Les propriétés des matériaux découlent en partie de leur organisation à l’échelle nano ou microscopique. Dans cette thèse, on montre qu’en contrôlant la chimie aux interfaces, des organisations très régulières peuvent être obtenus spontanément dans divers matériaux polymères.Dans une première, la chimie supramoléculaire a été utilisée pour contrôler l’organisation en masse de polymères greffés à une ou deux de leurs extrémités par la thymine (Thy) ou la 2,6-diamino-1,3,5-triazine (DAT), deux unités supramoléculaires complémentaires s’associant par liaisons hydrogène. Quelque soit la nature de la chaine polymère (PE, PDMS, PPG), les matériaux présentent des organisations lamellaires nanoscopiques très régulières lorsque l’unité terminale (Thy) et/ou la chaine (PE) cristallisent. Les contributions respectives à ces organisations de la ségrégation de phase, de la cristallisation, des liaisons supramoléculaires et des interactions secondaires ont été déterminées. Il a été montré que le confinement des chaines polymères dans les lamelles empêche la formation de chaines de grandes masses molaires. Cependant, les interactions supramoléculaires Thy/DAT permettent de former des copolymères à blocs supramoléculaires en mélangeant des chaines incompatibles fonctionnalisées par ces unités.Dans une seconde partie, nous avons montré que la texturation spontanée de films acrylates photopolymérisés à l’air est gouvernée à l’interface formulation/air par l’équilibre des cinétiques de polymérisation et d’inhibition par l’oxygène. Des morphologies microscopiques très régulières, hexagonales, lamellaires ou cacahuètes, sont obtenues en contrôlant différents paramètres expérimentaux et ce pour une large gamme d’épaisseur de film (6 µm – 2 mm). L’auto-texturation confère aux films des propriétés optiques singulières (flou, clarté) qui peuvent être modulées en ajustant les caractéristiques de la morphologie. / Materials properties very often derive from their nano or micro-scale organization. In this thesis, we evidence that controlling the chemistry at the interfaces allows obtaining spontaneously very regular organizations in various polymer materials.In the first part, supramolecular chemistry has been used to control the organization in the bulk of polymer grafted at one or both extremities by thymine (Thy) or 2,6-diamino-1,3,5-triazine (DAT), two self-complementary supramolecular units interacting via hydrogen bonds. Whatever the polymer nature (PE, PDMS, PPG), materials present very regular nanoscale long-range ordered lamellar organizations if the end group crystallize (Thy) and/or the chain crystallize (PE). Respective contributions to these organizations of phase segregation, crystallization, supramolecular interactions and secondary interactions have been determined. It was shown that the confinement of chains in lamellae prevent the formation of high molecular weight chains, resulting in poor mechanical properties. However, Thy/DAT interactions allow creating supramolecular block copolymers by mixing incompatible chains functionalized with these units.In the second part, we have studied the spontaneous formation of patterns at the film surface of acrylate film during their photopolymerization under air. This phenomenon occurs if there is a balance at the film surface between the polymerization and the oxygen inhibition rates. Very regular microscale patterns (hexagons, lamellae, peanuts) have been generated by controlling some experimental parameters (UV intensity, initiator concentration) for a wide range of film thicknesses (6 µm – 2 mm). Self-patterning gives interesting optical properties to the films (haze, clarity) which can be modulated by adjusting the patterns wavelength and amplitude.

Proton-coupled electron transfer (PCET) is one of the elementary reactions occurring in many chemical and biological systems, such as photosystem II where the oxidation of tyrosine (TyrZ) is coupled to deprotonation of the phenolic proton. This reaction is here modelled by the oxidation of a phenol covalently linked to a Ru(bpy)32+-moitey, which is photo-oxidized by a laser flash-quench method. This model system is unusual as mechanism of PCET is studied in a unimolecular system in water solution. Here we address the question how the nature of the proton accepting base and its hydrogen bond to phenol influence the PCET reaction. In the first part we investigate the effect of an internal hydrogen bond PCET from. Two similar phenols are compared. For both these the proton accepting base is a carboxylate group linked to the phenol on the ortho-position directly or via a methylene group. On the basis of kinetic and thermodynamic arguments it is suggested that the PCET from these occurs via a concerted electron proton transfer (CEP). Moreover, numerical modelling of the kinetic data provides an in-depth analysis of this CEP reaction, including promoting  vibrations  along the O–H–O coordinate that are required to explain the data. The second part describes the study on oxidation of phenol where either water or an external base the proton acceptor. The pH-dependence of the kinetics reveals four mechanistic regions for PCET within the same molecule when water is the base. It is shown that the competition between the mechanisms can be tuned by the strength of the oxidant. Moreover, these studies reveal the conditions that may favour a buffer-assisted PCET over that with deprotonation to water solution.

No description available.

