Cette thèse est consacrée à étudier et à améliorer les modèles mathématiques et les méthodes utilisées pour les modèles de solvatation implicite en chimie quantique. Ce manuscrit est composée de deux parties. Dans la première partie où nous analysons l'interface soluté-solvant, nous donnons, pour la première fois, une caractérisation complète de la surface moléculaire lisse, c'est-à-dire la surface exclue du solvant (SES). À partie de cette caractérisation, nous développons un algorithme de maillage par morceaux pour les surfaces moléculaires différentes, en particulier pour la SES, en utilisant la triangulation à front avançant. De plus, la cavité de la SES (la région entourée par la SES) est une description plus précise de la cavité de soluté. Dans la deuxième partie, nous construisons donc un modèle de continuum polarisable basé (PCM) sur la SES, dans lequel le paramètre de permittivité diélectrique est continu. Le problème électrostatique de ce modèle consiste à résoudre une équation de Poisson définie sur R3. Nous développons ensuite une méthode de Schwarz particulière, où seules les équations locales restreintes à des boules doivent être résolues. Enfin, nous étudions le modèle de solvatation de Poisson-Boltzmann, un autre modèle de solvatation implicite, qui tient compte à la fois de la permittivité diélectrique et de la force ionique du solvant. Une méthode de Schwarz similaire est proposée pour résoudre l'équation de Poisson-Boltzmann associée en résolvant des équations locales restreintes aux boules comme pour le PCM basé sur la SES. / This thesis is devoted to study and improve the mathematical models and methods used in implicit solvation models in quantum chemistry. The manuscript is composed of two parts. In the first part where we analyze the solute-solvent interface, we give, for the first time, a complete characterization of the so-called “smooth” molecular surface, i.e., the solvent excluded surface (SES). Based on this characterization, we develop a piecewise meshing algorithm for different molecular surfaces, especially the SES, using the advancing-front triangulation. Further, it has been pointed out in the literature that the SES-cavity (the region enclosed by the SES) is a more accurate description of the solute cavity. In the second part, we therefore construct an SES-based polarizable continuum model (PCM), in which the dielectric permittivity parameter is continuous. The electrostatic problem of this model involves solving a Poisson equation defined in R3. We then develop a particular Schwarz domain decomposition method where only local equations restricted to balls need to be solved. Finally, the Poisson-Boltzmann solvation model, another implicit solvation model, is also investigated, which takes into account both the dielectric permittivity and the ionic strength of the solvent. A similar Schwarz domain decomposition method is proposed to solve the associated Poisson-Boltzmann equation by solving local equations restricted to balls as it is for the SES-based PCM.

Nous étudions la dynamique d’anions hydroxyde et fluorure micro-solvatés dans un agrégat d’eau après photo-excitation. Du fait du coût numérique important des calculs ab-initio et de la faible transférabilité des potentiels modèles de la littérature, nous avons développé un nouveau modèle transférable permettant de décrire l’interaction d’un soluté quelconque avec une molécule d’eau. Nous avons également effectué une étude des propriétés statiques de F^-(H2O)n=1−7 et OH−(H2O)n=1−7 qui sert de référence pour la paramétrisation du modèle et fournit une base à l’interprétation des calculs de dynamique. De cette étude, nous avons déduit le nombre de molécules d’eau nécessaires pour stabiliser le premier état excité de F− et OH−. Nous avons aussi déterminé l’impact de la base sur la description des états excités. Enfin, nous avons mis en évidence un motif géométrique favorable à la recombinaison géminée. L’étude de trajectoires sur le premier état singulet excité pour F^-(H2O)3,5 et OH^-(H2O)3,5 montre des différences de comportement entre le fluorure et l’hydroxyde. Pour F^−, l’électron est très diffus et se transfère en une centaine de femtosecondes à l’eau. Dans le cas de OH^−, à cause du dipôle du radical OH qui maintient l’électron, le transfert de charge ne s’effectue que lorsque le radical OH tourne vers l’agrégat d’eau. Cette différence de comportement entre OH^−et F^−offre une piste pour la compréhension du phénomène de recombinaison géminée rapide observé pour OH^−. Nous avons également étudié le spectre d’énergie de détachement vertical de l’électron pour des agrégats d’eau négativement chargés qui constituent l’un des produits finaux de la dynamique des anions photo-excités. Ces résultats ont été discutés et