 2002). Good agreement between the models was found. The validation of parameterization and EEM was done using bifunctional molecules (tri-glucose and tetra-peptide) showing good agreement and robustness. However, analysis of permanent dipole moments of 250 molecules shown a serious caveat of EEM and GBEEM, beside the good agreement between EEM and CM1 charges. EEM has overestimated the dipole moments. Such result may be due to the truncated expansion in atomic charges and lacking of explicit treatment of exchange interaction. A new approximation was proposed constraining the charge transfer between groups within the molecule. This approximation corrected the caveat of EEM in the prediction of dipole moments in vacuum and condensed phase (Shimizu et al., 2004). Based on these results, a new solvation model was developed founded in GBEEM and Floris-Tomasi model. The parameterization was done with a training set of 62 neutral molecules (13 functional groups) and experimental hydration free energies as target. This new solvation model has produced a mean absolute deviation, MAD, of 0.71 kcal/mol comparing to experimental data.

Este trabalho visou compreensão da solvatação em solventes puros e misturas binárias, e aplicar as informações obtidas para analisar o efeito de solventes na síntese de líquido iônico, e na dependência das propriedades de filmes de acetatos de celulose, AC, sobre o grau de substituição do éster. Para a compreensão da solvatação utilizou-se compostos (sondas solvatocrômicas) cujos espectros Uv-Vis são sensíveis às propriedades do meio. Juntamente com tais sondas, foram usadas outras duas ferramentas: (i) Modelo de solvatação preferencial; proposto por nosso grupo e que descreve a composição da camada de solvatação da sonda, considerando a existência de um \"agregado\" água - solvente orgânico. (ii)Correlações multi-paramêtricas de energia livre de solvatação; que correlacionam uma propriedade dependente do meio com as propriedades dos solventes e suas misturas. Primeiramente, estudamos a solvatação de pares de sondas que possuíam pKas semelhantes e lipofilicidades diferentes em solventes próticos. Concluiu-se que a acidez e a dipolaridade/polarizabilidade dos solventes são as propriedades mais importantes. As conclusões foram corroboradas por cálculos teóricos, que mostraram a relação entre as características estruturais da sonda e suas susceptibilidades às propriedades do meio. O mesmo conjunto de sondas foi usado no estudo de misturas água-solventes próticos. Neste, aplicou-se com sucesso o modelo de solvatação acima mencionado e, de forma inédita, conseguimos racionalizar as constantes de equilíbrio para a troca das espécies presentes (água, solvente e água-solvente) na camada de solvatação com as propriedades dos solventes puros e/ou das misturas binárias. Os resultados revelaram que a composição da camada de solvatação é regida pelas propriedades de solventes, em particular a lipofilicidade e basicidade. As sondas RB e WB foram estudadas em misturas de água com alcoóis e com solventes apróticos. O intuito era ampliar a aplicabilidade do modelo de solvatação, para o qual precisávamos conhecer o volume molar do agregado, VSolv-A, e a constante de dissociação, Kdissoc, do agregado água-solvente. Estas duas grandezas eram obtidas de forma simultânea, através de dados de densidade. Desta vez, fizemos uso de cálculos teóricos para obter, de forma independente, o volume molar e depois utilizá-lo, como parâmetro constante (não ajustável) na cálculo de Kdissoc. A comparação dos resultados mostrou que, por ambas as abordagens, o desvio entre os valores de Kdissoc era mínimo. Por outro lado, em nenhum caso a ordem de Kdissoc se alterava. Esta observação deve-se ao fato de que o cálculo simultâneo de Kdissoc e VSolv-A foi sempre baseado em número grande de dados de densidade (18) de forma que os ajustes por interação não convergissem para um falso mínimo; o nível de teoria usado nos cálculos teóricos foi adequado. Quanto às aplicações, ficou evidente como a escolha do solvente afeta a velocidade da síntese do líquido iônico. Em relação aos filmes de AC, tentamos reproduzir as propriedades dos mesmos, através de uso de dois modelos etanol-acetato de etila e celulose-triacetato de celulose. Os dados da mistura líquida mostraram solvatação preferencial; foram tratados com sucesso pelo mesmo modelo aplicado para misturas binárias aquosas. O modelo sólido reproduziu os dados da AC qualitativamente.
