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1
Barnard, Edward S. "AtomicControl : a crystallography simulator." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/32853.
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Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2005.Includes bibliographical references (p. 51).
AtomicControl is a software package designed to aid in the teaching of crystallography and x-ray diffraction concepts to materials science students. It has the capability to create an arbitrary crystal structure based on the user's specification of a space group and atomic coordinates. It also can generate a simulated powder diffractogram based on the user's generated crystal. The program is fully interactive and allows the user to view the effects of changes to lattice and atoms in a 3D visualization of the crystal. AtomicControl's x-ray diffraction patterns have been shown to match well with experimental data, proving the validity of the algorithm. AtomicControl is available online.
by Edward S. Barnard.
S.B.
2
Jones, Adrian Howard. "The acquisition, analysis and correlation of low energy electron diffraction and scanning tunnelling microscopy data from silicon surfaces." Thesis, University of York, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.283430.
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Moro, Marjan. "Nano-Characterization of Ceramic-Metallic Interpenetrating Phase Composite Material using Electron Crystallography." Youngstown State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1340223324.
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Hobday, Denise Marie. "LEED analysis of Ge(111)(#sq root#3X#sq root#3)R30deg-Ag and Kikuchi electron diffraction." Thesis, University of York, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259880.
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Gopal, Kreshna. "Efficient case-based reasoning through feature weighting, and its application in protein crystallography." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1906.
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Shi, Rongpei. "Variant Selection during Alpha Precipitation in Titanium Alloys- A Simulation Study." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397655766.
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Gao, Yipeng. "Transformation Pathway Network Analysis for Martensitic Transformations." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385978073.
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Venter, Gerhard. "The effect of the crystalline state on the properties of the dative bond." Thesis, Stellenbosch : Stellenbosch University, 2005. http://hdl.handle.net/10019.1/20944.
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Thesis (PhD)--University of Stellenbosch, 2005.ENGLISH ABSTRACT: Density functional theory (DFT) has been used to investigate the effect of the surrounding molecules on the structure of selected boron-nitrogen compounds. It was found that a very limited number of molecules, orientated according to the experimental crystal structure, are needed to successfully reproduce the large changes in structure witnessed when HCN–BF3 and CH3CN–BF3 crystallises. Specifically, the addition of seven molecules shortens the B–N distance by 0.735 °A in (HCN–BF3)8 and 0.654A° in (CH3CN– BF3)8. Accompanying the large changes in B–N bond length are equally large changes in the N–B–F angle. Investigation of the structure of these complexes in terms of localised electron pairs shows that the availability of lone pairs, in close proximity to the B–N bond axis, plays an important role in the bond change. Through delocalisation of the fluorine lone pairs the antibonding σ ∗(B–N) orbital becomes increasingly occupied as the N–B–F angle lessens and vice versa. Further, an investigation of the specific effects of dipole-dipole interactions was performed by applying uniform electric fields of varying strength along the donor-acceptor bond axis of a series of compounds of the form X–Y; X=H3N, HCN, CH3CN; Y = BF3, BH3, SO3. All complexes investigated show sensitivity to the external electric field, however, only the compounds having nitrile donors and acceptors with fluorine atoms produce large changes, which in turn are dominated by a very sudden large change in B–N bond length occurring in a very narrow range of changing field strength. Analysis of the changes in bond character reveals that HCN–BF3 and CH3CN–BF3 have long bonds in the gas phase, formed primarily through electrostatic interaction between the donor and acceptor. In the short bond in the condensed phase the bond character changes considerably through the introduction of strong electron sharing interactions, i.e. covalent or orbital interactions. Fundamental changes in the nature of the bond, catalysed by surrounding molecules, thus lie at the heart of the large phase-dependent changes in these species.
AFRIKAANSE OPSOMMING: ’n Kohn-Sham elektrondigtheidsteorie (DFT) studie is gedoen op die effek van die omliggende molekules in die kristalstruktuur van sekere molekules wat boor-stikstof bindings bevat. Daar is gevind dat ’n klein aantal molekules, georienteer soos in die eksperimentele kristalstruktuur, benodig word om die groot veranderinge in stuktuur te veroorsaak wat eksperimenteel waargeneem word wanneer HCN–BF3 en CH3CN–BF3 kristaliseer. Spesifiek, die byvoeging van sewe molekules verminder die B–N bindingslengte met 0.735 °A in (HCN–BF3)8 en 0.654 A° in (CH3CN–BF3)8. Die groot veranderinge in B–N bindingslengte gaan saam met ewe groot veranderinge in die N–B–F hoek. ’n Ondersoek van die struktuur van die molekules in terme van gelokaliseerde elektronpare wys dat die beskikbaarheid van alleenpare, wat naby die B–N bindingsas lˆe, ’n belangrike rol speel in the verandering in bindingslengte. Deur delokalisasie van die fluoor alleenpare word die antibindende σ ∗(B–N) orbitaal toenemend beset soos die N–B–F hoek afneem en omgekeerd. Verder is die spesifieke effek van dipool-dipool interaksies ondersoek deur uniforme elektriese velde aan te lˆe langs the donor-akseptor bindingsas van ’n reeks komplekse van die vorm X–Y; X = H3N, HCN, CH3CN; Y = BF3, BH3, SO3. Al die komplekse toon sensitiwiteit teenoor die eksterne elektriese veld, maar net die verbindings wat nitriel akseptore en fluoor atome aan the donor fragmente het, toon groot veranderinge, wat op hulle beurt weer oorskadu word deur ’n skielike verandering in the B–N bindingslengte in ’n nou band van veranderende veldsterkte. Analise van die veranderinge in bindingskarakter toon dat HCN–BF3 en CH3CN–BF3 lang bindings in die gasfase het, wat hoofsaaklik gevorm word deur elektrostatiese interaksies tussen die donor en akseptor fragmente. In die kort binding in die kristalfase is daar ’n aansienlike verandering in the karakter as gevolg van die intrede van sterk elektrondelingsinteraksies, m.a.w. kovalente of orbitaalinteraksies. Fundamentele veranderinge in the manier wat die binding saamgestel word, wat gekataliseer word deur omliggende molekules, is dus die oorsaak van die groot faseafhanklike veranderinge.
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Blocher, Richard Paul. "Predictive Tools for the Improvement of Shape Memory Alloy Performance." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1556022653899471.
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Bryant, Mathew James. "Platinum pincer complexes : in pursuit of switchable materials." Thesis, University of Bath, 2016. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678854.
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The research presented within this thesis is concerned with the design, synthesis, characterisation, and analysis of a series of new compounds of platinum (II), with aims to produce compounds possessing switchable optical properties, and with potential applications as "smart-materials" for use as highly selective sensors.
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Muniz, Francisco Tiago LeitÃo. "Estudo dos Perfis pela Teoria DinÃmica da DifraÃÃo de Raios - X." Universidade Federal do CearÃ, 2012. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=8121.
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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel SuperiorA teoria dinÃmica da difraÃÃo de raios X Ã uma teoria que ao contrÃrio da teoria cinemÃtica tem sua origem nas equaÃÃes de Maxwell e na lei de Bragg e com um tratamento fÃsico mais completo e adequado levando em consideraÃÃo todas as interaÃÃes entre os campos de onda eletromagnÃticos dentro do cristal e logo, leva em conta tambÃm, as propriedades fÃsicas do meio cristalino. Estas interaÃÃes trazem consigo efeitos que sÃo desprezados na teoria cinemÃtica, teoria mais tradicional e mais comumente utilizada quando se trata de difraÃÃo de cristais pouco espessos. Este trabalho visa calcular os perfis de difraÃÃo pela teoria dinÃmica com o intuito de confirmar e analisar a presenÃa dos efeitos dinÃmicos que, por sua vez, se acentuam com o aumento da espessura da amostra. Esses efeitos sÃo a absorÃÃo anÃmala e os efeitos de extinÃÃo. Os cÃlculos foram feitos com o uso da linguagem de programaÃÃo Fortran 90 aplicados em monocristais de silÃcio, germÃnio, arseneto de gÃlio e fosfeto de Ãndio, com o objetivo de estudar a influÃncia da espessura do cristal e da razÃo entre as partes imaginÃria e real do fator de estrutura, nos perfis de difraÃÃo. Por fim, tendo-se a largura a meia altura, determinados pelos grÃficos dos perfis, em funÃÃo da espessura pÃde-se concluir que a equaÃÃo de Scherrer se aplica bem em cristais pouco espessos, regiÃo de espessura onde os efeitos dinÃmicos sÃo desprezÃveis.
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Broderick, Thomas Froats. "The Influence of Microstructure on the Deformation Behavior of Beta Solution Heat Treated and Aged Ti-6Al-2Sn-2Zr-2Mo-2Cr-0.18Si." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1263951781.
