Aujourd’hui, la diminution des ressources d’énergies fossiles corrélée à l’augmentation des besoins et à l’augmentation du taux de CO2 dans l’atmosphère nous poussent à développer de nouvelles énergies.L’utilisation de l’hydrogène comme vecteur énergétique est une solution. En effet, celui-ci est abondant et sa combustion est très énergétique (3 fois supérieure au pétrole). Cependant, son utilisation se heurte à des problèmes de production, de stockage et d’utilisation. Nous nous sommes ici intéressés au problème du stockage de l’hydrogène à l’état solide. Celui-ci permet d’obtenir des capacités volumiques de stockage importantes (environ 140 g/L) mais est freiné par des capacités massiques et des cinétiques de réaction faibles. Le magnésium se présentant comme un bon candidat en terme de capacité massique (7,6 %), nous nous sommes intéressés aux intermétalliques ternaires TR-M-Mg (TR = terres rares, M = métaux de transition). L’objectif était double : conserver la bonne capacité du magnésium et diminuer l’enthalpie de formation de l’hydrure. Le système TR4NiMg (avec TR = Y et Gd) et les solutions solides dérivées ont été étudiées. Un stockage irréversible de l’hydrogène de 2,5% massique ainsi qu’une transition d’antiferromagnétique à verre de spin ont été observés. Un travail plus exploratoire a permis de découvrir deux nouveaux composés riches en magnésium : LaCuMg8 et Gd13Ni9,5Mg77,5. Ils permettent tous deux l’obtention d’un mélange de phases issu de leur décomposition lors de la première absorption. Ce mélange permet une amélioration significative des propriétés de sorption de l’hydrogène par du magnésium. / Nowadays, the decrease of fossil fuel resources, and the increase of energy requirements and concentration of greenhouse gases in the atmosphere induces the development of new energies. The use of hydrogen as energetic vector is a solution. Indeed, it is abundant and its combustion is highly energetic (3 times more than petrol). However, its utilisation is limited by problems of production, storage and use. In this work, we have focused on the problem of solid hydrogen storage. It allows for high volumetric capacity (≈ 140 g/L) but is restricted by low weight capacity and by slow sorption kinetics. Because magnesium is potentially a good candidate according to its high weight capacity (7.6 %wt), we have chosen to work on the ternary compounds RE-M-Mg (RE = Rare earth, M = transition metal). The goal was double: to keep the good capacity of the magnesium and to decrease the enthalpy of formation of the hydride. The RE4NiMg system (with RE = Y and Gd) and the derived solid solutions were studied. An irreversible hydrogen uptake of 2.5% wt and a magnetic properties change from antiferromagnetic to spin glass behaviour were observed.A more exploratory work allowed us to discover two new magnesium rich compounds: LaCuMg8 and Gd13Ni9.5Mg77.5. Both lead to a phase mixture induced by their decomposition during the first absorption. This mixture allows a very significant improvement of the hydrogen sorption properties of magnesium.

Made available in DSpace on 2015-05-14T13:21:22Z (GMT). No. of bitstreams: 1 ArquivoTotal.pdf: 18195512 bytes, checksum: 6229ab5e9f367190d5f7b4336c07dfec (MD5) Previous issue date: 2013-08-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / This study was designed based on the concept of achiral / meso compound. The importance of preparing achiral compounds is based on their structural simplification, leading to new molecules which require no further investigations pharmacodynamics and pharmacokinetics of the enantiomers. Therefore, it is proposed to the synthesis of analogues tetrahydropyrans achiral/meso using the Prins cyclization reaction. The homoallylic alcohols synthesized in this work were derived from the Barbier reaction obtained in great yields, wherein these products are used as a synthesis intermediate for the preparation of tetrahydropyrans proposed. The Prins cyclization reaction is an efficient method for the preparation of tetrahydropyrans therefore proved to be a powerful tool for synthesis and versatile for the preparation of substituted tetrahydropyrans to give all the compounds synthesized in satisfactory yields. Through spectroscopic and crystallographic studies were possible to determine in detail the relative configuration of the molecules 40a, 41a, 44a, 45a, 46a, 46b and 48b. Furthermore, a theoretical study was developed using the density functional theory to obtain the molecular geometries optimized in the gas phase, making it possible to compare these preferred conformations with geometries defined by crystals. The tetrahydropyrans bioevaluated were synthesized in the leukemic cell line K562 and two types of normal L929 cells and PBMC. The results were very promising in cancer in vitro assays, highlighting the hydrazones 42a-c and the 43a-c aminoguanidines they were the only compounds that were active against resistant cell line K562, highlighting the tetrahydropyran 42c which showed higher activity series counterpart (present value of IC50 7.59 μM) and the tetrahydropyran 42b with an excellent IC50 (8.97 μM) value and a good selectivity index (2.2 in L929 and 1.6 in PBMC). / Este trabalho foi idealizado baseado no conceito de compostos aquirais/meso. A importância da preparação de compostos aquirais está baseada na sua simplificação estrutural, conduzindo a novas moléculas que não necessitam de posteriores investigações farmacodinâmicas e farmacocinéticas dos enantiômeros. Sendo assim, propomos neste trabalho a síntese de análogos tetraidropirânicos aquirais/meso utilizando a reação de ciclização de Prins. Os álcoois homoalílicos sintetizados foram provenientes da reação de Barbier obtidos em ótimos rendimentos, no qual estes produtos foram utilizados como intermediário de síntese para a preparação dos tetraidropiranos propostos. A reação de ciclização de Prins é um método eficiente na preparação dos tetraidropiranos, pois mostrou-se ser uma ferramenta de síntese poderosa e versátil para a preparação dos tetraidropiranos substituídos, obtendo-se todos os compostos sintetizados em rendimentos satisfatórios. Através de estudos espectroscópicos e cristalográficos foi possível determinar detalhadamente a configuração relativa das moléculas 40a, 41a, 44a, 45a, 46a, 46b e 48b. Além disso, foi desenvolvido um estudo teórico utilizando a teoria do funcional densidade para se obter as geometrias moleculares otimizadas em fase gasosa, tornando possível comparar estas conformações preferenciais com as geometrias definidas pelos cristais. Os tetraidropiranos sintetizados foram bioavaliados na linhagem de células leucêmicas K562 e dois tipos de células normais L929 e PBMC. Os resultados em câncer foram bastante promissores nos ensaios in vitro, dando destaque para as hidrazonas 42a-c e as aminoguanidinas 43a-c que foram os únicos compostos que se mostraram ativos contra a linhagem celular resistente K562, destacando-se o tetraidropirano 42c que apresentou maior atividade da série congênere (apresentando valor de CI50 7.59 μM) e o tetraidropirano 42b que apresentou excelente valor de IC50 (8.97 μM) e um bom índice de seletividade (2.2 em L929 e 1.6 em PBMC).