This work is aimed at understanding solvation in pure solvents and binary mixtures and, the application of the information obtained in order to analyze the solvents effects on the synthesis of an ionic liquid, and on the dependence of the properties of cellulose acetate films, CA, on the degree of substitution of the ester. To understand salvation, was have used compounds (solvatchromic probes), whose UV-vis spectra are susceptible to the environment properties. In addition to these probes, were used more two tools: (i) Preferential solvation model; it was proposed by our research group and describes the composition of the probe solvation shell, considering the existence of an aggregate between water and organic solvent. (ii) Multi-parameter solvation free energy equations that correlate the solvent dependent properties with solvents properties and their mixtures. At first, we have studied pairs of probes that have similar pKa values and different lipophilicity in protic solvents. We have concluded that solvent acidity and dipolarity/polarizability are the most important properties. These conclusions are supported by theoretical calculations, that have shown the relationship between structural features of the probe and its susceptibility to environment properties. The same set of probes was used in order to study water - protic solvents mixtures. In this, we have applied the above cited solvation model successfully and rationalized the equilibrium constants of the exchange of species present (water, solvent and water -solvent) in the solvation shell with the properties of pure solvents and / or binary mixtures. These results revealed that the composition of solvation shell is controlled by the properties of solvents, in special, lipophilicity and basicity. The probes RB and WB were studied in mixtures of water with alcohols and with aprotic solvents. The intention was to broaden the applicability of the solvation model, for which, we needed to know the molar volume of the aggregate VSolv-W, and the dissociation constant, Kdissoc, of the same. Previously, these two quantities were obtained, simultaneously, by iteration of density data. We have used theoretical calculations in order to obtain VSolv-W and then use it as constant parameter (not adjustable one) in the calculation of Kdissoc. Comparison of the results showed that, in both approaches, the differences between Kdissoc values were minimal. Moreover, the order of Kdissoc has not changed. This observation is due to the fact that the simultaneous calculation of Kdissoc and VSolv-W was always based on a large number of density data (18) so that the interation did not converge to a false minimum; the level of theory used in the theoretic calculations was appropriate. Regarding applications, our results showed the importance of the choice of solvent to the synthesis of an ionic liquid. We have attempted to reproduce the properties of CA by the use of two models, ethanol-ethyl acetate and cellulose triacetate-cellulose. The data of the liquid mixture showed preferential solvation; were successfully treated by the same model applied to aqueous binary mixtures. The solid model reproduces the CA data qualitatively.

La représentation des propriétés thermodynamiques de solutions d'électrolytes en mélange de solvants est un enjeu industriel fort. Cependant la modélisation thermodynamique de ces systèmes présente des difficultés spécifiques. Dans ce travail, nous avons réalisé un montage à base d'électrodes sélectives d'ions afin d'obtenir des grandeurs expérimentales propres à améliorer la représentation des solutions d'électrolytes en solvant non-aqueux et en mélange de solvants. Cette méthode permet non seulement la détermination de coefficient d'activité moyen mais aussi d'enthalpie libre de transfert, grandeurs indispensables pour exprimer les coefficients d'activité par rapport à un état de référence indépendant de la composition du mélange. Les déterminations ont porté sur les solutions de la naci et de nabr dans le méthanol puis dans des mélanges eau-méthanol. Notre dispositif a ensuite été utilisé pour déterminé la répartition de la naci entre les deux phases liquides du système eau-n-butanol
