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Dissertations / Theses on the topic 'Hydrogen bond network'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Matsumoto, Masakazu, and Iwao Ohmine. "A new approach to the dynamics of hydrogen bond network in liquid water." American Institute of Physics, 1996. http://hdl.handle.net/2237/7055.

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2

Kwong, Lam Elwood. "Investigating the Role of the Proximal Cysteine Hydrogen Bonding Network and Distal Pocket in Chloroperoxidase." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3898.

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Chloroperoxidase (CPO) is one of the most versatile heme enzyme isolated from the marine fungus, Caldariomyces fumago. Functionally, CPO can catalyze four types of reactions: peroxidation (peroxidase-like), dismutation (catalase-like), halogenation (halogenase-like), and peroxygenation (P450-like). Structurally, CPO has a distal and proximal pockets that can be best described as a hybrid of classical peroxidase and P450s. As a heme-thiolate protein, CPO contains the conserved proximal Pro28-Cys29-Pro30 stretch found in other members of the family. However, the structural and functional roles o

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3

Shersher, Elena. "The Influence of the Proximal Thiolate Ligand and Hydrogen Bond Network of the Proximal Helix on the Structural and Biochemical Properties of Chloroperoxidase." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2483.

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Chloroperoxidase (CPO) from Caldariomyces fumago is a versatile heme enzyme with great potential for environmental and pharmaceutical applications. It catalyzes a plethora of reactions including halogenation, dismutation, epoxidation, and oxidation. The diverse catalytic capabilities of CPO have long been attributed to the protein’s distinct active site that combines structural features of peroxidases and cytochromes P450. Particularly, the role of the axial thiolate ligand in CPO catalysis has been much debated. Furthermore, no data are available on the role of hydrogen bonding between Arg 26

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4

Näslund, Lars-Åke. "Probing unoccupied electronic states in aqueous solutions." Doctoral thesis, Stockholm University, Department of Physics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-294.

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<p>Water is one of the most common compounds on earth and is essential for all biological activities. Water has, however, been a mystery for many years due to the large number of unusual chemical and physical properties, e.g. decreased volume during melting and maximum density at 4 °C. The origin of the anomalies behavior is the nature of the hydrogen bond. This thesis will presented an x-ray absorption spectroscopy (XAS) study to reveal the hydrogen bond structure in liquid water.</p><p>The x-ray absorption process is faster than a femtosecond and thereby reflects the molecular orbital struct

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5

Mancini, Adauto Luiz. "Um sistema híbrido inteligente para previsão de posição de átomos de hidrogênio em proteínas." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-03072008-084623/.

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Os métodos existentes para a previsão da posição de átomos de hidrogênio em proteínas são todos baseados na simulação computacional de modelos construídos a partir de características físicas e (ou) químicas das moléculas. A abordagem proposta neste trabalho faz uso de técnicas inteligentes para a predição da posição de átomos de hidrogênio contidos em grupos hidroxilas (OH) pertencentes à cadeias laterais dos aminoácidos serina, treonina e tirosina. Estas técnicas inteligentes são utilizadas em duas fases para a solução do problema proposto: o preprocessamento dos dados e a predição da posição

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6

Kirch, Alexsandro. "Modelagem e caracterização de sistemas nanofluidos através de simulações moleculares em multiescala." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-28092018-152059/.

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As propriedades físicas incomuns exibidas por fluidos confinados em meios porosos desempenham um papel importante em diversos processos químicos, geoquímicos e ambientais. Atualmente, muitos aspectos da estrutura e dinâmica dos fluidos espacialmente confinados ainda são pouco compreendidos. Nesse contexto, fenômenos interfaciais influenciam consideravelmente os processos que ocorrem em meios nanoporosos, podendo resultar em efeitos relevantes para o desenvolvimento dos dispositivos nanofluidicos. Esses sistemas multifásicos e com fenômenos multifísicos podem apresentar propriedades eletrônico

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7

Koishi, Ayumi. "Mécanismes de nucléation des carbonates." Thesis, Université Grenoble Alpes (ComUE), 2017. http://www.theses.fr/2017GREAU032/document.

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La précipitation et la dissolution du carbonate de calcium (CaCO3) sont des processus clés dans les systèmes naturels en raison de leur association intime avec le cycle du carbone terrestre. La précipitation se produit généralement sur des substrats étrangers en abaissant les barrières énergétiques qui contrôlent la nucléation. Ce processus appelé nucléation hétérogène résulte d'une interaction entre la sursaturation du fluide et les différentes énergies d’interface entre substrat-noyau-fluide. Malgré l’importance des énergies d’interface sur le devenir de la nucléation hétérogène, la littérat

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8

Herrmann, Anna [Verfasser]. "Surface-Bound Functional Hydrogel Networks / Anna Herrmann." Berlin : Freie Universität Berlin, 2020. http://d-nb.info/1219070157/34.

