Hydration is known to be crucial in biomolecular interactions including ligand binding and self-assembly. In our earlier studies we have shown the key role of water in stabilizing the specific parts of the collagen triple helix depending on the imino acid content. We further showed that the primary hydration shell around collagen could act as a lubricating layer aiding in collagen assembly. But key details on the structure and dynamics of water near protein surfaces and its role in protein-protein interactions remain unclear. In the current study we have developed a novel method to analyze hydration maps around peptides at 1-A resolution around three self-assembling lament systems with known structures, that respectively have hydrated (collagen), dry non-polar and dry polar (amyloid) interfaces. Using computer simulations, we calculate local hydration maps and hydration forces. We find that the primary hydration shells are formed all over the surface, regardless of the types of the underlying amino acids. The weakly oscillating hydration force arises from coalescence and depletion of hydration shells as two laments approach, whereas local water diffusion, orientation, or hydrogen bonding events have no direct effect. Hydration forces between hydrated, polar, and non-polar interfaces differ in the amplitude and phase of the oscillation relative to the equilibrium surface separation. Therefore, water-mediated interactions between these protein surfaces ranging in character from ‘hydrophobic’ to ‘hydrophilic,’ have a common molecular origin based on the robustly formed hydration shells, which is likely applicable to a broad range of biomolecular assemblies whose interfacial geometry is similar in length scale to those of the present study. In a related study through simulations we show that the rate of tissue optical clearing by chemical agents correlated with the preferential formation of hydrogen bond bridges between agent and collagen. Hydrogen bond bridge formation disrupts the collagen hydration layer and facilitates replacement by a chemical agent to destabilize the tertiary structure of collagens thereby reducing light scattering. This study suggests that the clearing ability of an alcohol not only depends on its molecular size, but also on the position of hydroxyl groups on its backbone.

Thesis (Ph. D.)--Syracuse University, 2007. / "Publication number: AAT 3295517."

Orientadores: Edvaldo Sabadini, Munir Salomão Skaf / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-20T16:17:25Z (GMT). No. of bitstreams: 1 Cardoso_MarcusViniciusCangussu_D.pdf: 5363072 bytes, checksum: 77f8ee9c80c8ce3514b001281dfddae6 (MD5) Previous issue date: 2012 / Resumo: Soluções aquosas de mono, di, oligo, e polissacarídeos foram estudas nos níveis macroscópico e molecular, empregando-se enfoques termodinâmicos e espectroscópicos. A influência da intensidade da ligação de hidrogênio sobre a solubilidade dos carboidratos (lineares e cíclicos) mostrou-se fortemente dependente de suas solubilidades. Quanto menos solúvel o carboidrato, maior é o efeito da substituição isotópica do solvente (H2O por D2O). Este efeito sugere que carboidratos menos solúveis (e maiores) perturbam mais fortemente a estruturação das moléculas de água. Devido ao efeito cooperativo da transição coil-helix da k-carragena, o efeito isotópico sobre a gelificação é bastante intensificado. Segundo um perspectiva mais molecular, as taxas de troca protônicas, kb, entre os prótons da água e os grupos OH dos carboidratos dependem da natureza do açúcar, sendo os maiores valores observados para a forma linear, seguida pela forma piranosidea e por último pela forma furanosidea. Já as transferências de magnetização entre as populações de prótons da água e dos grupos CH-carboidratos são moduladas pelos movimentos moleculares e intermediadas pelas trocas protônicas com os grupos OH. Propõe-se que os prótons das moléculas de água interagem preferencialmente com os prótons OH e negligenciavelmente com os prótons CH. Estudos de relaxação H mostraram-se ricos para o estudo de processos moleculares de agregação micelar dos n-alquil-glicosídeos sendo possível demonstrar experimentalmente que a agregação leva a indisponibilização das hidroxilas ao interagirem com as moléculas de água / Abstract: Aqueous solutions of mono, di, oligo, and polysaccharides were studied on the macroscopic and molecular standpoints through thermodynamic and spectroscopic approaches. The effect of hydrogen-bonding strength on the solubility of a series of (linear and cyclic) saccharides showed to be strongly dependent of the solubility of the carbohydrate. As lower is the solubility of the carbohydrate, greater will be the deuterium isotopic effect of the solvent (H2O for D2O) on the carbohydrate solubilities. These results suggest that low soluble carbohydrates (and larger ones) perturb more strongly the water structure. Owing to the cooperativity of the coil-helix transition, the deuterium isotope effect on the gelling of k-carrageenan is intensified leading to stronger gels and double-helices more stable in D2O. Looking deeper onto a molecular perspective and based on spin-spin nuclear magnetic relaxation, the proton exchange rates, kb, between water and OH-carbohydrate, are dependent of the nature of the saccharide. The kb values are higher for linear than for pyranoside form, and the slowest value is found for fructofuranoside form. The transferring of magnetization between proton pools of water and CH-carbohydrates are modulated by molecular motions and intermediated by proton exchanging process between water and OH-carbohydrate protons. H NMR relaxation experiments of exchangeable protons provide to be rich in probing the micelar aggregation of n-alkyl-glucosides. It was possible to demonstrate experimentally that the aggregation of the surfactant molecules provoke a drastic reduction on the interactions between water and OH-saccharide head groups / Doutorado / Físico-Química / Doutor em Ciências