The representation of the thermodynamic properties of electrolytes solutions in mixed-solvent is a strong industrial stake. However the thermodynamics modelling of these systems presents specifics difficulties. In the present study, we carried out an electrochemical cell with ion selective electrodes in order to determine experimental measurements that could be used to improve the representation of non-aqueous and mixed-solvent electrolytes solutions. This method allows us to obtain not only experimental values of mean activity coefficient but also of the standard gibbs energy of transfer, a property necessary to express the mean activity coefficients in a reference state that does not depend on the mixture composition. The first measurements have been relative to solutions of naci and nabr in methanol and water-methanol mixtures. The new device was then used to determine the partition coefficient of naci between the two liquid phases produced by the water-n-butanol system

La production de bio-huiles par conversion thermochimique de la biomasse estun procédé prometteur pour le bio-raffinage. Alors que la cinétique en phase gazeuse de la conversion de la bio-huile est bien avancée, sa réactivité en phase liquide reste mal connue.L’objectif de cette thèse est de comprendre le mécanisme cinétique détaillé de la décomposition thermochimique de la biomasse à basse température en phase liquide. Comme indiqué par Basu et al. (June 2010) et Nakamura et al. (2007a,b)et Kawamoto (2017), une phase liquide est observée pendant la première étape de la pyrolyse de la biomasse. Dans cette étude, nous tenterons de modéliser le premier stade de la pyrolyse de la biomasse. A notre connaissance, aucune étude de modélisation de la réactivité en phase liquide n’a été proposée pour la pyrolyse de la biomasse. L’étude des réactions en phase liquide de ces systèmes complexes nécessite une bonne connaissance de l’influence du solvant sur la cinétique. Nous avons en premier temps comparé la prédiction des modèles COSMO-SAC avec celles du modèle de solvatation Abraham, en considérant la base de données COMPSOL de Moine et al. (2017) comme données de référence. Nous avons ensuite proposé une re-paramétrisation de ces modèles COSMO-SAC qui conduit à de bien meilleures prédictions et nous permets d’étendre ces modèles à l’utilisation des cavités CPCM (Nait Saidi et al. (2020)). Les méthodes prédictives basées sur des calculs ab initio peuvent être très précises pour prédire les propriétés thermochimiques en phase gazeuse et sont généralement plus polyvalentes que les méthodes de contribution de groupe. Une extension de la méthode ab initio de prédiction des enthalpies de formation de Paulechka et Kazakov (2017) a été proposée dans ce travail (Mielczarek et al. (2019)) et utilisée pour les composés de la biomasse. En troisième partie de cette étude, nous avons prédit les différents chemins réactionnels possibles de la décomposition des composés représentatifs de la partie lignine de la biomasse à l’aide du générateur de mécanismes réactionnels (RMG). Les composés choisis sont le créosol, le gaïacol et le méthoxy vinylphénol. Ce travail peut être considéré comme une extension du mécanisme en phase gazeuse de la pyrolyse proposé par Ranzi et al.(2017a,b) en considérant la recombinaison radicalaire et la polymérisation qui se produit à basse température entre100°C et 300°C. Pour modéliser la cinétique des réactions clés, nous les avons étudiés par l’approche des états de transition à l’aide de Gaussian09 et d’ORCA. L’estimation des paramètres cinétiques est ensuite déterminé par la théorie des états de transition à l'aide du Kisthelp tool (Canneaux et al. (2014)) pour la cinétique en phase gazeuse et cinétique en phase liquide à partir de l’approche Green (Jalan et al. July 2013)
Production of bio-oils through thermochemical biomass conversion is a promising process for biorefining. While gas phase kinetics of bio-oil conversion has been improving, its liquid phase reactivity is currently poorly understood. The aim work of my thesis is about the understanding of detailed kinetics mechanism of biomass thermochemical decomposition at low temperature range in the liquid phase. As mentionned by Basu (June 2010); Nakamura et al. (2007a,b); Kawamoto (2017) a liquid phase is observed during the initial stage of biomass pyrolysis. In this study, we will try to model the initial stage of biomass pyrolysis. To our knowledge, no modelling study of the rate of