Xylanases are xylan-degrading enzymes, belong to glycosyl hydrolases (GH). Xylanases from the two major families 10 (GH10) and 11 (GH11) catalyze the hydrolysis of internal β-, bonds of xylan backbone. Xylan is the second most abundant polysaccharide in nature. Nearly one third of the dry weight of the higher plants is xylan and therefore, xylanases have an important role in biomass conversions. Currently, the most effective application of xylanases is in prebleaching of kraft pulp to minimize the use of environmentally hazardous chemicals in the subsequent treatment stages. In recent years, therefore, attention is focused on to isolate and/or engineer the xylanases for the industrial requirements. The desirable roperties of xylanases in paper industry are stability and activity at high temperatures and alkaline pH. While he factors responsible for the thermal stability of GH10 xylanases have been analyzed, factors governing the alkaline stability of GH10 xylanases remain poorly understood. The present thesis reports the crystal structures of an alkali thermostable GH10 extracellular endo-xylanase (BSX) from an alkalophilic organism, Bacillus sp. NG-27 in free and xylosaccharides-bound form. The enzyme was purified from the native organism and crystallized. The structure was solved by molecular replacement method. The 2.2 Å crystal structure of the native BSX enzyme is the first structure of an alkali thermostable GH10 family xylanase from an alkalophilic organism. It has unveiled unique protein properties that can form the basis for improving the thermal, alkaline stability and activity by site directed mutagenesis. The comparative study, especially in relation to GH10 xylanases, deciphered important structural features which are likely to be responsible for the alkaline stability of the enzyme. The work exemplifies the mechanism of adaptation of enzymes to function under polyextreme conditions through changes in the nature and composition of solvent-exposed residues. As apparent from the comparative study, the enhanced stability of the protein can be attributed to the surface rich in acidic residues and less number of solvent-exposed Asn as seen in BSX. This situation which may be roughly described as “acidic residues outside and Asn inside”, is a notable feature of alkali-stable GH10 xylanases from alkalophilic organisms. In addition, the candidate has carried out the comprehensive database analysis of the occurrence of C-H…O hydrogen bonds in helices and helix termini of globular proteins. The study provides a compelling evidence that the main-chain Cα and the side-chains CH which participate in C-H…O hydrogen bonds collectively augment the cohesive energy and thereby contribute together with the classical N-H…O hydrogen bonds and other interactions to the overall stability of helix and therefore of proteins. Chapter 1 starts with a brief introduction of xylanases, their classifications and overall folds. At present, a little more than a dozen of crystal structures of GH10 xylanases are known and described in the literature. A brief mention about these structures and their optimum pH and temperature is outlined under a separate section. In view of the industrial importance of the study enzyme, the potential industrial and biotechnological applications of xylanases are detailed in this Chapter. A section is dedicated to describe the present study enzyme BSX, an alkali thermostable endo-xylanase from an alkalophilic bacterium, Bacillus sp. NG-27. BSX has a molecular mass of ~41 kDa and is optimally active at 343 K and at a pH of 8.4. The alkaline thermostability of the wild type BSX is likely to be industrially important. At the end, the scope of the present work is detailed. Chapter 2 presents the purification of xylanase (BSX) from Bacillus sp. NG-27, the crystallization of the native and xylosaccharides-bound BSX, the X-ray diffraction data collection on these crystals and processing of the data. Repeated attempts to crystallize the protein expressed in the chloroplast of transgenic tobacco plant were unsuccessful. However, crystallization was achieved with the protein sample purified from the native source by hanging drop vapour diffusion method. Crystals were grown at both acidic (4.6) and basic pH (8.5). The corresponding crystallization conditions are 0.2 M MgCl2, 0.1 M sodium acetate pH 4.6 and 20% PEG 550 MME and 0.1 M aCl, 0.01 M MgCl2, 0.1 M Tris-HCl pH 8.5 and 15% PEG 8000. Crystals grown at acidic pH were not suitable for X-ray diffraction study. Subsequently, crystal obtained at a basic pH of 8.5 was used for X-ray data collection and it diffracted X-rays to better than 2.2 Å at the home source at cryo-temperature (100 K). Native BSX crystals belong to monoclinic space group C2 with unit cell parameters a = 174.5 Å, b = 54.7 Å, c = 131.5 Å and β = 131.2°. Crystals of xylosaccharides-bound enzyme were grown in a slightly modified crystallization condition of native, 0.1 M NaCl, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5 and 15% PEG 8000 and the enzyme was incubated with xylan prior to setting up the crystallization. Crystals belong to primitive orthorhombic space group P212121 with unit cell parameters a = 59.2 Å, b = 83.8 Å and c = 174.4 Å. A data set was collected using synchrotron radiation of wave length 1.0 Å from a cryo-cooled crystal at Spring-8 BL26B1 beam line, Japan. The Matthews coefficient VM for native and xylosaccharides- bound crystals was calculated to be 2.8 and 2.7 Å3 Da-1, respectively, suggesting two molecules in each crystal asymmetric unit. No twinning was detected in both the