En dépit de l’importance considérable des matériaux alumino- et borosilicates pour la catalyse, l’origine moléculaire de leur activité demeure mal comprise. Ceci tient à la difficulté de caractériser le désordre structural local généré au sein du réseau silicaté par l’incorporation d’hétéroatomes. Le caractère local de la résonance magnétique nucléaire (RMN) à l’état solide en fait une technique adaptée pour résoudre cette question majeure. Les silicates en feuillés auto-assemblés en présence de surfactants sont d’excellents systèmes modèles pour l’étude de la structure locale autour d’hétéroatomes de B ou d’Al car la synthèse, la structure moléculaire et la signature RMN 29Si simple de leurs formes siliceuses sont parfaitement maîtrisées. L’incorporation dans leurs réseaux silicatés de différentes quantités d’Al ou de B et leurs conséquences ont été étudiées par des méthodologies avancées de RMN permettant de sonder les interactions à travers l’espace ou les liaisons chimiques entre noyaux de 29Si, 27Al, 11B et/ou 1H, une approche qui peut être étendue à la substitution atomique dans une argile aluminosilicate et un nouveau borosilicate de calcium. Ces résultats ont été combinés à la modélisation moléculaire pour construire et valider des modèles structuraux capables de décrire les distorsions et les réarrangements parfois profonds du réseau résultant de la substitution. Cela a révélé des différences frappantes entre les conséquences de l’incorporation d’Al ou de B dans deux matériaux de morphologie semblables mais de structures moléculaires différentes, et offre une occasion unique de comprendre les propriétés régissant l’incorporation d’hétéroatomes dans les silicates. / While alumino- and borosilicate materials have paramount importance in catalysis, the molecular origin of their activity is not completely understood. This is mainly because the incorporation of heteroatoms into the silicate framework deteriorates the molecular order by generating local disorder that is particularly difficult to establish. Because of its local vision of ordered and disordered environments, solid-state nuclear magnetic resonance (NMR) can play a key role to solve this long-standing issue. Surfactant-directed layered silicate materials with short-range molecular order are particularly interesting model systems to study the local structures around Al or B heteroatoms because the synthesis, molecular structures, and simple 29Si NMR signatures of their pure-silicate forms are well understood. Various amounts of Al and B atoms were incorporated into their frameworks, and their consequences on the local structure were investigated by state-of-the-art multidimensional NMR measurements probing spatial proximities or bonding interactions between 29Si, 11B, 27Al, and 1H nuclei, an approach that could be extended to atomic substitution in an aluminosilicate clay and a new calcium borosilicate. These results were combined with molecular modeling to build and evaluate structural models that capture the local framework distortions and sometimes profound rearrangements resulting from the atomic substitutions. This reveals remarkable differences between the consequences of the incorporation Al or B in two distinct frameworks of otherwise strongly-related materials, and offers a unique opportunity to understand the properties that drive heteroatom incorporation.

Knowledge of protein hot spots and the ability to successfully predict them while using only primary protein structure has been a worldwide scientific goal for several decades. This thesis describes the importance of hot spots and sums up advances achieved in this field of study so far. Besides that we introduce hot spot prediction algorithm using only a primary protein structure, based primarily on signal processing techniques. To convert protein sequence to numerical signal we use the EIIP attribute, while further processing is carried out via means of S-transform. The algorithm achieves sensitivity of more than 60 %, positive predictive value exceeds 50 % and the main advantage over competitive algorithms is its simplicity and low computational requirements.

