Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-05-25T14:19:15Z No. of bitstreams: 1 marianadasilvacunha.pdf: 6235170 bytes, checksum: e49cfdcb2f78bafd1146dd684a809c87 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-05-25T14:48:17Z (GMT) No. of bitstreams: 1 marianadasilvacunha.pdf: 6235170 bytes, checksum: e49cfdcb2f78bafd1146dd684a809c87 (MD5) / Made available in DSpace on 2017-05-25T14:48:17Z (GMT). No. of bitstreams: 1 marianadasilvacunha.pdf: 6235170 bytes, checksum: e49cfdcb2f78bafd1146dd684a809c87 (MD5) Previous issue date: 2017-02-21 / Neste trabalho foi investigada a influência da modificação dos ligantes Hidrogeno psulfobenzoato de potássio (PSB), Ácido 1,2,4,5-benzenotetracarboxílico (BTC) e Ácido 1,5-naftalenodissulfônico tetrahidratado (1,5NDS) nas interações com a molécula de Isoniazida (INH) em três novos compostos, PSB-INH, BTC-INH e 1,5NDS-INH, e também foi realizado um estudo sobre o composto 1,5NDS-INO no qual o ligante Isoniazida sofreu uma termodecomposição, levando à formação do Ácido isonicotínico (INO). Foi realizado um estudo das ligações de hidrogênio formadas entre os ligantes através da análise de superfície de Hirshfeld e gráficos de impressão digital. Estas análises são extremamente sensíveis ao ambiente químico da molécula e são únicas para cada molécula e, dessa forma, permitem a identificação das diferenças entre os empacotamentos cristalinos no estado sólido. Foi observado que, embora a conformação da molécula de Isoniazida seja praticamente idêntica nos compostos PSB-INH, BTC-INH e 1,5NDS-INH e as principais ligações de hidrogênio presentes envolvem interações do tipo N – H···O e O – H···N, os gráficos de impressão digital são diferentes e exibem a influência da modificação dos ligantes. Nos gráficos de impressão digital obtidos as contribuições mais importantes das interações estão relacionadas aos contatos O···H e N···H, que possuem valores de 31,3% e 6,0% para o composto PSB-INH, 49,9% e 6,9% para o composto BTC-INH e 44,8% e 5,0% para o composto 1,5NDS-INH. No composto 1,5NDS-INO as principais ligações de hidrogênio são do tipo O – H···O e O – H···N e a contribuição mais importante para o gráfico de impressão digital está relacionada ao contato O···H, que contribui com 41,9% para a superfície e também ao contato H···H, que contribui com 30,5%. Este trabalho demonstrou como as análises de superfície de Hirshfeld e dos gráficos de impressão digital conseguem identificar diferenças entre as moléculas no estado sólido e permitiu a análise das interações intermoleculares formadas nos diferentes compostos, comprovando a importância dessas novas ferramentas para a análise estrutural. / In this work was investigated the influence of the modification of the ligands Hydrogen p-sulfobenzoate of potassium (PSB), 1,2,4,5-benzenetetracarboxylic acid (BTC) and 1,5-naphthalenedisulfonic acid tetrahydrate (1,5NDS) in interactions with the molecule of Isoniazid (INH) in three new compounds, PSB-INH, BTC-INH and 1,5NDS-INH, and also a study on the compound 1,5NDS-INO in which the Isoniazid ligand underwent a thermodecomposition, leading to the formation of isonicotinic acid (INO). A study of the hydrogen bonds formed between the ligands was carried out through Hirshfeld surface analysis and fingerprint plots. These analysis are extremely sensitive to the chemical environment of the molecule and are unique to each molecule and thus allow identification of the differences between the crystalline packages in the solid state. It was observed that, although the conformation of the Isoniazide molecule is practically identical in the compounds PSB-INH, BTC-INH and 1,5NDS-INH and the main hydrogen bonds present involve N – H ··· O and O – H ··· N, the fingerprint plots are different and exhibit the influence of the modification of the ligands. In the fingerprint plots obtained, the most important contributions of the interactions are related to the contacts O···H and N···H, which have values of 31.3% and 6.0% for the compound PSB-INH, 49.9% and 6.9% for compound BTC-INH and 44.8% and 5.0% for the compound 1.5NDS-INH. In the compound 1,5NDS-INO the main hydrogen bonds are of the O – H ··· O and O – H ··· N type and the most important contribution to the fingerprint plot is related to the contact O···H, which contributes with 41.9% to the surface and also to the H···H contact, which contributes with 30.5%. This work demonstrated how Hirshfeld surface analysis and fingerprint plots can identify differences between molecules in the solid state and allowed the analysis of the intermolecular interactions formed in the different compounds, proving the importance of these new tools for structural analysis.

