La première partie de cette thèse concerne la synthèse et les études structurales de 2:1-[α/aza]-oligomères linéaires et cycliques possédant des acides aminés hydrophobes et/ou basiques. Les études RMN et IRTF ont démontré que les oligomères adopteraient des conformations de type coude β en solution. Les calculs de dynamiques moléculaires des oligomères à base de résidus lysine ont révèlé l’importance du motif aza dans le repliement de ces oligomères indépendamment de l’impact de la chaîne latérale. Les études par DRX, IRTF et RMN ont révélé que les deux hexamère cycliques (L- ou D-Phe-azaPhe-Ala)2 homo- et hétérochiraux adoptent des conformations de type coude ß en solution et à l’état solide. Ils s’organisent en structures 3D très ordonnées, stabilisées par des ponts hydrogènes et des empilements π. La deuxième partie démontre l'auto-assemblage de quelques 2:1-[α/aza]-oligomères dans certains solvants pour former des gels supramoléculaires. Le cyclooligomère hétérochiral (D-Phe-azaPhe-Ala)2 peut former des organogels. La spectroscopie et rhéologie des organogels ont révélé de bonnes stabilités thermique et mécanique avec un comportement de type solide. La MEB/MET de l'aérogel a montré une structure fibreuse 3D. De plus, deux hydrogels Fmoc-D- ou L-Phe-azaPhe-Ala-OH ont été obtenus aux pH 7.0 et 10.0. Les spectres UV et de fluorescence ont révélé une stabilisation des hydrogels par interaction π entre les groupes aromatiques. Leur analyse par CD montre que les trimères s'auto-assemblent sous forme de feuillet β en accord avec les résultats ATR/IRTF. Ainsi, leurs études rhéologiques ont révélé un comportement de type solide. La MEB des xérogels a montré une structure fibreuse. La troisième partie propose deux applications; (i) les oligomères à base de résidus lysine ont révélé de bonnes performances pour la séparation CO2/N2 dans des membranes polymères Pebax®, et (ii) le cyclohexamère hétérochiral (D-Phe-azaPhe-Ala)2 convient pour la gélification sélective avec un bon pourcentage de récupération / The first part of this thesis reported the synthesis and structural studies of linear and cyclic 2:1-[α/aza]-oligomers possessing hydrophobic and/or basic amino acids (lysine). NMR and FTIR results demonstrated that the oligomers could adopt β-turn conformations in solution. Molecular dynamic calculations for oligomers based lysine residues reflected the important role of the aza-motif(s) in structuring the backbones regardless the chirality and nature of the amino acids. In the other hand, X-ray, FTIR, and NMR studies showed that homo- and heterochiral cyclo-(L- or D-Phe-azaPhe-Ala)2-hexamers adopt β-turn conformations in solution and solid states. Both molecules could organize into 3D highly ordered structures stabilized by hydrogen bonds and π-stacking. The second part reflected the propensity of some 2:1-[α/aza]-oligomers to self-assemble in some solvents to form supramolecular gels. Interestingly, the heterochiral cyclo-(D-Phe-azaPhe-Ala)2-hexamer could form organogels. The spectroscopic and rheological studies of the organogels revealed good thermal and mechanical stability with solid-like behavior. SEM and TEM images of the aerogel showed fibrous structure. Furthermore, two hydrogelators, Fmoc-D- or L-Phe-azaPhe-Ala-OH, have been developed and they could achieve hydrogels at pHs 7.0 and 10.0. UV and Flu studies demonstrated that the hydrogels are supported by π-stacking between the aromatic groups. CD analysis reflected that the two hydrogelators self-assemble into β-sheet like structure in consistent with ATR-FTIR results. Both hydrogels exhibited solid-like behavior through rheological studies and the SEM analysis of the xerogels revealed fibrous structure. The third part offered two applications; (i) oligomers based lysine residues reflected good performances in CO2/N2 separation when used as additives in polymeric Pebax® membrane, and (ii) the heterochiral cyclo-(D-Phe-azaPhe-Ala)2-hexamer is suitable for phase selective gelation with good recovery percentages

<p>Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO₂ cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding.</p><p>This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified.</p><p>Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.</p>

Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO2 cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding. This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified. Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.

Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

The thesis entitled “Unravelling the Nature of Halogen and Chalcogen Intermolecular Interactions by Charge Density Analysis" consists of five chapters. A basic introductory section describes the topics relevant to the work and the methods and techniques utilized. The main focus of the present work is to characterize the interaction patterns devoid of strong classical hydrogen bonds. The case studies include halogen bonds and hydrogen bonds involving bromine (as a halogen bond donor and hydrogen bond acceptor), intermolecular chalcogen bond formation involving sulphur, type I Br Br contacts, type II F F and F S interactions and S-H S hydrogen bonds. Chapter 1 discusses experimental and theoretical charge density analyses on 2,2-dibromo-2,3-dihydroinden-1-one which has been carried out to quantify the topological features of a short C Br···O halogen bond with nearly linear geometry (2.922Å, C Br···O=172.7) and to assess the strength of the interactions using the topological features of the electron density. The electrostatic potential map indicates the presence of the “- hole” on bromine while the interaction energy is comparable to that of a moderate O-H O hydrogen bond. In addition, the energetic contribution of C-H···Br interaction is demonstrated to be on par with that of the C-Br···O halogen bond in stabilizing the crystal structure. Chapter 2 discusses an organic solid, 4,7-dibromo-5,6-dinitro-2,1,3-benzothiadiazole that has been designed to serve as an illustrative example to quantitatively evaluate the relative merits of halogen and chalcogen bonding in terms of charge density features. The compound displays two polymorphic modifications, one crystall zing in a non-centrosymmetric space group (Z =1) and the other in a centrosymmetric space group with two molecules in the asymmetric unit (=2). Topological analysis based on QTAIM clearly brings out the dominance of chalcogen bond over the halogen bond along with an indication that halogen bonds are more directional compared to chalcogen bonds. The cohesive energies calculated with the absence of both strong and weak hydrogen bonds as well as stacking interaction are indicative of the stabilities associated with the polymorphic forms. Chapter 3 discusses the role of a type I C-Br Br-C contact and what drives the contact i.e. how a dispersive interaction is stabilized by the remaining contacts in the structure. In the process we observe the role the Br2Cl motif which is quite unique in its nature. Also the role of the bromine atoms in stabilizing the stacking interactions has been shown by the electrostatic potentials which are oriented perpendicular to the plane of the benzene ring. Chapter 4 discusses the enigmatic type II C-F F-C and C-FS-C interactions in pentafluorophenyl 2,2- bithiazole. Both the interactions are shown to be realistic “-hole” interactions based on high resolution X-ray charge density analysis. As fluorine is the most electronegative element, its participation in halogen bonding wherein the electrostatic potential around the atom gets redistributed to form regions of electron depletion and accumulation had time and again been speculated but never observed. In this chapter the experimental charge dnsity analysis clearly identifies the “-hole” on fluorine and distinguishes the C-F S-C interaction as a halogen bond rather than the chalcogen bond. Chapter 5 discusses the experimental charge density analysis of the hitherto unexplored S-H S hydrogen bond in crystal structures. The work highlights how relatively small is the number of crystal structures which are constructed by the S-H S hydrogen bond compared to the X-H S hydrogen bond via Cambridge Structural Database (CSD) analysis. The potential S-H S hydrogen bond is studied in three isomeric mercaptobenzoic acids with experimental charge density collected on 2-mercaptobenzoic acid and theoretical estimates made on 3- and 4-mercaptobenzoic acid. The strength and directionality of the S-H S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of intramolecular S O halogen bond.

A interação da água com a celulose e com o amido é de grande importância para a compreensão das propriedades de ambos polissacarídeos e fundamental para o desenvolvimento de novas aplicações tecnológicas. Entre as novas aplicações estão em destaque a nanocelulose, como os nanocristais e microfibrilas. A preparação desses materiais é fortemente influenciada pela interação das ligações de hidrogênio presente nas fibras de celulose, tanto de caráter intra como intermolecular. Essas interações são responsáveis pelas propriedades mecânicas desses materiais uma vez que as moléculas estão ligadas umas às outras por meio de ligações de hidrogênio onde a água pode participar como elemento de ligação. Para o amido, dependendo da concentração da água, pode modifica-lo em termos da solubilidade e em propriedades pelo processo de gelatinização ou atuar como plastificantes como parcial despolimerização em amido termoplástico. Neste trabalho é descrito o estudo da interação do sistema água com a celulose e com o sistema água com amido por meio da análise termogravimétrica para a identificação de diferentes espécies de água: i) água livre, ii) água ligada congelável iii) água ligada não congelável. Para a realização deste estudo foi utilizado o método auto stepwise, método que permite uma maior resolução dos diversos fenômenos separadamente que ocorrem durante a dessorção da água. A dessorção da água no amido se demostrou mais complexa que a celulose devido à alternância da parte amorfa e cristalina em sua estrutura. Para o cálculo da energia de ativação da dessorção da água ligada e da degradação do polissacarídeo foi utilizado o método cinético de Osawa-Flynn-Wall, sendo possível estimar a energia de ativação dos fenômenos. Variando de 35-65 kJ/mol para dessorção da água ligada e 144,6-184 kJ/mol para degradação dos materiais. / The interaction of water with cellulose and starch are of great importance for understanding the properties of both polysaccharides and fundamental to the development of new technological applications. Among the new applications are highlighted to nanocellulose such as nanocrystals and microfibrils. The preparation of these materials is strongly influenced by the interaction of hydrogen bonds present in the cellulose fibers, both intra as intermolecular. These interactions are responsible for the mechanical properties of these materials since the molecules are linked to each other through hydrogen bonds where water can participate as a connecting element. For starch, depending on the concentration of the water, can modify it in terms of solubility and properties by gelatinization process or act as plasticizers as partial depolymerization of thermoplastic starch. This paper describes the study of the interaction of the water/cellulose system and the starch/water system by means of thermogravimetric analysis for the identification of different species of water: i) the free water or freezing water, ii) the freezing bound water and iii) the non-freezing bound water. For this study we used the auto stepwise method, that allows greater resolution of the various phenomena separately that occur during the water desorption. The water desorption in the starch is more complex that cellulose, due to alternating crystalline and amorphous parts of the structure. To calculate the bound water desorption activation energy and polysaccharide degradation energy was used kinetic method of Osawa-Flynn-Wall, that possible to estimate the phenomena of the activation energy, ranging from 35-65 kJ / mol for bound water desorption and from 144.6 to 184 kJ / mol for material degradation.

