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No. of bitstreams: 1 elgteelminborgesdepaula.pdf: 3380575 bytes, checksum: 18f97b33fbd0bd8930a6495505ebf65e (MD5) Previous issue date: 2009-07-30 / FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais / Este trabalho consiste na síntese e caracterização de complexos inéditos envolvendo as espécies oxocarbônicas ácido esquárico e croconato, o pseudo-oxocarbono croconato violeta, bem como os ligantes nitrogenados derivados piridínicos 4,4’-dimetil-2,2’-bipiridina (MBP), 1,3-bis(4-piridil)propano (BPP) e 2,3,5,6-tetraquis(α-piridil)pirazina (TPP) e os sítios metálicos de Co(II), Ni(II) e Cu(II). Adicionalmente realizou-se sínteses envolvendo o sítio metálico de Mn(II). Utilizou-se diversas técnicas analíticas e espectroscópicas para a caracterização dos compostos sintetizados, tais como, análise elementar (CHN), análise térmica (TG/DTA) e espectroscopia vibracional (IV e Raman). Foram obtidos seis complexos envolvendo a espécie esquarato, dos quais três contêm o ligante 4,4’-dimetil-2,2’-bipiridina (MBP), denominados: [Co(MBP)2(C4O4)] (1), [Ni(MBP)3](C4O4).3H2O (2) e {[Cu2(MBP)2(C4O4)2(H2O)4]}n (3) e três o ligante 2,3,5,6-tetraquis(α-piridil)pirazina (TPP): [Co2(TPP)(C4O4)2(H2O)2)]2H2O (4), [Ni2(TPP)(C4O4)(H2O)2Cl2]7H2O (5) e [Cu2(TPP) (H2O)2Cl2)] (C4O4)2H2O (6). Os complexos (2), (3) e (6) tiveram suas estruturas determinadas por difração de raios X de monocristal. O composto (3) apresentou-se como um polímero de coordenação que se estende em uma dimensão através do ligante esquarato, coordenado em ponte entre dois sítios de Cu(II) pelo modo µ-1,2-bis(monodentado). O referido ligante oxocarbônico apresentou-se nos compostos (2) e (6) como contra-íon. As sínteses envolvendo a espécie oxocarbônica croconato de potássio levaram à obtenção de sete compostos inéditos denominados: {[Co(MBP)2(NO3)]2+.[Co(C5O5)2(H2O)4]2-} .6H2O (7), [Ni(MBP)2(C5O5)] (8), [Cu(MBP)(C5O5)(H2O)] (9), {[Mn2(BPP)2(C5O5)2(H2O)4].3H2O}n (10), {[Co2(BPP)2(C5O5)2(H2O)4].2H2O}n (11), {[Ni2(BPP)3(C5O5)2(H2O)4].5H2O}n (12) e {[Cu(BPP)(C5O5)(H2O)3]}n (13), em que MBP consiste no ligante nitrogenado 4,4’-dimetil-2,2’-bipiridina e BPP no 1,3-bis(4-piridil)propano. Os compostos (7), (8) e (10) tiveram suas estruturas determinadas por difração de raios X de monocristal. O complexo (7) apresentou-se dinuclear, sendo constituído por uma porção catiônica e outra aniônica que apresenta dois íons croconato coordenados pelo modo monodentado, enquanto que (8) é mononuclear com o diânion croconato coordenado ao Ni(II) pelo modo 1,2-bidentado, tais complexos apresentaram arranjos supramoleculares, sendo que em (7) a presença de interações de hidrogênio estendem o arranjo em duas dimensões e em (8) interações do tipo empacotamento π estende o arranjo supramolecular em uma dimensão. O composto (10) apresentou-se como um polímero de coordenação bidimensional em que tanto o ligante nitrogenado BPP, numa conformação TG (trans-gauche), quanto um dos diânions croconato, apresentaram-se coordenados em ponte entre dois sítios metálicos de Mn(II). Tal rede polimérica apresenta caminhos fechados cuja topologia estrutural é (6,3). O referido polímero apresenta dois íons croconato com modos de coordenação distintos, um deles se coordena ao sítio de Mn(II) pelo modo 1,2-bidentado e outro em ponte pelo inusitado modo µ-1,2-bis(monodentado), o qual não apresenta relatos na literatura. Observou-se que a folha bidimensional apresentou-se entrelaçada paralelamente à outra folha equivalente, gerando uma estrutura interpenetrada. Através das sínteses envolvendo o pseudo-oxocarbono croconato violeta obteve-se dois compostos denominados: [Co(MBP)2(CV)] (14) que envolve o ligante nitrogenado 4,4’-dimetil-2,2’-bipiridina (MBP) e {[Mn(BPP)2(H2O)2](CV)2-.2H2O}n (15) que envolve o ligante 1,3-bis(4-piridil)propano (BPP). O composto (15) teve sua estrutura