Orientador: Roberto Rittner Neto / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-19T09:46:54Z (GMT). No. of bitstreams: 1 Cormanich_RodrigoAntonio_M.pdf: 17962045 bytes, checksum: e9b512f22b0c39e10dfff2d962a24647 (MD5) Previous issue date: 2011 / Resumo: São reportadas na presente dissertação as análises conformacionais dos aminoácidos da glicina, L-alanina, sarcosina e N,N-dimetilglicina e dos ésteres metílicos da L-valina, L-fenilalanina e L-tirosina, utilizando cálculos teóricos e espectroscopias de RMN de H e infravermelho. Todos os cálculos foram executados em nível B3LYP/aug-cc-pVDZ e comparados com os dados obtidos experimentalmente, para o caso dos ésteres metílicos da L-valina, L-fenilalanina e L-tirosina utilizando as espectroscopias de RMN de H e de infravermelho. Os valores de JHH em vários solventes forneceram informações importantes a respeito das variações populacionais com a mudança do meio para estes três sistemas moleculares. As populações relativas dos confôrmeros, obtidas em solventes com diferentes valores de constante dielétrica, foram também determinadas pela deconvolução da banda referente ao estiramento da ligação C=O dos espectros de infravermelho. Os resultados experimentais obtidos em cada solvente estão em boa concordância quando comparados com as estruturas obtidas utilizando cálculos teóricos de solvatação implícita IEFPCM (Integral Equation Formalism Polarized Continuum Model) e, portanto, validam estes últimos. Assim, em divergência aos dados da literatura, este trabalho sugere, baseado nas análises de orbitais naturais de ligação (NBO) e de teoria quântica de átomos em moléculas (QTAIM), que as preferências conformacionais destes importantes compostos são governados por efeitos estéricos e hiperconjugativos e não devido à possível formação de ligações de hidrogênio intramoleculares / Abstract: The conformational analysis of glycine, L-alanine, sarcosine and N,N-dimetilglycine aminoacids and L-valine, L-phenylalanine and L-tyrosine methyl esters, using theoretical calculations and H NMR and infrared spectroscopies, are reported in the present dissertation. All calculations were carried out at the B3LYP/aug-cc-pVDZ level of theory and compared with experimental data obtained for the L-valine, L-phenylanaline and L-tyrosine, using the H NMR and infrared spectroscopies. The JHH values in various solvents provided important informations about the populational variation with the environment changing to these three molecular systems. Conformer relative populations, obtained in solvents of different dieletric constant values, were also measured by the infrared spectra C=O stretching band deconvolution. The experimental results obtained in each solvent are in good agreement in comparison to the obtained structures using the implicit solvent model IEFPCM (Integral Equation Formalism Polarized Continuum Model) theoretical calculations and, therefore, validate the last ones. Indeed, in divergence with literature data, this work suggests, within the framework of natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) analysis, that these important compounds conformational preferences are ruled by steric and hyperconjugative effects and not as due to possible intramolecular hydrogen bonding formation / Mestrado / Quimica Organica / Mestre em Química