Este trabalho documenta o processo de desenvolvimento de um software didático-interativo para síntese e visualização de estruturas cristalinas intitulado CrystalWalk (CW). Sua criação foi justificada inicialmente pela percepção, colhida junto a atores sociais, de deficiências nas ferramentas de ensino-aprendizagem relacionadas ao estudo de estruturas cristalinas de materiais. Posteriormente, um levantamento do estado da arte dos softwares cristalográficos existentes revelou oportunidades para o desenvolvimento de um novo software com preocupação eminentemente didática. Na especificação e elaboração do CW, foram preconizados os princípios do software livre, da acessibilidade e da democratização do conhecimento. Adotou-se o estado da arte de tecnologias e serviços para desenvolvimento de aplicações web interativas, tais como plataforma HTML5/WebGL, arquiteturas orientadas a serviços (SOA) e sistemas distribuídos responsivos, resilientes e elásticos. Para facilitar o entendimento e a síntese de estruturas cristalinas, foi proposto um inédito processo passo a passo baseado no conceito \"rede + motivo = estrutura cristalina\", que exige a participação ativa e consciente do usuário. Inseriu-se também uma ferramenta denominada \"narrativa didática\", por meio por meio da qual o usuário registra sequências de visualização acompanhadas de anotações e que podem ser compartilhadas múltiplas narrativas permitem atender a diferentes perfis de aprendizagem. Também foram incorporadas com sucesso funcionalidades didáticas eficazes para garantir plena acessibilidade aos recursos do CW e para aumentar seu alcance social, tais como o suporte à interação avançada e às tecnologias de interface de realidade virtual, o suporte à impressão 3D e a oferta de uma plataforma de publicação online. Na avaliação dos produtos gerados, o principal critério foi o atendimento às demandas dos atores sociais, que foram empoderados ao final do processo. O CW é a primeira plataforma a superar a maioria dos problemas apontados e das limitações encontradas nos instrumentos didáticos existentes sobre a temática deste trabalho, impactando positivamente o acesso e a democratização do conhecimento, por meio da construção coletiva, do estímulo à colaboração e da autonomia e independência tecnológicas. / This work documents the process of development of an educational interactive software for synthesis and visualization of crystal structures (crystallographic software) named CrystalWalk (CW). The development of CW was justified by educational problems that were the identified and defined from direct stakeholders inquiry process about the lack of proper didatic tools for teaching crystal structure topic in materials science and engineering disciplines. Further, an evaluation of the existing crystallographic softwares has shown opportunities for the development of a new software, focused on the educational approach. The process of development and implementation of CrystalWalk was guided by principles of free software, accessibility and democratization of knowledge, adopting state of art technologies for the development of interactive web applications, such as HTML5/WebGL, service oriented architecture (SOA) and responsive, resilient and elastic distributed systems. CW proposes an unprecedented step-by-step crystal structure creation approach, imparting the concept of lattice and motif through active and conscious user interaction. Additionally, a comprehensive set of didactic functionalities was also successfully implemented, as an online content publication platform for sharing interactive crystal structures, a \"didactic narratives\" tool that enables users to generate interactive classes based on predefined animated sequences as well the support for advanced interaction and virtual reality technologies as Oculus Rift, Google Cardboard, LEAP Motion, multi-touch devices and 3D printing technologies. Project deliverables were evaluated under action-research premises based on identified problems resolution and overall stake-holders acquired knowledge or empowerment . CW has successfully resolved most of the identified problems identified, empowering students, professors and researchers through positive impact in the democratization of knowledge and technological autonomy and independence.