Les isonitriles sont des espèces connues depuis longtemps, mais étudiées depuis peu. Une approche théorique a permis de s'intéresser en détails aux réactions de Nef et de Ugi. Nous nous sommes tout d'abord focalisés sur la première. Après en avoir élucidé le mécanisme, nous avons étudié l'effet du solvant et nous avons proposé de nouvelles conditions expérimentales. Nous avons ensuite étudié l'influence des groupements de l'acyl, de l'isonitrile et du groupe partant. L'ensemble des variations considérées a pu être rationalisé en reliant l'énergie d'activation au pKa du groupe partant. En parallèle, nous avons étudié la réaction de Ugi. Le mécanisme proposé par Ugi pour cette réaction complexe n'avait toujours pas été vérifié 50 ans après sa découverte. Une étude quasi-exhaustive des différents mécanismes possibles a été menée, en utilisant une approche originale mêlant théorie et expériences. Le mécanisme de cette réaction a ainsi été démontré, tant dans le méthanol que dans le toluène. Les étapes cinétiquement déterminantes et les forces motrices ont été mises en lumière et diffèrent de celles proposées par Ugi. Une variation de la réaction de Ugi est le couplage Ugi-Smiles pour lequel de nombreux résultats expérimentaux n'ont toujours pas trouvé d'explications. Nous nous sommes donc intéressés au réarrangement de Smiles. Nous avons montré l'importance d'une liaison hydrogène intramoléculaire sur la faisabilité de la réaction, et nous avons étendu cette observation aux réactions intermoléculaires. Nous avons également étudié l'influence des substituants des quatre réactifs sur les barrières afin de construire un modèle prédictif. / Isocyanides are known for a long time, but have been studied only recently. A theoretical approach allowed us to investigate in details the Nef and the Ugi reactions. We first focused on the former. After elucidating its mechanism, we studied solvent effects and proposed new experimental conditions. We then studied the acyl moiety and isocyanide influences, such as the leaving group one. All the variations were rationalized by linking the activation energy to the leaving group pKa. Simultaneously, we studied the Ugi reaction. The mechanism proposed by Ugi for this complex reaction was still unverified 50 years after its discovery. A thorough and quasi-complete study of all the possible mechanisms were lead, using a mixed theoretical and experimental approach. The mechanism of this reaction was demonstrated, in both methanol and toluene. Rate determining steps and driving forces were highlighted and differ from those proposed by Ugi. A variation of the Ugi reaction is the Ugi-Smiles coupling, for which numerous experimental results are still unexplained. We thus studied the Smiles rearrangement. We showed the key-role of an intramolecular hydrogen bond on the reaction feasibility, and extended this observation to intermolecular reactions. We also studied the four substituent influence on the barrier, aiming to build a predictive model.

Experimental mole fraction solubilities of several carboxylic acids (2-methoxybenzoic acid, 4-methoxybenzoic acid, 4-nitrobenzoic acid, 4-chloro-3-nitrobenzoic acid, 2-chloro-5-nitrobenzoic acid,2-methylbenzoic acid and ibuprofen) and 9-fluorenone, thianthrene and xanthene were measured in a wide range of solvents of varying polarity and hydrogen-bonding characteristics. Results of these measurements were used to calculate gas-to-organic solvent and water-to-organic solvent solubility ratios, which were then substituted into known Abraham process partitioning correlations. The molecular solute descriptors that were obtained as the result of these computations described the measured solubility data to within an average absolute deviation of 0.2 log units. The calculated solute descriptors also enable one to estimate many chemically, biologically and pharmaceutically important properties for the ten solutes studied using published mathematical correlations.