Ce document contient un rapport scientifique résultant de plus de quatre années de recherche théorique et expérimentale sur un type particulier de systèmes physico-chimiques appelés hydrates de clathrates de gaz. Ces systèmes sont des composés d'inclusion constitués d'un cadre aqueux tridimensionnel contenant des molécules de gaz avec de faibles moments dipolaires dans leurs cavités. Les hydrates de clathrate de gaz sont très importants dans une grande variété de domaines scientifiques liés aux sciences de la vie ou à la planétologie, et ils sont également considérés comme une ressource naturelle principale pour l'industrie de l'énergie. Habituellement, les hydrates de clathrate de gaz nécessitent une pression élevée et une température basse pour être thermodynamiquement stables. En fonction de ces conditions, différentes phases ont été détectées, les plus courantes étant les structures cubiques sI et sII, la sH hexagonale et la structure de glace remplacée orthorhombique (FIS). Notre étude a considérablement progressé dans la connaissance du comportement du méthane et des hydrates de clathrate de dioxyde de carbone dans différentes conditions de pression et de température. En particulier, nous avons contribué à : (i) la détermination et la compréhension des régions thermodynamiques de stabilité, (ii) la caractérisation d'une structure haute pression controversée et (iii) la mise en place d'un nouvel équipement expérimental pour les mesures Raman dans une gamme de pression jusqu'à 1 GPa [...] / This document contains a scientific report resulting from more than four years of theoretical and experimental research on a particular kind of physicochemical systems called gas clathrate hydrates. These systems are inclusion compounds constituted by a three dimensional water framework hosting gas molecules with low dipolar moments in its cavities. Gas clathrate hydrates are very important in a great variety of scientific fields related to life sciences or planetology, and they are also considered as a main natural resource for the energy industry. Usually, gas clathrate hydrates need high pressure and low temperature to be thermodynamically stable. Depending on these conditions, differentphases have been detected being the most common ones the cubic structuressI and sII, the hexagonal sH, and the orthorhombic Filled Ice Structure(FIS). Our study has substantially advanced in the knowledge of the behaviorof methane and carbon dioxide clathrate hydrates under different pressure andtemperature conditions. In particular, we have contributed to: (i) the determination and understanding of stability thermodynamic regions, (ii) the characterizationof a controversial high-pressure structure, and (iii) setting up a new experimental equipment for Raman measurements in a pressure range up to 1 GPa [...] / Este documento contiene el informe científico resultante después de más de cuatro años de investigación teórica y experimental sobre un tipo particular de sistemas físico-químicos llamados clatratos hidratos de gas. Estos sistemas son compuestos de inclusión constituidos por un armazón tridimensional de agua que aloja en sus cavidades moléculas de gas con momentos dipolares bajos.Los clatratos hidratos de gas son muy importantes en una gran variedad de campos científicos relacionados con las ciencias de la vida o la planetología, y también se consideran como uno de los principales recursos naturales para la industria energética. Por lo general, los clatratos hidratos de gas necesitan alta presión y baja temperatura para ser termodinámicamente estables.Dependiendo de estas condiciones, se han detectado diferentes fases siendo las más comunes las estructuras cúbicas sI y sII, hexagonal sH y la estructura ortorrómbica de hielo relleno (FIS). Nuestro estudio ha avanzado sustancialmente en el conocimiento del comportamiento de los clatratos hidratos de metano y dióxido de carbono en diferentes condiciones de presión y temperatura, proporcionando (i) regiones termodinámicas de estabilidad, (ii) la caracterización de una estructura de alta presión controvertida y (iii) un nuevo equipo experimental para mediciones Raman en un rango de presión de hasta 1 GPa [...]