O objetivo do presente trabalho foi determinar as estruturas cristalinas e moleculares de cocristais de 2,4,6-trinitrofenol, ou ácido pícrico, com diversas bases orgânicas, bem como estudar as interações intermoleculares existentes nesses cocristais para tentar estabelecer um padrão de comportamento na formação de ligações de hidrogênio e de preferências estruturais, com a finalidade de contribuir para o entendimento do empacotamento cristalino. Foram sintetizados os seguintes compostos: 1:1 picrato/8-hidroxiquinolina, 1:1 picrato/isonicotinamida, 1:1 picrato/2-azaciclononanona, 1:2 picrato/2-azaciclotridecanona, 1:1 picrato/morfolina, 1:1 picrato/1,3 dimetiluréia, 1:1 picrato/4-metil-morfolina-N-óxido, 1:2 picrato/3-picolina-N-óxido, 1:2 picrato/glicina e 1:1 picrato/prolina. Esses compostos foram caracterizados por análise elementar CHN, para a confirmação da estequiometria, pelos pontos de fusão, e para o cocristal de picrato/prolina foram registrados espectros de emissão na região entre 430 e 650 nm e o espectro de excitação na região entre 360 e 500 nm, onde foi observado que o composto é transparente na região acima de 500 nm, sendo portanto favorável aos experimentos de duplicação de radiação laser Nd/YAG (λ = 1.064 nm), uma vez que não absorve na região da radiação duplicada (λ =532 nm). A coleta de dados, a obtenção das intensidades dos feixes difratados pelos monocristais, para a determinação das estruturas cristalinas foi realizada em um difratômetro Enraf-Nonius CAD4 Mach 3. As intensidades observadas medidas foram convertidas em fatores de estrutura observados através da correção pelos fatores de Lp e de absorção. As estruturas foram determinadas utilizando os chamados Métodos Diretos e refinadas por cálculos sucessivos de Fourier-Diferença e mínimos quadrados. Ao final da determinação das estruturas dos dez cocristais pôde-se analisar um total de 50 ligações de hidrogênio do tipo O-H...O, N-H...O e C-H...O. Essas ligações de hidrogênio foram analisadas geometricamente em relação às distâncias e ângulos de ligações, e também foram nomeadas e classificadas pelo método Graph-set. Através destas análises pode-se chegar a uma comparação entre as estruturas e a padrões comuns em relação às ligações intermoleculares existentes. Observa-se que as ligações de hidrogênio do tipo O-H...O mais fortes são aquelas formadas entre o grupo doador e os oxigênios fenólicos receptores do picrato. As distâncias d(H...O) das ligações de hidrogênio correspondentes a O-H...O (oxigênio fenólico) estão concentrados na região entre 1,51 e 1,82 Å, e os ângulos <OHO concentram-se na região entre 161 e 171º. As distâncias d(O...O) estão compreendidas entre 2,48 e 3,1 Å. Para as ligações O-H...O (oxigênio do grupo nitro) as distâncias d(H...O) estão entre 2,41 e 2,54 Å e ângulos <OHO na região entre 100 e 121º. Também é observado que as distâncias d(O...O) estão compreendidas entre 2,78 e 3,04 Å, mas predominantemente estão na faixa entre 2,4 e 2,55 Å. Para as interações do tipo N-H...O, observa-se que as distâncias d(H...O) estão em um intervalo entre 1,85 e 2,52 Å; e em relação aos ângulos <NHO, estão distribuídos no intervalo entre 121 e 171º. Um intervalo bastante largo é observado em relação as distâncias d(N...O), que estão compreendidas entre 2,6 e 3,2Å. Para as interações do tipo C-H...O, observa-se que as distâncias d(H...O) tem uma leve tendência crescente em função do aumento do ângulo <CHO, e encontram-se no intervalo entre 2,96 e 3,61 Å. / The objective of the present work is to determine the crystalline and molecular structures of 2,4,6 trinitrophenol (picric acid ) cocrystals, with several organic bases, as well as to study the intermoleculares interactions existent in those cocristals in order to establish a pattern of behaviour in the formation of hydrogen bonds and structural preferences, with the purpose of contributing for the understanding of crystalline packing. Was synthesized the following compounds: 1:1 picrate/8-hidroxiquinoline, 1:1 picrate/isonicotinamide, 1:1 picrate/2-azacyclononanone, 1:1 picrate/morfoline, 1:1 picrate/1,3 dimethylurea, 1:1 picrate/ 4-methyl-morfoline-N-oxide, 1:2 picrate/3-picoline-N-oxide, 1:2 picrate/glycine, 1:1 picrate/proline. Those compositions were characterized by elemental analysis (CHN) for the stoichiometry confirmation, melting points and, for the picrate/proline cocrystal, the emission and excitation spectra were recorded. It was observed that this compound is transparent above 500 nm, being therefore suitable to experiments of Nd/YAG laser radiation duplication (λ = 1.064 nm), since it does not absorb at the wavelength of the duplicated radiation (λ = 532 nm). Data collection for crystalline structure determination\'s was accomplished in an Enraf-Nonius CAD4 Mach 3 diffractometer. The observed intensities were transformed into structure factors observed through Lp and absorption corrections. The structures were determined using the direct method and refined by successive Fourier-difference calculations and least-square analysis. At the end of this determination some hydrogen bonds, O-H ...O, N-H ...O and C-H ...O could be analyzed. Those hydrogen bonds were geometrically analysed with relation to bond distances and angle, and they were also nominated and classified by the Graph-set method. Through these analyses it was possible a comparison among the structures and to common patterns in relation to intermolecular bonds. It was observed that the stronger hydrogen bonds are those formed between the donor group and the phenolic picrate oxygen. The O-H ...O (phenolic oxygen) distances d(H ...O) are concentrated in range 1.51 and 1.82 Å, and angles <OHO are concentrated between 161 and 171Å. The distances d(O...O) are between 2.48 and 3.1 Å. The distances of hydrogen bonds O-H ...O (nitro group oxygen), d(H ...0), are in the range 2.41 and 2.54 Å and angles <OHO between 100 and 121º. It is also observed that distances d(O ...O) lie between 2.78 and 3.04 Å. but predominantly they are in the interval between 2.4 and 2.55 Å. For interactions of the type N-H ...O. it is observed that distances d(H ...O) are between 1.85 and 2.52 Å, and angles <NHO, are between 121 and 171º. A quite wide area is observed with relation to the distance d(N ...O), that lie between 2.6 and 3.2 Å. For interactions of the type C-H ...O. it is observed that distances d(H ...O) increase in function of the angle <CHO; they lie between 2.96 and 3.61 Å.