comparés à l’expérience. Nous avons ainsi pu faire correspondre des structures géométriques aux pics des spectres mesurés expérimentalement. Nous discutons aussi du rôle de l’énergie interne des agrégats sur l’allure des spectres via son impact sur l’évaporation de molécules d’eau. / We study the dynamics of micro-solvated hydroxide and fluoride anions in water clusters after photoexcitation. Because ab-initio calculations are numerically expensive and model potentials from literature lack of transferability, we developed a transferable model, which allows us to describe the interaction between any solute and a water molecule. We have studied the statics properties of F^−(H2O)n=1−7 and OH^−(H2O)n=1−7. The results from this study serve as a basis for the parametrization of the model and for the interpretation of dynamics simulation. From this study, we deduced the number of water molecules needed to stabilize an excited state for F^−and OH^−. We investogated the impact of the basis on the description of the excited states At last, we highlight a favorable motif for geminate recombination. Study of trajectories on the first excited singlet states of F^−(H2O)3,5 and OH^−(H2O)3,5 shows differences in the dynamics between OH^−and F^− For F^−, the excess electron is very diffuse and transferred quickly to the water For OH−, because of the OH dipole, the excess electron remains bound to the neutral . OH, until charge transfer takes place when OH rotate to the water cluster. This difference provides a way to understand the fast geminate recombination process observed for OH^−. We also studied vertical detachment spectra of the electron for negatively charged water clusters which are the final products of the anions dynamics on the first excited state. These results are compared to experience from literature. We associate isomers to the experimentally observed peaks. We discuss the effect of internal energy on the shape of the spectra through water molecules evaporation

Ion-exchange membranes, conventionally utilized in separation processes of electrolyte solutions, are electroactive polymers that display a unique coupling between electrochemistry and mechanics. Previous experimental studies have demonstrated the possibility of actuating cation-exchange membranes in salt solution through the application of a remote external electric field. The use of anion-exchange membranes as contactless actuators, however, has never been documented and little is known about the physics of their actuation. Here, it is reported for the first time the possibility of contactless actuating anion-exchange membranes in salt solutions; such an actuation is mediated by the selection of anions in the external salt solution and the membrane. Actuation is attributed to the physical phenomenon of solvation, the interaction between ions and solvent in solution. Contrary to previous studies with cation-exchange membranes, the results show that anion-exchange membranes consistently bend toward the anode. The integration of anion-exchange and cation-exchange membranes in composites promises innovative programmable contactless actuators, with applications in underwater robotics and biomedical engineering.

A natureza das ligações de hidrogênio e a influência destas interações na estrutura eletrônica de complexos neutros, catiônicos, aniônicos e radicalares foi estudada utilizando-se análises geométricas, energéticas, eletrônicas e topológicas. Inicialmente, verificaram-se alterações na aromaticidade do cátion pirílio após a complexação com uma a três moléculas de água. Tais complexos foram ainda estudados em meio reacional com constante dielétrica igual a da água com o emprego do modelo PCM (Polarizable Continuum Model). Adicionalmente, os efeitos da hidroxilação na estrutura eletrônica dos cátions benzopirílio e flavílio foram considerados. Posteriormente, analisaram-se os efeitos das fortes ligações de hidrogênio na ressonância do grupo carboxila em complexos formados entre o radical hidroperoxil e os ácidos fórmico, acético e trifluoroacético. Como extensão desse trabalho, estudos envolvendo complexos obtidos com e sem restrições na otimização de geometria possibilitaram obter informações a respeito da ressonância dos grupos carboxila e carboxilato quando o fluoreto de hidrogênio interage linear ou perpendicularmente com todos os átomos do ácido fórmico e do ânion formiato. O desenvolvimento das atividades supracitadas compreendeu a análise da função de onda pelos métodos NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory) e AIM (Atoms in Molecules). As alterações em parâmetros geométricos e nas cargas atômicas foram consideradas. Uma análise energética foi realizada com o emprego do método de decomposição de energia proposto por