reactions in the liquid phase has been proposed for biomass pyrolysis. The investigation of liquid phase reactions of such complex systems requires a good knowledge of solvent effects. We compared the prediction capabilities of COSMO-SAC with those of the Abraham solvation model, by considering the COMPSOL database of Moine (2017) as the reference data. We then proposed a re-parametrization of these COSMO-SAC models that leads to much better predictions, and extended these models to CPCM cavities(Nait Saidi et al. (2020)). Predictive methods based on ab initio calculations can be very accurate for predicting gas phase thermochemical properties and are usually more versatile than group contribution methods. An extension of Paulechka and Kazakov (2017) ab initio prediction method of enthalpies of formation was proposed in this study (Mielczarek et al. (2019)) and used for biomass compounds. We then used Reaction Mechanism Generator (RMG) to investigate the possible reaction mechanism of different Tar surrogate compounds of biomass decomposition. The surrogate compounds that we chose are Creosol, guaiacol and methoxy vinylphenol to model the lignin. This work can be considered as an extension of the gas phase reaction mechanism of pyrolysis proposed by Ranzi(2017a,b) taking in consideration the primary tar recombination/polymerisation reaction that occur in the temperature range 100°C to 300°C.To model the kinetics of the key reaction, we investigated the transitional state using Gaussian 09 and ORCA. We then estimated the kinetics parameters using Transitional State Theory with Kisthelp tool (Canneauxet al. (2014)) and liquid phase kinetics approach based on the gas phase kinetics and solvation free energies correction (Jalan et al. July 2013)

Description théorique de l'interface entre un métal noble et une solution électrolytique. La description de l'interface solution-paroi solide est décrite par le modèle "civilisé" dans lequel les molécules sont des sphères dures portant un dipôle ponctuel et les ions de sphères dures chargées. Détermination du profil de densité des dipôles lorsque ceux-ci interagissent avec la surface ainsi que le profil de densité des ions. Pour l'interface métal noble-vide, calcul du travail de sortie et de l'énergie de surface. Utilisation d'un modèle simple permettant de traiter la surface et de rendre compte de l'hybridation s/d
Theoretical description of the interface between a noble metal and an electrolytic solution. The description of the solution-wall solid interface is described by the "civilized" model in which the molecules are hard spheres bearing a point dipole and the ions of charged hard spheres. Determination of the density profile of dipoles when they interact with the surface and the density profile of ions. For noble-vacuum metal interface, calculation of output work and surface energy. Use of a simple model to treat the surface and account for hybridization s/d

Absorção e Emissão de radiação eletromagnética por moléculas na região do UV-Vis fornece informações sobre os estados eletrônicos excitados, sendo propriedades de grande interesse devido a sua relação com processos biológicos, bem como suas possíveis aplicações em diagnósticos e tecnologia. Essas propriedades são sensíveis ao meio em que as moléculas se encontram, tornando-se assim natural a busca por métodos teóricos que possibilitam descrever essas interações. Neste trabalho, nós usamos a metodologia Sequential-Quantum Mechanics/Molecular Mechanics para estudar o espectro de absorção e de emissão de moléculas de relevância biológica, quando em solução. Simulações clássicas Monte Carlo foram usadas pra construir uma configuração eletrostática média do líquido para posterior cálculo das propriedades, feito através dos métodos multiconfiguracionais CASSCF e CASPT2. Cuidados especiais foram tomados para incluir a polarização eletrônica que o soluto sofre devido à presença do solvente. Nossa contribuição é a adaptação do método do Gradiente de Energia Livre para permitir a obtenção de geometrias de estados excitados do soluto em solução. A técnica foi implementada em um programa e aplicada com sucesso nos sistemas estudados. As perspectivas agora se abrem para a obtenção de intersecções cônicas em meio solvente, permitindo assim o estudo de decaimentos não-radiativos em sistemas solvatados.