Occasionally, crystallisation of proteins works in mysterious ways! One might obtain crystals of a protein of unknown identity in place of the protein for which crystallisation experiments were performed. If the investigator is not aware of such possibilities, valuable time and resources might be lost in attempting to determine the structure of such proteins. Instances of non-target protein getting crystallised may not come to light at all or may be realised only when attempts to determine the structure completely fail by conventional procedures after collecting and processing the diffraction data. Usually, it is not possible to reproduce the crystals of the same protein as their occurrence is serendipitous. Such rare instances of crystallisation are probably caused by fluctuating environmental or crystallisation conditions and are not reproducible. It could also be due to contaminating microbes, which is more likely when the experimentalist is not well experienced. Therefore, experimental phasing of the data collected on serendipitously obtained crystals could be a challenging task. With the rapid increase in the number of structures deposited in the protein data bank (PDB), molecular replacement has become the method of choice for structure determination in macromolecular X-ray crystallography. This is due to the fact that it is possible to select a suitable phasing model for most target proteins based on their sequence information. However, if the identity of the target protein itself is uncertain, all attempts of structure determination using phasing models selected on the basis of target protein sequence-dependent search would fail. Sequence-independent ab initio phasing techniques such as ARCIMBOLDO (Meindl et al., 2012), which has recently become available, could provide leads only if the non-target protein is an all-α-protein and the associated diffraction data extends to a resolution better than 2 Å. Even then, the success rate with this technique is low. Hence, it becomes important to employ a sequence-independent method of structure determination for such mysteriously obtained crystals. This thesis reports crystal structures of proteins which are serendipitously crystallised using a large-scale application of Molecular Replacement (MR) technique (referred in this thesis as MarathonMR). This thesis also presents an evaluation of molecular replacement strategies for structure determination. The thesis begins with an overview of crystallographic methods of structure determination with an emphasis on the method of molecular replacement (Chapter 1). The most prominent of the results obtained in the course of these investigations pertains to a crystal obtained during routine crystallisation of a viral protein mutant in the year 2011. The cell parameters were different from cell constants of crystals obtained with other known viral protein mutants crystallised earlier in the same laboratory. Unfortunately, this crystal could not be reproduced in the same form in subsequent crystallisation trials. All attempts to determine the structure through conventional molecular replacement techniques using a combination of domains from a nearly identical virus coat protein protomer as the phasing model had failed. The data was shelved as “not-solvable” in late 2011. However, the crystal had diffracted to 1.9 Å and had excellent merging statistics. Therefore, the data was retrieved recently and additional attempts were made to determine the structure through phasing techniques that have become available recently. Techniques such as AMPLE (Bibby et al., 2013) and Rosetta (DiMaio, 2013), which use large-scale homology models coupled with molecular replacement, did not lead to meaningful solutions. A couple of helices identified by ARCIMBOLDO (Meindl et al., 2012) were neither correct (retrospectively) nor sufficient to determine the entire structure. Given the excellent merging statistics of the crystal data, there was significant motivation to determine the structure, though it meant developing a fresh protocol. It was at this time that we came across the work of Stokes-Rees and Sliz (2010) in which they had demonstrated that it is possible to determine structure of proteins of unknown identity by employing almost every known protein structure as a potential phasing model. The work reported in the thesis is a result of an earlier project to examine the relationship between properties of phasing models and the quality of target protein model generated through MR by employing large scale molecular replacement runs. This project was initiated because of the realisation that the recent explosion in crystallographic structural studies has resulted in near complete exploration of the “fold-space” of proteins and PDB now has a representative structure for most plausible folds of proteins. Some folds are highly represented in the PDB. Hence, it is likely that there would be at least one homologue in the PDB which could be used as a phasing model to successfully determine the structure of a protein of unknown identity if the diffraction dataset is of excellent quality. Hence, the single dataset which had diffracted to 1.9 Å resolution was used to develop a MarathonMR procedure for structure determination. MarathonMR procedure takes sequence-independent approach to structure determination and employs large-scale molecular replacement calculations to identify the closest homologue (in structural terms initially). This protocol is described in Chapter 2 (Materials and methods) of the thesis. Through MarathonMR, structure of the dataset which had remained unsolved for 5 years was finally determined. Nearly complete sequence of the polypeptide could be deduced by inspecting the electron density map due to the high resolution and quality of the map. The protein was found to be a phosphate binding protein from a soil bacterium Stenotrophomonas maltophilia (SmPBP). The way in which the structure was determined and possible explanations for the mysterious source of this protein which had crystallised instead of the target protein is discussed in Chapter 3. Though MarathonMR procedure was developed to solve a single dataset, it was soon realised that the same procedure could be applied to other similar datasets, all of which had diffracted to reasonable resolutions with good merging statistics but had remained unsolved for unknown reasons. Among such datasets, one of the datasets which was collected in 2007 and had diffracted to 2.3 Å resolution had cell parameters very close to that of SmPBP. Hence, a poly-alanine model of the