This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules as expressed in terms of the C6 dipole-dipole dispersion coefficients. In a series of publications, it has been shown by us that the complex linear polarization propagator method provides accurate ab initio and first-principles density functional theory values of the C6 dispersion coefficients in comparison with those reported in the literature. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, n-alkanes, polyacenes, azabenzenes, and C60. It has been shown that the proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C6 dispersion coefficients for the first π → π* excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the π → π* excited state is smaller r than that of the ground state. It is found that the characteristic frequencies ω1 defined in the London approximation of n-alkanes vary in a narrow range and that makes it possible to construct a simple structure-to-property relation based on the number of -bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable for the interactions of the π-conjugated systems since their characteristic frequencies ω1 vary strongly depending on the systems. / <p>Report code: LIU-TEK-LIC-2006:2</p>

No description available.

O tema interações intermoleculares é um conceito central dentro do conhecimento químico por permitir, por exemplo, a interpretação de uma série de transformações e propriedades físicas dos materiais. Considerando a carência de estudos que investigam especificamente os processos de ensino e aprendizagem em nível superior, a presente pesquisa objetivou analisar o aprendizado de graduandos em química durante uma disciplina de química geral I, relacionando-o as aulas ministradas aos alunos e a abordagem do tema nos livros didáticos sugeridos para estudo. Para isso, as aulas da disciplina, oferecidas aos alunos ingressantes do curso de química do Instituto de Química da Universidade de São Paulo, foram acompanhadas e gravadas em vídeo; os estudantes responderam alguns questionários para o levantamento das principais dificuldades e lacunas na aprendizagem e os livros didáticos sugeridos foram analisados através de mapas conceituais. A análise dos livros mostrou a complexidade e amplitude do tema por apresentar uma rede de relações conceituais extensa e distribuídas ao longo de diferentes capítulos. Nas análises dos livros e das aulas chamou atenção a abordagem classificatória com que o tema é tratado começando pelas interações que envolvem moléculas polares e depois interações entre moléculas apolares. Na análise das explicações dos alunos foi possível perceber a presença de várias dificuldades ou lacunas como na interpretação das equações das energias potenciais das interações e identificação dos tipos de interações que atuam em distintos contextos. A partir das análises foi feita uma triangulação dos dados que permitiu elencar ideias fundamentais que os alunos precisam compreender sobre o tema sendo essas relacionadas a: uma melhor compreensão da estrutura molecular considerando a geometria da molécula e a distribuição da densidade eletrônica na mesma, parâmetro expresso pelos conceitos polaridade, polarizabilidade e nuvem eletrônica (propriedades moleculares); necessidade de fazer uma correta diferenciação entre as interações intermoleculares e as ligações químicas; compreender que as mudanças de estado físico estão correlacionadas aos diferentes tipos de interações intermoleculares que atuam nos sistemas; entender que vários tipos de interações intermoleculares podem estar atuando no mesmo sistema e que as forças dispersivas de London são universais; interpretar as equações das energias potenciais que são diretamente proporcionais a propriedade molecular e inversamente a distância; interpretar os valores de energia típicos das interações e também relacionar a intensidade e o alcance; considerar nas ligações de hidrogênio a direcionalidade da interação e a necessidade de sítios para esse tipo de interação (pares de elétrons livres). Essas ideias integraram sugestões para o ensino do tema que vão desde a repensar a forma como as interações intermoleculares são ensinadas na química geral até uma possível