Absorption and emission of electromagnetic radiation by molecules in the UV-Vis region yields information about the electronic excited states, being properties of great interest due its relation with biological process, as well as its possible applications in diagnostics and technology. These properties are sensible to the environment in which the molecules are, making natural the search for theoretical methods that describe these interactions. In this work, we have used the Sequential-Quantum Mechanics/Molecular Mechanics methodology to study the spectrum of absorption and emission of molecules of biological relevance, when in solution. Classical Monte Carlo simulations were carried out to construct an average solvent electrostatic configuration and used to represent the liquid in posterior quantum mechanics calculation of the properties, performed by using the multiconfigurational methods CASSCF and CASPT2. Special cares were taken to include the electronic polarization of the solute due the solvent. Our contribution is the adaptation of the Free Energy Gradient method to allow the determination of the solute excited states geometries in solution. The method was implemented in a computer program and successfully applied in the systems studied. The perspectives are now open to the calculation of conical intersection in solvent environment, enabling the study of nonradioactive decays in solvated systems.

Uma das propriedades fundamentais de soluções de micelas aquosas é sua capacidade de solubililizar uma ampla faixa de solutos orgânicos com diferentes graus de polaridade e hidrofobicidade. Recentemente Quina et. aI., estudaram as interações químicas específicas que governam a solubilidade para um ampla faixa de solutos orgânicos em micelas usando relações lineares de energia livre de solvatação (LSERs), baseado nos parâmetros empíricos do soluto desenvolvido por Abraham. O presente trabalho trata a solubilização de solutos orgânicos em micelas baseado em parâmetros obtidos unicamente da estrutura molecular do soluto através de cálculos de química quântica. Nossos resultados mostram que valores experimentais de Ks para solubilização de solutos orgânicos em detergentes aniônicos (micelas de SDS, dodecil sulfato de sódio e agregados de SDS com PEG-polietilenoglicol) podem ser reproduzidos usando parâmetros teóricos. A relação linear teórica de energia livre de solvatação resultante é quimicamente condizente com LSERs baseados em parâmetros empíricos do soluto. No caso de detergentes catiônicos e não iônicos, a metodologia apresenta limitações, por que o método de cálculo de cargas formais usando a definição de análise populacional de Mulliken não descreve de maneira apropriada o caráter ácido e básico das pontes de hidrogênio entre os solutos e a água. Alternativas para resolver o problema da limitação imposta pelos parâmetros teóricos, mantendo a aproximação linear de energia livre, são discutidas.
One of the most fundamental properties of aqueous micelar solutions is their ability to solubilize a wide variety of organic solutes with quite distinct polarities and degree of hydrophobicity. Recently Quina et al., studied the specific chemical interactions governing the solubilities of a wide range of solutes in micelles using linear solvation energy relationships (LSERs) based on empirical solute parameters developed by Abraham. This work reports an investigation of the solubilization of organic solutes in micelles based on the use of theoretical solute parameters derived from quantum chemical calculations Our results show that the experimental Ks values for solubilization of organic solutes in anionic detergents (micelles of SDS-sodium dodecyl sulfate and aggregate formed between SDS and PEG-poly(ethylene glycol)) can be reproduced using theoretical parameters. The resultant theoretical linear solvation energy relationships are chemically consistent with LSERs based on empirical solute parameters. In the case of cationic and nonionic detergents, the theoretical parameters used to describe hydrogen bonding fail because methods of calculating formal charges using the concept of Mulliken populational analysis cannot describe hydrogen bonding donor and acceptor character in an appropriate way. Possible strategies to solve the theoretical descriptor problem in the context of the linear free energy approximation are discussed.