determinada por difração de raios X de monocristal, a qual apresenta dois ligantes BPP, numa conformação TG (trans-gauche), coordenados em ponte entre dois sítios de Mn(II) gerando um arranjo polimérico unidimensional em que os diânions croconato violeta atuam como contra-íons. Observou-se a presença de interações de hidrogênio na estrutura, as quais foram responsáveis pelos arranjos supramoleculares bi e tridimensional. / This work presents the synthesis and characterization of novel complexes of Co(II), Ni(II) and Cu(II) involving the oxocarbons species, squaric acid and croconate ion, the pseudo-oxocarbon croconate violet dianion as well as the nitrogen ligands derived from pyridine 4,4’-dimethyl-2,2'-bipyridine (MBP), 2,3,5,6-tetrakis(α-pyridyl)pyrazine (TPP) and 1,3-bis(4-pyridyl)propane (BPP). Additionally, some syntheses involving the Mn(II) metal ion were realized. We used various analytical and spectroscopic techniques for characterization of the compounds such as elemental analysis (CHN), thermal analysis (TG/DTA) and vibrational spectroscopy (IR and Raman). We obtained six complexes involving the species squarate. Three of them contain the ligand 4,4’-dimethyl-2,2'-bipyridine (MBP), named: [Co(MBP)2 (C4O4)] (1), [Ni(MBP)3](C4O4).3H2O (2) and {[Cu2(MBP)2(C4O4)2(H2O)4]}n (3) and the other three contain the ligand 2,3,5,6 tetrakis(α-pyridyl)pyrazine (TPP): [Co2(TPP)(C4O4)2(H2O)2)]2H2O (4), [Ni2(TPP)(C4O4)(H2O)2Cl2]7H2O (5) and [Cu2(TPP)(H2O)2Cl2)](C4O4)2H2O (6). The complexes (2), (3) and (6) had their structures determined by single crystal X-ray diffraction analysis. The compound (3) is an one-dimensional coordination polymer extended through squarate ion coordinated to the Cu(II) sites in the µ-1,2-bis(monodentate) bridging mode. The oxocarbon ligand acts as counter-ion in compounds (2) and (6). The synthesis involving the croconate ion led to the taking of seven novel compounds named: {[Co(MBP)2(NO3)]2+[Co(C5O5)2(H2O)4]2-}.6H2O (7), [Ni(MBP)2(C5O5)] (8), [Cu(MBP)(C5O5)(H2O)] (9), {[Mn2(BPP)2(C5O5)2(H2O)4].3H2O}n (10), {[Co2(BPP)2(C5O5)2(H2O)4].2H2O}n (11), {[Ni2(BPP)3(C5O5)2(H2O)4].5H2O}n (12) and {[Cu(BPP)(C5O5)(H2O)3]}n (13). The compounds (7), (8) and (10) had their structures determined by single crystal X-ray diffraction analysis. The complex (7) is dinuclear, consisting of one cationic and one anionic portion that has two croconate ions coordinated to the metal center in a monodentate fashion, while compound (8) is mononuclear with croconate dianion coordinated to Ni(II) in the 1,2-bidentate mode. In compound (7) it can be noticed the presence of hydrogen interactions extending the arrangement into two dimensions, while in (8), π-π stacking interactions extend the supramolecular arrangement in one dimension. Compound (10) is a two-dimensional coordination polymer where both BPP nitrogen ligands adopt a TG (trans-gauche) conformation. The polymer has two croconate ions with different coordination modes, one adopts the 1,2-bidentate mode and the other acts in an unusual -1,2-bis(monodentate) bridging mode, which has no reports in the literature. This 2-D polymer network presents (6,3) structural topology. Two 2-D sheets interlocked each other in a parallel way generating an interpenetrated structure. Through the synthesis involving the croconate violet dianion was obtained two compounds, named: [Co(MBP)2(CV)] (14) and {[Mn(BPP)2(H2O)2](CV).2H2O)]}n (15). Compound (15) had its structure determined by single crystal X-ray diffraction analysis. It has two BPP ligands, in the TG (trans-gauche) conformation, bridging two sites of Mn(II) generating a one-dimensional polymeric array in which the croconato violet dianions act as counter-ions. There is the presence of hydrogen bonding interactions in the structure which are responsible for the extension of the supramolecular arrangements into two and three dimensions.