<p>U ovom radu kori&scaron;cen je spektroskopski, teorijski i hemometrijski pristup<br />proucavanju N-HO i N-H&middot;&middot;&middot; vodonicne veze koja se uspostavlja izmedu<br />amidnog protona i etarskog kiseonika tj aromaticnog sistema. U ovom radu<br />odredeni su parametri N-HO i N-H vodonicne veze za &scaron;esnaest Nsupstituisanih<br />amida sa tetrahidrofuranom i toluenom. Vecina ispitivanih amida do<br />sada nije bila izucavana sa stanovi&scaron;ta vodonicne veze. Uspostavljene su korelacije<br />izmedu spektorsopskih i teorijskih parametara. Izvr&scaron;eno je poredenje medu<br />osobinama vodonicno vezanih kompleksa za razlicite amide kao proton donore.<br />Svih 32 ispitivanih vodonicno vezanih kompleksa okarakterisano je<br />hemometrijskim metodama: Klaster analizom i analizom glavne komponente, na<br />osnovu spektroskopskih, teorijskih i Taftovih parametara</p> / <p> In this PhD thesis, N-H&times;&times;&times;O and N-H&middot;&middot;&middot; hydrogen bond beetwen the amide<br /> proton with ether oxygen and aromatic system has been investigated using the<br /> spectroscopic and theoretical approach. The study included sixteen N-substituted<br /> amides (formamides, acetamides, caproamides and benzamides) as well as<br /> tetrahydrofuran and toluene. The possibility of using chemometric methods was<br /> investigated in order to characterise N-H...O and N-H&middot;&middot;&middot; hydrgen bonded<br /> complexes. Hierarchial clustering and Principal Component Analysis (PCA) have<br /> been applied on infrared spectroscopic, PM3 theoretical and Taft parameters of 32 Nsubstituted<br /> amide complexes with tetrahydrofuran and toluene</p>

Die vorliegende Arbeit befasst sich mit den Synthesen, Charakterisierungen und umfassenden Reaktivitätsstudien von unterschiedlich substituierten Organosilanolverbindungen, die ausgehend von den niedervalenten Siliziumverbindungen Tetramesityldisilen Mes2Si=SiMes2 (Mes = 2,4,6-Trimethylphenyl) und Hexakisarylcyclotrisilan (ArN2Si)3 (ArN = 2-[(Dimethylamino)methyl]phenyl) dargestellt wurden. Das durch Oxygenierung und Hydrolyse synthetisierte Tetramesitylsiloxandiol Mes2Si(OH)O(OH)SiMes2 wurde hinsichtlich seiner Reaktivität gegenüber Wasser und verschiedenen Ethern untersucht und dabei eingehend durch NMR- und IR-spektroskopische Analysen charakterisiert. Die Isolierung von Einkristallen ermöglichte darüber hinaus die Charakterisierung dreier polymerähnlicher Siloxandiol-Ether-Addukte im Festkörper. Neben Unterschieden der Struktur und Reaktivität in Lösung und im Festkörper konnte zusätzlich durch eine Kooperation mit Prof. Schalley (FU Berlin) anhand eines Gasphasenexperimentes des 18O-markierten Siloxandiolanions, in einem FT-ICR-ESI-Massenspektrometer der vollständige Austausch aller Sauerstoffatome durch Wassermoleküle nachgewiesen werden. Darüber hinaus führte die Einführung intramolekular stabilisierender Liganden wie in dem Siloxandiol ArN2(OH)Si(O)Si(OH)ArN2 zur vollständigen Austauschreaktion in organischen Lösemitteln. Ausgehend von dem [(Dimethylamino)methyl]phenylsubstituierten Cyclotrisilan (ArN2Si)3 konnte das Silylen-Lewispaar ArN2Si–B(C6F5)3 unter Einsatz der starken Lewis-Säure B(C6F5)3 isoliert werden. Durch Hydrolyse wird das Silanolboran ArN2H2OSi–B(C6F5)3 gebildet, das sich durch starke Wasserstoffbrückenbindungen zu den