Os métodos existentes para a previsão da posição de átomos de hidrogênio em proteínas são todos baseados na simulação computacional de modelos construídos a partir de características físicas e (ou) químicas das moléculas. A abordagem proposta neste trabalho faz uso de técnicas inteligentes para a predição da posição de átomos de hidrogênio contidos em grupos hidroxilas (OH) pertencentes à cadeias laterais dos aminoácidos serina, treonina e tirosina. Estas técnicas inteligentes são utilizadas em duas fases para a solução do problema proposto: o preprocessamento dos dados e a predição da posição do átomo de hidrogênio. Na fase de preprocessamento, informações sobre os padrões de ligações hidrogênio existentes em moléculas de proteínas são extraídas da base PDB (Protein Data Bank) e reunidas em agrupamentos. A base de dados PDB é a principal base internacional que disponibiliza publicamente a estrutura espacial de biomoléculas, principalmente proteínas e ácidos nucléicos, cujas estruturas espacias foram determinadas através de métodos experimentais. Os padrões de ligações hidrogênio obtidos da base de dados são agrupados por similaridade através de um novo algoritimo proposto, o algoritmo de agrupamento por fusão. Este novo algoritmo de agrupamento foi criado com o propósito de tratar dados com distribuição não uniforme, isolando padrões de entrada muito diferentes da média em agrupamento separados. Após o agrupamento, os padrões de ligações hidrogênio contidos em um grupo têm suas estruturas espaciais superpostas (alinhamento das geometrias dos padrões) através de operações espaciais de translação e rotações, coordenadas pelo uso de um algoritmo genético. Na fase de predição, os padrões já superpostos contidos em cada agrupamento gerado, são utilizados para o treinamento de uma rede neural de arquitetura MLP (multi layer perceptron) para a predição da posição do átomo de hidrogênio contido no padrão. Uma parte dos padrões contidos no agrupamento não são usados para o treinamento da rede e reservados para o teste da capacidade da rede neural inferir a posição do hidrogênio após o treinamento. Para cada agrupamento é treinada uma rede individual, de forma que os parâmetros livres da rede neural sejam calibrados para os dados específicos do agrupamento para o qual a rede neural foi treinada. Após diversas alterações de metodogia ao longo dos experimentos computacionais realizados, a nova abordagem proposta mostrouse eficaz, com um bom índice de acerto na predição da posição do hidrogênio após o treino da rede neural, para padrões de ligações hidrogênio previamente superpostos em agrupamentos / The existing methods for the prediction of the position of hydrogen atoms in proteins are all based on computer simulation models constructed from physical and(or) chemical properties of molecules. The approach proposed in this paper makes use of intelligent techniques for clustering the patterns of hydrogen bonds by similarity, these patterns extracted from the spatial structure of protein molecules, recorded in the files of the PDB (Protein Data Bank). A new algorithm, which allows clustering of data with nonuniform distribution was developed for this purpose. To align spatialy these patterns already grouped in a cluster is used a genetic algorithm that rotates the patterns each other in a way to obtain the aligment of them. The prediction of the position of atoms of hydrogen is done by the training of a MLP (multi layer perceptron) neural network that uses as input the data of the patterns of hydrogen bond contained in a given cluster, previously aligned. The new approach proved to be effective, with a good rate of success in the prediction of the position of hydrogen atoms contained in a cluster after training the neural network

No / We describe the Δlog P method for the assessment of intramolecular hydrogen bonds (IMHBs), and show that it is not a very general method of distinguishing between molecules in which there is an IMHB and molecules in which there is no IMHB. The ‘double’ Δlog P method of Shalaeva et al. is a much more reliable method for the assessment of IMHB but requires the synthesis of a model compound and the determination of no less than four water-solvent partition coefficients. In addition, it is difficult to apply to compounds that contain more than one hydrogen bond acidic group capable of IMHB. We then describe our NMR method of assessing IMHB, based on 1H NMR chemical shifts in solvents DMSO and CDCl3. We have determined 1H NMR chemical shifts for a number of ortho-substituted anilines and show that the only compound we have studied that forms an IMHB is methyl 2-methylaminobenzoate though there is no IMHB present in methyl 2-aminobenzoate. This apparently anomalous result is supported by both MM and ab initio calculations. The NMR method is much simpler and less time consuming than other methods for the assessment of IMHB. It provides a quantitative assessment of IMHB and can be applied to molecules with more than one hydrogen bond acidic group.