datasets and the overall quality of the data sets was found to be good. Chapter 3 details the application of molecular replacement method to the structure solution of native and xylosaccharides-bound BSX, the course of iterative model building and the refinement carried out, and the quality of the final protein structure models. The native-enzyme structure solution was obtained by the molecular replacement method using as a search model the crystal structure (PDB code 1hiz) of the closest homologous, extracellular xylanase (GSX) from Geobacillus stearothermophilus. No non- crystallographic symmetry (NCS) restraint was applied between the two independent molecules in the crystal asymmetric unit at the final round of refinement. The final positional refinement of native BSX converged to R factors of R = 19.4% and Rfree = 23.5% for data between 20.0 to 2.2 Å. The final native model consists of 5704 protein atoms, two Mg2+ ions and 721 solvent water molecules. The final native model was taken as the search structure for the xylosaccharides-bound BSX and a solution with a correlation coefficient of 70.7% and an R-factor of 32.1% was obtained from the molecular replacement calculation. Unlike the native structure refinement, NCS restraint was imposed at all stages of the refinement. Bound xylosaccharides were clearly visible inthe difference Fourier electron density maps. The last round of refinement gave a model with R and Rfree of 21.8% and 25.7%, respectively. The final xylosaccharides-bound model consists of 5766 protein atoms, four Mg2+ ions, 85 atoms belong to bound xylosaccharides and 523 solvent water molecules. No residues were found in the disallowed region of the Ramachandran (φ, ψ) map for both the structures. Chapter 4 describes the native and xylosaccharides-bound BSX crystal structures and the structural comparison of BSX with other GH10 family xylanase crystal structures for which the optimum temperature and pH are known in the literature. BSX folds as the ubiquitous (β/α)8-barrel, a common structural superfold characteristic of GH10 xylanases. The two active site glutamic acid residues, Glu149 and Glu259, are located on opposite sides of the active site cleft and their side-chains are at a distance of 5.5 Å apart suggesting the enzymatic reaction takes place by the retaining mechanism. From the structural superposition of other xylotriose-bound xylanase structures on to the xylosaccharides-bound BSX, structural plasticity in the xylotriose binding can be inferred, implying that the xylose recognition at the subsite -3 displays plasticity and is less specific as opposed to that at -1 and -2 subsites. The stacking interaction of one of the xylose moieties of the xylobiose with the Trp235 seen in BSX provides, for the first time, a structural evidence for the direct involvement of Trp235 in xylosaccharides binding. The crystal structure revealed a metal binding site, found at the C-terminal end of catalytic domain. The presence of metal binding site was not anticipated from earlier theoretically modeled structure and biochemical studies. Further, we have shown experimentally the requirement of Mg2+ ion for the enzyme activity. We havedescribed a novel WP sequence-structure-interaction motif which is present in the (+) side of the active site region and presumably helps in the efficient binding of the carbohydrate moiety of the xylan in the active site cleft of BSX. The structural comparison of BSX with other GH10 xylanases solved to date and characterized to be active at a pH close to neutral was done for the first time. The comparative study revealed the essential structural features which may responsible for the alkaline stability of GH10 xylanases.Briefly, the alkalophilic GH10 xylanases from alkalophilic organisms have surface abundant in acidic residues, the heat and alkaline susceptible residue Asn depleted on the protein surface and increased number of salt bridges. Our study has unveiled the role of the nature and composition of protein surface amino acids in the adaptation of enzymes to polyextreme conditions. The observations reported in the thesis provide important lessons for engineering alkaline stability in xylanases for industrial applications and in general for the understanding of alkaline stability in related proteins. A comparison of the surface features of the BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in polyextremophilicity of proteins, where understanding structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. Chapter 5 summaries the important findings of the present study from the crystal structural analysis of BSX and its comparison with non-alkalophilic GH10 xylanases. Separate sections are made on conclusions and future prospects for the study on BSX. Chapter 6 describes the comprehensive database analysis of C-H…O hydrogen bond in helices of globular proteins. The C-H…O hydrogen bonds found in helices are predominantly of type 5 → 1 or 4 → 1.Our analysis reveals that the Cγ and Cβ hydrogen atom(s) are frequently involved in such hydrogen bonds. A marked preference is noticed for aliphatic β-branched residue Ile to participate in 5 → 1 C- H…O hydrogen bonds involving methylene Cγ1 atom as donor in α-helices. In addition, C-H…O hydrogen bonds are present along with helix stabilizing salt bridges and to some extent compensate for the side-chain conformational entropy loss. Our analysis highlights that a multitude of local C-H…O hydrogen bondsformed by a variety of amino acid side-chains and Cα hydrogen atoms occur in helices and more so at the helix termini. A majority of the helix