Secretion is the passage of macromolecules across cellular membranes. In bacteria, secretion is essential for virulence and survival. Gram-negative bacteria use specialized envelope-spanning multiprotein complexes to secrete macromolecules called type IV secretion system (T4SS). T4SSs mediate the secretion of monomeric proteins, multisubunit protein toxins and nucleoprotein complexes. Also, they contribute to the horizontal spread of plasmid-encoded antibiotic resistance genes. Consequently, they are potential targets for antivirulence drugs. Gram- negative bacteria have two membranes that the secretion complex spans. As a result, the T4SS consists of proteins inserted in the membranes and of soluble proteins that face into or out of the bacterial cell. The details of channel assembly and structure are not known, although recent advances have revealed the structure of the core secretion channel. VirB8 is an inner membrane protein of the complex that interacts with many other T4SS subunits and works as nucleation factor for T4SS channel assembly. Biophysical studies and NMR experiments in particular were conducted to characterize the structural aspects of VirB8 interactions. Dynamic regions of VirB8 during monomer-to-dimer transition were identified by NMR spectroscopy. X-ray crystal and NMR analyses revealed structural differences at the helical regions (α-1 and α-4) of wild-type VirB8 and its monomeric variant VirB8M102R. Fragment screening identified small molecules binding to the wild-type and monomeric variant. In silico docking analyses suggested that the surface groove in the VirB8 structure is important for effective binding of the small molecules. NMR experiments and biochemical assays demonstrated that the β-sheet domain (β1 in particular) is the binding interface of VirB8 for the interaction with VirB10. The identified interface has functional importance for T4SS-mediated conjugation. In addition, I used NMR spectroscopy to identify changes in the structure of VirB8 upon interaction with VirB5. Altogether, structural and biochemical studies on periplasmic and full length VirB8 enabled us to characterize the sequence of interactions between VirB8 and other VirB proteins during T4SS complex assembly and function. The results of this research may lead to an innovative strategy for the development of novel antimicrobial drugs. / La sécrétion est le passage de macromolécules à travers les membranes cellulaires. Chez les bactéries, la sécrétion est essentielle pour la virulence et la survie. Les bactéries à Gramnégatif utilisent le système de sécrétion de type IV (SST4) pour la sécrétion de toxines et de nucléoprotéines. Les SST4 contribuent notamment à la propagation des gènes de résistance aux antibiotiques. Pour cette raison, les composants du SST4 sont des cibles potentielles pour le développement de médicaments antivirulence. Le SST4 est un complexe protéique qui s’étend entre la double membrane de la bactérie à Gram-négatif. Les protéines qui le composent sont insérées dans les membranes cellulaires ou solubles. Bien que la structure du pore central du SST4 ait été résolue récemment, les détails de l'assemblage et la structure de ce complexe ne sont pas connus. VirB8 est une protéine de la membrane interne qui interagit avec de nombreuses autres sous-unités du SST4. Il s’agit d’un acteur central de l'assemblage du SST4. Des études biophysiques, et notamment des expériences de RMN ont ainsi été réalisées pour caractériser les aspects structuraux des interactions avec VirB8. Des regions dynamiques dans la structure de VirB8 ont été identifiées par spectroscopie RMN lors de la transition entre la forme monomérique et dimérique. Les analyses de cristallographie et de RMN ont révélé des différences structurales dans les régions hélicoïdales (α1 et α4) de VirB8 wild-type et du variant monomérique VirB8M102R. Le criblage de fragments a permis d’identifier de petites molécules capables de se lier à VirB8 ainsi qu’au variant monomérique. Les analyses d’arrimage moléculaire in silico suggèrent que la rainure de surface dans la structure VirB8 est importante pour laliaison de ces petites molécules. Les expériences de RMN et les essais biochimiques révèlent que le feuillet β (β1 en particulier) constitue l'interface d’interaction entre VirB8 et VirB10. Cette interface d’interaction est d’ailleurs importante pour la conjugaison du SST4. De plus, j'ai identifié des changements dans la structure de VirB8 lors de l'interaction avec VirB5. Les études sur la protéine VirB8 nous ont permis de caractériser la séquence d'événements entre VirB8 et d'autres protéines VirB, régulant l'assemblage et la fonction du SST4.

Le kétoprofène est un anti-inflammatoire non stéroïdien connu par ses propriétés analgésiques et antipyrétiques. Cependant, il présente une très faible solubilité dans l'eau, ce qui limite sa biodisponibilité. Afin de résoudre ce problème, le principe actif est administré sous forme de sels solubles dans l’eau avec le sodium, la lysine, l’arginine, la N-méthylglucamine et le trométamol. L’objectif de cette thèse était d’apporter pour la première fois la caractérisation structurale des sels de kétoprofène racémique et du S-kétoprofène avec la L-lysine et le trométamol, et de chercher à obtenir la structure cristalline de nouveaux co-cristaux ou sels de kétoprofène, pour analyser la relation structure-propriétés de ces formes solides. Nous avons réussi à faire la croissance cristalline des sels de kétoprofène racémique et de S-kétoprofène avec le trométamol et la L-lysine, ainsi qu’avec l’amine 2-amino-2-méthylpropanol. L’analyse des structures de ces sels a montré qu’ils sont tous formés par des couches anioniques de kétoprofènates entre les quelles s’insèrent les cations grâces aux liaisons hydrogène fortes de type N-H…O et O-H…O. Les cations forment des couches dans les sels avec le trométamol et la L-lysine. Cependant, ils ne sont connectés que par des interactions de Van der Waals dans les sels de 2-amino-2-méthylpropanol. La cohésion des couches anioniques est assurée par des interactions faibles de type C-H…O, C-H…π ou C-H…N. L’étude de l’épaisseur des couches anionique, ainsi que la surface et le volume occupé par un anion kétoprofènate dans une couche montre des variations significatives dans les différents sels. Ces variations peuvent être expliquées par des différences des conformations des anions kétoprofènates. L’étude des paramètres géométriques des anions kétoprofènates dans les sels et ceux des molécules de kétoprofène dans les principes actifs montre que les variations les plus importantes touchent les angles de torsions engageant le groupement carboxylate/acide carboxylique qui interagit avec les molécules/anions voisines par des liaisons hydrogène intermoléculaires