structure of SmPBP, which was determined by then, was used as the phasing model to run molecular replacement and the structure was readily solved. It was surprising to note that SmPBP had crystallised serendipitously not once but twice, once in 2011 resulting in crystals that diffracted to 1.9 Å resolution and earlier in 2007 in crystals that diffracted to 2.3 Å resolution independently by two different investigators in the same laboratory. Both the structures are nearly identical and a comparison of these structures is presented in Chapter 4. Structure of SmPBP determined at 2.3 Å resolution by MarathonMR also corresponds to the dataset that had remained unsolved for the longest period of time (9 years). This success of structure determination after the lapse of such a long period emphasises the importance of carefully preserving X-ray diffraction data irrespective of its immediate outcome. In Chapter 5 of the thesis, another instance of non-target protein crystallisation, the structure of which was determined using the MarathonMR procedure is described. The crystal was obtained while carrying out crystallisation of mutants of a survival protein (SurE) expressed in Salmonella typhimurium when the bacterium is subjected to environmental or internal stresses. The original investigator had used the structure of SurE as the phasing model to determine structure of the mutant crystals and obtained a model with R and Rfree of 35% and 40%, respectively. However, the model did not refine further to lower R-factors suggesting that the solution obtained may not be correct. MarathonMR indicated that the fold of the crystallised protein could be similar to that of glycerol dehydrogenase. As SurE shares some fold similarity with one of the domains of GlyDH, the original investigator might have been able to achieve a limited success with R/Rfree factors of 35% and 40%, respectively. As the merging statistics for this diffraction data set was poor, the diffraction images were reprocessed in XDS program on Xia2 automated spot processing pipeline. The data statistics indicated merohedral twinning (14%). However, using appropriate parameters, it was possible to refine the structure obtained by MarathonMR to acceptable R/Rfree using the Refmac program. Four protomers were present in the crystal asymmetric unit (ASU). Non-crytsallographic symmetry averaging of electron density over these four molecules further improved the electron density. As the data was limited to 2.7 Å resolution, it was not possible to deduce the identity of every residue of the protein unambiguously based solely on the resulting electron density map. With the identity of the amino acids that could be deduced with certainty, it was clear that the protein belongs to glycerol dehydrogenase from a species of Enterobacteriacea family. Though a similar structure of glycerol dehydrogenase has been reported from Serratia, there are clear differences in many unambiguously determined residues which suggest that the protein is not from Serriatia. The protein has been named EnteroGlyDH as the source of the protein is likely to be from a species of Enterobacteriacea family. The structure of the protein, its biochemical implications and possible reasons for the serendipitous crystallisation of a non-target are discussed. Chapter 6 discusses the structure determination of an inorganic pyrophosphatase and catalytic domain of Succinyl transferase, the crystals of which had diffracted to 2.3 Å and 3.1 Å, respectively, but had remained unsolved. Neither of the datasets corresponds to the intended target proteins. The dataset corresponding to the protein whose structure was determined as that of an inorganic pyrophosphatase was provided by a colleague from a different laboratory in the Indian Institute of Science. It is interesting to note that the investigator had carried this dataset to one of the CCP4 workshops and had tried to determine the structure with the help of experts in the workshop. The attempts to determine its structure had however failed for reasons that are obvious now. The original investigator was unfortunately making efforts with an erroneous assumption on the identity of the target protein. As these enzymes are well studied, their structures and functions are briefly discussed. It is already well established that molecular replacement is being used with increasing frequency as the phasing technique when compared to other experimental phasing techniques. With the ever growing number of structures in the PDB, high population of certain folds and a near-plateau attained in the identification and growth of new folds, it is reasonable to expect that molecular replacement will be used even more frequently in the years to come. Therefore, for carrying out molecular replacement for a given diffraction dataset of a target protein, it is very likely that several homologous structures would be available in the PDB that could be used as potential phasing models. Hence, it becomes important to understand the influence of phasing model on the quality and accuracy of model generated through MR to achieve the best structure solution. To understand this relationship between phasing model and model obtained by MR protocol, re-determination of already known structures deposited in the PDB starting with their respective structure factors and various phasing models was initiated. Structures belonging to TIM beta/alpha-barrel (SCOPe ID: c.1) and Lysozyme-like (SCOPe ID: d.2) folds were chosen as targets. The structure of each target was re-determined serially starting with poly-alanine models of all available unique homologues as phasing models. Due to the multi-dimensional nature of this study, the results obtained were represented in a graphical form with nodes and edges. Detailed methodology of the work carried out and the data representation model are discussed in the Chapter 2 (Materials and methods). It was found that after a certain sequence identity cut-off, sequence identity between phasing model and target seems to have little influence on the quality and accuracy of the model generated through MR. Instead, other qualities of the phasing model such as Rfree and RSCC influence the quality of MR models. These results are discussed in Chapter 7. Learning from the work reported in this thesis are discussed in concluding chapter. The possible logical and programmatic upgrades to MarathonMR protocol and future path in which the relationship between phasing models and models generated through MR can be studied are discussed in Chapter 8 (Conclusion and future prospects).