Aminsubstituenten auszeichnet. In Gegenwart von Base, H2O und Luft entsteht nach Dehydrogenierung und Kondensation das Borosiloxan [(HArN2(OB(C6F5)3)Si)2O]. Alle Verbindungen wurden isoliert und vollständig charakterisiert. Zusätzlich ergänzen DFT-Rechnungen (Prof. Kaupp, TU Berlin), die experimentell erhaltenen Beobachtungen. / The following thesis deals with the synthesis, characterization and detailed reactivity studies on differently substituted organosilanols, synthesized by the low valent silicon compounds tetramesityldisilene Mes2Si=SiMes2 (Mes = 2,4,6-trimethylphenyl) and hexakisarylcyclotrisilane (ArN2Si)3 (ArN = 2-[(dimethylamino)methyl]phenyl). Oxygenation and hydrolysis of tetramesityldisilene yielded tetramesitylsiloxanediol Mes2Si(OH)O(OH)SiMes2, the reaction behavior of which towards water and various ethers was studied by means of NMR and IR spectroscopy. Additionally, single crystal analysis delivered three different siloxanediol ether polymer-like structures in the solid state. Besides studies in solution and the solid state, gas phase reactions in a FT-ICR-ESI mass spectrometer of the 18O-labelled siloxanediol anion, showed complete exchange of all O-atoms in presence of gaseous water molecules (cooperation with Prof. Schalley, FU Berlin). Furthermore, we could show that altering the ligand system of the siloxanediol to the amine substituted siloxanediol ArN2(OH)Si(O)Si(OH)ArN2, resulted in a complete exchange of all oxygen atoms in solution when H217O was present. Starting from the [(dimethylamino)methyl]phenyl substituted cyclotrisilane (ArN2Si)3, formation of the Lewis acid stabilized silylene-borane ArN2Si–B(C6F5)3 was accomplished. In presence of water the silanolborane ArN2H2OSi–B(C6F5)3 was formed, showing characteristic strong intramolecular hydrogen bonding to its amino ligands. When reacted with a base and water under ambient air, a dehydrogenation reaction followed by condensation leads to the borosiloxane motif [(HArN2(OB(C6F5)3)Si)2O]. All compounds were isolated separately and fully characterized by means of NMR and IR spectroscopy, as well as X-ray diffraction analysis. In cooperation with Prof. Kaupp (TU Berlin), DFT-calculations were carried out to support the achieved experimental data.

Recent research has shown that small hydrogen bonding catalysts can catalyze the hetero Diels-Alder reaction. In this thesis such hydrogen bonding catalysts in conjunction with varying functional groups and their effect on the hetero Diels-Alder reaction have been investigated. The influence of the different solvents has been investigated as well. The activation barriers for the different region- and stereo isomeric pathways have been compared in order to determine the stereo specificity of the reactions. These calculations have been done using the B3LYP functional for the geometry optimizations and then M06-2X for single point calculations. For the solvated cases the cPCM model and the M06-2X functional were used. It was shown that for the catalyzed systems bulkier groups in the endo position tend to have a lower activation barrier, allowing for control over the stereoselectivity. Electron withdrawing groups have an activating effect and are also synergistic with the hydrogen bonding catalysts. The solvent with the lowest dielectric constant gave the lowest activation barrier.