favouring residues, Met, Glu, Arg, Lys, Leu and Gln which also have large side-chains with more donatable CH groups, have significant propensity to form side-chain to main-chain C-H…O hydrogen bonds in helix. The large side-chains are marked by their ability to shield from the solvent the polar atoms of the peptide backbone and at the same time participate in weak cohesive C-H…O interactions in the helix. This chapter also details the identification for the first time a novel chain reversal motif stabilized by 1 → 5 Cα-H…O interactions. The importance of these hydrogen bonds with respect to helix stability is discussed in the final section of the chapter. Appendix A details the crystallographic and structural analyses oftwares used for the present thesis work. Appendix B describes, in addition to the crystal structure analysis of BSX, the work carried out by the candidate on a comparative study of a thermostable xylanase from Thermoascus aurantiacus, solved in our laboratory at atomic 1.11 Å (293 K) and ultrahigh 0.89 Å (100 K) resolutions. From the comparison, we have for the first time pointed out the possibility of plasticity of ion pairs in proteins with water molecules mediating some of the alternate arrangements. The αβ-loops are relatively less flexible than the βα-loops. The β-strands are least affected structurally with the increase in temperature. Thus the TIM barrel fold in the study enzyme, though having a single domain, may be dissected into parts based on the relative flexibility and described as having a rigid core constituted by the β-barrel and a less rigid exterior formed by the surrounding α-helices. Appendix C presents the crystallization and the preliminary X-ray characterization work done by the author of the thesis on an alkali thermostable cellulase enzyme from Thermomonospora sp. The protein is an extracellular enzyme with molecular mass of 14.2 kDa and interestingly, has the dual activity for both cellulose and xylan. The primary structure of the enzyme is not known. The enzyme was purified from the source organism and crystallized. A complete diffraction data set was collected and processed to 2.3 Å in an orthorhombic space group P212121. Appendix D contains tables which give details about the analysed 5 → 1 Cα- H…O hydrogen bonds in helices and a novel chain reversal motif with 1 → 5 Cα-H…O hydrogen bonds. Appendix E encloses reprints of publications which have resulted from the work reported in the thesis.

BARBOZA, F. M. Estudo das propriedades vibracionais do cristal de timidina em condições extremas de pressão e temperatura. 2017. 187 f. Tese (Doutorado em Física) – Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2017. / Submitted by Giordana Silva (giordana.nascimento@gmail.com) on 2017-04-17T18:08:44Z No. of bitstreams: 1 2017_tese_fmbarboza.pdf: 14915098 bytes, checksum: 92c70871f92588cea1807a2552402d46 (MD5) / Approved for entry into archive by Giordana Silva (giordana.nascimento@gmail.com) on 2017-04-17T18:09:44Z (GMT) No. of bitstreams: 1 2017_tese_fmbarboza.pdf: 14915098 bytes, checksum: 92c70871f92588cea1807a2552402d46 (MD5) / Made available in DSpace on 2017-04-17T18:09:44Z (GMT). No. of bitstreams: 1 2017_tese_fmbarboza.pdf: 14915098 bytes, checksum: 92c70871f92588cea1807a2552402d46 (MD5) Previous issue date: 2017 / The unit of sugar and base connected by a N-β-glycosyl linkage is named a nucleoside. In the present work the nucleoside thymidine, whose molecular formula is C10N2O5H14, was studied by Raman spectroscopy, subjecting it extreme conditions of pressure and temperature, as well as X ray diffraction measurements. An auxiliary analysis of normal crystal vibration modes was performed using first principles calculations using the B3LYP functional together with the Gaussian bases 6-31G+(d) and potential energy distribution analysis (PED). These results, together with literature data and Raman spectroscopy measurements in several thymidine scattering geometries, allowed the identification of the various normal modes of crystal vibration. X-ray diffraction experiments were performed in the temperature range between 83 and 413 K. Experiments of Raman spectroscopy under extreme temperature conditions (20 to 380 K) were performed in the spectral range of 20 to 3400 cm-1. From the analysis of the results, it is possible to draw some conclusions. (i) The thymidine crystal remained stable throughout the investigated temperature range, indicating that the temperature effect is not sufficient to modify the hydrogen bonds present between the molecules in such a way as to modify the symmetry of the crystal. (ii) The material studied showed some slight changes in the vibrational spectra in the experiment performed at low temperatures, suggesting, if not a structural phase transition, at least some conformational modification of the thymidine molecules. Raman spectra of thymidine crystal were obtained for pressures up to 5.0 GPa in a diamond anvil cell. The results show the presence of anomaly in the Raman spectrum at pressures close to 3.0 GPa. This anomaly is characterized by disappearance of lattice modes, appearance of some internal modes, splitting of high wavenumbers modes, downshift of modes associated with hydrogen bonds, changes in the intensity of internal modes and discontinuities of the slopes of the wavenumbers versus pressure for several Raman modes. This set of modifications was interpreted as consequence of a phase transition undergone by thymidine close to 3.0 GPa. Further, decompression to atmospheric pressure generates the original Raman spectrum, showing that the pressure-induced