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Bucar, Dejan-Kresimir. "Crystal engineering of organic and metal-organic solids: design, structure and properties." Diss., University of Iowa, 2010. https://ir.uiowa.edu/etd/3435.
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Crystal engineering has recently emerged as a method of choice for the design and the construction of functional materials. Solid-state synthesis, of the most commonly studied aspects of crystal engineering, has been shown to provide access to molecular targets that are hardly obtainable using principles of conventional (i.e. solution-based) organic synthesis. Reactions in the solid state are, however, not routinely used in organic synthetic chemistry. The scarce use of solid-state reactions can be attributed to the difficulty of predicting molecular arrangements in the solid state, as well as to the lack of methodologies to control crystal packing. Template-directed solid-state synthesis is a recently developed modus operandi that enables control over reactivity within multi-component crystals. The thesis is focused on the application of template-directed solid-state approach to [2+2] photocycloaddition reactions in the solid state, as well as on the understanding of intermolecular interactions in crystals. Synthetic templates have been utilized to construct cocrystals that enable a class of hitherto underdeveloped organic solid-state reactions, namely [2+2] cross-photoaddition reactions. In addition, products derived form templated solid state reactions, namely tetrapyridylcyclobutanes, have been utilized to generate exceptional materials, such as thixothropic hydrogels based on nano-dimensional metal-organic particles. The utility of crystal engineering has also been expanded to the nanoscience and the development of nanomaterials. A crystallization method for the preparation of nano-dimensional cocrystals has been developed. The method has been shown to enable single-crystal-to-single-crystal [2+2] photodimerizations of olefins. In addition, nano-dimensional cocrystals have been shown to exhibit distinctive mechanical properties upon single-crystal-to-single-crystal transformations.
In addition to solid-state reactions and materials derived therefrom, we systematically studied hierarchies of supramolecular synthons in pharmaceutical cocrystals comprised of multi-functional molecules. Pharmaceutical cocrystals have been recently shown to exhibit physical properties superior to those of parent drugs. Our studies involved xanthine alkaloids as pharmaceutical agents and a series of hydroxylated benzoic acids as cocrystal formers. Synthon hierarchies have been established for three xanthine alkaloids. We also discovered pharmaceutical salts that formed where cocrystallization was expected to occur. Reasons contributing to such unexpected salt formation were investigated using X-ray crystallography and computational methods. The established synthon hierarchies are expected to contribute to a better understanding of self-assembly processes in cocrystals that is crucial for the development of state-of-art drugs, and the design of organic reactions in the solid state.
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Davis, Harrison Olivia. "Copper, Silver, and Gold Clusters: A Synthetic and Structural Investigation." Kent State University Honors College / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1557352298361181.
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Xu, Qifang. "Statistical Analysis of Biological Interactions from Homologous Proteins." Diss., Temple University Libraries, 2008. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/25686.
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Computer and Information SciencePh.D.
Information fusion aims to develop intelligent approaches of integrating information from complementary sources, such that a more comprehensive basis is obtained for data analysis and knowledge discovery. Our Protein Biological Unit (ProtBuD) database is the first database that integrated the biological unit information from the Protein Data Bank (PDB), Protein Quaternary Server (PQS) and Protein Interfaces, Surfaces and Assemblies (PISA) server, and compared the three biological units side-by-side. The statistical analyses show that the inconsistency within these databases and between them is significant. In order to improve the inconsistency, we studied interfaces across different PDB entries in a protein family using an assumption that interfaces shared by different crystal forms are likely to be biologically relevant. A novel computational method is proposed to achieve this goal. First, redundant data were removed by clustering similar crystal structures, and a representative entry was used for each cluster. Then a modified k-d tree algorithm was applied to facilitate the computation of identifying interfaces from crystals. The interface similarity functions were derived from Gaussian distributions fit to the data. Hierarchical clustering was used to cluster interfaces to define the likely biological interfaces by the number of crystal forms in a cluster. Benchmark data sets were used to determine whether the existence or lack of existence of interfaces across multiple crystal forms can be used to predict whether a protein is an oligomer or not. The probability that a common interface is biological is given. An interface shared in two different crystal forms by divergent proteins is very likely to be biologically important. The interface data not only provide new interaction templates for computational modeling, but also provide more accurate data for training sets and testing sets in data-mining research to predict protein-protein interactions. In summary, we developed a framework which is based on databases where different biological unit information is integrated and new interface data are stored. In order for users from the biology community to use the data, a stand-alone software program, a web site with a user-friendly graphical interface, and a web service are provided.
Temple University--Theses
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Sugar, Joshua D. "Mechanisms of microstructure development at metallic-interlayer/ceramic interfaces during liquid-film-assisted bonding." Berkeley, Calif. : Oak Ridge, Tenn. : Lawrence Berkeley National Laboratory ; distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2003. http://www.osti.gov/servlets/purl/825347-j6A0Su/native/.
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Thesis (M.S.); Submitted to the University of California, Berkeley, CA (US); 1 Dec 2003.Published through the Information Bridge: DOE Scientific and Technical Information. "LBNL--54185" Sugar, Joshua D. USDOE Director. Office of Science. Basic Energy Sciences (US) 12/01/2003. Report is also available in paper and microfiche from NTIS.
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Spiers, Ian D. "Synthesis, crystallography and biological activity of myo-inositol phosphates." Thesis, Aston University, 1996. http://publications.aston.ac.uk/11047/.
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The antioxidant property of myo-inositol hexakisphosphate is important in the prevention of hydroxyl radical formation which may allow it to act as a 'safe' carrier of iron within the cell. Here, the hypothesis that the recently discovered natural product, myo-inositol 1,2,3-trisphosphate represents the simplest structure to mimic phytate's antioxidant activity has been tested. The first synthesis of myo-inositol 1,2,3-trisphosphate has been completed, along with its X-ray structure determination and that of key synthetic intermediates. Iron binding studies of myo-inositol 1,2,3-trisphosphate demonstrated that phosphate groups with the equatorial-axial-equatorial conformation are required for complete inhibition of hydroxyl radical formation. myo-Inositol monophosphatase is a key enzyme in recycling myo-inositol from its monophosphates in the brain and its inhibition is implicated in lithium's antimanic properties. Current synthetic strategies require inositol compounds to be protected (often with more than one group), resolved, phosphorylated and deprotected to produce the desired optically active myo-inositol phosphates. Here, the synthesis of myo-inositol 3-phosphate has been achieved in only 4 steps from myo-inositol. The stereoselective addition of the chiral phosphorylating agent (2R,4S,5R)-2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidin-2-one to a protected inositol intermediate allowed separation of diastereoisomers and easy deprotection to myo-inositol 3-phosphate. This strategy also allows the possible introduction of labels of oxygen and sulphur to give a thiophosphate of known stereochemistry at phosphorus which would be useful for the analysis of the stereochemical course of phosphate hydrolysis catalysed by inositol monophosphatase.
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Eberman, Kevin W. (Kevin Wilmot) 1971. "Crystallographic origins of fast-ion conduction in pyrochlore." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/50456.
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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1998.Includes bibliographical references (p. 129-132).
We have examined the crystallographic origins of fast-ion conduction in oxides with the pyrochlore structure-type, ideally A2B2O7, a superstructure of (A,B)20 3.5 defect fluorite-like array. These materials have technological promise for use in electrochemical devices such as oxygen sensors and solid-oxide fuel-cells. The pathway for ion conduction proposed by several authors has been a jump between equivalent nearest-neighbor oxygen sites through the tetrahedral edges of the relatively-immobile cation array. Substitution of a third cation species in slid-solution in the B site, A2(B-yB'y)2O7, results in a marked change in the structure and properties of the materials which is not fully understood. As the average radius of the cations occupying the B-site increases (with changing composition) towards that of the larger average radius of the cations occupying the Asite, a tendency for increasing disorder has been observed, where complete disorder corresponds to the fluorite structure. A decrease in Frenkel-defect formation-energy and an increase in the migration enthalpy accompanies the disordering. We have executed several studies of pyrochlore structures employing neutron and x-ray powder diffraction. In particular, we have focused on high-temperature in-situ experiments that should better correspond to the structure for which the conductivity measurements were made at elevated temperature ...
by Kevin W. Eberman.
Ph.D.
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Schiffrin, Agustin. "Self-assembly of amino acids on noble metal surfaces : morphological, chemical and electronic control of matter at the nanoscale." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/798.
