Dissertations / Theses: 'Molecular structure'

1

Pounds, Andrew J. "A generalized discrete dynamical search method for locating minimum energy molecular geometries." Diss., Georgia Institute of Technology, 1994. http://hdl.handle.net/1853/27144.

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O'Dubhthaigh-Orgel, Joseph Patrick Rosen. "The molecular structure of collagen." Thesis, University of Stirling, 2000. http://hdl.handle.net/1893/1968.

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This thesis describes the study of the molecular packing and organisation of collagen molecules within a fibril. The first two chapters describe the background to the study. In Chapter 1, a review of the extracellular matrix concentrates on the structure and organisation of type I collagen. Chapter 2 summarises the theory of X-ray diffraction by fibres, and Chapter 3 describes X-ray sources and equipment used in data collection. Data treatments and data extraction methods (such as simulated annealing) are also discussed. Chapters4 and 5 present the results of the study. Chapter 4 describes the determination of the one-dimensional structure of type I collagen to 0.54 nm resolution using X-ray diffraction and isomorphous derivative phase determination. The significance of the electron density map is interpreted in light of the known amino acid sequence, showing possible variations in the nature of the helix pitch. More importantly, the conformations of the intermolecular crosslink forming non-helical telopeptides were determined. Chapter 5 provides a detailed background to the current understanding of the three dimensional packing structure of collagen, and presents the first model-independent phase determined structure of a natural fibre - the lateral packing structure of type I collagen in rat tail tendon. The data extraction methods described in Chapter 3 are employed to calculate an electron density map of anisotropic resolution, from which the 4 crosslink forming telopeptide segments within the quasi-hexagonal packing structure are identified. Conclusions are drawn concerning the nature of order/disorder within collagen fibrils and the validity of the compressed microfibril model of collagen molecular packing and organisation is discussed. Chapter 6 summaries the results and evaluates the success of the study. The potential for development of the techniques and results found for further studies are also discussed.

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Forsyth, G. A. "Molecular structure by diffraction methods." Thesis, University of Reading, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.384586.

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Santos, Flavio Bezerra dos. "Molecular structure and liquid crystallinity." Thesis, University of Southampton, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243176.

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Rowles, Jonathan Henry. "The structure of molecular clouds." Thesis, University of Kent, 2011. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.544095.

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Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.

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Jarvis, Vern Marshall. "Studies of molecular cluster ions." Diss., Georgia Institute of Technology, 1994. http://hdl.handle.net/1853/30074.

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Ahmed, Syed Muzaffor. "Molecular Shock Structure in Multifluid MagnetohydrodynamicS." Thesis, University of Leeds, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486150.

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We present an investigation on the effects of magnetic dissipation and cooling due to spontaneous radiative emission in multifluid magnetohydrodynamic (MHD) shocks. Ideal MHD allows n small amplitude waves and therefore we can associate a shock with each. But, only non-linear fast and slow shocks are evolutionary. On smaller scales the structure ofshocks is determined by the non-ideal MHD equations and from neutral cooling. Therefore in a dense weakly ionised medium there exist three generic types of shock; C-type, J-type and C*-type. The shooting method can be used to calculate simple steady solutions, with constant ambipolar resistivity and radiative cooling. In this approach only coplanar transverse fields can vary i.e., these shocks are coplanar. But, this method is restricted to C-type non-reacting fluidÃ‚Â· shocks, since J-type and C*-type contain a point of singularity in the transonic phase. For time dependent equations an upwind conservative scheme (Godunov's scheme) in one dimension is used. This method is less restricted; we have shown that it is extremely accurate in second order and that we call also capture all three generic interstellar shocks successfully. For completeness we : give expressions for the sources of mass, momentum and energy in a five fluid reacting model. We show that studies in zero dimensions can be used to reveal important shock structure parameter.s. Five fluid MHD shocks show that ionisation, recombination and . grain dynamics can have profound effects on the structure. Firstly we show that slow shock length scales are significantly enhanced and that cooling from molecular rotational and atomic fine structure lines contributes significantly in fast shocks. Thus the structure of the weakest and strongest shocks are characteristically adiabatic and characteristically finite cooling respectively. Conditions are such that both ambipolar resistivity and Hall resistivity can dominate, hence the waves are characteristically dissipative and dispersive, but, only in the fast regime a significant non-coplanar transverse field is induced. In slow shocks grain fluids are decoupled from the field, but in the fast regime they can reconnectÃ‚Â· with the field and this is also dependent on their dimensions. We predict that slow shocks are generally C*-type, and that such shocks are more likely to be responsible for the: condensation of dense cores and therefore the formation of protostellar objects and stars.

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9

Legha, Prem, University of Western Sydney, of Science Technology and Environment College, and of Science Food and Horticulture School. "Molecular structure and odor mixture perception." THESIS_CSTE_SFH_Legha_P.xml, 2004. http://handle.uws.edu.au:8081/1959.7/549.