Xantheas. As freqüências vibracionais e a intensidade das bandas do estiramento do grupo X-H, doador da ligação de hidrogênio, foram analisadas. As densidades de spin para os complexos radicalares também foram obtidas. A influência das ligações de hidrogênio e o efeito do substituinte na aromaticidade dos cátions foram verificados com o emprego dos métodos e índices NICS (Nucleus Independent Chemical Shifts), HOMA (Harmonic Oscillator Model of Aromaticity), HOSE (Harmonic Oscillator Stabilization Energy) e PDI (para-Delocalization Index). Os cálculos foram efetuados com os modelos B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd) e UB3LYP/6-311++G(3df,3pd). Ocasionalmente, outras funções de base (EPR-III e cc-pVDZ), assim como o método MP2, foram utilizados para testar a confiabilidade dos resultados obtidos. As interações intermoleculares pouco alteraram a estrutura eletrônica e a aromaticidade do cátion pirílio. Analogamente, a substituição de um átomo de hidrogênio por um grupo hidroxila em diversas posições dos cátions benzopirílio e flavílio também não provocou modificações muito significativas na estrutura eletrônica desses cátions, embora tenha se verificado uma dependência da aromaticidade com a posição da hidroxila. Por outro lado, a distorção geométrica associada às ligações de hidrogênio foram responsáveis pelo incremento ou diminuição da ressonância do grupo carboxila nos ácidos fórmico, acético, trifluoroacético e do grupo carboxilato no ânion formiato. Os efeitos dos grupos doador e sacador de elétrons na estabilização dos complexos radicalares foram evidenciados. Adicionalmente, pode-se atribuir um caráter covalente parcial em algumas ligações de hidrogênio. / The nature of hydrogen bonds and their influence on electronic structure of neutral, cationic, anionic, and radical complexes was studied by using geometric, energetic, electronic, and topological analysis. The changes in aromaticity of the pyrylium cation upon complexation with one up to three water molecules were investigated. The PCM (Polarizable Continuum Model) model was employed to study the pyrylium-water complexes in a water reaction medium. In addition, the effects of hydroxylation on electronic structure of the benzopyrylium and flavilium cations were also considered. In addition, the effects of strong hydrogen bonds on carboxyl group resonance in the complexes formed between the hydroperoxyl radical and formic, acetic, and trifluoroacetic acids were analyzed. In extension of this work, studies including complexes, obtained with and without geometric restrictions, provided information about the resonance of the carboxyl and carboxylate groups when the hydrogen fluoride interacts, linear or perpendicularly, with all atoms of formic acid and formate anion. The analysis of the wavefunction by using NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory), and AIM (Atoms in Molecules) methods was necessary to the development of the above mentioned activities. The changes in geometric parameters and atomic charges were also considered. An energetic analysis of complexes was done with the energy decomposition method proposed by Xantheas. The vibrational frequencies and the intensity of the X-H (hydrogen bond donor group) stretching bands were studied. The spin densities for the radical complexes were also obtained. The Nucleus Independent Chemical Shifts (NICS), Harmonic Oscillator Model of Aromaticity (HOMA), HOSE (Harmonic Oscillator Stabilization Energy), and PDI (para-Delocalization Index) aromaticity criteria were employed to verify the hydrogen bond influence and the effect of hydroxylation in the aromaticity of the cations. The calculations were carried out by using B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd), and UB3LYP/6-311++G(3df,3pd) models. Occasionally, other basis set (EPR-III and cc-pVDZ), as well as the MP2 method, were applied to test the accuracy of the results. The intermolecular interactions lead to small alterations in the electronic structure and aromaticity of pyrylium cation. Similarly, the substitution at different positions of the benzopyrylium and flavilium cations by a hydroxyl group does not cause significant changes in the electronic structure of these cations. However, a dependence of the hydroxyl group position on aromaticity was observed. On the other hand, for formic, acetic, trifluoroacetic acids, as well as for the formate anion, the resonance of the carboxyl and carboxylate groups is affected not only by the geometric distortions but also by the hydrogen bonds. The effects of the electron-donating and electron-withdrawing groups in the stabilization of radical complexes were characterized. Furthermore, a partial covalent character can be attributed to some hydrogen bonds.