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Designing novel nanostructures which exploit the self-assembly capabilities of biomolecules yields a promising approach to control matter at the nanoscale. Here, the homochiral molecular self-assemblies of the methionine and tyrosine amino acids on the monocrystalline Ag(111) and Cu(111) surfaces are characterized by means of scanning tunneling microscopy (STM) and spectroscopy
(STS), helium atom scattering (HAS), x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) in ultrahigh vacuum (UHV). On Ag(111), methionine self-assembles into supramolecular chains following the <110> substrate axis, forming regular nanogratings with tunable periodicity. Within the nanowires, a zwitterionic dimerization scheme is revealed. STS shows that the biomolecular nanostructures act as tunable one-dimensional quantum resonators for the surface state electrons. Zero-dimensional electronic confinement is achieved by positioning single iron atoms in the molecular trenches. This shows a novel approach to control the dimensionality of surface state electrons. The nanogratings
were exploited to steer the spontaneous one-dimensional ordering of cobalt and iron atoms. For T > 15 K, the metal species self-align into homogeneously distributed chains in between the biomolecular trenches with ~25 Å interatomic distace. For Co, the dynamics of the self-alignment was monitored,
revealing a reduced mobility in comparison with isolated Co atoms on bare Ag(111). On Cu(111), the self-assembly of methionine is influenced by the substrate reactivity and its temperature during molecular deposition.
For T < 273 K, the biomolecules assemble in anisotropic extended clusters oriented with a -10° rotation off the <110> substrate orientations, whereas above 283 K a regularly ordered 1D phase arises with a +10° rotation off these high-symmetry axis. XPS reveals a structural transformation triggered by a thermally activated deprotonation of the zwitterionic ammonium group. On Ag(111), tyrosine self-assembles above a critical temperature into linear
structures primarily following the substrate crystalline symmetry. A zwitterionic non-covalent molecular dimerization is demonstrated, NEXAFS data providing evidence of a non-flat adsorption of the phenyl ring. This recalls the geometrical pattern of methionine on Ag(111) and supports a universal self-assembling scheme for amino acids on close-packed noble metal surfaces,
the different mesoscopic ordering being determined by the side chain reactivity.
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Brust, Alexander Frederick. "Applications of Graph Cutting for Probabilistic Characterization of Microstructures in Ferrous Alloys." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1555523646156822.
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Candela, Emily. "Mid-century molecular : the material culture of X-ray crystallographic visualisation across postwar British science and industrial design." Thesis, Royal College of Art, 2015. http://researchonline.rca.ac.uk/1773/.
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This thesis investigates the use and significance of X-ray crystallographic visualisations of molecular structures in postwar British material culture across scientific practice and industrial design. It is based on research into artefacts from three areas: X-ray crystallographers’ postwar practices of visualising molecular structures using models and diagrams; the Festival Pattern Group scheme for the 1951 Festival of Britain, in which crystallographic visualisations formed the aesthetic basis of patterns for domestic objects; and postwar furnishings with a ‘ball-and-rod’ form and construction reminiscent of those of molecular models. A key component of the project is methodological. The research brings together subjects, themes and questions traditionally covered separately by two disciplines, the history of design and history of science. This focus necessitated developing an interdisciplinary set of methods, which results in the reassessment of disciplinary borders and productive cross-disciplinary methodological applications. This thesis also identifies new territory for shared methods: it employs network models to examine cross-disciplinary interaction between practitioners in crystallography and design, and a biographical approach to designed objects that over time became mediators of historical narratives about science. Artefact-based, archival and oral interviewing methods illuminate the production, use and circulation of the objects examined in this research. This interdisciplinary approach underpins the generation of new historical narratives in this thesis. It revises existing histories of the cultural transmissions between X-ray crystallography and the production and reception of designed objects in postwar Britain. I argue that these transmissions were more complex than has been acknowledged by historians: they were contingent upon postwar scientific and design practices, material conditions in postwar Britain and the dynamics of historical memory, both scholarly and popular. This thesis comprises four chapters. Chapter one explores X-ray crystallographers’ visualisation practices, conceived here as a form of craft. Chapter two builds on this, demonstrating that the Festival Pattern Group witnesses the encounter between crystallographic practice, design practice and aesthetic ideologies operating within social networks associated with postwar modernisms. Chapters three and four focus on ball-and-rod furnishings in postwar and present-day Britain, respectively. I contend that strong relationships between these designed objects and crystallographic visualisations, for example the appellation ‘atomic design’, have been largely realised through historical narratives active today in the consumption of ‘retro’ and ‘mid-century modern’ artefacts. The attention to contemporary historical narratives necessitates this dual historical focus: the research is rooted in the period from the end of the Second World War until the early 1960s, but extends to the history of now. This thesis responds to the need for practical research on methods for studying cross-disciplinary interactions and their histories. It reveals the effects of submitting historical subjects that are situated on disciplinary boundaries to interdisciplinary interpretation. Old models, such as that of unidirectional ‘influence’, subside and the resulting picture is a refracted one: this study demonstrates that the material form and meaning of crystallographic visualisations, within scientific practice and across their use and echoes in designed objects, are multiple and contingent.
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Clemens, Miles A. "Normally Supportive Sublattices of Crystallographic Space Groups." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7705.
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Normal subgroups can be thought of as the primary building blocks for decomposing mathematicalgroups into quotient groups. The properties of the resulting quotient groups are oftenused to determine properties of the group itself. This thesis considers normal subgroups of threedimensionalcrystallographic space groups that are themselves three-dimensional crystallographicspace groups; for convenience, we refer to such a subgroup as a csg-normal subgroup. We identifypractical restrictions on csg-normal subgroups that facilitate their tabulation. First, the point groupof an csg-normal subgroup must be a normal subgroup of the crystallographic point group of thespace group, which we refer to for convenience as a cpg-normal subgroup. For each of the cpgnormalsubgroups, which are all well known, we identify the abstract quotient group. Secondly,we identify necessary conditions on the sublattice basis of any csg-normal subgroup, and tabulatethe “normally supportive“ sublattices that meet these conditions, where some tables are symbolicforms that represent infinite families of sublattices. For a given space group, every csg-normalsubgroup must be an extension of such a normally supportive sublattice, though some normallysupportive sublattices may not actually support such extensions.
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Mason, Jeremy K. (Jeremy Kyle). "Analysis of crystallographic texture information by the hyperspherical harmonic expansion." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/53251.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2009.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 223-230).
The field of texture analysis is fundamentally concerned with measuring and analyzing the distribution of crystalline orientations in a given polycrystalline material. Traditionally, the orientation distribution function describing crystallographic orientation information is written as a linear combination of the generalized spherical harmonics. Since the use of generalized spherical harmonics requires that orientations be described by sets of Euler angles, the field of texture analysis suffers from the inherent limitations of Euler angles. These include difficulty of presentation and interpretation, discontinuous changes in the description of a changing orientation, and singularities in many equations of Euler angles. An alternative expansion of the orientation distribution function as a linear combination of the hyperspherical harmonics is therefore proposed, with the advantage that this expansion allows rotations to be described by angles that directly relate to the axis and angle of a rotation. Apart from the straightforward and intuitive presentation of orientation statistics that this allows, the utility of the hyperspherical harmonic expansion rests on the fact that the orientation distribution function inherits the useful mathematical properties of the hyperspherical harmonics. The relationship of the hyperspherical harmonics to the three- and four-dimensional rotation groups is investigated, and expressions for the matrix elements of the irreducible representatives of these rotation groups as linear combinations of the hyperspherical harmonics are found.
(cont.) These expressions allow an addition formula for the hyperspherical harmonics to be derived, and provide the means to write a simple conversion between the generalized spherical harmonic and hyperspherical harmonic expansions. This allows results derived via the hyperspherical harmonic expansion to be related to the texture analysis literature. Furthermore, a procedure for calculating the symmetrized hyperspherical harmonics consistent with crystal and sample symmetries is indicated, and used to perform the expansion of an orientation distribution function significantly more efficiently. The capability of the hyperspherical harmonic expansion to provide results not traditionally accessible is demonstrated by the generalization of the Mackenzie distribution to arbitrary textures. Finally, further areas where the application of the hyperspherical harmonic expansion is expected to advance the field of texture analysis are discussed.
by Jeremy K. Mason.
Ph.D.
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Harrington, Daniel John. "Crystallographic Studies of the Pathological Polymerization of Human Hemoglobin." eScholarship@UMMS, 1998. http://escholarship.umassmed.edu/gsbs_diss/211.
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Sickle cell disease is caused by the intracellular polymerization of human hemoglobin containing a mutation of a glutamic acid to a valine residue at the sixth position of the β chain. This substitution of a hydrophobic residue for a hydrophilic residue greatly decreases the solubility of the hemoglobin tetramer, promoting the formation of ordered fibers in deoxygenated red blood cells. These fibers are composed of double strands of hemoglobin tetramers, which effectively bury the valine side chain in a hydrophobic pocket, eliminating its unfavorable interaction with solvent. Inhibition of fiber formation would greatly alleviate the symptoms of sickle cell disease; therefore, the elucidation of the structure of the fiber is critical to developing treatments for the disease. In this thesis, an analysis of the crystal structures of the double strand component of the fibers formed by HbS and other site-directed mutants displaying altered sickling properties is undertaken.