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The sense of smell is a primal sense for humans as well as animals.In everyday life the smells encountered are composed of dozens, even hundreds of odors; few arise from a single odorant. Enormous numbers of odors occur due to the vast variation in the concentration, size and structure of odorant molecules that makes olfaction differ from simpler visual or auditory dimensions. Accordingly, little is known about the ways in which changes in molecular structure and concentration of individual odorants change odor quality. Also, currently not much is understood about synergism/antagonism, how one odorant masks or suppresses another in mixtures and there is no method for predicting which odor will be suppressed. The two main objectives of this thesis were to determine whether a part of a molecular structure rather than the whole structure plays a key role in odor quality and whether a key part of a molecule can be used to choose antagonists for that odorant. For this study three classes of musks and two potential antagonists were used. The results of the study are discussed in some detail. It is concluded that future studies of the importance of molecular structure in mixture interactions require substantially more information on the relation between structure and odor quality to allow systematic studies to be developed. In summary the two hypotheses investigated were not supported by the results. Importantly, however, they do support the view that it is likely that odor quality is dependent on the whole structure of an odorant not a single feature.
Master of Science (Hons)

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Hellier, P. R. "The molecular structure of future fuels." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1387437/.

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Future fuels will be developed from a variety of biomass and fossil sources, and must seek to address the adverse environmental impacts of current fossil fuel usage. To this end, understanding how the molecular structure of a fuel impacts on the processes of combustion and emissions production is critical in selecting suitable feed-stocks and conversion methods. This work presents experimental studies carried out on a compression ignition engine equipped with a novel low volume fuel system. This system was designed and manufactured so as that several series of single-molecule fuels, and also binary fuel mixtures, could be tested to investigate the effect of fuel molecular structure on combustion and emissions. Features of fuel molecular structure that were studied include: alkyl chain length and degree of saturation, double bond position and isomerisation and the fatty acid ester alcohol moiety. The interactions between cyclic molecules and $n$-alkanes were also studied, as was the potential of carbonate esters and terpenes as future sustainable fuels; the latter produced from genetically modified micro-organisms. The engine tests were carried out at constant injection timing and they were repeated at constant ignition timing and at constant ignition delay, the latter being achieved through the addition to the various fuels of small quantities of ignition improver (2-ethylhexyl nitrate). In tests conducted at constant injection and constant ignition timing the ignition delay of the molecule was found to be the primary driver of combustion phasing, the balance between premixed and diffusion-controlled combustion and, thereby, exhaust emissions. The various features of molecular structure were found to influence the duration of ignition delay, and an effect of interactions of binary fuel mixtures was also visible. Physical properties, such as viscosity, impacted on the production of exhaust emissions, and in extreme cases also influenced combustion phasing and heat release.

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Daldrop, Peter. "Structure and molecular recognition in riboswitches." Thesis, University of Dundee, 2011. https://discovery.dundee.ac.uk/en/studentTheses/db338d42-75c1-43a6-be6a-11399f04989e.

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Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docking but known from the far more explored field of protein-ligand docking.The SAM-I riboswitch was also subjected to virtual ligand screening. This receptor is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the docking setup based on previously published data, a set of compounds selected from the in-house database of commercially available compounds was screened. One compound identfied in silico was cofirmed to bind experimentally.The k-turn motif found in the SAM-I riboswitch was investigated with respect to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identfied which fold in context of the riboswitch but do not fold in isolation. This confirms the contribution of tertiary interactions to k-turn folding. This conclusion was backed up with structural data is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identi ed which fold in context of the riboswitch but do not fold in isolation. This con rms the contribution of tertiary interactions to k-turn folding. This conclusion was backed

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Kazantsev, Andrey. "Molecular flexibility in crystal structure prediction." Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/9079.

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The packing of molecules in solids greatly affects the properties of the bulk materials. This is particularly important for the pharmaceutical industry, where the discovery of crystal forms at a late stage of process development can have disastrous consequences. As a result, the importance of polymorphism in crystal structures of organic molecules has been recognised for many years. This thesis presents computational developments that can complement experimental form screening of molecules for which conformational flexibility is significant. Current methods for crystal structure prediction are limited by the extent of molecular flexibility that can be practically handled due to the prohibitive computational cost associated with quantum mechanical calculations integrated in most of the successful approaches. In order to reduce the number of quantum mechanical evaluations, local approximate models can be defined for the estimation of the intramolecular energy, molecular geometry and the conformationally dependent intermolecular electrostatic model. A novel algorithm, CrystalOptimizer, for the accurate local minimisation of the lattice energy of crystals involving flexible organic molecules is presented. The main novelty of the algorithm is the use of dynamically constructed and updated local approximate models which essentially make available the full accuracy of quantum mechanical models at each and every iteration of the minimisation algorithm, requiring only a small number of explicit quantum mechanical calculations. This has made possible the accurate treatment of molecules involving a relatively large numbers of atoms with significant flexibility in torsional and bond angles and even bond lengths. The performance of the algorithm is critically assessed and demonstrated on a set of single and multi-component crystals. An extension of an existing algorithm for the identification of low energy crystal structures of flexible molecules, CrystalPredictor, is also described. In the proposed modification, the intramolecular energy and the molecular conformation are modelled using local approximate models. This provides a more realistic model for the effects of the flexible degrees of freedom on the molecular geometry and lattice energy. The use of deterministic low-discrepancy sequences ensures an extensive and uniform coverage of the multivariable search space. A parallelised implementation of the algorithm allows minimisations from several hundreds of thousands of initial guesses to be carried out in reasonable time. A further computational benefit is derived by the storage of the information used to construct the local approximate models in databases, which can be re-used in subsequent re-minimisation of structures with more accurate models for the lattice energy. The usefulness of these modifications is demonstrated on the ROY molecule, for which the structures of all experimentally known polymorphs are identified by the algorithm. By combining the above algorithms, a comprehensive multi-stage methodology for ab initio determination of the crystal structure of a given molecule based solely on its atomic connectivity is presented. The application of the methodology to two large and flexible molecules of pharmaceutical interest is also demonstrated.