courtes et fortement directionnelles. Les interactions dans lesquelles les cycles aromatiques sont engagés sont plutôt faibles, par conséquent les angles de torsions mettant en jeu ces cycles varient peu dans les différentes structures cristallines. Différentes techniques ont été également utilisées pour caractériser les sels : diffraction des rayons X sur poudre, calorimétrie différentielle à balayage (DSC), spectroscopie infrarouge (IR), analyse thermogravimétrique (ATG) et résonance magnétique nucléaire à l’état solide (RMN). Les résultats obtenus ont été corrélés aux structures cristallines. Les mesures de solubilité du sel de kétoprofène racémique-trométamol et des deux polymorphes des sels de S-kétoprofène avec le trométamol confirment que ces derniers ont des solubilités très améliorées par rapport aux principes actifs purs / Ketoprofen is a non-steroidal anti-inflammatory drug known by its analgesic and antipyretic properties. However, it has a very low water solubility, which limits its bioavailability. To solve this problem, the active pharmaceutical ingredient is administered as a water soluble salt with sodium, lysine, arginine, N-methylglucamine or trometamol. The scope of this thesis is to study, for the first time, the crystal structures of salts of both racemic and S-ketoprofen with L-lysine and trometamol, and to obtain the crystal structure of new ketoprofen co-crystals or salts, in order to analyze the relationship between the structure and the properties of these solid forms. We succeeded to control the crystal growth of the salts of racemic and S-ketoprofen with trometamol and L-lysine, and with 2-amino-2-methyl propanol. The analysis of these salt structures has shown that they are formed by anionic layers of ketoprofenates which are inserted between the cations thanks to strong N-H...O and O-H...O hydrogen bonds. The cations form layers in trometamol and L-lysine salts. However, they are only connected by van der Waals interactions in the salts of 2-amino-2-methylpropanol. The cohesion of the anionic layers is ensured by weak C-H...O, C-H...π or C-H...N interactions. The study of the thickness of anionic layers, as well as that of the surface and the volume occupied by a ketoprofenate anion in each anionic layer, shows significant differences in the salts. These variations may be explained by differences in the conformations of ketoprofenates anions. The study of geometrical parameters of ketoprofenate anions in the salts and those of the ketoprofen molecules in the pure active ingredients shows that the most important changes affect the twisting angles engaging the carboxylate/carboxylic acid that interacts with neighboring molecules/anions by short and highly directional intermolecular hydrogen bonds. The interactions in which the aromatic rings are incurred are rather weak, therefore the twisting angles involving these cycles slightly vary in the different crystal structures. Various techniques have also been used to characterize the salt, such as powder X-ray diffraction, differential scanning calorimetry (DSC), infrared (IR) spectroscopy, thermogravimetric analysis (TGA) and solid state nuclear magnetic resonance (NMR). The results were correlated with the crystal structures. The solubility measurements of the racemic ketoprofen-trometamol salt and the two polymorphs of S-ketoprofen-trometamol salts confirm that they have greatly improved solubility compared to the pure active ingredients

Mon projet a porté sur la caractérisation du mécanisme moléculaire des enzymes d'arenavirus (une 3'-5' exoribonucléase et une endonuclease) impliquées dans l'inhibition de la réponse innée IFN de type I et dans le vole de coiffe respectivement, et le développement d'une stratégie thérapeutique basée sur leur structures. Premièrement, j'ai résolu deux structures cristallographiques à haute résolution du domaine exoribonucléases du virus Mopeia (NP-exo MOPV) -un homologue du virus Lassa pathogène- en complexe avec deux ions différents. Ensuite, j'ai effectué une caractérisation fonctionnelle de l’activité exoribonucléase 3'-5' codée par ce domaine. Une corrélation entre la structure et la fonction de NP-exo MOPV démontre que; L’activité exoribonucléase 3'-5' est conservée chez les arenavirus pathogènes ainsi que chez les non-pathogènes. J'ai démontré pour la première fois que l'exoribonucléase est capable d'exciser un ARN misapparié, suggérant ainsi une potentielle activité de correction d'erreur par cette enzyme. Avec la structure de NP-exo MOPV, j'ai développé une stratégie in silico pour identifier des inhibiteurs potentiels spécifiques contre son activité et un inhibiteur a était identifié.En parallèle, nous avons résolu deux structures cristallographiques du domaine de l'endonuclease du virus de la LCMV en complexe avec deux ions catalytiques et deux composés appartenant a la famille des diketo. En résumé, ce travail éclaircit le rôle des exoribonucléases de la famille d'Arenaviridae allant de l’évasion de l'immunité innée à son implication directe dans la réplication. Il ouvre également la voie au développement des inhibiteurs contre ces nucléases. / My PhD work focused on the characterization of the molecular mechanism of two arenavirus enzymes - a 3'-5' exoribonuclease and an endonuclease - implicated in type I IFN suppression and mRNA cap-snatching respectively and the design of a structure based-drug strategy against them. First I solved two high resolution crystal structures of the exoribonuclease domain of Mopeia virus (NP-exo MOPV) -a non pathogenic homologue of the highly pathogenic Lassa virus- in complex with different metal ions. Next I performed an in depth functional characterization of the 3'-5' exoribonuclease activity encoded by this domain. By correlating the structure and function of NP-exo MOPV, I showed that; the 3'-5' exoribonuclease activity is conserved in pathogenic as well as in non-pathogenic arenaviruses. Also, I showed for the first time that this enzyme is able to excise a mismatched RNA suggesting that, arenaviruses might posses a mechanism to limit error incorporation by the RdR polymerase during replication. Using the crystal structure of NP-exo MOPV I designed a structure-based strategy to identify potential inhibitors specific for the 3'-5' exoribonuclease activity and have identified a potential inhibitor.Alongside, we solved two crystal structures of the endonuclease domain of LCMV in complex with two catalytic ions and two compounds belonging to the diketo family.In conclusion, this work has a deep implication extending the role of the Arenaviridae exoribonuclease from innate immunity evasion to direct implication in replication. It also paves the way for the development of inhibitors against these arenavirus nucleases.