Cette thèse présente l'étude de la dynamique d'un atome ou d'une molécule en interaction avec un agrégat en vue d'étudier comment un petit système (l'atome, la molécule) échange de l'énergie électronique, cinétique et vibrationnelle avec un système possédant de très nombreux degrés de liberté (l'agrégat).Le premier système est l'étude, expérimentale et théorique, de la dynamique en temps réel d'un atome de baryum déposé sur agrégat d'argon (BaArn). L'atome de baryum est excité dans des niveaux de Rydberg, il en résulte une dynamique extrêmement riche entre le chromophore et l'agrégat. L'interprétation théorique a nécessité la conception d'une méthode de dynamique originale, permettant de traiter à la fois le grand nombre d'états excités mis en jeu, couplés à de nombreux degrés de libertés atomiques. La mise en commun des informations théoriques et expérimentales a permis d'établir l'ensemble du chemin réactionnel ayant lieu au cours de cette dynamique.Le deuxième système concerne l'étude par fluorescence de la photo-dissociation de Ca2 déposé sur agrégat d'hélium ou sur agrégat mixte hélium-argon (Ca2Hen ou Ca2ArmHen). Ces résultats sont comparés à ceux obtenu sur agrégat d'argon pur (Ca2Hen). Les différences entre ces trois types de solvant montrent que les interactions sont différentes suivant que le solvant est ``quantique'' (l'hélium) ou ``classique'' (l'argon). Plusieurs canaux réactionnels ont été mis en évidence selon que l'atome de calcium excité qui résulte de la photo-dissociation est libre ou reste solvaté par de l'hélium et/ou de l'argon. Les rapports de branchement entre ces différents canaux ont également été mesurés. / The dynamics of the interaction of an atom or a molecule with a large cluster has been studied in this manuscript in view of characterising the exchange of electronic vibrational and kinetic energy between a small system with another having a large number of degrees of freedom, the cluster.We have first studied experimentally and theoretically, the real time dynamicsof a barium atom deposited on argon clusters , (BaArn). The Ba atom was excited in high Rydberg states. A rich dynamics ensues between the chromophore an the cluster. For the theoretical interpretation a new method has been developed. It its designed to take into account the large number of electronically accessed states and their coupling with the numerous nuclear degrees of freedom of the atomic movements. The combination of the experimental and theoretical informations has allowed the characterisation of a reaction path for these dynamics. The second system studied is the photodissociation of the Ca2 molecule deposited on helium clusters pure or doped with argon (Ca2Hen or Ca2ArmHen), fluorescence emission. A comparison is also made with the Ca2Hen system. Important differences appear depending upon the nature of the solvating medium be it quantal (helium) or classical (argon). Several reaction channels have been characterised and measured for the formation of the resulting calcium atom in helium or argon solvating media.

CETTE THESE RASSEMBLE DIVERSES CONTRIBUTIONS MATHEMATIQUES ET NUMERIQUES A LA CHIMIE QUANTIQUE. LE CHAPITRE 1 EST CONSACRE A UNE PRESENTATION DE L'ESPRIT ET DES MODELES DE LA CHIMIE QUANTIQUE. LE CHAPITRE 2 TRAITE DE LA CONVERGENCE D'ALGORITHMES POUR LA RESOLUTION DES EQUATIONS DE HARTREE-FOCK. LES CHAPITRES SUIVANTS PORTENT SUR DES PROBLEMES SPECIFIQUES AUX SYSTEMES MOLECULAIRES IN SITU, C'EST-A-DIRE EN INTERACTION AVEC UN ENVIRONNEMENT EXTERIEUR. UNE PREMIERE APPROCHE POUR SIMULER LES EFFETS D'ENVIRONNEMENT CONSISTE A TRAITER L'INTERACTION ENTRE LE SYSTEME MOLECULAIRE ET LE MILIEU EXTERIEUR COMME UNE PERTURBATION. AU CHAPITRE 3, ON ETEND LA THEORIE DES PERTURBATIONS DES OPERATEURS LINEAIRES AU CADRE NON LINEAIRE DU MODELE DE HARTREE-FOCK. L'INTERACTION D'UN SYSTEME MOLECULAIRE AVEC UN ENVIRONNEMENT EST SOUVENT UN PROCESSUS DYNAMIQUE. C'EST LE CAS BIEN EVIDEMMENT DES QU'ON ETUDIE UNE REACTION CHIMIQUE. LE CHAPITRE 4 CONSISTE EN L'ANALYSE MATHEMATIQUE D'UNE DES APPROXIMATIONS DE L'EQUATION DE SCHODINGER DEPENDANT DU TEMPS QUI DECRIT LA DYNAMIQUE DU SYSTEME : LE MODELE DE HARTREE-FOCK NON ADIABATIQUE. LA QUASI-TOTALITE DES REACTIONS CHIMIQUES INTERESSANT L'INDUSTRIE OU LES SCIENCES DE LA VIE SE DEROULENT EN PHASE LIQUIDE, OU LES EFFETS DE SOLVANTS JOUENT UN ROLE DETERMINANT. LES CHAPITRES 5, 6 ET 7 CONCERNENT LA RESOLUTION NUMERIQUE DES MODELES DE CONTINUUM QUI SONT LES MODELES DE SOLVATATION OFFRANT A L'HEURE ACTUELLE LE MEILLEUR COMPROMIS ENTRE QUALITE DES RESULTATS ET TEMPS DE CALCUL.