phase transition undergone by thymidine crystals is reversible. A comparison with results on other nucleosides submitted to high pressure is also furnished. / Quando a pentose (glicose) e uma base nitrogenada unem-se por meio de uma ligação N-β glicosídica forma-se uma molécula denominada de nucleosídeo. No presente trabalho o nucleosídeo timidina, cuja fórmula molecular é C10N2O5H14, foi estudado através de espectroscopia Raman, submetendo-o a condições extremas de pressão e de temperatura, além de medidas de difração de raios X. Uma análise auxiliar a respeito dos modos normais de vibração do cristal foi realizada através de cálculos de primeiros princípios utilizando-se o funcional B3LYP em conjunto com as bases gaussianas 6-31G+(d) e análise de distribuição de energia potencial (PED). Esses resultados, juntamente com dados da literatura e medidas de espectrocopia Raman em diversas geometrias de esplalhamento na timidina permitiram uma identificação dos vários modos normais de vibração do cristal. Os experimentos por difração de raios X foram realizados no intervalo de temperatura entre 83 e 413 K. Experimentos de espectroscopia Raman sob condições extremas de temperatura (20 a 380 K) foram realizados no intervalo espectral compreendido entre 20 e 3400 cm-1. Da análise dos resultados, é possível tirar algumas conclusões. (i) O cristal de timidina manteve-se estável em todo o intervalo de temperatura investigado, indicando que o efeito de temperatura não é suficiente para modificar as ligações de hidrogênio presentes entre as moléculas de tal forma que haja modificação da simetria do cristal. (ii) O material estudado apresentou algumas leves mudanças nos espectros vibracionais no experimento realizado a baixas temperaturas, sugerindo, se não uma transição de fase estrutural, pelo menos alguma modificação conformacional das moléculas da timidina. Experimentos submetendo o cristal a pressões de até 5 GPa foram realizados utilizando-se uma célula de pressão a extremos de diamantes. Os resultados mostraram anomalias nos espectros Raman por volta de 3.0 GPa. Essas anomalias foram caracterizadas pelo desaparecimento de alguns modos de rede, surgimento de alguns modos internos, deslocamento para menores números de onda de modos associados a ligações de hidrogênio e descontinuidades dos coeficientes lineares de vários modos nos gráficos de número de onda em função da pressão. Essa série de modificações foram interpretadas como consequência de uma transição de fase sofrida pela timidina por volta de 3.0 GPa. Além disso, a descompressão da amostra até a pressão atmosférica mostrou que a transição de fase é reversível. Também fornecemos uma comparação com resultados de outros nucleosídeos submetidos a altas pressões.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In this work was synthesized and determined the crystal and molecular structure of two silver triazenide complexes, two cadmium triazenide complexes and a zinc triazenide complex. The complexes {Ag[C12H9N2NNNC6H4(NO2)](C5H5N)}2 (1) and {Ag[C6H3Br2NNNC6H3Br2](C5H5N)}2 (2) crystallize in the monoclinic crystal system, space group P2(1)/c and P2(1)/n respectively. The refinement of those structures converge to de follow discordance indexes R1 = 0,0473 and 0,0503 respectively. The structures of complexes (1) and (2) consist of binucleated neutral silver complexes, centrosymmetric and acentric, respectively, in which metal ions are coordinated by two desprotonated molecules of the ligand (L1) and (L2), respectively, and a neutral molecule of the pyridine. Both complexes (1) and (2) show Ag···Ag interactions allowing an expansion of the coordination geometry of distorted tetrahedral from the distorted T in the case of complex (1) and distorted T to a distorted pyramid with square base in the case of complex (2). In addition, the complex (1) shows the formation of 2-D supramolecular arrangement, forming centrosymmetric dimers through interactions Ag-arene- η2, η2 π and hydrogen centrosymmetric bonding C-H···O and formation of supramolecular 3-D to the complex (2) through non-classic centrosymmetric hydrogen bonds C-H···Mi, weak interactions Br2···Br2ii and Br3···Br3ii . The cadmium complex Cd[(C6H3Br2NNNC6H3Br2)(C5H5N)]2 (3) and [Cd(C6H3Br2NNNC6H3NO2OCH3)2(C5H5N)2] (4) are mononucleated. The complex (3) present a distorted octahedral geometry of coordination and the complex (4) present a distorted tetrahedral geometry of coordination. They crystallized on the monoclinic and triclinic crystal system and P2(1)/c and P(-1) space group, respectively. The refinement of those structures converge to the discordance indexes R1 = 0,0310 and 0,0693 respectively. The structure of the complex (3) consists of a neutral mononuclear complex of cadmium, centrosymmetric, in which the ion metal is hexacoordenated, presenting a coordination geometry distorted octahedral with two molecules of ligand (L2) connected in a bidentate chelating and two molecules of pyridine trans. The structure of the complex (4) consists of a neutral mononuclear complex of cadmium, acentric, in which the ion metal is tetracoordenated, with distorted tetrahedral coordination geometry with two molecules of ligand (L3) linked monodentate and two molecules of pyridine. The complex (3) provides 2-D supramolecular arrangement according to the non-classical hydrogen bonds centrosymmetric C16-H16···Bri and Br2···Br4ii and the complex (4) shows 2-D supramolecular arrangement via hydrogen bonds non-classical centrosymmetric C-H···O. The zinc complex Zn(C6H3Br2NNNC6H3Br2)2(C5H5N)2] (5), has distorted tetrahedral coordination