Estudamos as propriedades estruturais e eletrônicas da molécula emodina (EM), em diferentes condições, do ponto de vista experimental e teórico. Numa primeira parte, realizamos medidas do espectro eletrônico de absorção da EM, em meio solvente (água, clorofórmio e metanol). Nessa parte, obtivemos que o solvente provoca pouco efeito nos deslocamentos das bandas. Numa segunda parte, estudamos a EM, isoladamente e nos três solventes, através de cálculos quânticos com funcional de densidade (B3LYP), conjunto de função base de Pople (6-31G*) e modelo contínuo polariz ável (PCM). Como principais resultados obtivemos que a EM é rígida a menos da orientação relativa das 3 hidroxilas. A mudança orientacional nessas hidroxilas pode provocar formação de até 2 ligações de hidrogênio intramolecular (o que estabiliza sua geometria) e conseqüente uma diminuição no momento dipolo de 5.5 a 1.7D (o que desestabiliza sua interação com a água). Numa terceira parte, realizamos simulações com método Monte Carlo e Dinâmica Molecular em solução. Nessa parte, obtivemos que as ligações de hidrogênio intramoleculares são raramente quebradas devido as interações com o solvente e isso atribui a EM um caráter hidrofóbico. Adicionalmente, utilizando Teoria de Perturbação Termodinâmica nas simulações, calculamos a variação de energia livre de solvatação da EM em partição água/clorofórmio e água/- metanol e obtivemos -2.6 e -4.9 kcal/mol, respectivamente. Esse resultado está em boa concordância com o resultado experimental de -5.6 kcal/mol para partição de água/octanol. Por último, realizamos cálculos do espectro eletrônico de absorção da EM, isoladamente e nos três solventes, considerando as moléculas através do modelo, contínuo de solvente (SCRF) e explícito de solvente, com o método INDO/CIS. Nessa parte, obtivemos que o efeito do solvente é bem descrito teoricamente.
We study the structural and electronic properties of the emodin (EM) in different solvents of experimental and theoretical the point of view. We started performing measurements of the UV-Vis absorption spectrum of the EM in solution (water, chloroform and methanol). Our main result is that the solvent causes little effect on shifts the bands. In the second part of this work, we performing quantum calculations of isolated EM and in the three solutions using density functional (B3LYP), a set of Pople basis function (6-31G*) and the polarizable continuum model (PCM). In this part, our result is that EM presents a rigid conformation unless the orientation of its 3 hydroxyls. The change in these hydroxyls orientation can form up to 2 intramolecular H-bonds (which stabilizes its geometry) and causes a decrease in the dipole moment from 5.5 to 1.7D (which destabilizes its interaction with water). In the third part of this work, we performing Monte Carlo and Molecular Dynamics simulations in solution. Our main result is that the intramolecular H-bonds are rarely broken, even in aqueous solution, and these give to EM a hydrophobic character. Additionally, using Thermodynamics Perturbation Theory in the simulations, we calculate variations of free energy of solvation of EM in partition of water/chloroform and water/methanol and obtained -2.6 and -4.9kcal/mol, respectively. This last result is in good agreement with the experimental result[3] of -5.6kcal/mol for partition of water/octanol. Finally, we performing calculations of UV-Vis absorption spectrum of isolated EM and in the three solutions. In this calculations, we considering the molecules through the continuum solvent (SCRF) and explicit solvent model with the method INDO/CIS. In this part, we obtaining that effect of solvent is well described theoretically.

La preorganització electrostàtica del centre actiu s'ha postulat com el mecanisme genèric de l'acció dels enzims. Així, alguns residus "estratègics" es disposarien per catalitzar reaccions interaccionant en una forma més forta amb l'estat de transició, baixant d'aquesta manera el valor de l'energia dactivació g cat. S'ha proposat que aquesta preorientació electrostática s'hauria de poder mostrar analitzant l'estabilitat electrostàtica de residus individuals en el centre actiu.
Ras es una proteïna essencial de senyalització i actúa com un interruptor cel.lular. Les característiques estructurals de Ras en el seu estat actiu (ON) són diferents de les que té a l'estat inactiu (OFF). En aquesta tesi es duu a terme una anàlisi exhaustiva de l'estabilitat dels residus del centre actiu deRas en l'estat actiu i inactiu.
The electrostatic preorganization of the active site has been put forward as the general framework of action of enzymes. Thus, enzymes would position "strategic" residues in such a way to be prepared to catalyze reactions by
interacting in a stronger way with the transition state, in this way decreasing the activation energy g cat for the catalytic process. It has been proposed that
such electrostatic preorientation should be shown by analyzing the electrostatic stability of individual residues in the active site.