A natureza das ligações de hidrogênio e a influência destas interações na estrutura eletrônica de complexos neutros, catiônicos, aniônicos e radicalares foi estudada utilizando-se análises geométricas, energéticas, eletrônicas e topológicas. Inicialmente, verificaram-se alterações na aromaticidade do cátion pirílio após a complexação com uma a três moléculas de água. Tais complexos foram ainda estudados em meio reacional com constante dielétrica igual a da água com o emprego do modelo PCM (Polarizable Continuum Model). Adicionalmente, os efeitos da hidroxilação na estrutura eletrônica dos cátions benzopirílio e flavílio foram considerados. Posteriormente, analisaram-se os efeitos das fortes ligações de hidrogênio na ressonância do grupo carboxila em complexos formados entre o radical hidroperoxil e os ácidos fórmico, acético e trifluoroacético. Como extensão desse trabalho, estudos envolvendo complexos obtidos com e sem restrições na otimização de geometria possibilitaram obter informações a respeito da ressonância dos grupos carboxila e carboxilato quando o fluoreto de hidrogênio interage linear ou perpendicularmente com todos os átomos do ácido fórmico e do ânion formiato. O desenvolvimento das atividades supracitadas compreendeu a análise da função de onda pelos métodos NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory) e AIM (Atoms in Molecules). As alterações em parâmetros geométricos e nas cargas atômicas foram consideradas. Uma análise energética foi realizada com o emprego do método de decomposição de energia proposto por Xantheas. As freqüências vibracionais e a intensidade das bandas do estiramento do grupo X-H, doador da ligação de hidrogênio, foram analisadas. As densidades de spin para os complexos radicalares também foram obtidas. A influência das ligações de hidrogênio e o efeito do substituinte na aromaticidade dos cátions foram verificados com o emprego dos métodos e índices NICS (Nucleus Independent Chemical Shifts), HOMA (Harmonic Oscillator Model of Aromaticity), HOSE (Harmonic Oscillator Stabilization Energy) e PDI (para-Delocalization Index). Os cálculos foram efetuados com os modelos B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd) e UB3LYP/6-311++G(3df,3pd). Ocasionalmente, outras funções de base (EPR-III e cc-pVDZ), assim como o método MP2, foram utilizados para testar a confiabilidade dos resultados obtidos. As interações intermoleculares pouco alteraram a estrutura eletrônica e a aromaticidade do cátion pirílio. Analogamente, a substituição de um átomo de hidrogênio por um grupo hidroxila em diversas posições dos cátions benzopirílio e flavílio também não provocou modificações muito significativas na estrutura eletrônica desses cátions, embora tenha se verificado uma dependência da aromaticidade com a posição da hidroxila. Por outro lado, a distorção geométrica associada às ligações de hidrogênio foram responsáveis pelo incremento ou diminuição da ressonância do grupo carboxila nos ácidos fórmico, acético, trifluoroacético e do grupo carboxilato no ânion formiato. Os efeitos dos grupos doador e sacador de elétrons na estabilização dos complexos radicalares foram evidenciados. Adicionalmente, pode-se atribuir um caráter covalente parcial em algumas ligações de hidrogênio. / The nature of hydrogen bonds and their influence on electronic structure of neutral, cationic, anionic, and radical complexes was studied by using geometric, energetic, electronic, and topological analysis. The changes in aromaticity of the pyrylium cation upon complexation with one up to three water molecules were investigated. The PCM (Polarizable Continuum Model) model was employed to study the pyrylium-water complexes in a water reaction medium. In addition, the effects of hydroxylation on electronic structure of the benzopyrylium and flavilium cations were also considered. In addition, the effects of strong hydrogen bonds on carboxyl group resonance in the complexes formed between the hydroperoxyl radical and formic, acetic, and trifluoroacetic acids were analyzed. In extension of this work, studies including complexes, obtained with and without geometric restrictions, provided information