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9

Mooney, Barbara Logan. "An Integrated Graph-Theoretic Approach to Understanding Solvation Using a Novel Data Mining Tool, moleculaRnetworks." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/243096.

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An integrated graph-theoretic and geometric approach to the analysis of aqueous solvation of atomic ions is presented. This analysis makes use of a novel data-mining tool, moleculaRnetworks, to process data from molecular dynamics simulations. The workings and structure of this tool are discussed, along with the development and testing of its PageRank algorithm-based rapid solvation polyhedra classifier. The ability to classify instantaneous solvation polyhedra enables a finely detailed understanding of shell structure-behavior relationships, as water molecules simultaneously rearrange about i

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10

Ni, Yiping. "Polymer networks architecture using supramolecular interactions." Phd thesis, Université Jean Monnet - Saint-Etienne, 2012. http://tel.archives-ouvertes.fr/tel-00952090.

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Supramolecular polymer networks are prepared basing on two different supramolecular interactions, ionic interaction and hydrogen bonds interaction. Ionic interaction was introduced in P(BMA-co-MA) with CaCO3 as a filler. The presence of Ca2+ is confirmed with X-ray diffraction by the apperence of specific ionic peak. The hydrogen bond interaction was introduced by two approaches. One is to first prepare a supramolecular monomer bearing DA moiety then supramolecular polymer P(MAAM-co-St) and P(MAP-co-St) are prepared by polyaddition. In the other approach, the supramolecular polymer is synthesi

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11

Walch, Hermann. "Molecular Networks Through Surface-Mediated Reactions - From Hydrogen Bonds to Covalent Links." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-127102.

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12

Delcey, Nicolas. "Tectonique moléculaire : réseaux moléculaires à propriétés optiques assemblées par des liaisons hydrogène chargées." Phd thesis, Université de Strasbourg, 2012. http://tel.archives-ouvertes.fr/tel-00832512.

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La conception et la préparation de réseaux moléculaires organiques et hybrides à l'état cristallin ont été envisagées par un processus itératif d'auto-assemblage entre des briques de construction moléculaires préprogrammées et complémentaires appelées tectons. Cette approche est basée sur la reconnaissance moléculaire de modules dicationiques, donneurs de liaisons hydrogène, et d'unités anioniques, accepteurs de liaisons hydrogène. Ainsi, la combinaison des tectons moléculaires de la famille des bis-benzimidazoliums, intrinsèquement luminescents, avec des anions polycyanométallates conduit à l

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13

Djidi, Dalila. "Synthèse et caractérisation de nouveaux réseaux polymériques thermoréversibles à base d'acide poly-lactique grâce aux interactions dynamiques." Thesis, Saint-Etienne, 2015. http://www.theses.fr/2015STET4010/document.

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Dans le contexte actuel de constante amélioration des propriétés des matériaux polymères et de l’optimisation de leur impact environnemental, la recherche se tourne de plus en plus vers les polymères biosourcés et biodégradables. Le travail de cette thèse consiste en la synthèse et le développement de nouveaux réseaux thermoréversibles à base d’acide polylactique (PLA). Cette thermo-réversibilité est assurée grâce à des interactions dynamiques comme les liaisons hydrogène et la réaction réversible de Diels-Alder. Une biomolécule, le gluthation, a été conjuguée au polymère et utilisée comme gén

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14

Adolf, Cyril. "Cristaux moléculaires : des cristaux coeur-coquille aux réseaux de cristaux." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAF026/document.

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L’agencement relatif de systèmes cristallins moléculaires, par une méthode d’organisation avancée est une stratégie de premier plan. Le développement de tels systèmes permet la conception de dispositifs innovants dans le domaine des matériaux poreux, magnétiques ou optiques.Les travaux menés dans le cadre de cette étude ont pour objectif l’élaboration d’architectures macroscopiques hiérarchisées concernant l’état cristallin, de type « réseaux de cristaux ». Dans un premier temps, le développement et la caractérisation de réseaux iso-structuraux ont été réalisés. Ces séries, formées par liaison

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15

Liang, Ji-Ming, and 梁誌明. "A Study of Hydrogen Bond Cooperativity by Model Systems of Network with Oxygen, Nitrogen and Carbon Hydrogen Bonds." Thesis, 1999. http://ndltd.ncl.edu.tw/handle/64086584075918582947.

