Na presente Tese, vamos desenvolver teorias para eletrólitos próximos de interfaces e para suspensões coloidais carregadas. No caso de interfaces, a nova teoria permite-nos calcular quantitativamente tensões e potenciais superficiais, e perfis de densidade para ambas interfaces água-ar e água-óleo. Para suspensões coloidais hidrofóbicas, a teoria permite-nos calcular as concentrações críticas de coagulação (CCC) para várias soluções eletrolíticas. Os resultados teóricos estão em excelente acordo com dados experimentais. A interação iônica com interfaces é relacionada com a classificação dos íons em caotrópicos e cosmotrópicos. A teoria, portanto, traz novo enfoque a série de Hofmeister que governa a estabilidade de soluções proteicas. Em suspensões coloidais, estudamos também o papel das correlações eletrostáticas na distribuição de íons multivalentes próximos da superfície coloidal. Uma nova teoria é introduzida que nos permite incluir as correlações interiônicas como uma nova condição de contorno renormalizada para a equação de Poisson-Boltzmann. Os perfis de densidade calculados são comparados com simulações de Monte Carlo, demonstrando uma boa concordância. Finalmente, exploramos o papel da polarizabilidade coloidal na distribuição iônica. Encontramos que a polarizabilidade causa a repulsão superficial dos contraíons e pode afetar a mobilidade eletroforética de partículas coloidais. / In the present Thesis we will develop theories for electrolytes near interfaces and for charge stabilized colloidal suspensions. In the case of interfaces the new theory allows us to quantitatively calculate surface tensions, surface potentials, and the ionic density profiles both for the water-air and the water-oil interfaces. For the hydrophobic colloidal suspensions, the theory allows us to calculate the critical coagulation concentrations (CCC) for various electrolyte solutions. The theoretical results are found to be in excellent agreement with the experimental data. The ionic interaction with the interfaces is found to be related to the classification of ions into chatropes and kosmotropes. The theory, therefore, sheds new light on the Hofmeister series which governs the stability of protein solutions. For colloidal suspensions, we also study the role of electrostatic correlations on the distribution of multivalent ions near the colloidal surface. A new theory is introduced which allows us to include the interionic correlations as a renormalized boundary condition for the Poisson-Boltzmann equation. The calculated ionic density profiles are then compared with the Monte Carlo simulations, showing a good agreement. Finally, we explore the role of colloidal polarizability on the ionic distribution. We find that polarizability causes the counterion repulsion from the surface and can affect the electrophoretic mobility of colloidal particles.

Thermodynamically, native cellulose nano fibrils are more stable in an aggregated state. The aggregated state is however not useful from a material development perspective. Therefore much research has been done to stabilize the dispersal of the fibrils. One method to overcome this instability is by surface substitution of the O6 hydroxyl group with carboxylate groups, to make highly charged fibrils in aqueous solutions. It is therefore of much interest to understand the interaction of highly charged fibrils in aqueous solutions. In this study, we aim to model the interaction potential energy between native and surface modified cellulose nanofibrils in order to understand under what conditions the contribution from the dipole interactions can be neglected. To achieve this we propose to use a continuum electrostatic approach, modeling the electrostatic interactions as a function of the fibrils relative dipole orientation, separation, surface charge as well as ionic strength of the solution, by means of using the Poisson-Boltzmann equation.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Hur elektrolytlösningar interagerar med laddade ytor är viktigt för många fenomen. I detta arbete undersöktes samspelet mellan flera joner med en negativt laddad yta som exponerade sulfonat funktionella grupper mot lösning. Särskild vikt lades på deprotoneringsbeteendet vid ytan. Samspelet mellan olika joner och sulfonatgruppen hade inte tidigare beaktats ur ett molekylärt perspektiv. Här användes ett Langmuir-monolager bestående av dokosan-1-sulfonsyra deponerat på olika elektrolytlösningar som modellsystem. För att studera molekylära interaktioner mellan ytan och elektrolyterna användes Vibrational Sum Frequency Spectroscopy (VSFS). Denna inneboende ytkänsliga teknik gör det möjligt att observera små förändringar i vibrationsenergier i sulfonagruppen vid kontakt med olika joner, här hydronium, litium, natrium och cesium. Ett av huvudsyftena med detta arbete var att jämföra de experimentellt bestämda parametrarna med teoretiska modeller av det elektriska dubbelskiktet vid laddade gränssnitt, såsom Gouy-Chapman-teorin och andra mer avancerade Poisson-Boltzmann-baserade modeller, för att utforska deras lämplighet och gränser av giltighet. Docosan-1-sulfonsyra packades snyggt i monolager, med packningstätheten ökande med starkare jonstyrka I underfasen. Två toppar i vibrationsspektra sågs för sulfonatgruppen, den symmetriska och asymmetriska sträckningen vid 1048 cm-1 respektive 1150 cm-1. Dessa band sågs blåskiftas vid bindning av litium- och natriummotjoner. Amplituden för den symmetriska sträckningen kunde kopplas direkt till mängden laddade arter. Den teoretiska Gouy-Chapman-modellen var tillräcklig att användas för relativt låga ytpotentialer (<|150mV|). För högre potentialer var motjonens storlek nödvändig att inkludera i modellen för mer exakta förutsägelser. Sulfonsyrans surhetsgrad uppmättes till att vara pKa=-1.8±0.4 och bindningskonstanterna för olika hårda joner till den sulfonatfunktionella gruppen uppskattades vara pKLi=0 och pKNa=-0.7. Däremot binder den mjuka jonen, cesium, inte till sulfonatgruppen. Implikationen är att sulfonatgruppen bör betraktas som en hård jon I enlighet med Collins lag om matchande vattenaffiniteter. / How electrolyte solutions interact with charged surfaces is essential for many phenomena in physics, chemistry and biology. In this work, the interactions of several ions with a negatively charged surface exposing sulfonate functional groups to solution were investigated. Specific emphasis was made on the deprotonation behaviour at the surface. The interplay between different ions and the sulfonate moiety had not been previously considered from a molecular perspective.  Here, a Langmuir monolayer consisting of docosane-1-sulfonic acid deposited on top of different electrolyte solutions was used as model system. To study the molecular interactions between the surface and the electrolytes, Vibrational Sum Frequency Spectroscopy (VSFS) was used. This intrinsically surface sensitive technique allows observing small changes in vibrational energies of the sulfonate functional group when in contact with different ionic species, here hydronium, lithium, sodium and cesium. One of the main objectives of this work was to compare the experimentally determined parameters with theoretical models of the electric double layer at charged interfaces, such as the Gouy-Chapman theory and other more advanced Poisson-Boltzmann based models, to explore their suitability and limits of validity. Docosane-1-sulfonic acid packed nicely into monolayers, with the packing density increasing with stronger ionic strength in the subphase. Two peaks in the vibrational spectra were seen for the sulfonate functional group, the symmetric and asymmetric stretch at 1048 cm-1 and 1150 cm-1, respectively. These bands were seen to blue-shift upon binding of lithium and sodium counterions. The amplitude of the symmetric stretch could be directly linked to the amount of charged species. The Gouy-Chapman theoretical model was adequate to use for relative low surface potentials (<|150mV|). For higher potentials, the size of the counterion was necessary to include in the model for more accurate predictions. The acidity of the sulfonic acid was measured to be pKa=-1.8±0.4 and the binding constants for different hard ions to the sulfonate functional group were estimated to be pKLi=0 and pKNa=-0.7. In contrast, the soft ion, cesium, does not bind to the sulfonate. The implication is that the sulfonate moiety should be considered a hard ion in accordance with Collins law of matching water affinities.