geometry similar to the complex (4) since it comprises the ligand (L3), which is coordinated in the same way as observed in the complex (4), and crystallizes in the triclinic crystal system, space group P (-1). The refinement of this structure converged to the discordance indexes R1 = 0.0757. The complex (5) shows 2-D supramolecular arrangement through no-classical hydrogen bonds centrosymmetric C-H···O. / Neste trabalho sintetizou-se e determinou-se a estrutura cristalina e molecular de dois complexos triazenidos de prata, dois complexos triazenidos de cádmio e um complexo triazenido de zinco. Os complexos {Ag[C12H9N2NNNC6H4(NO2)](C5H5N)}2 (1) e {Ag[C6H3Br2NNNC6H3Br2](C5H5N)}2 (2) cristalizam no sistema cristalino monoclínico, grupo espacial P2(1)/c e P2(1)/n respectivamente. O refinamento dessas estruturas convergiu aos índices R1 = 0,0473 e 0,0503 respectivamente. As estruturas dos complexos (1) e (2) são constituídas de complexos binucleados neutros de prata, acêntrico e centrossimétrico, respectivamente, no qual os íons metálicos são tricoordenados por duas moléculas do ligante (L1) e (L2), respectivamente, desprotonados e uma molécula neutra de piridina. Ambos os complexos (1) e (2) apresentam interações Ag···Ag, o que permite uma expansão da geometria de coordenação de T distorcida para tetraédrica distorcida no caso do complexo (1) e T distorcida para uma geometria de coordenação pirâmide de base quadrada distorcida no caso do complexo (2). Além disso, o complexo (1) apresenta a formação de arranjo supramolecular 2-D, formando dímeros centrossimétricos através das interações Ag-areno-η2, η2 π e ligações de hidrogênio não clássicas centrossimétricas C-H···O e formação de arranjo supramolecular 3-D para o complexo (2) via ligações de hidrogênio não clássicas centrossimétricas C-H···Mi, interações fracas do tipo Br2···Br2ii e Br3···Br3ii . Os complexos de Cádmio Cd[(C6H3Br2NNNC6H3Br2)(C5H5N)]2 (3) e [Cd(C6H3Br2NNNC6H3NO2OCH3)2(C5H5N)2] (4) são mononucleados, sendo o complexo (3) com geometria de coordenação octaédrica distorcida e o complexo (4) apresentar uma geometria de coordenação tetraédrica distorcida, cristalizam no sistema cristalino monoclínico e triclínico, grupo espacial P2(1)/c e P(-1), respectivamente. O refinamento dessas estruturas convergiu aos índices R1 = 0,0310 e 0,0693 respectivamente. A estrutura do complexo (3) é constituída de um complexo mononucleado neutro de cádmio, centrossimétrico, no qual o íon metálico é hexacoordenado, apresentando uma geometria de coordenação octaédrica distorcida, com duas moléculas do ligante (L2) ligados de forma quelante bidentada e duas moléculas de piridina em trans. A estrutura do complexo (4) é constituída de um complexo mononucleado neutro de cádmio, acêntrico, no qual o íon metálico é tetracoordenado, apresentando geometria de coordenação tetraédrica distorcida, com duas moléculas do ligante (L3) ligados de forma monodentada ao íon e duas moléculas de piridina. O complexo (3) apresenta arranjo supramolecular 2-D em função das ligações de hidrogênio não clássicas centrossimétricas C16-H16···Bri e das interações Br2···Br4ii e o complexo (4) apresenta arranjo supramolecular 2-D via ligações de hidrogênio não-clássicas centrossimétricas C-H···O. O complexo de zinco Zn(C6H3Br2NNNC6H3Br2)2(C5H5N)2] (5), apresenta geometria de coordenação tetraédrica distorcida semelhante ao complexo (4) já que é composto pelo mesmo ligante L3, o qual se coordenada da mesma forma que observado no complexo (4), cristaliza no sistema cristalino e triclínico, grupo espacial P(-1). O refinamento dessa estrutura convergiu aos índices R1 = 0,0757. O complexo (5) apresenta arranjo supramolecular 2-D via ligações de hidrogênio não-clássicas centrossimétricas C-H···O.

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.

Les résultats présentés dans ce manuscrit décrivent la synthèse et l'étude de silices hybrides organiques-inorganiques visant des applications dans le domaine de la santé. Les précurseurs polysilylés synthétisés sont des dérivés de la triazine comportant des motifs de reconnaissance moléculaire du type donneur-accepteur-donneur qui peuvent complexer des molécules complémentaires, tel que l'acide cyanurique, via des liaisons H. La préparation de matériaux hybrides à partir de ces précurseurs complexés ou non, ainsi que leur mise en forme pour obtenir des nanoparticules, sont réalisées dans des conditions nucléophiles. Ces matériaux sont sensibles aux pH puisque des pH légèrement acides peuvent entrainer la dissociation du complexe. Des précurseurs du même type sont également utilisés pour la fonctionnalisation de nanoparticules de type MCM-41 afin de créer des nanomachines. Ces dernières se sont révélées très efficaces lors d'études in vitro en présentant une mort cellulaire significative pour le cancer du sein. / In this thesis hybrid organic-inorganic silicas have been synthesized and studied for applications in health field.The synthesized polysilylated precursors are based on triazine derivatives including donor-acceptor-donor molecular recognition motifs which can complex complementary compounds, like cyanuric acid, via hydrogen bonds. Hybrid bulk materials as well as nanoparticles, with or without complex, are obtained upon nucleophilic catalysis from these precursors and are shown to be pH-sensitive since a slightly acidic pH could destabilize the complex.In addition, such type of precursors is also used to functionalize MCM-41 nanoparticles in order to prepare nanomachines. In vitro studies showed the efficiency of these systems with significant cell death for breast cancer.