The binding of different proteins involved in processes such as transcription, replication and chromatin compaction to regions of the genome is regulated by the structure of DNA. Thus, DNA structure acts as the crucial link modulating evolutionary selection of the DNA sequence based on its own function, and the function of the proteins it encodes. The aim of this work is to examine the role of intrinsic, sequence-dependent structural variations vis-a -vis the protein-induced variations, in allowing DNA to assume geometries necessary for binding by proteins. For this purpose, we carried out analyses of datasets of X-ray crystal structures of free and protein-bound DNA, and molecular dynamics simulation studies of few free DNA structures and a protein-DNA complex. Each of the projects described below will appear as a separate chapter in the thesis. Analysis of X-ray crystal structure datasets Dataset of high-resolution X-ray crystal structures of free and protein-bound DNA This project was initiated with the aim of investigating the variation in A-and B-forms of DNA and the role they play in the binding of proteins. However, a survey of the existing literature indicated that the terms ‘A-DNA’ and ‘B-DNA’ were being used rather loosely and several different parameters at the local structural level were being used by various investigators to characterise these structures. Hence a systematic study was taken up to analyse all high-resolution free DNA structures comprising of sufficient number of contiguous Watson-Crick basepairs, irrespective of how they were classified by the existing databases. We also carried out a study of double-helical, Watson-Crick basepaired, free RNA structures for comparison. The structures in the RNA dataset were observed to rigidly assume the A-form and hence the average values of different parameters for that dataset were used to characterise the A-form. The analysis of free DNA and RNA structures was accompanied by an analysis of protein-bound DNA crystal structures. DNA structures bound to the helix-turn-helix motif in proteins were also analysed separately. The analysis of free DNA and RNA structures allowed us to pinpoint the parameters suitable for discriminating A-and B-forms of DNA at the local structural level. The results illustrated that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A-and the B-forms. Most protein-bound DNA structures, including those with large, smooth curvature, were observed to assume the B-form. The A-form was observed to be limited to a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. Thus our study highlighted the structural versatility of B-form DNA, which allowed it to take up a range of global geometries to accommodate most DNA-binding protein motifs. Dataset of X-ray crystal structures of the nucleosome The study of high-resolution structures of free and protein-bound DNA was followed by an analysis of a dataset of X-ray crystal structures of the nucleosome, which is the fundamental repeating unit of the eukaryotic chromosome, and has been shown to play an important role in transcription regulation. Our results indicated that there is an ensemble of dinucleotide and trinucleotide level parameters that can give rise to similar global nucleosome structures. We therefore raise doubts about the use of the best resolved nucleosome structure as the template to calculate the energy required by putative nucleosome-forming sequences for adopting the nucleosome structure. Based on our results, we have proposed that the local and global level structural variability of DNA may act as a significant factor influencing the formation of nucleosomes in the vicinity of high-plasticity genes, and in determining the probability of binding by regulatory proteins. Molecular dynamics simulation studies of free and protein-bound DNA structures The analysis of crystal structure databases was complemented by molecular dynamics (MD) studies to investigate the dynamic evolution of the DNA structure in its free and protein-bound states. The following three simulation studies were carried out: Study to examine the biological relevance of the presence of 5-methyl group in thymine nucleotides An investigation of the biological relevance of the 5-methyl group in thymine nucleotides was carried out. For this purpose, comparison of molecular dynamics studies on structures with sequences d(CGCAAAUUUGCG)2and d(CGCAAATTTGCG)2was carried out. Our results showed that the presence of the thymine 5-methyl group was necessary for the A-tract to assume characteristic properties such as a narrow minor groove. It was also shown to modulate local level structural parameters and consequently, the curvature of the longer DNA fragment in which the A-tract was embedded. The analysis also provided possible explanation for the experimentally observed interaction of A-tracts with drugs and DNase-I in the presence and the absence of the thymine 5-methyl group. This project was the first of a series of MD studies, and hence several protocols were tested before finalising the correct protocol. Simulations were carried out using the Berendsen temperature equilibration scheme as well as the Langevin temperature equilibration scheme on both the structures. The Langevin temperature equilibration scheme was found to be unsuitable for nucleic acid simulations, as it caused long-term and possibly permanent disruption of the double-helical structure at the terminal and the neighbouring two positions in the sequence. The Berendsen temperature equilibration scheme was not observed to cause such disruptions. Simulations were also carried out on both structures, with or without initialising the initial ion positions. The position of minimum electrostatic potential, where AMBER8 placed the first counterion, was observed to act as a minimum energy trap from which the counterion could not escape even during the course of several nanoseconds of simulation. Hence, the actual simulations were carried out using the Berendsen temperature equilibration scheme, and after randomisation of initial ion positions. The results of protocol testing have been reported in an appendix. Study of DNA bending and curvature An analysis of DNA bending and curvature was carried out, by MD simulation on structures of three, ∼thirty basepair long sequences, namely, d(G-3(CA4T4G)-C)2, d(G-3(CT4A4G)-C)2and d(T-GACTA5T-GACTA6T-GACTA5T-G). For each molecule, snapshots belonging to a particular global geometry (linear, curved, bent in a particular direction etc.) were grouped together, and the average values of the dinucleotide step parameters for different groups were compared. It was observed that for all the three molecules, the average values for groups corresponding to different global geometries were within 1of each other, indicating that ensemble average values of dinucleotide level parameters are incapable of predicting the global geometry of a DNA molecule. Study of the TraR-Trabox complex The study on DNA bending and curvature was followed by simulations of a protein-DNA