about the resonance of the carboxyl and carboxylate groups when the hydrogen fluoride interacts, linear or perpendicularly, with all atoms of formic acid and formate anion. The analysis of the wavefunction by using NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory), and AIM (Atoms in Molecules) methods was necessary to the development of the above mentioned activities. The changes in geometric parameters and atomic charges were also considered. An energetic analysis of complexes was done with the energy decomposition method proposed by Xantheas. The vibrational frequencies and the intensity of the X-H (hydrogen bond donor group) stretching bands were studied. The spin densities for the radical complexes were also obtained. The Nucleus Independent Chemical Shifts (NICS), Harmonic Oscillator Model of Aromaticity (HOMA), HOSE (Harmonic Oscillator Stabilization Energy), and PDI (para-Delocalization Index) aromaticity criteria were employed to verify the hydrogen bond influence and the effect of hydroxylation in the aromaticity of the cations. The calculations were carried out by using B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd), and UB3LYP/6-311++G(3df,3pd) models. Occasionally, other basis set (EPR-III and cc-pVDZ), as well as the MP2 method, were applied to test the accuracy of the results. The intermolecular interactions lead to small alterations in the electronic structure and aromaticity of pyrylium cation. Similarly, the substitution at different positions of the benzopyrylium and flavilium cations by a hydroxyl group does not cause significant changes in the electronic structure of these cations. However, a dependence of the hydroxyl group position on aromaticity was observed. On the other hand, for formic, acetic, trifluoroacetic acids, as well as for the formate anion, the resonance of the carboxyl and carboxylate groups is affected not only by the geometric distortions but also by the hydrogen bonds. The effects of the electron-donating and electron-withdrawing groups in the stabilization of radical complexes were characterized. Furthermore, a partial covalent character can be attributed to some hydrogen bonds.

Mis à part les liaisons hydrogène, d’autres interactions non covalentes participent dans les réseaux de reconnaissance ARN et ARN protéines. Parmi celles-ci, j’ai étudié les interactions oxygène-pi. Cette interaction prend la forme phosphate-pi dans les U turns et O4'-pi dans les motifs ARN-Z. Je propose une nouvelle classification des boucles de quatre nucléotides, décrivant les U turn et les Z turn à partir d’interactions oxygène-pi. De plus, les motifs "Z like" présents dans tous les ARN, sont aussi reconnus par certaines protéines immunologiques. Pour mieux comprendre les réseaux de reconnaissance biomoléculaire, nous avons examiné les interactions entre cations/anions et ARN. Nous avons trouvé de nombreuses erreurs dans les structures de la PDB et proposé des règles pour améliorer l'attribution d’espèces ioniques. Les résultats de cette thèse amélioreront notre connaissance des réseaux de reconnaissance biomoléculaire et aideront aux techniques de modélisation structurale des ARN. / Together with hydrogen bonds, uncommon non-covalent interactions are fundamental for recognition networks in RNA and RNA-protein systems. Among them, I focused on oxygen-pi stacking. This interaction takes the form of phosphate-pi within U-turns and of ribose O4’-pi within “Z-RNA” motifs. In that respect, a novel classification of tetraloops is proposed, defining U-turns and Z-turns based on their oxygen-pi stacking properties. Further, “Z-like” motifs are found to pervade small and large RNAs, being also a recognition pattern for immunology-related proteins. To better understand biomolecular recognition networks, we reviewed the binding of metal ions and anions within RNA, finding many examples of ions misattribution in PDB structures. We propose rules to avoid attribution errors. The results of this thesis will improve our knowledge and understanding of biomolecular recognition networks, as well as assist structural determination and structural modelling techniques of RNA systems.