La chitotriosidase (CHIT1) est une chitinase humaine appartenant à la famille glycosyl hydrolase 18 (GH18) qui hydrolyse la chitine. CHIT1 présente plusieurs caractéristiques enzymatiques conservées dans la famille GH18 qui ne sont pas complètement comprises. Pour renforcer nos connaissances sur le mécanisme catalytique de CHIT1 et de la famille GH18, j'ai amélioré la résolution des structures obtenues par diffraction de rayon-X du domaine catalytique de CHIT1. Ces structures correspondent à la forme apo de CHIT1, pseudo-apo ainsi qu’en complexe avec la chitobiose ont été obtenues à des résolutions comprises entre 0.95Å et 1.10Å. Mes résultats m’ont permis de proposer un nouveau mécanisme d’hydrolyse des chaines chito-oligosaccharidiques. En outre, grâce à une nouvelle stratégie de cristallisation, la première structure cristalline de CHIT1 complète a pu être obtenue à une résolution de 1.95Å. Mon étude donne de nouvelles perspectives sur le mode d'action de CHIT1 et les caractéristiques enzymatiques conservées dans la famille GH18. / Chitotriosidase (CHIT1) is a human chitinase belonging to the glycosyl hydrolase family 18 (GH18), a highly conserved enzyme family. GH18 enzymes hydrolyze chitin, a N-acetyl glucosamine polymer. CHIT1 is characterized by many enzymatic features that are conserved in GH18 and not completely understood. To increase our knowledge on the catalytic mechanism in CHIT1 and GH18 family, I improved the X-ray resolution crystal structure of CHIT1 catalytic domain in apo and pseudo apo forms as well as in complex with a synthetic substrate to a resolution range between 0.95Å and at 1.10Å. My results allow me to suggest a new mechanism for chito-oligosaccharide chains hydrolysis. Moreover, thanks to a new a crystallogenesis strategy, I obtained the first crystal structure of full length CHIT1 at 1.95Å resolution. My study presents many structural and mechanistic aspects of CHIT1 which gives new insights onto its mode of action and shed light into the conserved enzymatic features in GH18 chitinase family.

Les glutathion transférases (GSTs) constituent une famille multigénique d’enzymes présentes dans les trois domaines du vivant. Cette présence ubiquitaire souligne l’origine sans doute très ancienne de ces enzymes ainsi que des fonctions fondamentales conservées au cours de l’évolution. Ces enzymes sont impliquées notamment dans la détoxication cellulaire de molécules toxiques et dans le métabolisme secondaire. Les analyses phylogénétiques regroupent les GSTs des organismes photosynthétiques au sein de quatorze classes qui peuvent être séparées en deux grands groupes selon le résidu catalytique : les GSTs à sérine catalytique qui possèdent des activités de conjugaison du glutathion (GSH) et/ou peroxydase tandis que les GSTs à cystéine catalytique présentent des activités thioltransférase, déshydroascorbate réductase et de déglutathionylation. Les GSTs à sérine catalytique de la classe Phi (GSTF) sont présentes chez les organismes photosynthétiques et certains basidiomycètes. Chez les plantes, cette classe comprend un nombre de gènes plus important que les autres classes de GSTs. Ceux-ci sont parmi les plus régulés en réponse à divers stress et ils ont été fortement étudiés chez les plantes céréalières en raison de l’activité de détoxication des herbicides des protéines correspondantes. Pourtant, à quelques exceptions près, les rôles physiologiques des GSTFs restent inconnus et la redondance d’isoformes dans cette classe reste incomprise. Par des approches moléculaires, biochimiques et structurales, l’analyse structure-fonction des huit GSTFs de l’arbre modèle Populus trichocarpa a été réalisée au cours de cette thèse. L’analyse phylogénétique des GSTFs chez les organismes photosynthétiques a montré que cette classe est apparue au moment de l’apparition terrestre des végétaux et que différents groupes pouvaient être identifiés avec des motifs catalytiques distincts. L’analyse transcriptionnelle a montré que les gènes relatifs aux GSTFs de peuplier sont principalement exprimés dans les fleurs femelles, les pétioles et les fruits. Certains aspects du mécanisme réactionnel ont été caractérisés en déterminant notamment les paramètres cinétiques et d’interaction des huit GSTFs et de plusieurs variants mutés pour des résidus clés vis-à-vis de substrats modèles. Les structures de cinq des huit GSTFs ont été résolues et ces protéines dimériques adoptent un repliement GST canonique et des spécificités structurales au niveau du site actif ont pu être observées. De plus, au regard de la capacité des orthologues des GSTFs à lier des hormones et des flavonoïdes ainsi que de l’expression récurrente des GSTFs de peuplier dans les fruits et les fleurs femelles, deux organes riches en ces molécules, il peut être supposé qu’elles ont aussi des propriétés de type ligandine. Des résultats préliminaires ont également été obtenus pour la recherche de substrats physiologiques à partir de métabolites extraits de différents organes de peuplier. A terme, l’identification de ces substrats permettra de déterminer le mode d’action (catalytique vs ligandine) de chaque enzyme et d’identifier clairement les fonctions in planta de ces enzymes / Glutathione transferases (GSTs) belong to a multigenic family whose presence in most eukaryotes, prokaryotes and archaea reflects their widespread nature and very likely important functions. These enzymes represent a major group of enzymes involved in xenobiotic detoxification and secondary metabolism. From the most recent genomic and phylogenetic analyses, the GST family is subdivided into 14 classes that can be separated into two main groups based on the catalytic residue which is either a serine (Ser-GST) or a cysteine (Cys-GST). Ser-GSTs usually catalyze