complex comprising of the bacterial quorum sensing transcription factor TraR with its promoter region known as Trabox. Simulations of a protein-free wild-type Trabox and a Trabox with two mutations in the spacer region were also carried out. Grouping of DNA snapshots in all the three simulations based on average values of dinucleotide parameters in the spacer region shows how selection of the ‘right’ DNA geometry by proteins works at several levels. The number of snapshots of free mutated Trabox assuming a geometry favourable for protein-binding in terms of average twist alone are less than one-fourth of the corresponding number for free wild-type Trabox. When one applies further selection criteria in terms of other parameters such as roll and slide, the number of mutated Trabox snapshots with a geometry favourable for protein-binding drops to less than 0.5%ofthe total number of MD snapshots. Thus our results highlight how sequence-dependent changes in the structrure of DNA regions, adjacent to those that directly hydrogen-bond to proteins, can also critically influence processes such as transcription. General Conclusion Overall, our results indicate that intrinsic, sequence-dependent structural variations in free B-DNA allow it to sample a large volume of the double-helical conformational space, and assume global geometries that can accomodate most DNA-binding proteins.

Crystal engineering underlies the essence of natural affiliation between the molecule on the one side and the crystal as a supramolecular assembly on the other. Molecular recognition is the fundamental cause for this efficient transformation and if we consider the crystal as a supramolecular entity then it is not at all difficult to conceive crystallization as an outstanding example of molecular recognition. In general, organic compounds often facilitate closed packed crystal structures as described by A. I. Kitaigorodskii in the form of the close packing principle but based on chemical features, there is still a small window to understand, to rationalize and to fashion new crystal structures. Extending the chemical viewpoint as first proposed by J. M. Robertson, the supramolecular synthon model as a descriptor of collective crystal structures has been invoked that enables one to trail the molecular behaviour from an entropy dominated situation in solution to an enthalpy driven progression in the solid state. After 20 years, the concept of the supramolecular synthon has stood the test of time because of its simplicity and effectiveness towards the implementation in complex crystal structures and has led the scientific community to further handle complex and interesting ideas in structural chemistry and supramolecular synthesis. The complexity of dynamic and progressive behavior of molecules during crystallization may be understood by the analogous argument of protein folding; both these complex phenomena decode the emergence of multiple metastable forms before the final structures are attained. These intermediate kinetically driven species may be high energy polymorphs and pseudopolymorphs of the compound in question or semicompact random globules for proteins. Understanding the role of these species in their respective processes is of critical importance in elucidating mechanisms. As an alternative approach, crystal structure prediction (CSP) is also of fundamental importance in the context of understanding the crystallization process. All energy based computational methods of CSP address this problem by scanning the multi-dimensional energy hypersurface. This is performed by computing lattice energy changes with respect to parameters like unit cell dimensions, space group symmetry and the positional coordinates of atoms in the asymmetric unit. Further, the computational prediction of the crystal structure of an organic compound results in several choices, and it is possible that a collection of some of these when taken together forms a pattern that mimics the course of the crystallization process very much in the manner that structure correlation mimics covalent bond breaking and making. With all these developments, one is truly at the stage today when any experimental or computed crystal structure is just that, a crystal structure of the molecule in question and it is part of a complex and dynamic structural space which may include a part of the supramolecular reaction trajectory for crystallization itself. Accordingly, this thesis emphasizes the importance of kinetic events during crystallization and proposes some strategies to access the inaccessible domains of this structural space of a given compound. I have exploited the supramolecular synthon model to understand the kinetics of the crystallization process and have further extended this understanding towards the isolation of stoichiometric ternary solids. The synthon model also helps one to provide a logical step to explore these remote domains of the complex hyperenergy surface that have collectively been termed as the crystal structure landscape of the compound in question. The precise descriptions of the chapters are mentioned below. Chapter 2 describes fluorosubstitution as a unique chemical probe to explore the high energy crystal structures of benzoic acid in ambient conditions. This landscape exploration of benzoic acid is based on the robust (kinetically favoured) supramolecular homosynthon as well as consistent fluorosubstitution in native compound. This analysis is also supported by synthon based crystal structure prediction which is one of the best ways of monitoring high energy virtual crystal structures. Chapter 3 extends the idea of landscape exploration towards multicomponent systems. The incorporation of an additional compound during crystallization facilitates even complex kinetic environments but using fluorosubstitution as a chemical probe, it again helps to analyse the high energy virtual domains of the given multicomponent system. Similar to chapter 2, the landscape exploration of multicomponent system is also based on the robust (kinetically favoured) supramolecular heterosynthon as well as consistent fluorosubstitution in the native multicomponent system. Chapter 4 emphasizes the importance of synthon modularity as a chemical probe to traverse in the crystal structure landscape of the given multicomponent system. Here, I have quantified the role of the definitive synthon, by using the supramolecular synthon based fragment approach (SBFA), in the emergence of polymorphism in cocrystals. In latter part of this chapter, I utilized this collective kinetic information in order to realize the combinatorial nature of the crystallization process and showed the complex combinatorial synthesis of ternary solids which itself is considered to be an arduous exercise. Chapter 5 discusses the importance of kinetic information which were fetched from the corresponding multicomponent landscapes and were further utilized for combinatorial synthesis of ternary solids. Although the combinatorial idea is well established