Structure of HbS at high resolution: The structure of HbS was solved at 2.05 Å resolution. This high-resolution analysis produced significant improvements in the previous 3.0 Å model. In particular, the accurate positioning of side chains, and the placement of more than 500 solvent molecules was achieved. Some side chains in the physiologically relevant contacts were moved by as much as 3.5 Å away from their locations in the lower resolution model. The structure also demonstrates that well ordered water molecules are located in both the axial and lateral contacts, some of which may be exploited in the design of sickling inhibitors.
Structures of Hbβ6L and Hbβ6W: The crystal structures of two human hemoglobins with mutations at the β6 position that display altered sickling behavior were solved and refined at high resolution. Both mutants were crystallized under conditions similar to those used with HbS. Hbβ6L showed a greater tendency to polymerize, and displayed reduced delay times in aggregation assays. The refined structure was very similar to that of HbS, with changes confined mostly to the lateral contacts. However, the packing of Leu β6 in the linear crystalline double strands is sub-optimal. This has important ramifications for the differences between the crystalline double strands and those within the physiological HbS fiber. Hbβ6W, on the other hand, showed a reduced tendency to polymerize and shorter delay times in polymerization assays. The protein crystallized in a different space group from the other two mutants (HbS and Hbβ6L) under the same crystallization conditions, and formed fundamentally different double strands in the crystals. This structure demonstrates conserved interactions at the axial contacts, but very different interactions at the lateral contacts. The alternate double strand formed by this protein in the crystal may be useful as a model for tetramer interactions within the physiological fiber, or as a structural model for heterogeneous nucleation. The structures of each of these mutants help explain their altered polymerization behavior.
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Strand-Tibbitts, Kristen. "Crystallographic Studies of Rrythrocruorin from Lumbricus Terrestris: a Dissertation." eScholarship@UMMS, 2004. http://escholarship.umassmed.edu/gsbs_diss/309.
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The viability of multicellular aerobic organisms requires the binding and transport of molecular oxygen from the atmosphere to sites of metabolism. In the earthworm, Lumbricus terrestris, erythrocruorins are freely dissolved multi-subunit protein complexes that serve the same functions as red blood cells The aims of this study were to 1) determine the overall arrangement of hemoglobin chains and non-hemoglobin chains in Lumbricus erythrocruorin, 2) determine the stereochemical determinants specifying erythrocruorin's hierarchical symmetry, and 3) investigate the molecular and chemical basis for the remarkable cooperative binding of ligands to earthworm hemoglobin. Erythrocruorin is a highly cooperative oxygen-carrying protein with Hill coefficients measured at some pH's as high as n = 7.9. Crystallographic analysis of the whole erythrocruorin molecule structure to 5.5 Å resolution reveals a hierarchical organization of 144 oxygen-binding polypeptides and 36 non-hemoglobin linker polypeptide chains. The hemoglobin chains are arranged in a novel dodecameric substructure at the periphery of the complex, whereas 36 linker chains comprise the inner core and projected triple-stranded, helical coiled-coil spokes towards the center of the complex. Interdigitation of these spokes appears crucial for stabilizing the complex. Crystallographic analysis of crystals from isolated hemoglobin chains provides greater detail (resolution = 2.6 Å) and complete atomic models for the hemoglobin polypeptides. Comparison of these models with other hemoglobins reveal unique features in the distal heme pocket, including large aromatic residues at the B10 position in three of the four hemoglobin chains. Aromatic residues at this position have been implicated in other hemoglobins to confer resistance to oxidation. Molecular interactions across each subunit include pH-dependent interactions that are consistent with the observed Bohr effect on oxygen binding. Specifically a π-cation interaction between an arginine of one subunit to a histidine of the opposing subunit is likely an important molecular switch in the allosteric transition from a low to high affInity ligand-binding state.
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Blanco, Carcache Peter Josephin. "Chemical Characterization and Biological Evaluation of Secondary Metabolites Isolated from Glycosmis ovoidea." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1580383951030389.
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Singaraju, Aditya Bharadwaj. "Crystallographic and spectroscopic assessment of pharmaceutical material mechanics." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6643.
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Despite the advent of alternative dosage forms, solid dosage forms constitute a major proportion of dosage forms not only on the market, but also in many pharmaceutical companies’ pipelines. This is because of their superior stability and ease of manufacturing relative to other dosage forms. Although solid dosage forms have been the topic of discussion for decades, the process of compaction of these dosage forms is considered an art rather than science because of the empiricism that exists in this area. With the introduction of Quality by Design (QbD), it is imperative that the drug development process is guided by structured scientific principles. It has been hypothesized that crystal structure of organic solids plays a pivotal role in understanding the properties, processing and eventually performance of solids. In this regard, the intermolecular interactions within a solid play a paramount role in dictating the materials response to stress. One important parameter that is weakly addressed in the literature is the concept of strength of intermolecular interactions. In the current work, we utilize the concept of elasticity as a metric for strength of intermolecular interactions. We introduce powder Brillouin light scattering; an inelastic light scattering technique to measure the elasticity of organic solids and try to correlate the mechanical moduli extracted from the spectra to the compaction performance of solids. We hypothesize that any redistribution of intermolecular interactions would be reflected in the BLS spectrum of these materials and the material properties can be used to explain the differences in compaction performance. Before we tested our hypothesis, we validated our powder BLS technique using aspirin as model system. We then applied the same analysis to four model systems that involved different ways of reorganizing the intermolecular interactions upon subtle modifications to the molecular structure.
In Chapter 4, we investigated the effect of alkyl chain length and crystal structure on the mechanical properties and compaction performance of p-aminobenzoic acid (PABA) and its esters. For the entire ester series, a similar hydrogen bonding pattern was observed with strong N-H…O (carbonyl) and supportive N-H…N interactions. While the ethyl and butyl esters exhibited a layered structure, the methyl ester displayed a 3-D isotropic structure. The crystal structure for PABA exhibited a three-dimensional, quasi-isotropic distribution of the hydrogen-bonding interactions that connected the PABA dimers. The powder BLS spectra for these materials revealed low velocity shear modes for the layered structures and a spectrum consistent with an isotropic structure for Me-PABA and PABA. This was in good agreement with the compressibility behavior under load, with Et-PABA and Bu-PABA more compressible than PABA. However, due to greater particle-particle adhesion, PABA compacts showed greater tensile strength at higher pressures. The moduli calculated also showed that both Et-PABA and Bu-PABA had lower shear and Young’s modulus relative to the other materials. Attachment energies corroborated the above results. These studies showed that weak dispersive forces play an important role in understanding material properties.
In Chapter 5, a series of nitrobenzoic derivatives were used to study the effect of secondary interactions on the crystal reorganization and material properties. The materials used in the study include p-nitrobenzoic acid (4-NBA), m-nitrobenzoic acid (3-NBA, 4-chloro-3-nitrobenzoic acid (Cl-NBA), 4-bromo-3-nitrobenzoic acid (Br-NBA), and 4-methyl-3-nitrobenzoic acid (Me-NBA). Crystal structures of the materials revealed different organization of C-H…O interactions. Two types of C-H…O interactions were prevalent namely C-H…O (nitro) and C-H…O (carboxy). The reorganization of these two types of interactions led to different packing motifs and different mechanical behavior. These structural features were reflected in their mechanical properties assessed by powder Brillouin light scattering. Cl-NBA and Br-NBA displayed an isotropic spectrum similar to polystyrene and aspirin. 3-NBA, 4-NBA and Me-NBA displayed different spectra from Cl-NBA and Br-NBA with high frequency tailing in the longitudinal mode distribution indicating a specific direction of extended molecular interactions. The Young’s modulus and shear modulus followed the order: 3-NBA < Me-NBA< 4-NBA < Cl-NBA < Br-NBA. The maximum longitudinal modulus Mmax was the highest for 3-NBA and was significantly greater than rest of the materials. From the compaction studies, it was observed that the tabletability followed the rank order 3-NBA > 4-NBA > Me-NBA ≈ Br-NBA ≈ Cl-NBA which is the same order as Mmax. 3-NBA by virtue of its low shear and Young’s modulus to be the most compressible material, but the compressibility rank order was 4-NBA > Me-NBA ≈ 3-NBA > Cl-NBA > Br-NBA. However, 3-NBA by virtue of its greater particle-particle adhesion was the most compactable material. The yield pressures obtained from Heckel plots revealed that 4-NBA and Me-NBA were relatively more plastic when compared to the other materials. This study demonstrated that subtle changes to the molecular structure can result in drastically different crystal packing which in turn would influence the mechanical properties and the compaction performance of organic solids.