The hydrophobic effect and hydrogen bonding interactions have long been considered to be the dominant forces in protein folding. However, the contribution of hydrogen bonds to stabilizing proteins has been difficult to clarify. As the intramolecular hydrogen bonds are formed in place of hydrogen bonds with solvent during folding, measures of stability fail to give a significant change in free energy. Previous studies on hydrogen bonding interactions have shown that they are only marginally important. Three long-range side chain-main chain hydrogen bonds have been found in the alpha subunit of tryptophan synthase (αTS), a (βα)8TIM barrel protein. These long-range noncovalent interactions connect either the N-terminus of one β-strand with the C-terminus of the succeeding and anti-parallel α-helix (F19-D46 and I97-D124) or the N-terminus of an α-helix with the C-terminus of the succeeding β-strand (A103-D130). By analogy, these interactions are designated as βα- or αβ-hairpin clamps. Surprisingly, the removal of any one of these clamp interactions, by replacement of the aspartic acid with alanine, results in significantly decreased thermodynamic stability for the native state and a substantial loss of secondary structure. When compared to several other side chain-side chain and short-range side chain-main chain interactions in αTS, these hairpin clamps clearly play a unique role in the structure and stability of αTS. The generality of these observations for βα-hairpin clamps in TIM barrel proteins was tested by experimental analysis of the clamps in a pair of homologous indole-3-glycerol phosphate synthase (IGPS) TIM barrels of low sequence identity. The results suggest that only the subset of conserved βα-hairpin clamps with hydrogen bond length less than 2.80 Å make substantive contributions to stability and/or structure. Those clamps with longer hydrogen bonds make modest contributions to stability and structure, similar to other types of side chain-main chain or side chain-side chain hydrogen bonds. The role of these clamps in defining the structures of the super-family of TIM barrel proteins was examined by a survey of 71 TIM barrel proteins from the structural database. Conserved features of βα-hairpin clamps are consistent with a 4-fold symmetry, with a predominance of main chain amide hydrogen bond donors near the N-terminus of the odd-number β-strands and side chain hydrogen bond acceptors in the loops between the subsequent α-helices and even-numbered β-strands. In this configuration, the clamps provide an N-terminal cap to odd-number β- strands in the β-barrel. Taken together, these findings suggest that βα-hairpin clamps are a vestigial signature of the fundamental βαβ building block for the (βα)8 motif and an integral part of the basic TIM barrel architecture. The relative paucity of βα-hairpin clamps remaining in TIM barrel structures and their variable contributions to stability imply that other determinants for structure and stability of the barrel have evolved to render a subset of the clamp interactions redundant. Distinct sequence preferences for the partners in the βα-hairpin clamps and the neighboring segments may be useful in enhancing algorithms for structure prediction and for engineering stability in TIM barrel proteins.

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Rewritable photochrome-based 3D optical data storage requires photochromic molecules with high two-photon absorption (2PA) cross sections. Currently, the low value of two-photon absorption cross sections of existing photochromes makes them unsuitable for practical application in 3D data storage. Worldwide attempts to increase the cross section of photochromic molecules by altering the chemical structure have yielded poor results. In this work, two ways to increase the two-photon absorption cross sections of photochromes were investigated. In the first method, partial success demonstrated by extending the conjugation of a photochromic molecule, a high two-photon absorption cross section of the closed form isomer and high photoconversion to the closed form were realized. At the same time, a decrease in photoswitching quantum yield and low photoconversion to open form was observed. A discussion is provided to explain the results, suggesting that the proposed method of extending the conjugation may not solve the problem. For this reason a new method for effective two-photon absorption cross section enhancement of photochromes was proposed. As a proof of principle, a new two-photon absorbing dye with a hydrogen bonding moiety was synthesized and used for the formation of supramolecular structures with a photochromic compound. Theoretical reasoning and experimental demonstration of energy transfer from the dye to the photochrome under one and two-photon excitation confirmed the practical value of the method. The effects of a 2PA dye on the photochromic properties of a diarylethene were investigated using a model compound to simplify data analysis. Formation of supramolecular structures was revealed using ¹H NMR spectroscopic methods. The model compound, having the same hydrogen bonding moiety as 2PA dye, has been demonstrated to bind with photochrome molecules at very low concentrations. Photochromic properties of 2,3-bis(2,4,5-trimethyl-3-thienyl)maleimide, including conversions at the photostationary state, extinction coefficients, photoisomerization reaction rates and quantum yields, were shown to be affected by hydrogen bonding with the model compound - 2,6-bis-(acetamido)pyridine. The extent of this change was determined and discussed, demonstrating a balanced supramolecular strategy to modulate photochemical and photophysical properties of this important class of photochromic material.