in solution, this chapter highlights the first experimental evidence of this idea in the solid state and shows preferred amplification of certain supramolecular synthons from corresponding libraries in the supersaturated crystallizing medium. Chapter 6 extends the combinatorial idea of crystallization even further by using highly flexible organic compounds that collectively provide larger structural space during crystallization. Using the delicate kinetic information about the molecular and supramolecular features, this chapter describes the preferential selection of molecular conformation and supramolecular synthons from the supersaturated solution during the molecule→crystal pathway. In summary, the idea of the crystal structure landscape provides an extended interpretation about some of the complex ideas namely, crystal energy landscape and polymorphism in modern crystal engineering. The crystallization of an organic compound often depends upon intrinsic chemical features and accordingly one selects optimized crystallization routes in the corresponding landscape through decisive experimental conditions. As a final note, the idea of the crystal structure landscape enables one to (at least qualitatively) understand the importance of crystallization kinetics which is understandably a difficult task.

Perovskite oxides have provided a wide variety of exotic functionalities based on their unique physical and chemical properties. By combining different perovskite oxides, interesting physical phenomena have been observed at the interfaces of perovskite heterostructures. The most interesting among these phenomena is the formation of two dimensional electron gas at the interface of two perovskite materials SrTiO3 and LaAlO3 which led to a number of fascinating physical properties such as metal-insulator transition, super-conductivity, large negative magnetoresistance and so on. This has raised the interest in exploiting the interface of various hybrids structures built on the perovskite oxide backbone. On the other hand, the two dimensional (2D) van der Waals materials such as graphene, MoS2, boron nitride etc. represent a new paradigm in the 2D electron-ics. The functionalities of these individual materials have been combined to obtain new enriched functionalities by stacking different materials together forming van der Waals heterostructures. In this work, we present a detailed study of the interface in hybrid structures made of vander Waals materials (graphene and MoS2) and their hybrids with a perovskite material namely, SrTiO3 which is known as the building block of complex oxide heterostructures. In graphene-MoS2 vertical heterostructure, we have carried out a detailed set of investigations on the modulation of the Schottky barrier at the graphene-MoS2 interface with varying external electric field. By using different stacking sequences and device structures, we obtained high mobility at large current on-off ratio at room temperature along with a tunable Schottky barrier which can be varied as high as ∼ 0.4 eV by applying electric field. We also explored the interface of graphene and SrTiO3 as well as MoS2 and SrTiO3 by electrical transport and low frequency 1/f noise measurements. We observed a hysteretic feature in the transfer characteristics of dual gated graphene and MoS2 field effect transistors on SrTiO3. The dual gated geometry enabled us to measure the effective capacitance of SrTiO3 interface which showed an enhancement indicating the possible existence of negative capacitance developed by the surface dipoles at the interface of SrTiO3 and the graphene or MoS2 channel. Our 1/f noise study and the analysis of higher order statistics of noise also support the possibility of electric field-driven reorient able surface dipoles at the interface.

Since NiTi shape memory alloy (SMA) was discovered in the early 1960s, great progress has been made in understanding the properties and mechanisms of NiTi SMA and in developing associated products. For several decades, most of the scientific research and industrial interests on NiTi SMA has focused on its superelastic applications in the biomedical field and shape memory based “smart” devices, which involves the low strain rate (around 0.001 s^-1) response of NiTi SMA. Due to either stress-induced martensite phase transformation or stress induced martensite variant reorientation under the applied load, NiTi SMA has exhibited a high damping capacity in both austenitic and martensitic phase. Recently, there has been an increasing interest in exploitation of the high damping capacity of NiTi SMA to develop high strain rate related applications such as seismic damping elements and energy absorbing devices. However, a systematic study on the influence of strain, strain rate and temperature on the mechanical properties, phase transformation, microstructure and crystal structure is still limited, which leads to the difficulties in the design of products being subjected to high strain rate loading conditions. The four main objectives of the current research are: (1) achieve the single loading and the control of strain, constant strain rate and temperature in high strain rate compression tests of NiTi SMA specimens using Kolsky (split Hopkinson) compression bar; (2) explore the high strain rate compressive responses of NiTi SMA specimens as a function of strain (1.4%, 1.8%, 3.0%, 4.8%, and 9.6%), strain rate (400, 800 and 1200 s^-1), and temperature (room temperature (294 K) and 373 K); (3) characterize and compare the microstructure, phase transformation and crystal structure of NiTi SMAs before and after high strain rate compression; and (4) correlate high strain rate deformation with the changes of microstructure, phase transformation characteristics and crystal structure. Based on the results from this study, it was found that: (1) the compressive stress strain curves of martensitic NiTi SMAs under quasi-static loading conditions are different from those under high strain rate loading conditions, where higher strain hardening was observed; (2) the critical stress and stress plateau of martensitic NiTi SMAs are sensitive to the strain rate and temperature, especially at 373K, which results from the interplay between strain hardening and thermal softening; (3) the microstructure of martensitic NiTi SMA has changed with increasing strain rate at room temperature (294 K), resulting in the reduction in the area of ordered martensite region, while that area increases after deformation at elevated temperature (373K); (4) the phase transformation characteristic temperatures are more sensitive to deformation strain than strain rate; (5) the preferred crystal plane of martensitic NiTi SMA has changed from (11 ̅1)M before compression to (111)M after compression at room temperature (294 K), while the preferred plane remains exactly the same for martensitic NiTi SMA before and after compression at 373 K. Lastly, dynamic recovery and recrystallization are also observed after deformation of martensitic NiTi SMA at 373K.