In Chapter 6, we investigated the effect of cocrystallization on the compaction performance of caffeine(CAF). The series of halo-nitrobenzoic acids (F-NBA, Cl-NBA and 3-NBA) were used as coformers. The cocrystals CAF: F-NBA, CAF: Cl-NBA and CAF: NBA Form 1 adopted a flat layered structure that can undergo deformation with ease. This increased the compressibility of the cocrystals relative to CAF. In addition to the improved compressibility, by virtue of increased particle-particle contacts, the cocrystals also displayed superior tabletability. In contrast to the layered structures adopted by the three cocrystals, the CAF: NBA Form 2 displayed a columnar structure that exhibited resistance to stress. The compressibility and the tabletability of CAF: NBA Form 2 was significantly compromised when compared to that of Form1. All the compaction characteristics of the cocrystals were in good agreement with moduli and parameters obtained from powder BLS spectra. The layered materials showed the presence of low velocity shear modes corroborating the earlier studies. There was a clear difference in the spectra of the polymorphs, indicating that powder BLS can be used for mechanical screening of polymorphs.
In Chapter 7, we examined the effects of crystal structure and coformer functionality on the compaction performance of theophylline (THY). The coformers employed include 4-fluoro-3-nitrobenzoic acid (FNBA), acetaminophen (APAP), and p-aminobenzoic acid (PABA). While THY-APAP and THY-FNBA exhibited layered structures, the THY-PABA displayed a interdigitated columnar structure. Powder BLS spectra showed the presence of low frequency shear modes relative to THY for all the three cocrystals. However, the order of frequencies followed: THY-FNBA < THY-APAP < THY-PABA. The shear modulus calculated followed the order THY-APAP≈ THY-FNBA < THY < THY-PABA which is in agreement with the crystal structures discussed. The Young’s modulus followed the order THY-FNBA < THY-APAP < THY < THY-PABA. The two layered structures (THY-APAP, THY-FNBA) showed distinct compaction performance (similar compressibility but different compactability and tabletability). The layered structures were more compressible than THY which is hypothesized to undergo deformation through multiple mechanisms. THY-PABA showed poor compaction properties. This highlights the fact that although the coformer (PABA) is molecularly similar to FNBA, the resultant cocrystals are structurally and mechanically distinct. These observations were well supported by the moduli calculated from powder BLS studies. The order of yield pressures obtained from Heckel analysis followed the same order as shear modulus. The tensile strength of the compacts of the cocrystals level off at around 150 MPa but the tensile strength of THY compacts continues to increase. From a manufacturing perspective the cocrystals can prove to be a better option as they as more compactable at higher porosities or they possess greater tabletability at low compaction pressures.
Overall, we have used model systems to demonstrate that the redistribution of intermolecular forces upon point substitution or cocrystallization have a dramatic effect on the material properties. It is also worth noting that elasticity along with plasticity can provide important information about the strength of interactions which would help in understanding the role of weak intermolecular forces in the performance of organic materials. To gain a better perspective of the compaction process and move towards a QbD approach, it is also imperative to understand the link between crystal structures, intermolecular interactions which is possible with the help of novel characterization techniques (BLS, AFM).
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Sood, Geeta. "Base modified peptidic nucleic acids: synthesis and crystallographic analysis of intermediates." Thesis, Aston University, 1998. http://publications.aston.ac.uk/10967/.
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Peptidic Nucleic Acids (PNAs) are achiral, uncharged nucleic add mimetics, with a novel backbone composed of N-(2-aminoethyl)glycine units attached to the DNA bases through carboxymethylene linkers. With the aim of extending and improving upon the molecular recognition properties of PNAs, the aim of this work was to synthesjse PNA building block intermediates containing a series of substituted purine bases for subsequent use in automated PNA synthesis. Four purine bases: 2,6~diaminopurine (D), isoGuanine (isoG), xanthine (X) and hypoxanthine (H) were identified for incorporation into PNAs targeted to DNA, with the promise of increased hybrid stability over extended pH ranges together with improvements over the use of adenine (A) in duplex formation, and cytosine (C) in triplex formation. A reliable, high-yielding synthesis of the PNA backbone component N -('2- butyloxycarbonyl-aminoethyl)glycinate ethyl ester was establishecl. The precursor N~(2-butyloxycarbonyl)amino acetonitrile was crystallised and analysed by X-ray crystallography for the first time. An excellent refinement (R = 0.0276) was attained for this structure, allowing comparisons with known analogues. Although chemical synthesis of pure, fully-characterised PNA monomers was not achieved, chemical synthesis of PNA building blocks composed of diaminopurine, xanthine and hypoxanthine was completely successful. In parallel, a second objective of this work was to characterise and evaluate novel crystalline intermediates, which formed a new series of substituted purine bases, generated by attaching alkyl substituents at the N9 or N7 sites of purine bases. Crystallographic analysis was undertaken to probe the regiochemistry of isomers, and to reveal interesting structural features of the new series of similarly-substituted purine bases. The attainment of the versatile synthetic intermediate 2,6-dichloro~9- (carboxymethyl)purine ethyl ester, and its homologous regioisomers 6-chloro~9- (carboxymethyl)purine ethyl ester and 6-chloro-7-(carboxymethyl)purine ethyl ester, necessitated the use of X-ray crystallographic analysis for unambiguous structural assignment. Successful refinement of the disordered 2,6-diamino-9-(carboxymethyl) purine ethyl ester allowed comparison with the reported structure of the adenine analogue, ethyl adenin-9-yl acetate. Replacement of the chloro moieties with amino, azido and methoxy groups expanded the internal angles at their point of attachment to the purine ring. Crystallographic analysis played a pivotal role towards confirming the identity of the peralkylated hypoxanthine derivative diethyl 6-oxo-6,7-dihydro-3H-purlne~3,7~djacetate, where two ethyl side chains were found to attach at N3 and N7.
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Horrell, Sam. "Development of crystallographic techniques and their application to several protein targets." Thesis, University of Liverpool, 2015. http://livrepository.liverpool.ac.uk/2036862/.
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Since its first use to solve the structure of sodium chloride in 1915 X-ray crystallography has developed significantly to become the premier technique for obtaining 3D structural information of small molecules and macromolecules alike. As the technique continues to develop and focus its attention on weak diffraction from the likes of micro-crystals and poorly packed crystals of membrane proteins and large protein complexes; as well as ultra-high resolution data and weak anomalous signal from native atoms, data quality is becoming more and more important. Data quality is particularly important in the wake of long wavelength macromolecular crystallography (MX) for phasing using anomalous signal from native sulphur and phosphorous atoms in proteins and DNA. This thesis first investigated the use of a new sample handling technique using a humidity controlled stream to preserve macromolecular crystals while excess surrounding solvent is removed (Chapter 2). Following the successful development of this technique the effects of excess surrounding solvent on data quality was assessed when collecting at standard MX X-ray wavelengths (~ 1 Å) and longer X-ray wavelengths (~ 2 Å). Datasets were collected from large populations of control and test crystals at standard and longer wavelengths to allow robust statistical methods to be applied; a practice not widely adopted in method development studies in X-ray crystallography. This made it possible to assess the small differences in data quality in the presence and absence of excess surrounding solvent. The effects of surrounding solvent at longer wavelengths appear to be protein dependent with some proteins tested showing no significant difference and others a significant decrease in data quality at longer wavelengths (Chapter 3). Originally this project aimed to use the new long wavelength in-vacuum MX beamline, I23, at Diamond Light Source UK to carry out phasing experiments using native sulphurs for structure solution. However, the considerable complexity involved in developing in-vacuum MX meant these experiments could not be carried out during the time frame of this thesis. Chapters 4 and 5 outline the production of a novel cancer protein (cancerous inhibitor of protein phosphatase 2A) and two protein targets from the Achromobacter xylosoxidans (Ax) genome intended for sulphur single wavelength anomalous dispersion phasing experiments on I23. Of these proteins the structure of Ax-α/β hydrolase was solved by conventional methods, the structure of which is discussed in Chapter 5. Of the protein crystals used in long wavelength data quality experiments in Chapter 3 the molecular biology of PA3825-EAL, a biofilm regulating protein essential to the swarming ability of Pseudomonas aeruginosa, was investigated further. The crystal structure of PA3825-EAL was solved in the resting, substrate bound and product bound states to high resolution. Comparison of the crystal structures of monomeric and dimeric PA3825-EAL with the inactive dimeric structure of MucR-EAL suggests dimerisation via helix 8 plays a role in inhibition of EAL domains. Prior to this, dimerisation was thought to be an activating factor in EAL domains. The product bound state of PA3825-EAL showed the presence of a previously unreported third metal binding site which may form an essential component of the reaction mechanism of EAL domains. Inability of MucR-EAL to incorporate this third metal due to dimerisation may explain the lack of activity despite possessing the conserved catalytic residues necessary. The fast detector technology and improvements in automated data processing software that allowed diffraction data for large populations of crystals to be collected in Chapters 2 and 3 have also been applied to development of a serial data collection technique. Of 159 datasets collected from 8 crystals of a copper nitrite reductase from Achromobacter cycloclastes, 45 datasets from a single crystal were analysed to observe the reaction mechanism using high resolution crystal structures. X-ray radiolysis initiated the reaction and high resolution data allowed the conversion of nitrite (NO2) to nitric oxide (NO) to be observed in the crystal. Other aspects of the reaction were investigated from the data series including a conserved water chain connecting the copper sites which may act as a proton wire to donate a proton and produce NO. This technique may have wide applications to the study of the reaction mechanisms of other metallo-proteins.