The research work reported in this thesis is focused on the chiral analysis, quantification of enantiomeric composition, assignment of absolute configuration of molecules with chosen functional groups. The weak intra-molecular hydrogen bonding interactions are detected by exploiting several multinuclear and multi-dimensional techniques. Pulse sequences have been designed to manipulate the spin dynamics to derive specific information from the complex NMR spectra encountered in diverse situations. Broadly, the thesis can be classified in to three sections. The section I containing two chapters reports the introduction of new chiral auxiliaries and protocols developed for enantiomeric discrimination, measurement of enantiomeric contents, assignment of absolute configuration for molecules possessing specific functional groups using chiral solvating and derivatizing agents. The section II, reports NMR experimental evidence for the observation of the rare type of intramolecular hydrogen bonds involving organic fluorine in biologically important organic molecules, that are corroborated by extensive DFT based theoretical calculations. The section II also discusses the H/D exchange mechanism as a tool for quantification of HB strengths in organic building blocks. The section III reports the two different novel NMR methodologies designed for deriving information on the scalar interaction strengths in an orchestrated manner. The designed sequences are able to completely eradicate the axial peaks, prevents the evolution of unwanted couplings and also yields ultrahigh resolution in the direct dimension, permitting the accurate measurement of scalar couplings for a particular spin. The brief summary about each chapter is given below. Chapter 1 provides a general introduction to one and two dimensional NMR spectroscopy. The pedagogical approach has been followed to discuss the conceptual understanding of spin physics and the NMR spectral parameters. The basic introduction to chirality, existing approaches in the literature for discrimination of enantiomers and the assignment of absolute configuration of molecules with chosen functional groups and their limitations are briefly discussed. The brief introduction to hydrogen bond, experimental methods to obtain the qualitative information about the strengths of hydrogen bonds, and the theoretical approaches employed in the thesis to corroborate the NMR experimental findings have been provided. The mechanism of H/D exchange, the utilization of exchange rates to derive strengths of intra-molecular hydrogen bond in small molecules have also been discussed. This chapter builds the bridge for the rest of the chapters. Each of these topics are discussed at length in the corresponding chapters. Part I: NMR Chiral Analysis: Novel Protocols Chapter 2 discusses a simple mix and shake method for testing the enantiopurity of primary, secondary and tertiary chiral amines and their derivatives, amino alcohols. The protocol involves the in-situ formation of chiral ammonium borate salt from a mixture of C2 symmetric chiral BINOL, trialkoxyborane and chiral amines. The proposed concept has been convincingly demonstrated for the visualization of enantiomers of a large number of chiral and pro-chiral amines and amino alcohols. The protocol also permits the precise measurement of enantiomeric composition. The significant advantage of the protocol is that it can be performed directly in the NMR tube, without any physical purification. The structure of the borate complex responsible for the enantiodifferentiation of amines has also been established by employing multinuclear NMR techniques and DFT calculations. From DOSY and 11B NMR experiments it has been ascertained that there are only two possible complexes or entities which are responsible for differentiating enantiomers. From the combined utility of DFT calculations and the 11B NMR chemical shifts, the structure of the borate complex has been determined to be an amine-coordinated complex with the N atom of the amine. Chapter 3 discusses a simple chiral derivatizing protocol involving the coupling of 2-formylphenylboronic acid and an optically pure [1,1-binaphthalene]-2,2-diamine for the rapid and accurate determination of the enantiopurity of hydroxy acids and their derivatives, possessing one or two optically active centers. It is established that this protocol is not only rapid method for discrimination of enantiomers but also highly effective for assigning the absolute configuration of various chiral hydroxy acids and their derivatives. The developed protocol involves the coupling of 2-formylphenylboronic acid with (R)-[1,1-binaphthalene]-2,2-diamine, and 2-formylphenylboronic acid with (S)-[1,1-binaphthalene]-2,2-diamine as chiral derivatizing agents. The absence of aliphatic peaks from the derivatizing agent, large chemical shift separation between the discriminated peaks of diastereomers, and the systematic change in the direction of displacement of peaks for an enantiomer in a particular diastereomeric complex, permitted the unambiguous assignment of absolute configuration. Part II : Rare Type of Intramolecular Hydrogen Bonding In chapter 4 The rare occurrence of intramolecular hydrogen bonds of the type N–H˖˖˖F–C, in the derivatives of imides and hydrazides in a low polarity solvent, is convincingly established by employing multi-dimensional and multinuclear