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13

Legha, Prem. "Molecular structure and odor mixture perception." Thesis, View thesis, 2004. http://handle.uws.edu.au:8081/1959.7/549.

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The sense of smell is a primal sense for humans as well as animals.In everyday life the smells encountered are composed of dozens, even hundreds of odors; few arise from a single odorant. Enormous numbers of odors occur due to the vast variation in the concentration, size and structure of odorant molecules that makes olfaction differ from simpler visual or auditory dimensions. Accordingly, little is known about the ways in which changes in molecular structure and concentration of individual odorants change odor quality. Also, currently not much is understood about synergism/antagonism, how one odorant masks or suppresses another in mixtures and there is no method for predicting which odor will be suppressed. The two main objectives of this thesis were to determine whether a part of a molecular structure rather than the whole structure plays a key role in odor quality and whether a key part of a molecule can be used to choose antagonists for that odorant. For this study three classes of musks and two potential antagonists were used. The results of the study are discussed in some detail. It is concluded that future studies of the importance of molecular structure in mixture interactions require substantially more information on the relation between structure and odor quality to allow systematic studies to be developed. In summary the two hypotheses investigated were not supported by the results. Importantly, however, they do support the view that it is likely that odor quality is dependent on the whole structure of an odorant not a single feature.

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14

Legha, Prem. "Molecular structure and odor mixture perception." View thesis, 2004. http://library.uws.edu.au/adt-NUWS/public/adt-NUWS20040723.142239/index.html.

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Thesis (M.Sc. (Hons)) -- University of Western Sydney, 2004.
"This thesis was submitted in fulfilment of the requirements for the degree of Master of Science (Hons) in the Centre for Advanced Food Research, University of Western Sydney, June 2004" Includes bibliography.

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15

Huang, Tian He. "Investigation of cyclodextrin formulations by combined experimental and molecular modeling techniques." Thesis, University of Macau, 2018. http://umaclib3.umac.mo/record=b3952153.

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16

Bliven, Spencer Edward. "Structure-Preserving Rearrangements| Algorithms for Structural Comparison and Protein Analysis." Thesis, University of California, San Diego, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3716489.

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Protein structure is fundamental to a deep understanding of how proteins function. Since structure is highly conserved, structural comparison can provide deep information about the evolution and function of protein families. The Protein Data Bank (PDB) continues to grow rapidly, providing copious opportunities for advancing our understanding of proteins through large-scale searches and structural comparisons. In this work I present several novel structural comparison methods for specific applications, as well as apply structure comparison tools systematically to better understand global properties of protein fold space.

Circular permutation describes a relationship between two proteins where the N-terminal portion of one protein is related to the C-terminal portion of the other. Proteins that are related by a circular permutation generally share the same structure despite the rearrangement of their primary sequence. This non-sequential relationship makes them difficult for many structure alignment tools to detect. Combinatorial Extension for Circular Permutations (CE-CP) was developed to align proteins that may be related by a circular permutation. It is widely available due to its incorporation into the RCSB PDB website.

Symmetry and structural repeats are common in protein structures at many levels. The CE-Symm tool was developed in order to detect internal pseudosymmetry within individual polypeptide chains. Such internal symmetry can arise from duplication events, so aligning the individual symmetry units provides insights about conservation and evolution. In many cases, internal symmetry can be shown to be important for a number of functions, including ligand binding, allostery, folding, stability, and evolution.

Structural comparison tools were applied comprehensively across all PDB structures for systematic analysis. Pairwise structural comparisons of all proteins in the PDB have been computed using the Open Science Grid computing infrastructure, and are kept continually up-to-date with the release of new structures. These provide a network-based view of protein fold space. CE-Symm was also applied to systematically survey the PDB for internally symmetric proteins. It is able to detect symmetry in ~20% of all protein families. Such PDB-wide analyses give insights into the complex evolution of protein folds.

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Bianchi, Laurent. "The structure of molecular liquids : neutron diffraction and molecular dynamics simulations." Thesis, University of Dundee, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312329.

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Spivak, Mariano Alejo. "Electronic structure calculations on extended metal atom chains. Insights on structural, magnetic and transport properties." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/399580.

