No description available.

No description available.

Calculating the solvation energies of surfactants is a way to predict the cmc. The solvation energies were determined for a homologous series of betaines, (CH₃)₃N+(CH₂)nCOO- where n = 1 to 6. Their structure is composed of only the hydrophilic head group of a surfactant. The solvation energies were determined from both the gas phase energy and free energy of solution. Conformational analysis was performed on each molecule to locate the lowest energy structures and determine the Boltzmann population of each conformation for each molecule. The final solvation energies for each molecule are expectation values based on their energies and Boltzmann populations. The plotted solvation energies versus n form a parabolic curve that is similar to the literature cmc data where the betaine has a long hydrocarbon tail. However, the solvation energies peak at n = 3 and the cmc data peaks at n = 4. The dipole moments were also examined. The gas phase dipole moments were graphed and have a maximum at n = 3, similar to the solvation energy. The solution dipole moments have a linear graph, not comparable to the solvation energies. Therefore, the stability of the gas phase structures contributes more to the final solvation energy than the stability of the molecule in water. The correlation between the plots of log cmc vs n and solvation energy vs n indicates that it is possible to computationally predict the cmc with this method. The hydrophobic contribution can be accounted for based on a known correlation between chain length and the cmc, and the hydrophilic contribution can be examined with this method. Therefore, it is possible to design a new surfactant molecule that has a cmc within the range of the biological activity to be sent for synthesis. / Master of Science

The molecular conformations, potential energy functions and vibrational spectra of several cyclic molecules have been investigated by ab initio and density functional theory calculations and by infrared and Raman spectroscopy. The ab initio computations of 3-cyclopenten-1-ol predict that its lowest energy conformer has a weak pi-type intramolecular hydrogen bonding. The three other conformers lie 301 to 411 cm^-1 higher in energy. The infrared and Raman spectra of this molecule confirm the presence of the four conformers. The energy difference between the two conformers of lowest energy was also determined from the experimental spectroscopic data and was found to be 435 plus/minus 160 cm^-1, in reasonable agreement with the ab initio computations results. Ab initio calculations for cyclopentane and d1, 1,1-d2, 1,1,2,2,3,3-d6, and d10 isotopomers confirm cyclopentane confirmed that has twist and bent structures and that these differ in energy by less than 10 cm^-1. The bending angle is 41.5 degrees and the twisting angle is 43.2 degrees. A complete vibrational assignment for each of the isotopomers was achieved. Ab initio calculations were also carried out for methylcyclopropane, cyclopropylsilane, cylopropylgermane, cyclopropylamine, cyclopropanethiol and cyclopropanol. The structure and the potential energy function for internal rotation was calculated for each and compared to available experimental results determined from infrared and Raman spectra. The calculated barriers to internal rotation agree very well with the experimental data. The structures, relative energies, and frequencies for the lowest energy vibrations of the twisted, bent, and planar forms of cyclohexene and four of its oxygen analogs were calculated and compared to experimental results. The calculated structural data agree very well with that from the microwave work, but the computed barriers are somewhat lower than those based on far-infrared data. 4-Silaspiro-(3,3)-heptane possesses two four-membered rings, each puckered with and angle of 34 degrees. The molecule possesses a two-dimensional ring-puckering potential energy surface with four equivalent minima. The ab initio calculations predict a barrier to planarity of each ring of 582 cm^-1 while the energy of the structure with both rings planar is 1220 cm^-1 higher. The calculated infrared and Raman spectra were compared to those previously published, and the agreement is excellent.

Examinations of the effects of (a.) alkyl carbon chain length and (b.) perfluorination of acyl chlorides; propionyl chloride, butyryl chloride, valeroyl chloride, and perfluorinated acyl chlorides; perfluoropropionyl chloride and perfluorobutyryl chloride, are reported and compared using CP-FTMW spectroscopy. All of these molecules are already published in various journals except for valeroyl chloride. The chapters are organized by molecule alkyl chain length and include some background theory. Conformational stability, internal rotation, helicity, and ionic character of the C-Cl bond via the nuclear electric quadrupole coupling constant (χzz) are analyzed. Results show syn, syn-anti/syn-gauche, and syn-anti-anti/syn-gauche-anti stable conformations. Internal rotation was only seen in propionyl chloride. Helicity was not observed. (χzz) was observed to be inert to alkyl chain length, ~ 60 MHz and ~ 65 MHz for the nonfluorinated and fluorinated acyl chlorides. Partial fluorination and varying functional groups are recommended.