Les oxydes d’azotes (NOx) sont un des groupes majeurs de polluants primaires émis dans l’atmosphère, principalement par les transports et l’industries, dont leur réduction constitue un enjeu sociétal crucial. Afin de répondre à l’évolution de normes environnementales plus exigeantes, la diminution des NOx est notablement explorée via la réaction clef de Réduction Catalytique Sélective par l’ammoniac (NH3-RCS) en employant des catalyseurs à base de cuivre et de fer. Le développement maîtrisé et perfectionné de cette solution requiert une profonde compréhension du système catalytique et ce à différentes échelles. Cette étude vise ainsi à développer un modèle cinétique multi-sites pour la représentation des performances NH3-RCS, par l’exploration des propriétés physico-chimiques, de surface et catalytiques d’une série de catalyseurs zéolitiques microporeux (Chabazite) supportant le cuivre. Cette série de catalyseurs imprégnés, échangés et « One-pot » permit la profonde caractérisation de différentes configurations de sites actifs dont les impacts sur les comportements catalytiques furent étudiés et identifiés selon différentes conditions opératoires. Ainsi, le modèle permit de prendre en considération, via la distinction selon leur nature, de 5 sites majeurs : la compétition d’adsorption, l’impact de l’eau, la formation et décomposition d’intermédiaires clefs et un schéma réactionnel précis, de représenter les activités des différents catalyseurs. De plus, l’étude In-situ de la surface de ces catalyseurs via spectrométrie infra-rouge à réflexion diffuse (DRIFT) fut complémentaire à la compréhension des dynamiques de surface et l’identification des mécanismes du procédé catalytique / The reduction of atmospheric pollution from stationary and mobile engines is a serious challenge associated with stringent environmental regulations. For nitrogen oxides (NOx) abatement in particular, the selective catalytic reduction using urea or ammonia (urea- or NH3-SCR) over copper- and iron-based catalysts is one of most effective and economic technologies. In this respect, revisiting after-treatment systems by a deep comprehension of the catalyst behavior at different scale may significantly improve their eco- and health-friendliness. This study targets the development of a multi-site kinetic model using a series of copper chabazite-based catalysts, as a selected model SCR catalyst. To qualify these materials as beyond-state-of-the-art catalysts and to better understand the impact on different active site configurations, three catalysts were synthetized by different preparation methods (impregnation, ionic exchange and one-pot), finely characterized by different techniques and their ability to abate NOx via the ubiquitous NH3-SCR reaction was extensively assessed under several operating conditions. Each catalyst behavior was quantified and associated to their respective main active sites (five different configurations described). The diffusion, water impact, adsorption competition between key reactants and storage sites were also ones of the main points spotlighted in this study. In-situ characterization of these catalysts was also performed, using Diffuse Reflectance Infrared Fourier-Transform Spectroscopy (DRIFTS) to understand the surface dynamical properties of the catalyst, and to unveil the mechanistic of the catalytic processes

In recent years, the potential benefits of high-throughput virtual screening to the drug discovery community have been recognized, bringing an increase in the number of tools developed for this purpose. These programs have to process large quantities of data, searching for an optimal solution in a vast combinatorial range. This is particularly the case for protein-ligand docking, since proteins are sophisticated structures with complicated interactions for which either molecule might reshape itself. Even the very limited flexibility model to be considered here, using ligand conformation ensembles, requires six dimensions of exploration - three translations and three rotations - per rigid conformation. The functions for evaluating pose suitability can also be complex to calculate. Consequently, the programs being written for these biochemical simulations are extremely resource-intensive. This work introduces a pure computer science approach to the field, developing techniques to improve the effectiveness of such tools. Their architecture is generalized to an abstract pattern of nested layers for discussion, covering scoring functions, search methods, and screening overall. Based on this, new stratagems for molecular docking software design are described, including lazy or partial evaluation, geometric analysis, and parallel processing implementation. In addition, a range of novel algorithms are presented for applications such as active site detection with linear complexity (PIES) and small molecule shape description (PASTRY) for pre-alignment of ligands. The various stratagems are assessed individually and in combination, using several modified versions of an existing docking program, to demonstrate their benefit to virtual screening in practical contexts. In particular, the importance of appropriate precision in calculations is highlighted.