retomada da abordagem do tema em disciplinas mais avançadas ampliando e ressignificando a compreensão dos conceitos. Defende-se aqui a necessidade de superar o ensino classificatório do tema interações intermoleculares abordando separadamente os tipos de interações intermoleculares: íon-dipolo, dipolo-dipolo, dipolo-dipolo induzido, forças dispersivas de London e ligação de hidrogênio para um ensino com ênfase na estrutura molecular e propriedades moleculares. / The subject of intermolecular interactions is a central concept within the chemical knowledge because it allows, for example, the interpretation of a series of transformations and physical properties of the materials. Considering the lack of studies that specifically investigate teaching and learning processes at the higher level, the present study is aimed at analyzing the chemistry students\' learning in during a general chemistry course, relating the classes given to the students and the approach to the subject suggested textbooks for study. For this, the classes of the course, offered to the incoming chemistry\'s course students of the Institute of Chemistry of the University of São Paulo, were accompanied and recorded in video; the students answered some questionnaires to survey the main difficulties and gaps in learning and the suggested textbooks were analyzed through concept maps. The analysis of the books showed the complexity and amplitude of the theme by presenting a network of extensive conceptual relationships distributed throughout different chapters. In the analysis of books and classes, the classificatory approach with which the topic is treated, starting with the interactions involving polar molecules and then interactions between apolar molecules, was called attention. In the analysis of the students\' explanations, it was possible to perceive the presence of several difficulties or gaps as in the interpretation of the equations of the potential energies of the interactions and identification of the types of interactions that operate in different contexts. From the analyzes, a triangulation of the data was made which allowed to list fundamental ideas that the students need to understand about the subject being related to: a better understanding of the molecular structure considering the geometry of the molecule and its distribution of the electronic density in, expressed parameter by the concepts polarity and polarizability and electronic cloud (molecular properties); the need to make a proper differentiation between intermolecular interactions and chemical bonds; to understand that the changes of physical state are correlated to the different types of intermolecular interactions that operate in the systems; to understand that various types of intermolecular interactions may be operating in the same system and that London\'s dispersive forces are universal; interpret the equations of potential energies that are directly proportional to the molecular property and inversely the distance; interpret the energy values typical of the interactions and also relate intensity and range; to consider in the hydrogen bonds the directionality of the interaction and the need of sites for this type of interaction (free electron pairs). These ideas have included suggestions for teaching the subject, ranging from rethinking how intermolecular interactions is taught in general chemistry to a possible resumption of the subject approach in more advanced courses by broadening and redefining the understanding of concepts. It is argued here the need to overcome classificatory teaching of intermolecular interactions by addressing separately the types of intermolecular interactions: ion-dipole, dipole-dipole, dipole-induce dipole, London\'s dispersive forces and hydrogen bonding for teaching with an emphasis on molecular structure and molecular properties.

This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19197号 / 農博第2136号 / 新制||農||1034(附属図書館) / 学位論文||H27||N4943(農学部図書室) / 32189 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 西尾 嘉之, 教授 木村 恒久, 教授 髙野 俊幸 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

No description available.

No description available.