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Pontius, Joan. "Atomic volumes in protein crystallographic structures and their use in structure validation." Doctoral thesis, Universite Libre de Bruxelles, 1997. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/212217.
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Yu, Lock See. "The effect of low energy ion bombardment on the crystallographic orientation of thin films." Thesis, Massachusetts Institute of Technology, 1985. http://hdl.handle.net/1721.1/15310.
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Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1985.MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE.
Includes bibliographical references.
by Lock See Yu.
M.S.
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Sutton, Karim J. "Determining structure and atomic properties of materials using resonant X-ray diffraction." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:3944a985-9339-4c8c-970b-4b460848f200.
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X-ray crystallography is a widely used analytical technique for the structure solution of small molecules. Since the determination of the rock salt structure in 1913 by Henry and Lawrence Bragg the technique has developed allowing the solution of larger and more complex structures. The information that can be determined about these structures has increased as X-ray sources, detectors, and computational methods have improved. However, certain properties of molecules cannot always be directly determined from single wavelength X-ray diffraction. These include, inter alia: the site specific oxidation or spin state of an element in compounds where more than one state of the same element exist; discrimination between consecutive heavy elements in the periodic table. As the size of molecules being studied increases, reduced data resolution also becomes a problem. The aim of this research was to determine whether these problems can be addressed by measuring the changing anomalous scattering contribution of heavy atoms within structure through careful selection of the X-ray energy. Firstly, I report an investigation into the problemof discriminating oxidation state, spin state and elements of near identical scattering by exploiting their anomalous signal. I first present DetOx, a program written during the course of the project to deconvolute the fluorescence signal from materials containing more than one state of the same element into their respective spectra. This allows the calculation of anomalous scattering factors for both atomic states of an atom, which can subsequently be used to refine the occupancy of the different states at ambiguous sites within the crystal structure. The approach taken here, to determine differences due to relatively small anomalous signals, is analogous to the refinement of the Flack parameter whereby small changes in many hundreds or thousands of observations can be used to fit a parameter with a high degree of precision and accuracy. I show the application of this technique to the mixed oxidation state compound, GaCl2, and the two-step spin crossover material, Fe(btr)3(ClO4)2. Refinement of the occupancy of charged ions on multiple sites using data at a single, carefully selected wavelength proved successful for these compounds, although upon extension to materials containing a larger number of anomalous scatterers, the absorption became a major issue in the data along with problems associated with simultaneously refining occupancies at more sites in the structure. We have demonstrated that calculations can be made to select specific experimental data to collect in order to improve the measured signal. However, due to limitation of the current collision model on the diffractometer used we have not yet been able to construct data collection strategies to take advantage of this. I next present a new ratio refinement technique to overcome this absorption problem due to the increased number of scatterers. By using ratios between datasets close in energy, but below the absorption edge, we were able to exploit small changes in f' without encountering absorption problems associated with the increase in f''. These ratio values were then refined against a lab structure using a modified version of CRYSTALS to reveal the site specific occupancies of different atomic species within a given structure. For mixed-valence compounds, e.g. Mn3 and Mn6 clusters, the difference in anomalous signal between the different states proved too small for a stable least-squares refinement solution. However, we have shown that using a simulated annealing algorithm (to refine only occupancies), we can consistently obtain the expected structure. For mixed-metal structures e.g. the Mn5Co4 cluster, there was enough contrast in the data to refine occupancies with a least-squares approach, and these results were supported using simulated annealing. Lastly, I describe the application of structure solution techniques based on methods used in macromolecular crystallography to 'large' small molecules. Traditionally these have been reserved for non-centrosymmetric protein structures, however with the trend of synthesising larger and larger small molecules, problems encountered in macromolecular crystallography leading to low resolution datasets are becoming increasingly common. I have shown that it is possible to solve the structure of centrosymmetric structures by exploiting the anomalous signal in multiple wavelength diffraction experiments. The technique is applied successfully to two relatively small molecules, however the results are promising for moving to larger structures in the future.
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Deshpande, Tanvi. "SYNTHESIS, TESTING AND CRYSTALLOGRAPHIC STUDIES OF ALLOSTERIC MODIFIERS OF HEMOGLOBIN." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/543.
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The major physiological function of hemoglobin (Hb) is to bind, transport and deliver oxygen to tissues; made efficient by endogenous effectors, such as protons and 2,3-diphosphoglycerate. Synthetic allosteric effectors of Hb (AEHs) are also known to modulate Hb oxygen affinity, showing potential for the treatment of sickle cell disease (SCD) and ischemic-related diseases. In this project, AEHs which increase Hb affinity for oxygen, including derivatives of the anti-sickling compounds, 5HMF and benzaldehydes, as well as an AEH that decreases Hb affinity for oxygen, RSR-13, were synthesized for their effects on Hb oxygen binding property and their capability to release NO from substituted nitrate ester moieties. Compounds that were found to increase Hb affinity for oxygen were further tested for their anti-sickling activities. Structural studies were carried out to gain insight into the compound’s mode of action. Development of these agents could be a therapeutic strategy for SCD or ischemic-related diseases.
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Young, Callum A. "Local structure/property relationships in functional materials." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:8eea6d96-5a48-4ed9-adad-e2b1fdc97acb.
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It is increasingly being realised that localised deviations from the average structure can play an important role in a material's properties, and hence an understanding of these deviations is essential when constructing a coherent picture of a system. In this thesis, both neutron and X-ray total scattering data have been collected and used to reveal information on three canonical systems: the high-temperature superconductor YBa2Cu3O7-x; the parent compound of the colossal magnetoresistive manganites, LaMnO3; and the oldest known magnetic material, Fe3O4. Reverse Monte Carlo refinements-using the RMCProfile implementation of the algorithm-have been used as the principal analysis technique, and the functionality of the RMCProfile program has been extended to allow the refinement of magnetic systems involving substitutional disorder. For YBa2Cu3O7-x, the focus of this thesis is on the apical Cu{O bond length. This is shown to have a bimodal distribution, but correlations in the displacements of both atoms disguise this fact in the average structure, thus resolving the apparent controversy that had existed between local- and average-structure probes. LaMnO3 displays (what was thought to be) a simple order{disorder transition that results in the Jahn-Teller distortion becoming invisible in the average structure above ~ 750 K. Here it is shown that in fact the transition is more complicated, and involves a change in the symmetry of the Jahn-Teller distortion, whereby the long Mn-O bonds move from being opposite one another in the octahedra to being adjacent to one another. This new distortion still breaks the degeneracy of the system, and is consistent with a wide range of existing observations. Finally the low temperature structure of Fe3O4 is examined using the updated RMCProfile code. The refinements show sensitivity to local structure variations, producing a bimodal Fe atom bond valence distribution. In addition, the refined magnetic spin configuration is presented, providing the first detailed description of the low-temperature magnetic structure. It is found to be a canted ferrimagnet, and appears to be consistent with Cc symmetry.
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Linaburg, Matthew Ronald. "Studies of Halide Perovskites CsPbX3, RbPbX3 (X=Cl-, Br-, I-), and Their Solid Solutions." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1449074303.
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Malet, Loïc. "The formation of plate martensite in a Fe-High Ni alloy: Crystallography and Variant Selection." Doctoral thesis, Universite Libre de Bruxelles, 2015. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/227689.