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En aquest treball, es van utilitzar diferents mètodes computacionals per estudiar les propietats de cadenes esteses de metalls de transició (EMACs en anglès). Es va simular la flexibilitat estructural de cadenes de tres àtoms de crom, amb CASSCF/CASPT2 i es van identificar estructures simètriques i asimètriques en un entorn de baixa energia. Basats en aquests resultats, vam realitzar dinàmiques moleculars de primers principis (AIMD) per entendre l'efecte de l'energia tèrmica i com aquesta modifica la proporció d'estructures. També es van estudiar els enllaços metall-metall en compostos de crom, utilitzant el model d'ordre d'enllaç efectiu (EBO) amb els números d'ocupació naturals de la funció d'ona CASSCF. Es van calcular constants d'acoblament magnètic per a compostos bimetàl·lics i EMACs de níquel mitjançant dues estratègies. MC-PT2 amb espai actiu mínim utilitzant orbitals moleculars millorats a partir d'un càlcul d'estats-mitjanats, i es va utilitzar un mètode nou (MCPDFT) per al magnetisme de EMACs grans, que ha mostrat bons resultats en el compost de cinc níquels. Finalment, estudiem propietats del transport d'electrons per dos EMACs de ruteni. Proposem l'ús d'un elèctrode gate metàl·lic per modular els nivells moleculars dels compostos i obtenir espècies redox actives. També utilitzem un mètode químicament més intuïtiu, que proposa crear parells iònics dins de la cel·la.
En este trabajo, se utilizaron diferentes métodos computacionales para estudiar las propiedades de cadenas extendidas de metales de transición (EMACs en inglés). Se simuló la flexibilidad estructural de cadenas de tres átomos de cromo, con CASSCF/CASPT2 y se identificaron estructuras simétricas y asimétricas en un entorno de baja energía. Basados en estos resultados, realizamos dinámicas moleculares de primeros principios (AIMD) para entender el efecto de la energía térmica y como ésta modifica la proporción de estructuras. También se estudiaron los enlaces metal-metal en compuestos de cromo, utilizando el modelo de orden de enlace efectivo (EBO) con los números de ocupación naturales de la función de onda CASSCF. Se calcularon constantes de acoplamiento magnético para compuestos bimetálicos y EMACs de níquel mediante dos estrategias. MC-PT2 con espacio activo mínimo utilizando orbitales moleculares mejorados a partir de un cálculo de estados-promediados, y se utilizó un método nuevo (MCPDFT) para el magnetismo de EMACs grandes, que ha mostrado buenos resultados en el compuesto de cinco níqueles. Finalmente, estudiamos propiedades del transporte de electrones para dos EMACs de rutenio. Proponemos el uso de un electrodo gate metálico para modular los niveles moleculares de los compuestos y obtener especies redox activas. También utilizamos un método químicamente más intuitivo, que propone crear pares iónicos dentro de la celda.
In this work we use different computational methods in the study of the properties of Extended Metal Atom Chains. The structural flexibility of trichromium chains has been simulated with CASSCF/CASPT2 and symmetric and asymmetric structures were identified in an extremely flat energy landscape. Based on these results, Ab initio molecular dynamic simulations were performed to understand how the thermal energy modifies the proportion of cited structures. In addition, the metal-metal bonding of chromium compounds was characterized using the Effective Bond Order (EBO) model with the natural occupation numbers of the CASSCF wave function. Furthermore, magnetic coupling constants were computed for nickel bimetallic and EMACs compounds, using two different approaches. Minimal active space MC-PT2 was performed with improved molecular orbitals based on state-average calculations, and a recently developed method (MCPDFT) used for the magnetism of large EMACs, showing good results in the five-nickel compound. Finally, the electron transport properties were simulated for two ruthenium EMACs. We propose the use of a metallic gate electrode to modulate the molecular levels of the compounds and achieve redox active species. In addition, another more chemically intuitive approach was tested, that consist of forming an ionic pair in-situ.

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Sabir, Kenneth Spencer. "Visual Analytics Of 3D Macro Molecular Structure." Thesis, The University of Sydney, 2018. http://hdl.handle.net/2123/18860.

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Currently, molecular biology research is dominated by the rapid advances in DNA sequencing and related technologies. However, interpreting these data, and gaining insight into underlying molecular processes, remains challenging. Of the many strategies being pursued in this effort to understand the biomolecular machinery of life, one of the most enduring involves considering three-dimensional structure. Increasingly, experimental data is providing information on this 3D structure and dynamics of chromosomes in living cells –– these data, in turn, promise new insight into fundamental genomic processes. Similarly, the flood of DNA and protein sequence data provides a vast resource that can be used to greatly extend our ability to predict the 3D structure of proteins. In this thesis I describe Score, a visual analytics framework I have created to help biologists understand the 3D structure of chromosomes and proteins, and to explore how this structure relates to the underlying biological function. Usage of the Score framework is demonstrated through two case studies: Aquaria and Rondo. Aquaria is a web-based protein sequence structure viewer allowing users to find and navigate through structures for any given protein sequence. Rondo is a web-based chromosome structure viewer that can superimpose feature track information.

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Miller, Paul Francis. "Luminescence studies of molecular materials." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342250.

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Kobayashi, Yusuke. "Molecular structure and evolution of chloroplast nucleoids." 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225437.

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Knight, Matthew John. "Molecular Adsorbate Structure Determination by Photoelectron Diffraction." Thesis, University of Warwick, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.491931.