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碩士<br>國立清華大學<br>化學系<br>87<br>The hybrid density functional calculations (B3LYP) have been performed to elucidate the profound meanings of hydrogen-bonding cooperativities in the modeling systems of serine protease and we further proposed the three significant ideas about enzyme catalysis, especially hydrolases. It is found that molecules, with electron donors and electron acceptors, have qualitatively and structurally intrinsic hydrogen-bonding cooperativities. Further, the results are extended to far indirect hydrogen-bonding cooperativities. The direct and indirect hydrogen-bonding cooperati

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16

Bruner, Barry D. "Ultrafast memory loss and energy redistribution in the hydrogen bond network of liquid water /." 2006. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=442598&T=F.

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17

Machczynski, Michael Christopher. "Physical characterization of the rack effect and hydrogen bond networks in blue copper proteins." Thesis, 2001. https://thesis.library.caltech.edu/8154/1/Machczynski_mc_2001.pdf.

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<p>A summary of previous research is presented that indicates that the purpose of a blue copper protein's fold and hydrogen bond network, aka, the rack effect, enforce a copper(II) geometry around the copper(I) ion in the metal site. In several blue copper proteins, the C-terminal histidine ligand becomes protonated and detaches from the copper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were made to alter the hydrogen bond network and quantify the rack effect by pK<sub>a</sub> shifts.</p> <p>The pK<sub>a</sub>'s of mutant amicyanins have been measured by p

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18

Walch, Hermann [Verfasser]. "Molecular networks through surface-mediated reactions : from hydrogen bonds to covalent links / Hermann Walch." 2010. http://d-nb.info/1010299484/34.

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19

Chen, Yen-Jung, and 陳彥蓉. "3D Printable Bone Repairing Biomaterial of ALG / HEMA Semi-Double Network Hydrogel Embedded Hydroxyapatite." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/n5e4ce.

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碩士<br>國立臺灣科技大學<br>化學工程系<br>107<br>A new bone repairing biomaterial, ALG/HEMA-HAp, was a semi-double network (S-DN) hydrogel fabricated from 2-hydroxyethyl methacrylate (HEMA) and ethylene glycol dimethacrylate (EGDMA) in the aqueous mixed dispersion of hydroxyapatite (HAp) and sodium alginate (ALG). The mechanical properties, moisture, shrinkage and morphology of all samples were investigated. Among them, The ALG/HEMA-HAp 10% xerogel showed the stress is 16.378 MPa and the elongation is 4.61%, which might be comparable to the human’s trabecular having the tensile strength of 10 to 20 MPa and e

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20

Gunawardana, Chamara Abeywickramasinghe. "Crystal engineering with coordination, hydrogen- and halogen-bonds, and the construction of porous solids." Diss., 2018. http://hdl.handle.net/2097/39092.

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Doctor of Philosophy<br>Department of Chemistry<br>Christer B. Aakeröy<br>A set of multifunctional molecules [isomeric forms of 1-(pyridylmethyl)-2,2'-biimidazole] was synthesized and subjected to systematic co-crystallizations with selected hydrogen- and halogen-bond donors in order to explore the impact of interaction type, geometry and electrostatics on the resulting supramolecular architectures. The structural outcome with hydrogen-bond donors (carboxylic acids) is somewhat unpredictable because of the presence of the acid···biimidazole heterosynthon that can compete with biimidazole···bi

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21

Lie, Chin Cheong Sharon. "Molecular Networks Created by Charge-Assisted Hydrogen Bonds Between Bis(aminidinium) Cations and Carboxylates, Sulfonates, Phosphonates and Phosphates." Thèse, 2013. http://hdl.handle.net/1866/10666.

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L'objectif de cette étude est d'apprendre à créer de nouveaux matériaux moléculaires par design. À l'heure actuelle, il n'existe aucune méthode générale pour la prédiction des structures et des propriétés, mais des progrès importants ont été accomplis, en particulier dans la fabrication de matériaux moléculaires ordonnés tels que des cristaux. En ces matériaux, l'organisation peut être contrôlée efficacement par la stratégie de la tectonique moléculaire. Cette approche utilise des molécules appelées “tectons”, qui peuvent s’associer de manière dirigée par des interactions non covalentes prévis

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22

Sathyapriya, R. "Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches." Thesis, 2007. http://hdl.handle.net/2005/624.

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The flow of genetic information from genes to proteins is mediated through proteins which interact with the nucleic acids at several stages to successfully transmit the information from the nucleus to the cell cytoplasm. Unlike in the case of protein-protein interactions, the principles behind protein-nucleic acid interactions are still not very (Pabo and Nekludova, 2000) and efforts are still underway to arrive at the basic principles behind the specific recognition of nucleic acids by proteins (Prabakaran et al., 2006). This is mainly due to the innate complexity involved in recognition of

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