glutathione (GSH) conjugation and/or peroxide reduction. On the other hand, Cys-GSTs cannot perform GSH-conjugation reactions but instead catalyze thiol-transferase, dehydroascorbate reductase and deglutathionylation reactions. Ser-GSTs from the Phi class (GSTF) are present in photosynthetic organisms and some basidiomycetes. This class is composed of a large number of genes compared to other GST classes which are amongst the most stress-inducible. The corresponding proteins have been extensively studied in crops with regard to their detoxification activities toward herbicides. However, with a few exceptions, very little is known about their roles in planta and it is not well understood why this class has expanded. By combining molecular, cellular, biochemical and structural approaches, the eight isoforms from the model tree Populus trichocarpa have been characterized during this PhD project. Phylogenetic analysis of GSTFs in the green lineage shows that the apparition of this class is concomitant with the appearance of terrestrial plants and that different groups can be distinguished based on the active site signature. RT-PCR analysis of the eight isoforms of GSTFs showed that transcripts mostly accumulate in female flowers, petioles and fruits. Some aspects of the reaction mechanism have been characterized by determining kinetic parameters of the eight poplar GSTFs and of several mutated variants for key residues towards model substrates. The structures of five GSTFs have been solved and these dimeric proteins display a typical GST fold but specificities have been observed at the catalytic site level. Moreover, considering the demonstrated capacity of GSTF orthologs to bind hormones, anthocyanins or flavonoids, and the consistent high expression of poplar GSTFs in female flowers and fruits, two organs rich in these molecules, we speculate that they may also possess ligandin properties. Preliminary results have been obtained regarding the nature of the substrates in various poplar organs by analyzing protein thermostability in the presence of putative ligands. In order to assess whether a functional redundancy between poplar Phi GSTs exists and to identify their mode of action (catalytic vs ligandin functions), we started to isolate and identify physiological substrates

Ziel dieser Arbeit war es, Beziehungen zwischen den kristallchemischen Eigenschaften und dem beobachteten anomalen Verhalten im spezifischen elektrischen Widerstand (nicht-magnetischer Kondo-Effekt) aufzuzeigen und zusammenhängend zu interpretieren. Verbindungen, an denen dieser Effekt beobachtet wurde, werden aus einem Übergangs-, oder Actinidmetall mit je einem Vertreter der 15. (Pniktogene) und 16. Gruppe (Chalkogene) des Periodensystems gebildet und kristallisieren im PbFCl-Strukturtyp. Da zu ternären Actinidmetall-Pniktid-Chalkogeniden (z.B. ThAsSe, UPS) nur sehr wenige chemische und kristallographische Informationen existieren, wurden in dieser Arbeit umfassende Untersuchungen zur Kristallchemie ternärer Phasen aus den Systemen M-Pn-Q (M = Zr, Hf, La-Ce; Pn = As, Sb; Q = Se, Te durchgeführt. Der Schwerpunkt lag dabei auf der strukturellen Lokalisierung der beobachteten Widerstandsanomalie und der Erarbeitung chemisch-physikalischer Eigenschaftsbeziehungen. Die Darstellung der untersuchten ternären Phasen in Form von Einkristallen gelang über exothermen Chemischen Transport mit Jod. Da die erhaltenen Kristalle bis zu mehreren Millimetern groß sind, konnten an ein und demselben Kristallindividuum sowohl die stoffliche Charakterisierung (EDXS, WDXS, ICP-OES, LA-ICP-MS, CIC) und die strukturelle Charakterisierung, als auch die Messung der physikalischen Eigenschaften erfolgen. Es konnte u.a. gezeigt werden, dass ZrAs1,4Se0,5 und HfAs1,7Se0,2 ein ähnlich ungewöhnliches Verhalten im temperaturabhängigen elektrischen Widerstand zeigen, welches bereits an Thorium-Arsenid-Seleniden und Uran-Phosphid-Sulfiden beobachtet wurde. Desweiteren gelang es den beobachteten Verlauf im elektrischen Widerstand, mit seinem Minium bei etwa T = 15 K, auf intrinsische strukturelle Merkmale in der anionischen Arsen-Teilstruktur zurückzuführen. / The aim of this work was, to evaluate and interpret a relationship between the crystal-chemical properties and the observed unusual behavior in the electrical resistivity (non-magnetic Kondo-effect). Compounds, which show such an effect, are formed by a transition- or actinide-metal with both a group 15 element and a group 16 element of the periodic table. All these compounds crystallizing in the PbFCl type of structure. Because of less crystallographic and chemical information about actinide-metal-pnictide-chalcogenides (i.e. ThAsSe, UPS), intensive investigation were made concerning the crystal-chemistry of ternary phases of the systems M-Pn-Q (M = Zr, Hf, La-Ce; Pn = As, Sb; Q = Se, Te. Our studies were focused on the structurally localization of the observed anomaly in the electrical resistivity and the evaluation of chemical-physical relations of properties. The synthesis of the investigated ternary phases was realized by exothermically Chemical Transport with iodine as transport agent. The dimension of the synthesized crystals allowed a chemical (EDXS, WDXS, ICP-OES, LA-ICP-MS, CIC) and structurally characterization, as well as a determination of the physical properties on one large single crystal. It could be shown, that ZrAs1,4Se0,5 and HfAs1,7Se0,2 reveal a similar unusual behavior in the temperature dependent electrical resistivity, as it was observed in thorium-arsenide-selenides and uranium-phosphide-sulphides. In conclusion, the non-magnetic Kondo-effect, which was found in the low-temperature range (about 15 K), arises from structurally features of the anionic sublattice with arsenic.