Cette thèse présente deux sujets de recherche indépendants concernant l'application de méthodes stochastiques à des problèmes issus de la dynamique moléculaire. Dans la première partie, nous présentons des travaux liés à l'interprétation probabiliste de l'équation de Poisson-Boltzmann qui intervient dans la description du potentiel électrostatique d'un système moléculaire. Après avoir introduit l'équation de Poisson-Boltzmann et les principaux outils mathématiques utilisés, nous nous intéressons à l'équation linéaire parabolique de Poisson-Boltzmann. Avant d'énoncer le résultat principal de la thèse, nous étendons des résultats d'existence et unicité des équations différentielles stochastiques rétrogrades. Nous donnons ensuite une interprétation probabiliste de l'équation non-linéaire de Poisson-Boltzmann sous la forme de la solution d'une équation différentielle stochastique rétrograde. Enfin, dans une seconde partie prospective, nous commençons l'étude d'une méthode proposée par Paul Malliavin de détection des variables lentes et rapides d'une dynamique moléculaire.

No description available.

<p>Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding.</p><p>The thermodynamic integration technique is used to calculate p<i>K</i>_a values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated p<i>K</i>_a values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine p<i>K</i>_a shifts in wild-type and mutant epoxide hydrolase. The calculated p<i>K</i>_a values support a model that can explain some of the pH dependent properties of this enzyme.</p><p> Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase.</p><p>Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.</p>

Les récepteurs muscariniques à l'acétylcholine sont des protéines transmembranaires jouant des rôles dans de nombreux processus physiologiques. La toxine MT7 est un puissant modulateur allostérique de ces récepteurs. De plus, cette toxine est le seul ligand connu spécifique du sous-type 1 des récepteur muscariniques (hM1). Nous avons étudié les bases moléculaires de l'interaction entre la toxine MT7 et le récepteur hM1 par modélisation. Tout d'abord un échantillonnage des structures des deux partenaires a été réalisé par dynamique moléculaire. Les mouvements de grande amplitude de la boucle e2 du récepteur ont été prédits par dynamique activée. Puis la toxine a été arrimée sur le récepteur par des calculs de dynamique moléculaire sous contraintes ambigües dérivées de données de mutagénèse. Ce modèle a ensuite été optimisé par une simulation de dynamique moléculaire libre, en environnement membranaire explicite. Enfin, des calculs en retour des valeurs d'énergie libre de liaison ont été effectués afin de valider le modèle. Nous prédisons que la toxine se lie sur un dimère de récepteurs hM1. Le cœur de l'interaction est localisé sur un des monomères en contact avec les boucles II et III de la toxine. Cette interaction est complétée par des interactions hydrophobes au niveau de la boucle I sur le second monomère. L'analyse de ce modèle apporte des éléments de compréhension à la fois sur bases structurale de la haute affinité de cette toxine ainsi que sur sa sélectivité pour ce sous-type de récepteur. Il apparaît que cette sélectivité est essentiellement portée par la boucle extracellulaire e2 du récepteur.

Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme. Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.