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Mainly two different morphologies of martensite can be obtained in steels depending on the amount of alloying elements. The first morphology, referred to as lath martensite, forms in low alloy, low carbon steels. It is, by far, the most extensively studied form of martensite due to its industrial applications. The second morphology of martensite, referred to as plate martensite, forms in highly alloyed and in high carbon steels and in particular in Fe-High Ni alloys. In this case, the transformation product is disc shaped and internally twinned. This morphology is the only form of martensite that has the potential to exhibit shape memory properties. It is therefore of great interest to understand the mechanisms of its formation. This is investigated in the present dissertation through the study of the martensitic transformation occurring in a Fe-30.5%Ni-0.155%C alloy. More precisely, the influence of stress and grain size on the crystallography of plate martensite is discussed in the general framework of the phenomenological theory of martensite crystallography. This theory allows associating a unique shape deformation to each orientational variant. In this way, the experimental observations carried out at different length scales by means of optical microscopy, EBSD and TEM can be used to infer the transformation path followed under different conditions. Firstly, the burst configurations of variants observed in coarse-grained austenite under stress free conditions are rationalized by considering the mechanical couplings between the variants. It is shown that self-accommodating and autocatalytic couplings are responsible for the formation of hierarchical configurations of variants. More precisely, the transformation is shown to occur through the alternate formation of perpendicular plate groups of variants. Self-accommodation is the dominant coupling between variants of the same plate group while autocatalytic couplings are responsible for the transfer of the transformation from one generation to the next. It is suggested that the plastic accommodation of the shape deformation plays a dominant role in propagating the transformation to a lower length scales. Secondly, the influence of a uniaxial stress state on the transformation is studied. It is seen experimentally that only the most favoured variants are systematically formed in coarse Cube grains while coarse non-Cube grains generally transform into plate groups of variants that are only moderately favoured by the stress. These observations are well explained by considering the interaction energy between the applied stress and the shape deformation associated with the transformation. Thirdly, the influence of the austenitic grain size on the transformation is also studied. A decrease in grain size is seen to decrease the martensite start temperature. For a grain size below about 10µm, the thermal transformation in liquid nitrogen is indeed suppressed in the present alloy. This observation is related to the increasing yield strength of austenite as the grain size is reduced. A noticeable change in the morphology of martensite also accompanies the decrease in grain size. Indeed, martensite forming in coarse-grained austenite is mostly lens shaped and partially twinned while it appears plate shaped and fully twinned in smaller grains. Furthermore, martensite forming in fine-grained austenite develops self-accommodating configurations suggesting that most of the transformation deformations are elastically accommodated in this case. This is believed to be related to the observance of a shape memory effect in the present alloy in its fine-grained condition.Doctorat en Sciences de l'ingénieur et technologie
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Alexopoulos, Eftichia. "Crystallographic and modeling studies of intermolecular interactions of biological interest." Doctoral thesis, [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972659137.
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Wu, Xianping Kalidindi Surya Doherty R. D. "Prediction of crystallographic texture evolution and anisotropic stress-strain response during large plastic deformation in alpha-titanium alloys /." Philadelphia, Pa. : Drexel University, 2006. http://hdl.handle.net/1860/1122.
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Cingolani, Gino. "Biochemical and crystallographic analysis of the human importin [alpha]/[bêta] complex." Grenoble 1, 1999. http://www.theses.fr/1999GRE10096.
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Le travail presente dans cette these decrit l'analyse structurale du complexe forme par les proteines humaines et importin. Le projet a debute par la caracterisation biochimique des 2 proteines, seules en solution, et du complexe qu'elles forment. Nous avons observe que dans le complexe la proteine importin est resistante a la chymotrypsine. La meme protection a ete observee lorsque la proteine -importin est incubee en presence d'un peptide, synthetise chimiquement, contenant les domaines ibb de la proteine importin. La co-cristallisation de la proteine -importin avec le peptide a donne naissance a 2 formes cristallines dans le groupe d'espace p21, diffractant respectivement a une resolution de 2. 5a et 2. 3a. La structure du complexe a ete resolue dans la premiere forme cristalline par diffusion anomale en utilisant la proteine -importin exprimee en presence de selenio-methionine. La structure a ensuite ete affinee a 2. 5 a de resolution. La deuxieme forme cristalline a ete resolue par remplacement moleculaire et le modele affine jusqu'a 2. 3 a de resolution. Un important changement conformationel a ete observe entre les deux formes cristallines donnant des informations sur la flexibilite interieure de la proteine importin. L'analyse de la structure du complexe ainsi que la comparaison avec les donnees biochimiques obtenues nous ont permis 4 observations majeures : - l'architecture caracteristique des proteines de la superfamille- a ete observe pour la premiere fois. - l'interaction intime entre les proteines et -importin a ete decrite au niveau moleculaire. - le double changement conformationel des proteines et importin observe par les methodes biochimiques a pu etre confirme grace a la structure tridimensionnelle. - une similarite de structure entre le complexe importin : domaines ibb et importin : sequence de localisation nucleaire (nls) a ete observe, confirmant une possible evolution commune de ces proteines.
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Accorsi, Gina Marie. "Fingerprinting Wolframite: An Atomic/crystallographic, Chemical And Spectroscopic Study Along The Solid Solution Series." ScholarWorks @ UVM, 2017. http://scholarworks.uvm.edu/graddis/710.
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In accordance with the 2010 Dodd-Frank Act, conflict minerals refer to gold, tantalum, tin, and tungsten bearing minerals sourced from the Democratic Republic of Congo (DRC) that have been mined illegally and used to funnel funds to rebel forces. In response to an increasing demand for these metals used in cellphones, computers, and other popular technologies, Dodd-Frank mandates that industrial consumers demonstrate due diligence and assure that the materials they use have been extracted legally. Because current chain-of-custody methods have not been effective in sourcing ores, a study was undertaken whereby the range of mineralogical characteristics of 15 samples along the wolframite solid solution series were determined in order to ascertain if differences in these characteristics would permit fingerprinting of the source deposit of wolframite, of which the DRC is the world's fifth largest producer.
For these 15 samples, single-crystal X-ray structure and powder X-ray diffraction studies have been conducted; major, minor and trace element chemistry has been determined using ICP-MS and ICP-OES; and Raman spectroscopy has been carried out.
Finally, statistical methods were used to determine relationships between samples, and the results of that mathematical work show that there is no firm method at the present time of determining the provenance of a sample based on the information of the crystal structure, diffraction patterns, vibrational frequencies/scattering, or major and trace elemental chemistry.
This study elucidates the range of mineralogical properties along the hübnerite-ferberite solid solution series while working towards to development of an analytical technique that is affordable, practical, accessible and effective for industrial consumers seeking product certification and compliance with the 2010 Dodd-Frank Act.
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Cuesta, Seijo Jose Antonio. "Crystallographic studies on echinomycin bisintercalation on DNA and an alternating D-alanyl,L-homoalanyl PNA." Doctoral thesis, [S.l.] : [s.n.], 2005. http://webdoc.sub.gwdg.de/diss/2005/cuesta_seijo.
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Richard, Laura Amanda. "A study of the crystallographic, magnetic and electronic properties of selected ZrM2-H systems." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:276c59fe-cf45-42d2-a5a0-8c534c8b46bd.
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Dissolution of hydrogen into intermetallic compounds characteristically occurs at interstitial sites, causing little alteration to the base metal substructure but often bringing about substantial electronic and magnetic changes to the material. These hydrogen-induced alterations in the intermetallic hydrides are of interest both on a fundamental research level and in terms of technological applications; however, there exists no general theory as to how and why these alterations arise. The objective of this research is to elucidate to general effect of hydrogen on intermetallic compounds through the study of crystallographic, magnetic and electronic properties. An investigation has been carried out on the properties of three intermetallic compound - hydrogen systems of general formula ZrM₂, where M = V, Cr, Mn. All three compounds reversibly absorbed hydrogen with no change in crystal symmetry: powder diffraction studies showed that hydrogen was accommodated in interstitial sites of the existing metal sublattice via lattice expansion. The measurement of the magnetic properties of these systems was combined with the determination of conductivity and dielectric properties in order to describe the electronic e¤ects of hydrogen absorption. Despite the lack of signi
cant structural alteration in these systems, electron transfer between the metal sublattice and hydrogen may occur, as manifested in the appearance/disappearance of magnetic phenomena and the increase/decrease of electrical conductivity. Whilst the hydrogen addition in ZrM₂-H occurs simply via an expansion of the crystal structure, hydrogen does not act purely as null dilutant - there exist subtle electronic changes connected with the hydriding process as well.
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Chivers, Claire Elizabeth. "Investigating high-affinity non-covalent protein-ligand interaction via variants of streptavidin." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:631c65ed-08d9-484e-a8df-309a4c95df45.