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Scanned-energy mode photoelectron diffraction (PhD) has been used to determine the adsorption geometries and structural parameters of a selection of molecular adsorption systems. Furan on Pd(111) has been investigated with the support of 0 K-edge near-edge X-ray absorption fine 'structure (NEXAFS) measurements. Adsorption at temperatures below 160 K is molecular, with decomposition of the molecule occurring after heating the surface to 340 K via the reaction: C4H40 -+ CO + C3H3 + H. Low coverage molecular furan phase NEXAFS measurements determined that the plane of the molecule is approximately parallel to the surface, in agreement with previous scanning tunnelling microscopy (STM) measurements. C 1s PhD measurements of C which is bonded to the 0 heteroatom (denoted aC) were used in the identification of several adsorption geometries, all with the aC atoms in off-atop sites. The results show agreement with those of a previous density functional theory (OFT) study. C 1s measurements found that CO bonds via the C atom, equally occupying both the fcc and hcp hollows. The structural parameters determined show good agreement with a previous PhD study of pure CO on Pd(111). For C3H3, PhD analysis found two possible structures within experimental variance. Comparison of the structural parameters revealed that C3H3 adsorbs with the molecular plane parallel to the surface, centred over an hollow site. The adsorption geometry of S02 and S03 on Ni(111) has been investigated. S 2p and 0 1s measurements were obtained for S02 at 145 K, which determined that the S atom adopts an off-atop site, with the 0 atoms situated between atop and hollow sites, in general accord with previous experimental studies. 0 1s PhD measurements for S03, prepared by heating the S02 covered surface to 210 K, identified an adsorption geometry in which one 0 atom is off-atop with two 0 atoms in off-bridge sites and the S atom centred above. The adsorption geometry determined is different to the results of OFT and normal incidence X-ray standing waves (NIXSW) studies, however the geometry found here identifies an alternative fit of the NIXSW data. C 1s PhD measurements were made to determine the adsorption geometry of CCl2 on Ag(111), prepared by heating a CCl4 covered surface to 198 K. The strongest modulations were observed at grazing emission angles suggesting adsorption in the hollow sites. Extensive analysis failed to yield a geometry which showed a good fit between theory and experiment in inequivalent azimuths. Examination of the experimental data revealed that the presence of spectral features, in particular the CI (LMM) Auger peak, led to modulations with unphysical characteristics precluding reliable structural determinations.

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Nguyen, Kim Trong. "Molecular dynamics study of the wurtzite structure." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq22368.pdf.

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Roney, Alfred B. "Structure and dynamics of heterogeneous molecular systems." [Tampa, Fla] : University of South Florida, 2006. http://purl.fcla.edu/usf/dc/et/SFE0001678.

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Hobson, Michael Paul. "The small-scale structure of molecular clouds." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282113.

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Karamertzanis, Panagiotis. "Prediction of crystal structure of molecular solids." Thesis, Imperial College London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.411320.

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Fattah, Jamila. "Structure and dynamics of some molecular crystals." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303690.

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Tongdang, Taewee. "Molecular structure of native and processed rices." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368246.

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Moorcroft, D. "Molecular structure studies using NMR relaxation methods." Thesis, University of Salford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.353972.

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Yates, P. C. "Investigation of molecular structure of macrocyclic complexes." Thesis, University of Reading, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373770.

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Rowan, Alan Edward. "NMR studies of molecular structure in solution." Thesis, University of Liverpool, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.291884.

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Thompson, Laura. "Synthesis and structure determination of molecular cocrystals." Thesis, University of Birmingham, 2013. http://etheses.bham.ac.uk//id/eprint/4007/.

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Research into cocrystals is just a small field within crystallography, though the significant rise of investigation into cocrystals has made it an exciting area of research. This thesis initially introduces the phenomenon of cocrystals, including the design, formation, structure solution and the properties of cocrystals. This thesis presents a number of new multi-component crystalline adducts that have been synthesised using dicarboxylic acids as coformers with isonicotinamide, nicotinamide or adenine. The first results chapter discusses a number of molecular adducts that contain distinct hydrogen bonding networks and includes the discovery of a new polymorph and the potential of adenine to tautomerise. The following two results chapters focus on molecular structures of nicotinamide and isonicotinamide with the dicarboxylic acids in which trends in crystal packing, cocrystal property studies and twisting of the acid backbone are discussed in detail. In conjunction with the crystal structure and property studies, several powder X-ray diffraction datasets were collected from a synchrotron source. The final results chapter shows that a cocrystal structure, such as nicotinamide : succinic acid, can be solved without the need of single crystal X-ray diffraction data.

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Sharman, Gary Jonathon. "Structure and molecular recognition in secondary metabolites." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627506.

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Hughes, Alan Nigel. "The structure and spectra of molecular ions." Thesis, University of Newcastle upon Tyne, 2013. http://hdl.handle.net/10443/2217.

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I give a review of the theory of the hydrogen molecular ion H2+ and its isotopomers D2+ and HD+ including the direct analytical solution and the standard adiabatic approximation. I discuss dissociation limits for homonuclear and heteronuclear species; the effect of an external electric field; non adiabatic calculations, relativistic and radiative effects; and spectroscopic measurements of H2+ and D2+ with a comparison of theoretical to experimental values. I give a detailed description of the fast ion-beam spectrometer as used for both laser-beam and microwave spectroscopy and describe the challenges involved in making high resolution spectroscopic measurements. An account is given of theory, experimental details and measurements of transition frequencies and intensities of the forbidden rotational transition (v = 19, N = 1) - (v = 19, N = 0) in the ground electronic state (X2Σg+, also represented as 1sσg) of H2+. Theory has predicted that the transition has measurable intensity due to the Fermi contact hyperfine interaction causing a breaking of electronic g/u symmetry resulting in the mixing of ortho-para states. The measurements were made in both single and double resonance using a fast ion beam/microwave spectrometer at a transition frequency of 14961.7 ± 1.1 MHz, in agreement with the theoretical prediction of 14960 ± 3 MHz. An account is also given of a further search that was conducted for a second forbidden rotational transition (v = 0, N = 1) - (v = 0, N = 0) in the first excited electronic state (2pσu) of H2+. A discussion is given on the possibility of making further observations of forbidden rotational transitions and the experimental difficulties involved; and of adapting the experimental techniques used in order to observe the recently discovered (v = 1, N = 0) in the first excited electronic state (2pσu) of H2+.