Les protéines et acides ribonucléiques sont les principaux acteurs de nombreux processus cellulaires.Comprendre leurs fonctions, structures et interactions est un challenge important.Les méthodes expérimentales fournissent des informations sur la structure et la dynamique des molécules.Cependant les méthodes expérimentales sont limitées par le nombre de molécules qu'elles peuvent observer et les moyens qu'elles requièrent.Les méthodes de prédiction permettent d'obtenir des informations structurelles de façon quasi-automatique.Pour s'assurer de leur fiabilité, elles sont testées sur des données expérimentales.Nous présentons une procédure basée sur la cinétique inverse pour trouver une transition entre deux conformations d'un ARN tout en conservant sa structure secondaire.Nous obtenons des résultats comparables à l'état de l'art, ce qui montre que notre sélection des degrés de liberté est pertinente.De plus, nous utilisons des données partielles, ce qui permet d'utiliser différents types de résultats expérimentaux.Nous abordons aussi le problème du repliement protéique par une approche de théorie des jeux.Nous représentons une protéine par un jeu où les joueurs sont les acides aminés et les stratégies, les angles dièdres.La prédiction de structure peut alors être vue comme la recherche d'un équilibre dans un jeu multi-joueur où les fonctions d'utilité correspondent à la qualité du repliement.Nous montrons que l'algorithme de non-regret, appelé Hedge, garantit l'élimination des stratégies dominées et la convergence locale vers un équilibre de Nash.Puis, en limitant notre analyse aux jeux de potentiel, nous montrons qu'une classe plus large d'algorithmes, les algorithmes de régularisation, convergent vers un équilibre de Nash presque surement. / Proteins and Ribonucleic Acids are the workhorses of many cellular processes.Understanding their functions, structures and interactions is an important challenge.Experimental methods provide actual information on structure and dynamics of molecules.However they have limitations : they cannot be applied to all molecules, and they need a lot of resources.Prediction methods are almost automatic ways of obtaining structural information.They are tested on experimental data to attest their reliability.We present, here, approaches tackling different problems.We develop a kinematics-based procedure to morph a RNA molecule between conformations while preserving its secondary structure.We obtain results comparable to state of the art methods showing that our selection of degrees of freedom is efficient.Furthermore we only use sparse information allowing for various kinds of experimental inputs.We also look at the protein structure prediction problem from a game theory angle.We represent the protein dynamics as a game, in which players are amino acids and strategies are dihedrals angles.The structure prediction can thus be seen as finding equilibrium in a multi-players game where all players have utility functions corresponding to the quality of the protein structure.We showed that a well-known no-regret algorithm, called Hedge, guarantees dominated strategies to vanish and a local convergence toward Nash equilibria.Furthermore restricting our analysis to potential games we showed that dual-averaging regularized learning algorithms converge toward a Nash equilibrium almost surely.

No description available.

Yes / The 13C NMR chemical shifts of the three Edaravone tautomers (keto, enol, and amine) were calculated using a combined molecular mechanics (Pcmod 9.1/MMFF94) and ab initio (GIAO (B3LYP/DFT, 6–31 + G(d)) model. This method gave such good agreement with experiment that the assignment of the complex spectrum of Edaravone in solution, which is a mixture of the three tautomers could be made. This has been attempted previously by various methods with diverse results. In CDCl3 solution, the observed spectra show only one form, the keto tautomer, and this is also the case with acetonitrile solvent. Acetone solvent reacts with Edavarone in the NMR tube. In the other solvents studied, methanol, pyridine, DMSO, trifluoroethanol (TFE), there is a mixture of the tautomers with populations which vary with the solvent. The application of the shift predictions allows the assignment of the 13C spectra to the three tautomers and from this the proportions of the tautomers in the solution. The results at times differ significantly from previous studies, and this is discussed.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal. / L'inférence d'un modèle tridimensionnel (3-D) d'une molécule d'ARN à partir d'informations biochimiques de faible résolution est une tâche complexe. Le développement de méthodes efficaces et objectives de modélisation est essentiel à la compréhension des mécanismes moléculaires impliquant des ARN. Le présent travail propose trois ajouts importants de ce domaine. Dans un premier temps, une définition de l'espace des conformations d'un ARN est établie et la technique de retour-arrière est décrite de façon à permettre une exploration complète de cet espace. Ensuite, un formalisme basé sur la logique floue est présenté. Cette approche permet d'utiliser l'information provenant de séquences multiples et est appliquée pour la modélisation du ribozyme activé par le plomb. Finalement, la flexibilité d'un système de modélisation 3-D utilisant une approche de satisfaction de contrainte est mise en évidence par l'ajout d'un nouveau type de contrainte dans l'engin de recherche, permettant la modélisation efficace de multimères cycliques. Ces ajouts permettent d'élargir le spectre des informations utiles à la modélisation 3-D des ARN et facilite l'intégration de nouveaux types d'informations à l'intérieur d'une méthode systématique. Les résultats obtenus sur des projets de modélisation spécifiques (ribozyme activé par le plomb et pRNA de çi>29) permettent de confirmer la pertinence de cette approche.

Notre travail s'effectue dans le but de fournir une méthode pour permettre le séquençage des oligosaccharides, des biopolymères jouant un rôle clé dans le domaine de la santé comme dans certains domaines industriels tels que l'énergie ou l'alimentation.Les méthodes utilisées pour séquencer les protéines sont limitées pour l'étude des oligosaccharides.En revanche, nous montrons que l'alliance entre la méthode expérimentale de spectroscopie d'action (IRMPD) et les calculs théoriques est une méthode prometteuse pour le séquençage des oligosaccharides.Notre méthode théorique consiste à obtenir des minima de la surface d'énergie potentielle.Les spectres infrarouges de ces minima sont calculés avec la DFT et en utilisant une grande base.Les spectres calculés sont alors comparés aux spectres expérimentaux afin d'obtenir des informations sur la structure des constituants ou la composition du mélange dans l'échantillon.Notre approche alliant les calculs théoriques aux mesures IRMPD s'est avérée particulièrement efficace pour obtenir les structures des mono ou disaccharides présents dans l'échantillon.De plus elle permet d'identifier des signatures spécifiques à des anomères ou à des conformères / Our work aims to develop a method to allow the sequencing of oligosaccharides, which are biopolymers playing a key role in the field of Health as in several industrial fields such as energy or nutrition.The methods used for sequencing proteins are limited in the study of oligosaccharides.However, we show that the combination of action spectroscopy experimental method (IRMPD) and theoretical calculations is a promising method to sequence oligosaccharides.Our theoretical method consist of obtaining minima of the potential energy surface.The infrared spectra of these minima are computed with DFT and a large basis.The calculated spectra are then compared to the experimental ones to gain informations on the structure of the compounds or on the composition of the mixture in the sample.Our approach combining theoretical computations to IRMPD measurements is particularly effective to obtain the structures of mono and disaccharides present in the sample.Moreover, it allows to identify specific signatures of anomers and conformers