Ras protein is an essential signaling molecule and functions as a switch in the
cell. The structural features of the Ras protein in its active state (ON state) are different than those in its inactive state (OFF state). In this thesis, an exhaustive analysis of the stability of residues in the active and inactive Ras active site is performed.

Electrolyte solutions play a central role in many processes from industry to biology. Understanding and building predictive models of their properties has therefore been a fundamental goal of physical chemistry from its beginnings. The challenge remains. In this thesis I outline a continuum solvent model of univalent monatomic ions in water. This model calculates the free energy of: 1) a single ion in bulk, 2) of an ion approaching the air–water interface and 3) of two ions approaching each other. Its central advancements are to include quantitatively accurate ionic dispersion interaction energies, missing from classical theories, including the higher order multipole moment contributions to these interactions. It also includes the contribution from the cavity formation energy consistently, including the effect of changes in the cavity’s shape. Lastly, it uses a quantum mechanical treatment of the ions and provides satisfactory values for their size parameters. Because one consistent framework is used with the same assumptions to calculate the free energies in these three different situations the number of parameters can be minimised and the model can be properly tested. These three calculations can be used to reproduce experimental solvation free energies, solvation entropies, partial molar volumes, surface tensions and activity/osmotic coefficients of the alkali-halide electrolyte solutions. A minimum of parameters are used and crucially no salt–specific fitting parameters are necessary. The model is quantitative and predictive and is therefore a satisfactory model of electrolyte solutions. It provides an explanation of several key qualitative puzzles regarding these properties. Namely that ions of the same size can have different solvation energies, that large ions can adsorb to the air–water interface and that ions in solution that have similar solvation energies are more strongly attracted to each other than ions that have dissimilar solvation energies. The continuum solvent model and separate ab initio calculations show that dispersion interactions play a key role in controlling these effects. In particular, dispersion energies explain the attraction of large ions for each other in water and the difference in solvation energy of ions of the same size. The success of the model implies that it is possible to understand the key properties of electrolyte solutions using a continuum solvent model. This is an important conclusion considering the massive computational demands of explicit solvent treatments.

(EN) The solvation model based on LSER was applied to study the retention behaviour of analytes in liquid and gas chromatography. In a first chapter, a retention description of 21 solutes was investigated by using the solvation model in a wide range of mobile phase composition methanol-water and acetonitrile-water. Generally, the retention of aromatic compounds was better described by the solvation model, compared to aliphatic compounds. Effect of the particular analytes used to formulate the LSER model on ability of retention description was studied. Different results of a retention estimation was achieved by using the regression set of compounds including aromatic solutes only or by contrast aliphatic solutes only. The solvation model developed on the basis of oxygen derivatives provided distinct results in comparison to model formulated with nitrogen derivatives only. The second chapter of this work, focused on gas chromatography, dealt with a description of retention of 152 isomers C5-C8 alkenes by the LSER model. The solvation descriptor L was obtained by using two estimation methods Havelec-Ševčík (HS) and Platts-Butina (PB), the descriptor E was calculated according to its definition. Two models for retention description of alkenes were constructed, the HS model and the PB model, derived...

(EN) This dissertation thesis is focused on physicochemical and chromatographic characterization of polyaniline-coated stationary phases. In the first part, surfaces of bare silica and octadecyl silica sorbents were modified by in-situ chemical polymerization of aniline hydrochloride and their subsequent systematic characterization was performed by using the linear solvation energy relationship approach in the HILIC mode of capillary LC. In addition, several common physicochemical techniques were used to characterize properties of these altered materials. The modified sorbents were then packed into capillary columns. The retention interactions taking place between solute and the separation system were evaluated on the basis of retention data of a number of various solutes. The results showed that polyaniline coating had a significant effect on the retention promoting interactions of both polyaniline-coated stationary phases. The assumed mixed-mode retention mechanism was proven for both the stationary phases. The second part dealt with investigation of the separation potential of polyaniline- coated silica stationary phase in different chromatographic modes. The retention factor curves of structurally similar solutes were constructed as a function of organic modifier portion in the mobile phase....