Hybridstrukturen aus organischen und anorganischen Halbleitern (HIOS) vereinen die besten Eigenschaften beider Materialklassen zu Konjugaten mit großem Anwendungspotential. Ihre engen Struktur-Eigenschafts-Beziehungen, eröffnen viele interessante wissenschaftliche Herausforderungen. Um z.B. ihre optoelektronischen Eigenschaften vorherzusagen, müssen die früher Stadien des Dünnschichtwachstums erforscht werden. Das erste Ziel dieser Arbeit ist es, den Einfluss der Entropie auf die Oberflächendiffusion von kurzen Polyphenyl Molekülen auf amorphem Siliziumdioxid, a-SiO2 zu untersuchen. Das zweite Ziel ist es, den Einfluss partieller Fluorierung auf para-Sexiphenyls (p-6P) zu untersuchen. Des Weiteren untersuchen wir Selbstdiffusion von p-6P auf einer Zinkoxid (ZnO) Oberfläche und Selbstorganisation bzw. Schichtwachstum auf a-SiO2. Hierfür verwenden wir klassische atomistische Molekular- und Langevin-Dynamik-Simulationen, kombiniert mit klassischer Diffusionstheorie. In Bezug auf das erste Ziel quantifizieren wir die entropischen Beiträge zu den Freie-Energie-Barrieren für die Oberflächendiffusion von Polyphenylen unterschiedlicher Länge und zeigen, dass die Entropie zum dominierenden Teil der freien Energie für längere Moleküle wird. Zweitens demonstrieren wir, dass die Erhöhung der Anzahl fluorierter Gruppen im p-6P die Diffusion in der apolaren Richtung der ZnO-Oberfläche verringert, aber die Diffusion in der polaren Richtung erhöht. Drittens untersuchen wir den Einfluss der Fluorierung auf die Nukleation und das Wachstum von p-6P auf a-SiO2 mit einem Simulationsmodell, das experimentelle Gasphasenepitaxie nachahmt. Wir reproduzieren korrekte Einheitszellen bei Raumtemperatur und zeigen, dass die Erhöhung der Anzahl fluorierter Gruppen zu einem Schicht-für-Schicht-Wachstum auf der Oberfläche führt. Diese Arbeit ebnet den Weg für zukünftige Simulationen von Dünnschichtwachstum kleiner organischer Moleküle auf anorganischen Oberflächen. / Hybrid structures of organic molecules and inorganic semiconductors (HIOS) combine favorable properties of each material into conjugates with great application potential. The optoelectronic properties of hybrid materials depend on the structure of individual molecules and their alignment relative to the inorganic surface. It is an interesting scientific challenge to predict the optoelectronic properties of HIOS based on studying the early stages of thin film growth and interface formation. The aim of this thesis is to investigate the effect of entropy in surface diffusion of short polyphenyl molecules on an amorphous silicon dioxide, a-SiO2. Second objective is to study the influence of partial fluorination of the organic para-sexiphenyl molecule (p-6P) on self-diffusion on an inorganic zinc oxide (ZnO) surface and on self-assembly and growth on the a-SiO2. For this we employ all-atom molecular dynamics and Langevin dynamics simulations, combined with classical diffusion theory. In respect to the first aim, we quantify entropic contributions to the free energy barrier of surface diffusion for short oligophenyls of varying length and demonstrate that entropy becomes even the dominant part of the free energy for longer molecules. For the second aim, we demonstrate that the increase in the number of fluorinated groups inside of the p-6P decreases the diffusivity in the apolar direction of the ZnO surface but increases the diffusivity in the polar direction. Thirdly, we study the influence of fluorination on nucleation and growth on a-SiO2 with a simulation model that mimics experimental deposition from the vapor. We reproduce the structures with correct room-temperature unit-cell parameters and demonstrate that the increase in the number of fluorinated groups leads to a layer-by-layer growth on the surface. This work can stimulate ideas for future simulations of nucleation and growth of small organic molecules with high tuning potential, on inorganic surfaces.

The synthesis and characterization of an isomorphous series of copper-containing microporous metal-organic frameworks (MOFs) based on triazolyl isophthalate linkers with the general formula 3 ¥[Cu4(m3-OH)2(R1-R2-trz-ia)3(H2O)x] are presented. Through size adjustment of the alkyl substituents R1 and/or R2 at the linker, the impact of linker functionalization on structure-property relationships was studied. Due to the arrangement of the substituents towards the cavities, the porosity (pore fraction 28%–39%), as well as the pore size can be adjusted by the size of the substituents of the triazole ring. Thermal analysis and temperature-dependent PXRD studies reveal a thermal stability of the MOFs up to 230 C due to increasing framework stability through fine-tuning of the linker substitution pattern. Adsorption of CO2 (298 K) shows a decreasing maximum loading with increasing steric demand of the substituents of the triazole ring. Furthermore, the selective oxidation of cyclohexene with tert-butyl hydroperoxide (TBHP) is studied over the MOFs at 323 K in liquid chloroform. The catalytic activity increases with the steric demand of the substituents. Additionally, these isomorphous MOFs exhibit considerable robustness under oxidizing conditions confirmed by CO2 adsorption studies, as well as by the catalytic selective oxidation experiments.