Ziel der Untersuchungen war die Charakterisierung der Protonierungs-, Komplexbildungs- und Verteilungseigenschaften von tripodalen Azaliganden unter Anwendung thermodynamischer und spektroskopischer Verfahren. Im Vordergrund stand dabei der Einfluß des Lösungsmittels auf die zugrundeliegenden Gleichgewichte. Ausgehend von dem Aminopodanden Tris(2-aminoethylamin) (tren) wurden für eine Reihe abgeleiteter Verbindungen mit unterschiedlichen Stickstoffdonorfunktionen und Substituenten Faktoren untersucht, welche die beteiligten Gleichgewichte beeinflussen. Das Protonierungsverhalten der Polyaminverbindungen ist im starken Maße von elektrostatischen, elektronischen und Solvenseinflüssen abhängig, welche durch den Abstand der benachbarten Aminfunktionen, die Substitution am Aminstickstoffatom und die sterischen Eigenschaften der Substituenten bestimmt werden. Faktoren, welche die Solvatation der Aminfunktionen verringern, führen zu einer Verringerung der Protonierungskonstanten. Zudem beeinflussen die Zusammensetzung der verwendeten Methanol-Wasser-Gemische sowie das verwendete Leitsalz die Protonierungskonstanten z.T. deutlich. Die Komplexbildung der untersuchten Azapodanden mit Ag+ in Methanol zeigt Unterschiede, welche hauptsächlich auf die unterschiedliche Basizität von Imin- bzw. Aminstickstoffatomen sowie Substituenteneffekte zurückzuführen sind. Von sterisch aufwendigen Substituenten an den Donorfunktionen der Podandarme können zudem destabilisiernde Effekte infolge der Beeinflussung der Koordinationsgeometrie von Ag+ ausgehen. Heteroditope Tetraazacryptanden zeigen gegenüber abgeleiteten offenkettigen Podanden erhöhte Stabilitätskonstanten, wobei auch die Verknüpfungsposition der tripodalen Einheiten am Phenylspacer und die Bindung von Wasser im Käfighohlraum eine Rolle spielen. Lösungsmittelpolarität und Gegenion haben einen deutlichen Einfluß auf die Komplexbildung mit Ag+. Der Schwerpunkt von Untersuchungen an Zweiphasensystemenen wäßrig-organisch lag auf dem Übergang von Wasser in die organische Phase unter dem Einfluß von extrahierten Spezies bei der Kationen- und Anionenextraktion. Mit der Verteilung von Liganden und Kationen- bzw. Anionenkomplexen lassen sich Änderungen des Wassersättigungsgehaltes in der niedrigpolaren organischen Phase registrieren, die mit der unterschiedlichen Hydratation der Spezies korrelieren. Qualitativ wurde die Hydratation von Azapodanden mittels IR- und 1H-NMR-Spektroskopie nachgewiesen, wobei auch Hinweise auf bestimmte, die Hydratation verringernde Faktoren, wie intramolekulare Wasserstoffbrücken, erhalten wurden. Quantitativ konnten mittels Karl-Fischer-Titration und Verteilungsmessungen Hydratationszahlen für ausgewählte Ligansysteme bestimmt werden. Extrahierte Komplexe der Verbindungen mit Ag+, Co2+, Ni2+ und Zn2+ zeigen eine gegenüber den freien Komplexbildnern veränderte Hydratation. Bei Ag+ kann in allen Fällen von einer deutlichen Verringerung der Hydratationszahlen ausgegangen werden. Für die zweifachgeladenen Kationen konnte kein klarer Nachweis erbracht werden. Es ergeben sich aber Hinweise, wonach zum Teil keine Verringerung auftritt, was auf eine zusätzliche Koordinationsstellen von Wasser am Kation hinweist. Bei der Iodidextraktion treten bei gleichzeitiger pH-Abhängigkeit mehrere Komplexspezies auf, was die Bestimmung von Hydratationszahlen erschwert. Als hilfreich erwies sich die Simulation für verschiedene mögliche Zusammensetzungen. Dabei stellte sich heraus, daß der 1:1-Komplex des untersuchten monoprotonierten Aminopodanden in Chloroform wahrscheinlich stärker hydratisiert ist als der freie Ligand, während die entsprechende 1:2-Spezies (Ligand:Iodid) eine ähnliche oder schwächere Hydratation aufweist als der Ligand.