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35

Brass, Andrew Michael. "Molecular dynamics simulations of fluorite structure crystals." Thesis, University of Edinburgh, 1987. http://hdl.handle.net/1842/12714.

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Uzoh, O. G. "Modelling molecular flexibility for crystal structure prediction." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1460832/.

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In the crystal packing of molecules wherein a single bond links aromatic groups, a change in the torsion angle can optimise close packing of the molecule. The improved intermolecular interactions, Uinter, outweigh the conformational energy penalty, ΔEintra, to give a more stable lattice energy, Elatt = Uinter + ΔEintra. This thesis uses this lattice energy model hierarchically in a new Crystal Structure Prediction (CSP) algorithm, CrystalPredictor version 1.6, which varies the low-barrier torsion angles at the start of generating hypothetical crystal structures. The crystal structure of 1-benzyl-1H-tetrazole was successfully predicted in an informal ‘blind test’ when given the chemical diagram and the number of molecules in the asymmetric unit cell. Then, the concept of whether specific molecular fragments favour polymorphism (i.e. polymorphophore) was investigated by analysing the crystal energy landscapes of the monomorphic fenamic acid and the polymorphic derivative tolfenamic acid. The CSP results show that the polymorphophore promotes but does not guarantee polymorphism and that the substituents on the polymorphophore fragment decide the relative energies of the crystal structures. Molecular Dynamics (MD) cannot use this lattice energy model because many ab initio calculations of ΔEintra on a single molecule are expensive. However, the examination of the physical origin of the torsional barrier in fenamates aided the derivation of an analytical model fo ΔEintra. This thesis develops codes for fitting analytical intramolecular force fields to ab initio conformational profiles of fenamates. An intramolecular exp-6 atom-atom term (for the non-bonded repulsion-dispersion contributions) plus a cosine term (that represents the changes to the Molecular Orbitals) accurately model the ab initio conformational energy surfaces of fenamic and tolfenamic acids. This thesis provides a first step in extending ΔEintra data generated from CSP studies to help MD on condensed phases of pharmaceutical-like organic molecules.

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Abildgaard, Jens. "Quantum chemical models in molecular structure elucidation /." Roskilde : Roskilde University, Department of Life Sciences and Chemistry, 1998. http://hdl.handle.net/1800/535.

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Rodger, Alison. "Molecular aspects of biomolecule structure and function." Thesis, The University of Sydney, 2002. http://hdl.handle.net/2123/516.

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All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

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39

Rodger, Alison. "Molecular aspects of biomolecule structure and function." University of Sydney. Chemistry, 2002. http://hdl.handle.net/2123/516.

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All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

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40

Culberson, Lori. "Molecular Electronic Structure via Photoelectron Imaging Spectroscopy." Diss., The University of Arizona, 2013. http://hdl.handle.net/10150/301677.

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This dissertation explores the use of photoelectron imaging spectrometry to probe the molecular electronic structure of various chemical systems, with an emphasis on photoelectron angular distributions. Experimental ion generation, mass selection, laser photodetachment, and photoelectron ion imaging were all done in a photoelectron imaging spectrometer described in detail. Results from simplistic systems, OH- and CH-, are used to illustrate the general and fundamental capabilities of imaging spectroscopy and angular distributions. This illustration is then expanded when both qualitative and quantitative analyses of photoelectron angular distributions are used to aid in the understanding of the electronic structure of several heterocyclic aromatic systems. First a qualitative analysis aids in the exploration of the electronic structure of thiophenide, C₄H₃S⁻, and furanide, C₄H₃O⁻. Ground and excited C₄H₃S and C₄H₃O radical states are observed, and bond dissociation energies are defined. Next, a new model used to qualitatively analyze photoelectron angular distributions resulting from mixed s - p hybrid states is presented and applied to detachment from pyridinide, C₅H₄N⁻; as a benchmark system. Before further exploring this model, the synthesis of several deuterated heterocyclic compounds is presented in order to determine the experimentally produced systems in our experimental setup. The electronic structure of the resultant molecules oxazolide, C₃H₂NO⁻, and thiazolide, C₃H₂NS⁻; are then investigated. Using this new qualitative model, the mixed s - p states model, to evaluate the angular distributions of the systems, the hybridization of the anion molecular orbitals is probed. Comparison of the photoelectron angular distributions that are modeled for each heterocyclic aromatic system yields several trends relating aromatic stabilization, molecular hybridization, and bond dissociation energies. A new qualitative model is then presented to evaluate photoelectron angular distributions resulting from mixed p - d states and applied to detachment from NO⁻. Finally, new ideas and directions are proposed.

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MARCHESAN, DOMENICO. "ELECTRONIC STRUCTURE THEORY CALCULATIONS OF MOLECULAR PROPERTIES." Doctoral thesis, Università degli studi di Trieste, 2005. http://thesis2.sba.units.it/store/handle/item/13198.

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Pham, Cong Huy. "Molecular crystal structure prediction with evolutionary algorithm." Doctoral thesis, SISSA, 2015. http://hdl.handle.net/20.500.11767/4884.