<p><br />U disertaciji su opisane sinteze i fizičko-hemijske karakterizacije 32 kompleksa kobalta(III), nikla(II) i bakra(II) sa ligandima S-metilizotiosemikarbazonom 2-acetilpiridina (HL&sup1;), bis(S-metilizotiosemikarbazonom) 2,6-diacetilpiridina (H₂L&sup2;), tiosemikarbazonom-S-metilizotiosemikarbazonom 2,6-diacetilpiridina (HL&sup3;), 1-adamantoilhidrazonom 2-acetilpiridina (HL⁴) i 1-adamantoilhidrazonom di(2-piridil)-ketona (HL⁵).</p><p>Kako ligandi HL&sup3;, HL⁴ i HL⁵ do sada nisu bili sintetisani, dobijeni rezultati ujedno predstavljaju i prve iz njihove koordinacione hemije. Iako je sa S-metilizotiosemikarbazonom 2-acetilpiridina poznato nekoliko kompleksa, do sada nijedan od njih nije strukturno okarakterisan, tako da su rezultati prikazani u ovoj disertaciji dali jasnu sliku o načinima koordinacije HL&sup1;. Takođe, kako je sa H₂L&sup2; poznat vrlo malo broj kompleksa, dobijeni rezultati su dali značajan doprinos razumevanju koordinacione hemije ovog liganda.</p><p>Gotovo svi sintetisani kompleksi (njih 27 od 32) su strukturno okarakterisani metodom rendgenske kristalografije. Odabrana jedinjenja su ispitana metodama termičke analize, a utvrđena je njihova antimikrobna i citotoksična aktivnost.</p><p>&nbsp;</p> / <p>This thesis describes syntheses and physico-chemical characterizations of 32 complexes of cobalt(III), nickel(II) and copper(II), with ligands 2-acetylpyridine S-methylisothiosemicarbazone (HL&sup1;), 2,6-dicetylpyridine bis(S-methylisothiosemicarbazone) (H₂L&sup2;), thiosemicarbazone-S-methylisothiosemicarbazone 2,6-dicetylpyridine (HL&sup3;), 2-acetylpyridine 1-adamantoylhydrazone (HL⁴), and di(2-pyridil)-ketone 1-adamantoylhydrazone (HL⁵).</p><p>Since the ligands HL&sup3;, HL⁴, and HL⁵ were not synthetized hitherto, the obtained results are the first regarding their coordination chemistry as well. Even though there are several complexes reported with 2-acetylpyridine S-methylisothiosemicarbazone as a ligand, none of them was structurally characterized. Therefore, here presented results gave clear insight into coordination modes of the HL&sup1;. Moreover, since there is limited number of complexes with H₂L&sup2; reported hitherto, the obtained results gave significant contribution to understanding of its coordination chemistry.</p><p>Almost each synthetized complex (27 out of 32) was structurally characterized by means of single crystal X-ray crystallography. The selected compounds were characterized by thermal analysis, and their antimicrobial and cytotoxic activity were determined.</p>

The new phases Ca3Pt4+xGe13−y (x = 0.1; y = 0.4; space group I213; a = 18.0578(1) Å; RI = 0.063; RP = 0.083) and Yb3Pt4Ge13 (space group P42cm; a = 12.7479(1) Å; c = 9.0009(1) Å; RI = 0.061, RP = 0.117) are obtained by high-pressure, high-temperature synthesis and crystallize in new distortion variants of the Pr3Rh4Sn13 type. Yb3Pt4Ge13 features Yb in a temperature-independent non-magnetic 4f14 (Yb2+) configuration validated by X-ray absorption spectra and resonant inelastic X-ray scattering data. Ca3Pt4+xGe13−y is diamagnetic (χ0 = −5.05 × 10−6 emu mol−1). The Sommerfeld coefficient γ = 4.4 mJ mol−1 K−2 for Ca3Pt4+xGe13−y, indicates metallic properties with a low density of states at the Fermi level in good agreement with electronic structure calculation (N(EF) = 3.3 eV−1/f.u.)); the Debye temperature (θD) is 398 K. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.