Gegenstand der Untersuchungen war die Reduktion von Stickoxiden (NOx und N2O) an verschiedenartig präparierten Eisenkatalysatoren (Fe-MF, Fe-beta, Fe-SBA-15). Die Katalysatoren wurden nach Synthese, Kalzinierung und Katalyse mittels EPR und UV/VIS-DRS charakterisiert, und darüber hinaus auch in-situ während des Kalzinierens. Isolierte Eisenspezies aggregieren im Verlauf der Kalzinierung bei 873 K. Sowohl höhere Heizraten beim Kalziniervorgang, als auch ein höheres Si/Al-Verhältnis des Trägermaterials verstärken die Neigung zur Aggregatbildung leicht. Die Verwendung des Katalysators für die SCR von NO führt zu weiterem Wachstum und zur Restrukturierung der FexOy-Cluster. Die Eisenkatalysatoren wurden weiterhin mittels in-situ Methoden (EPR, UV/VIS-DRS, FTIR) untersucht während der SCR von NO durch NH3 und Isobutan, der SCR von N2O mit CO, und im Strom der entsprechenden reinen Eduktgase. Die Ergebnisse korrelieren mit dem katalytischen Verhalten der Materialien. Verschiedene Fe3+-Spezies, welche sich durch ein unterschiedliches Redoxverhalten auszeichnen, wurden identifiziert. UV/VIS-Messungen erlauben die Schlußfolgerung, daß isolierte, oktaedrisch koordinierte Fe3+?Spezies leichter zu reduzieren sind als tetradrisch koordinierte. Im Gegensatz zu isoliertem Fe3+ lassen sich FexOx-Cluster leichter oxidieren als reduzieren, und verbleiben daher unter Reaktionsbedingungen trivalent. Durch ihr hohes Oxidationspotential kommt es, vor allem für die Reaktion mit Isobutan, zur unerwünschten Totaloxidation des Reduktanden. Der Anteil isolierter Fe3+ Spezies korreliert mit der Aktivität der Katalysatoren für die SCR von NO und N2O. Weiterhin hängt zumindest für die Reaktion zwischen N2O und CO der Reaktionsmechanismus von der Art der vorliegenden Eisenspezies ab: an isolierten Plätzen erfolgt die Reduktion des N2O an dem an Fe3+ gebundenen CO. An FexOy-Clustern hingegen läuft die Reaktion als Redoxprozeß (Fe3+ / Fe2+) unter Bildung eines radikalischen Intermediates O-. Der Einfluß der Porengeometrie des Trägermaterials auf die katalytische Aktivität wurde an Katalysatoren mit ähnlichem Eisengehalt und ähnlicher Art und Verteilung der Eisenspezies studiert (Fe-MFI, Fe-SBA-15). Die drastisch höhere Aktivität von Fe-MFI belegt, daß die Lokalisierung der aktiven Komponente in einer Pore mit passender Geometrie (Größe und Struktur) essentiell für die katalytischen Eigenschaften ist. Als weitere, die Aktivität stark beeinflussen Größe, wurde für die Reaktion von NO mit Ammoniak und auch mit Isobutan die Azidität identifiziert, die jedoch für die katalytische Zersetzung oder Reduktion mit N2O keine Rolle spielt. / The reduction of nitrogen oxides (NOx and N2O) was investigated over Fe-catalysts (Fe-MFI, Fe-beta and Fe-SBA-15) which were prepared by different methods have been analyzed by EPR and UV/VIS-DRS ex situ after synthesis, calcination and use in catalysis as well as in situ during calcination. It was found that aggregated species are formed at the expense of isolated Fe species upon calcination at 873 K, and that aggregate formation is slightly favored by calcination with higher heating rates as well as by high Si/Al ratio of the support. Use in SCR of NO leads to further growth and restructuring of FexOy clusters. These Fe-catalysts were studied by in situ EPR, in situ UV/VIS-DRS and in situ FT-IR spectroscopy during SCR of NO with NH3 or isobutane and during SCR of N2O with CO as well as during interaction with single feed components. The results were related to the catalytic behaviour. Different types of isolated Fe3+ sites with different reducibility were identified. Based on FT-IR results which revealed that NO reacts preferably with trivalent Fe, it is concluded that Fe3+ ions reduced under reaction conditions to Fe2+ do probably not contribute to catalytic activity. In general, the degree of steady-state Fe site reduction during NH3-SCR is markedly lower than during isobutane-SCR. This might be the reason for the lower activity of Fe-catalysts in the latter reaction. UV/VIS-DRS results suggest that isolated Fe3+ in octahedral coordination is easier reduced than tetrahedral Fe3+. In contrast to isolated Fe3+ species, FexOy clusters are much faster reoxidized than reduced and, thus, remain essentially trivalent under reaction conditions. Due to their higher oxidation potential, they cause undesired total oxidation of the reductant being much more severe in the case of isobutane. A correlation was found between the fraction of isolated Fe+3 sites in the catalysts and their activity for SCR of NO and N2O. The reaction mechanism of SCR of N2O with CO is Fe site dependent. Over isolated Fe sites, the reduction of N2O occurs via coordinated CO species on Fe3+ sites. The reaction over FexOy sites proceeds via a redox Fe3+/Fe2+ process with intermediate formation of O- radicals. The effect of pore geometry of the support on the catalytic activity was studied by comparing catalytic performance of Fe-MFI and Fe-SBA-15 which contain similar iron content and show similar nature and distribution of Fe species as evidenced by UV/VIS-DRS and EPR. Fe-MFI revealed to be much more active than Fe-SBA-15 in all reactions studied. This clearly illustrates that the confinement of the iron species in pores of suitable geometry (structure and size) is essential to originate their remarkable catalytic properties. Acidity is essential for SCR of NO with NH3 or isobutane but it is not mandatory for direct decomposition or SCR of N2O.