solution state NMR experiments. The observation of 1hJFH, 2hJFN, and 2hJFF of significant strengths, where the spin polarization is transmitted through space among the interacting NMR active nuclei, provided strong and conclusive evidence for the existence of intra-molecular hydrogen bonds. Solvent induced perturbations and the variable temperature NMR experiments unambiguously supported the presence of intramolecular hydrogen bond. The two dimensional HOESY and 15N–1H HSQC experiments reveals the existence of multiple conformers in some of the investigated molecules. The 1H DOSY experimental results discarded any possibility of self or cross-dimerization of the molecules. The results of DFT based calculations, viz., Quantum Theory of Atoms In Molecules (QTAIM) and Non Covalent Interaction (NCI), are in close agreement with the NMR experimental findings. In chapter 5 the rates of hydrogen/deuterium (H/D) exchange determined by 1H NMR spectra have been utilized to derive the strength of hydrogen bonds and to monitor the electronic effects in the site-specific halogen substituted benzamides and anilines. The theoretical fitting of the time dependent variation in the integral areas of 1H NMR resonances to the first order decay function permitted the determination of H/D exchange rate constants (k) and their precise half-lives (t1/2) with high degree of reproducibility. The comparative study also permitted the determination of relative strengths of hydrogen bonds and the contribution from electronic effects on the H/D exchange rates. Part III: Novel NMR Methodologies for the Precise Measurement of 1H-1H Couplings Chapter 6 describes two novel NMR methodologies developed for the precise measurement of 1H-1H couplings. Poor chemical shift dispersion and the pairwise interaction among the entire coupled network of protons results in the severely complex and overcrowded one dimensional 1H NMR spectra, hampering both the resonance assignments and the accurate determination of nJHH. The available two-dimensional selective refocusing (SERF) based experiments suffer from the evolution of magnetization from uncoupled protons as intense uninformative axial peaks. This creates ambiguity in the identification of peaks belonging to the coupled partners of a selectively excited proton, hindering the extraction of their interaction strengths. This challenge has been circumvented by designing two novel experimental technique, cited as “Clean-G-SERF” and “PS-Clean-G-SERF”. The Clean-G-SERF technique completely eradicates the axial peaks and suppresses the evolution of unwanted couplings while retaining only the couplings to the selectively excited proton. The method permits the accurate determination of spin-spin couplings even from a complex proton NMR spectrum in an orchestrated manner. The PS-Clean-G-SERF technique has been designed for the complete elimination of axial peaks and undesired couplings, with a blend of ultra-high resolution achieved by real time broad band homonuclear decoupling has been discussed in this chapter. The spin dynamics involved in both these pulse sequences have been discussed. The diverse applications of both these novel experiments have been demonstrated.

La formation des liaisons non covalentes et plus particulièrement des liaisons hydrogène joue un rôle majeur dans de nombreux processus biologiques, atmosphériques et astrophysiques. Les complexes hydratés (1:n) entre une molécule de diacétyle (C4H6O2) et une à plusieurs molécules d’eau (H2O) ont été étudiés selon des approches théoriques et expérimentales dans le but de caractériser leur structure et leur spectre vibrationnel. Sur le plan théorique les propriétés énergétiques, géométriques et vibrationnelles des complexes C4H6O2:(H2O)n ont été déterminées et une étude topologique spécifique a été réalisée sur le complexe 1:1 C4H6O2:H2O. A travers cette étude théorique, les premières étapes du mécanisme d’hydratation du diacétyle ont été mises en évidence et analysées en détail. En s’appuyant sur les techniques spectroscopiques infrarouges d’isolation en matrice de néon et de jet supersonique, plusieurs modes de vibration des isomères du complexe 1:1 ont été identifiés et leurs fréquences déterminées Enfin, un jeu de constantes de couplage anharmonique a été obtenu à partir de l’analyse des bandes harmoniques et de combinaison. / The formation of non-covalent bonds and more particularly hydrogen bonds play a major role in several biological, atmospheric and astrophysical chemistry issues. The theoretical and experimental investigation of hydrated complexes (1:n) between a diacetyl molecule (C4H6O2) and one or several water molecules (H2O) have been studied to characterize their structure and their vibrational spectrum. Energetical, geometrical and vibrational properties of C4H6O2:(H2O)n complexes have been determined from ab initio and DFT calculations. Moreover a topological analysis of the 1:1 C4H6O2:H2O complex has been carried out. Such theoretical investigations enabled to evidence and analyze in detail the first steps of diacetyl hydration. From neon matrix isolation and supersonic jet techniques coupled to infrared spectroscopy, several vibrational modes of 1:1 isomers have been detected and therefore their frequencies have been determined. Finally a set of anharmonic coupling constants have been derived from the spectral analysis of harmonic and combination bands.