Ziel der Untersuchungen war die Charakterisierung der Protonierungs-, Komplexbildungs- und Verteilungseigenschaften von tripodalen Azaliganden unter Anwendung thermodynamischer und spektroskopischer Verfahren. Im Vordergrund stand dabei der Einfluß des Lösungsmittels auf die zugrundeliegenden Gleichgewichte. Ausgehend von dem Aminopodanden Tris(2-aminoethylamin) (tren) wurden für eine Reihe abgeleiteter Verbindungen mit unterschiedlichen Stickstoffdonorfunktionen und Substituenten Faktoren untersucht, welche die beteiligten Gleichgewichte beeinflussen. Das Protonierungsverhalten der Polyaminverbindungen ist im starken Maße von elektrostatischen, elektronischen und Solvenseinflüssen abhängig, welche durch den Abstand der benachbarten Aminfunktionen, die Substitution am Aminstickstoffatom und die sterischen Eigenschaften der Substituenten bestimmt werden. Faktoren, welche die Solvatation der Aminfunktionen verringern, führen zu einer Verringerung der Protonierungskonstanten. Zudem beeinflussen die Zusammensetzung der verwendeten Methanol-Wasser-Gemische sowie das verwendete Leitsalz die Protonierungskonstanten z.T. deutlich. Die Komplexbildung der untersuchten Azapodanden mit Ag+ in Methanol zeigt Unterschiede, welche hauptsächlich auf die unterschiedliche Basizität von Imin- bzw. Aminstickstoffatomen sowie Substituenteneffekte zurückzuführen sind. Von sterisch aufwendigen Substituenten an den Donorfunktionen der Podandarme können zudem destabilisiernde Effekte infolge der Beeinflussung der Koordinationsgeometrie von Ag+ ausgehen. Heteroditope Tetraazacryptanden zeigen gegenüber abgeleiteten offenkettigen Podanden erhöhte Stabilitätskonstanten, wobei auch die Verknüpfungsposition der tripodalen Einheiten am Phenylspacer und die Bindung von Wasser im Käfighohlraum eine Rolle spielen. Lösungsmittelpolarität und Gegenion haben einen deutlichen Einfluß auf die Komplexbildung mit Ag+. Der Schwerpunkt von Untersuchungen an Zweiphasensystemenen wäßrig-organisch lag auf dem Übergang von Wasser in die organische Phase unter dem Einfluß von extrahierten Spezies bei der Kationen- und Anionenextraktion. Mit der Verteilung von Liganden und Kationen- bzw. Anionenkomplexen lassen sich Änderungen des Wassersättigungsgehaltes in der niedrigpolaren organischen Phase registrieren, die mit der unterschiedlichen Hydratation der Spezies korrelieren. Qualitativ wurde die Hydratation von Azapodanden mittels IR- und 1H-NMR-Spektroskopie nachgewiesen, wobei auch Hinweise auf bestimmte, die Hydratation verringernde Faktoren, wie intramolekulare Wasserstoffbrücken, erhalten wurden. Quantitativ konnten mittels Karl-Fischer-Titration und Verteilungsmessungen Hydratationszahlen für ausgewählte Ligansysteme bestimmt werden. Extrahierte Komplexe der Verbindungen mit Ag+, Co2+, Ni2+ und Zn2+ zeigen eine gegenüber den freien Komplexbildnern veränderte Hydratation. Bei Ag+ kann in allen Fällen von einer deutlichen Verringerung der Hydratationszahlen ausgegangen werden. Für die zweifachgeladenen Kationen konnte kein klarer Nachweis erbracht werden. Es ergeben sich aber Hinweise, wonach zum Teil keine Verringerung auftritt, was auf eine zusätzliche Koordinationsstellen von Wasser am Kation hinweist. Bei der Iodidextraktion treten bei gleichzeitiger pH-Abhängigkeit mehrere Komplexspezies auf, was die Bestimmung von Hydratationszahlen erschwert. Als hilfreich erwies sich die Simulation für verschiedene mögliche Zusammensetzungen. Dabei stellte sich heraus, daß der 1:1-Komplex des untersuchten monoprotonierten Aminopodanden in Chloroform wahrscheinlich stärker hydratisiert ist als der freie Ligand, während die entsprechende 1:2-Spezies (Ligand:Iodid) eine ähnliche oder schwächere Hydratation aufweist als der Ligand.