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The layout of the thesis is as follow: In Chapter 1, we present the theoretical background of DFT, Projector-Augmented-Wave (PAW) and Gauge-Including Projector-Augmented-Wave (GIPAW) methods. In Chapter 2, we introduce the crystal structure prediction problem and present evolutionary algorithms as one solution to perform crystal structure search for molecular crystals. Chapter 3 and Chapter 4 are dedicated to the detailed results when using evolutionary algorithm in crystal structure search for the studies of glycine and cholesterol respectively

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Aleksandrov, Alexey. "Protéines : Structure fonction et évolution." Phd thesis, Ecole Polytechnique X, 2008. http://pastel.archives-ouvertes.fr/pastel-00004205.

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Tétracyclines (TC) sont une famille d'antibiotiques important, qui se lient SPECI ャ ... allié aux protéines du ribosome et solidaire. Le mécanisme le plus important de la résistance à la tétracycline est régie par sa reliure en Tc: Mg2 + complexe à la protéine Tet Repressor (TetR). Il est donc d'intérêt pour améliorer notre compréhension des deux Tc: TetR et Tc: liaison au ribosome. Les structures cristallines des tétracyclines dans plusieurs complexes avec les protéines et les ribosomes ont fourni des informations essentielles. Une approche complémentaire consiste à développer des modèles de simulation par ordinateur, qui peut être utilisée pour étudier la structure, la dynamique et la thermodynamique de Tc: protéines ou Tc: complexes ribosome. Malgré son importance, à la tétracycline a rarement été soumis à la modélisation informatique, en partie en raison de la nécessité de ャ> St développer un modèle de mécanique moléculaire pour le TC. Ici, nous avons développé un tel modèle, de manière à être compatible avec le ャ CHARMM27 force »ld pour les protéines et les acides nucléiques, de 12 analogues de tétracycline importants, notamment la tétracycline plaine. paramètres ld ャ forces intermoléculaires ont été dérivées de supermolécule une approche standard. Le modèle reproduit la géométrie ab initio et Fxibility ャ de chaque Tc. Comme les tests, nous avons fait des simulations d'un cristal de Tc, Tc: Mg2 + et Tc: complexes Ca2 + en solution aqueuse, et d'un complexe solvaté entre TC: Mg2 + et le TetR. Le modèle se compare bien avec un large corpus de données expérimentales. Nous ャ> St utilisé notre modèle pour l'étude Tc: reconnaissance TetR qui est un problème complexe. Nous avons utilisé des simulations d'énergie libre pour étudier les interactions électrostatiques entre la protéine et ligand et le rôle éventuel de ャ induite "en Tc contraignant. Nous avons constaté que la tétracycline préfère une étendue, l'état zwitterioniques fois en solution et en complexe avec la protéine. Tc est donc préorganisés pour la reliure. En l'absence de Tc, TetR est étroitement liée à son ADN opérateur; lors de la liaison de Tc il se dissocie de l'ADN, permettant l'expression des gènes réprimés. Son contrôle serré par Transports Canada fait TetR largement utilisables dans le génie génétique. Le Tc site de liaison est plus de 20 ヒ A partir de l'ADN, de sorte que le signal de liaison doivent se propager sur une longue distance. Nous utilisons des simulations de dynamique moléculaire et calculs continuum électrostatique pour élucider le mécanisme allostérique. Lorsque [TC: Mg] lie +, l'ion Mg2 + permet des interactions avec hélice 8 de TetR un monomère et Helix 6 de l'autre monomère, et Helix 6 est tiré en direction du noyau central de la structure. Hy- interactions drophobic avec hélice 6 puis tirez hélice 4 dans un mouvement pendulaire, avec un déplacement maximum à son extrémité N-terminale: l'interface de l'ADN. Le résidu N-terminal de l'hélice 4, Lys48, est très conservée dans l'ADN de liaison des protéines régulatrices de la classe TetR et fait la plus grande contribution de tout acide aminé à l'TetR: l'ADN d'énergie libre contraignant. Ainsi, les changements de conformation conduire à une réduction drastique de la TetR: la liaison d'un ADN lité ャハ, permettant TetR se détacher de l'ADN. Nous avons ensuite utilisé le modèle pour l'étude Tc liaison au ribosome et de facteur d'élongation Tu (EF-Tu). Les structures cristallines de Tc lié à la Thermus thermophilus 30S sous-unité montrer le même site Tc primaire obligatoire (appelé TET1), avec la plus forte densité d'électrons Tc, à proximité du site A-, compatible avec un rôle inhibiteur. Un site secondaire Tc-contraignant, TET5 appelé a également été observée dans les deux structures. Nous avons fait de la dynamique moléculaire (MD) des simulations de sous-unités 30S du ribosome pour caractériser Tc contraignant et aider à résoudre l'ambiguïté en ce qui concerne le nombre et la force de Tc sites de liaison. Nous avons présenté des preuves pour les lier à TET1 prédominante, indiquant que d'autres sites de liaison signalés sont plus faibles et pas très occupés à des concentrations physiologiques Tc. Récemment, la structure cristalline d'un complexe entre le facteur d'allongement Tu (EF-Tu) et Tc a été résolu, ce qui soulève la question de savoir si Tc 窭冱 contraignant à EF-Tu a un rôle dans l'inhibition de la synthèse protéique. Nous montrons que la contribution directe de EF-Tu à l'énergie libre de Tc contraignant à l'EF-Tu: PIB: complexe Mg est négligeable, mais plutôt la liaison peut être attribuée uniquement à Tc interactions avec l'ion Mg et le phosphate PIB groupes . Nous montrons aussi que EF-Tu ne présente pas de préférence contraignant pour le TC sur la non-antibiotiques, 4-dedimethyl-Tc, et EF-Tu ne lie pas la tigécycline analogique Tc, qui est un antibiotique puissant. Globalement, nos résultats appuient l'idée que les EF-Tu n'est pas la cible principale de la tétracycline. Les articles présentés ci-dessous comprennent à la fois de calcul et les résultats expérimentaux. Tout le travail expérimental a été réalisé par Winfried Hinrichs et ses collabora-teurs. Tout le travail de calcul a été fait par moi-même. Les connaissances acquises dans ce travail et les techniques de modélisation employées doivent être d'intérêt pour l'amélioration des techniques antibiotiques Tc et TetR protéines améliorées pour la régulation des gènes.

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Nenov, Artur. "Relation between molecular structure and ultrafast photoreactivity with application to molecular switches." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-150470.

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45

O'Neill, Andrew. "Investigations in molecular structure : from scattering to molecular complexes of brominated compounds." Thesis, University of Glasgow, 2010. http://theses.gla.ac.uk/1709/.

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The main focuses of this research were to examine the capabilities of solution techniques to attempt to monitor the nucleation process in crystallisation, and to investigate structural outcomes of crystallisation processes, with reference to polymorphism and intermolecular interactions. To achieve this, work on the investigation of nucleation and early-stage crystallisation was carried out at the Department of Pharmaceutical Sciences at the University of Strathclyde and also at the central synchrotron facility of Station 2.1 at the SRS Daresbury. Small angle X-ray scattering (SAXS) was carried out on solutions of methyl-4-hydroxybenzoate (pMHB) and 2-bromobenzoic acid. These studies were carried out after developing solution methods to enable us to determine the point at which crystals emerged from solution. This was achieved using Focussed Beam Reflectance Measurements. Structural studies were also carried out on pMHB to examine its polymorphic behaviour and crystal structures were solved at various temperatures from 100K to 300K. The crystal structure of methyl-2,5- dibromobenzoate was also solved at 100K after discovering it sublimes at room temperature. This structure could only be solved from a twinned crystal and indicated the appearance of interesting halogen interactions occurring. Structural studies have also been carried out using the bromanilic acid molecule as a focus to generate a number of co-crystal complexes to examine their halogen bonding capability and to determine any structural significances in their formation. Co-crystal complexes of bromanilic acid and a variety of molecules were made in 1:1 and 1:2 ratios to see if any additional halogen interactions could be observed or induced, in addition to the expected hydrogen-binding interactions. The co-crystals included a range of picolines and lutidines as well as bromo-substituted pyridines to attempt to induce halogen interactions. This generated a number of new compounds whose structures were determined using single crystal X-ray diffraction and the interactions were monitored to observed whether any defined patterns with regards to the tendency of bromanilic acid co-crystallisations to produce predictable patterns of intermolecular interactions could be determined.

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Jiménez, Rosés Mireia. "Structure and function of GPCRs." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667278.

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Los receptores acoplados a proteínas G (GPCRs) son la superfamilia más grande y diversa de proteínas transmembrana en Eucariotas. Estos receptores transducen una gran variedad de señales exógenas y endógenas como fotones, hormonas o neurotransmisores para iniciar la respuesta biológica en el interior de la célula. Son, por lo tanto, muy interesantes como dianas farmacológicas. Esta Tesis Doctoral se centra en la comprensión de la estructura y función de los GPCRs, mediante el uso de técnicas de la química computacional como son el modelado por homología, el anclaje molecular y las simulaciones de dinámica molecular. En concreto, la tesis aborda los determinantes estructurales asociados al mecanismo de activación, la regulación por moduladores alostéricos, la oligomerización con otro GPCR o proteínas adicionales, asícomo el acoplamiento de transductores (proteínas G o arrestinas).
G protein-coupled receptors (GPCRs) are the largest and most diverse superfamily of transmembrane proteins in Eukaryotes. GPCRs transduce a huge variety of exogenous and endogenous signals such as photons, hormones or neurotransmitters to initiate biological responses in the cell interior. Therefore, they are very interesting therapeutic targets. This Doctoral Thesis focusses on the understanding of the structure and function of GPCRs, by applying computational chemistry techniques such as homology modelling, docking and molecular dynamics simulations. Particularly, the thesis addresses the structural determinants associated to the activation mechanism, the regulation by allosteric modulators, the oligomerization with other GPCR or additional proteins and the coupling to transducers (G proteins or arrestins).

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Banerjee, Sangeeta. "Host cell response to coronavirus infection." Access restricted to users with UT Austin EID Full text (PDF) from UMI/Dissertation Abstracts Internataional, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3025137.

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Lakins, Johnathon N. "Structure and activity of human clusterin." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0021/NQ45178.pdf.

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Wu, Tao. "Structure-function analysis of vascular tethering molecules using atomic force microscope." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/31844.

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Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2009.
Committee Chair: Zhu, Cheng; Committee Member: Barry, Bridgette; Committee Member: Boyan, Barbara; Committee Member: McEver, Rodger; Committee Member: McIntire, Larry. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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Watson, Aleksandra. "Molecular structure and function of C-type lectin-like molecules in innate immunity." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504625.

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Dissertations / Theses on the topic 'Molecular structure'

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