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The Streptomyces avidinii protein streptavidin binds the small molecule biotin (vitamin H / B₇) with extraordinary stability, resulting in the streptavidin-biotin interaction being one of the strongest non-covalent interactions known in nature (Kd ~ 10-14 M). The stable and rapid biotin-binding, together with high resistance to heat, pH and proteolysis, has given streptavidin huge utility, both in vivo and in vitro. Accordingly, streptavidin has become a widely used tool in many different biotechnological applications. Streptavidin has also been the subject of extensive research efforts to glean insights into this paradigm for a high-affinity interaction, with over 200 mutants of the protein reported to date. Despite the high stability of the streptavidin-biotin interaction, it can and does fail under certain experimental conditions. For example, streptavidin-biotin dissociation is accelerated by an increased temperature or lower pH (conditions often encountered in cellular imaging experiments), and by mechanical stress, such as the shear force arising from fluid flow (encountered when streptavidin is used as a molecular anchor in biosensor chips and arrays). This study details efforts made at increasing further the utility of streptavidin, by increasing the stability of biotin and biotin-conjugate binding. A rational site-directed mutagenesis approach was used to create 27 mutants, with eight of these mutants possessing higher-stability biotin-binding. The most stable biotin-binding mutant was named traptavidin and was extensively characterised. Kinetic characterisation revealed traptavidin had a decreased dissociation rate from biotin and biotin-conjugates when compared to wildtype streptavidin, at both neutral pH and pH 5. Atomic force microscopy and molecular motor displacement assays revealed the traptavidin-biotin interaction possessed higher mechanical stability than the streptavidin-biotin interaction. Cellular imaging experiments revealed the non-specific cell binding properties of streptavidin were unchanged in traptavidin. X-ray crystallography was also used to generate structures of both apo- and biotinbound traptavidin at 1.5 Å resolution. The structures were analysed in detail and compared to the published structures of streptavidin, revealing the characteristics of traptavidin arose from the mutations stabilising a flexible loop over the biotin-binding pocket, as well as reducing the conformational change on biotin-binding to traptavidin. Traptavidin has the potential to replace streptavidin in many of its diverse applications, as well as providing an insight into the nature of ultra-stable noncovalent interactions.
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Hore, Katie. "Ammonia borane and its derivatives : high weight percentage hydrogen storage materials." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:8625aca3-fb03-4a11-a621-4ef835ad5372.
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Ammonia borane and ammonium borohydride have been considered extensively as potential hydrogen storage materials. This thesis reports their structure and functional properties, emphasising the key role that dihydrogen bonding plays in both materials. The formation of a 'mobile phase' is considered to be the preliminary step in the decomposition of ammonia borane. The formation of this mobile phase has been studied using neutron diffraction, inelastic neutron spectroscopy and NMR. It has been found that in the mobile phase, 'end-to-end' flipping of the ammonia borane molecule occurs. This is an important precursor to the next step in the decomposition: the formation of the diammoniate of diborane. The dihydrogen bonding networks which occur in both the orthorhombic and the tetragonal phases of ammonia borane, and are the controlling factor in the decomposition process, were investigated using Density Functional Theory Molecular Dynamics (DFT-MD) simulations. It was hence shown that in the high-temperature tetragonal phase of ammonia borane, dihydrogen bonding is still an important stabilising interaction and there is little to distinguish between the three crystallographically distinct dihydrogen bonds. A closely related hydrogen storage material, ammonium borohydride, was also studied using the same techniques. Its low temperature phase progression was examined using variable temperature neutron diffraction. The vibrational modes of ammonium borohydride were assigned by comparing vibrational spectra determined using inelastic neutron spectroscopy with the results of DFT-MD simulations. Quasielastic neutron spectroscopy was used to show that both the ammonium and borohydride groups in ammonium borohydride perform discrete 'hopping' reorientational motions at a wide range of temperatures, and that the ammonium group has a mean residence time approximately 100 times less than that of the borohydride group. Hydrogen atom densities in the ammonium group were determined from DFT-MD simulations, and from refinements of high-resolution neutron diffraction data using cubic harmonic basis functions.
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Ryan, Katharine Rachel. "A study of ammonia borane and its derivatives." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:56384446-e80a-42f2-afdd-3c8a8ea33ce8.
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This thesis reports the investigation of molecular materials for hydrogen storage applications with a particular emphasis on alkali-metal amidoboranes. I have developed new routes for the synthesis of $alpha$-LiNH$_{2}$BH$_{3}$ and NaNH$_{2}$BH$_{3}$, and have studied their hydrogen storage properties by thermogravimetric analysis, variable temperature X-ray and neutron diffraction and inelastic neutron scattering. I report the synthesis and full structural characterization of two new materials, KNH$_{2}$BH$_{3}$ and $beta$-LiNH$_{2}$BH$_{3}$, and have performed initial studies on a tetragonal phase of a variant of LiNH$_{2}$BH$_{3}$ with a preliminary structure solution. I have also performed variable temperature neutron diffraction on ammonium borodeuteride, ND$_{4}$BD$_{4}$, and report the full structural characterisation of the three phases identified as a result of these measurements. Furthermore, variable temperature inelastic neutron scatting (INS) measurements were performed on ammonia borane, NH$_{3}$BH$_{3}$, and the results are discussed in terms of crystallographic phase changes.
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Pluchino, Kristen Marie. "Generation of chimeric P-glycoprotein for functional and structural investigations." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:4f5c9dcc-401c-4123-9b2f-c5d17e0d7bc2.
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A major challenge in cancer treatment is acquired or intrinsic multidrug resistance (MDR) to chemotherapeutics. A notorious mediator of MDR is P-glycoprotein (P-gp, ABCB1), product of the human MDR1 gene, which actively effluxes cytotoxic drugs from cancer cells, resulting in sub-therapeutic intracellular concentrations. Understanding how P-gp interacts with drugs has been severely limited by the lack of high-resolution structures of P-gp. Although numerous efforts to obtain an X-ray crystal structure of P-gp have been attempted, human P-gp has never been crystallized. However, mouse P-gp (87% homologous to human P-gp) has been crystallized, and several structures of mouse P-gp have been recently reported. Despite a high degree of homology, it is currently unknown why mouse P-gp can be crystallized while human P-gp cannot. The studies presented in this thesis describe the creation of novel chimeras of mouse and human P-gp as an approach to investigate whether specific protein domains are responsible for differences in the ability to form crystals between mouse and human P-gp. A range of chimeras, created by protein domain swapping, were expressed in mammalian cells and all were found to retain MDR transport function demonstrating that P-gp can tolerate major structural changes. High-level expression of all chimeras was achieved by baculovirus-mediated heterologous protein expression. Chimeric proteins were purified by a multi-step process including immobilized metal affinity chromatography and size exclusion chromatography. Crystallization screening obtained protein crystals for two of the chimeras, indicating the approach adopted is a successful strategy, and an advance along the path towards a high-resolution structure of human P-gp.
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Clayton, Amber Jayne. "Structural, biophysical and cellular analysis of synaptic receptors and organizers." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:86579b80-d0de-4f69-a247-b9753882abca.
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Smith, Christopher. "p-block hydrogen storage materials." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:6dd710a5-baf2-4fd2-918c-d1df97c229bf.
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The development of a clean hydrogen economy will aid a smooth transition from fossil fuels which is required to stem the environmental impact and economic instability caused by oil dependency. For vehicular application, in addition to being cheap and safe, a commercial hydrogen store must contain a certain weight percentage of hydrogen to provide a reasonable range (~300 miles). It must also be able to release hydrogen under near-ambient conditions (80-120°C) and have a reasonable cycling capacity (~1000 cycles). The primary motivation of this thesis is to gain a fundamental understanding into the sorption processes of hydrogen on carbon- and aluminium-based materials to improve their hydrogen storage capacity. The sorption processes of hydrogen on mechanically milled graphite have been investigated, primarily using Electron Spin Resonance Spectroscopy and Inelastic Neutron Scattering. An investigation into the storage properties of tetrahydroaluminates, primarily NaAlH4 and LiAlH4, is performed in the presence and absence of a catalyst, and a new phase of NaAlH4 is observed prior to its decomposition. Variable temperature neutron and synchrotron diffraction, in conjunction with gravimetric and mass spectroscopy data were obtained for several mixtures of tetrahydroaluminates and alkali amides and the hydrogen desorption processes are shown to be quite different from the constituent materials. The structure of Ca(AlH4)2 has been experimentally determined for the first time and a complete set of equations describing its decomposition pathway is given.
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Lee, Wei Lin. "The structural basis of the disabling of the actin polymerization machinery by Yersinia." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:53f9b7cb-ff29-4606-8a7b-d0aae77b61a3.
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Yersinia pestis is a human pathogen and the causative agent of bubonic plague, responsible for causing three massive pandemics, resulting in hundreds of millions of deaths in the 14th century alone. Yersinia’s virulence stems from its ability to overcome host immune defences by the injection of six Yersinia outer proteins (Yops) into the host cells via its Type III secretion system. One of these Yops, YopO specifically disables the actin polymerization machinery, leading to the crippling of phagocytosis. YopO consists of a GDI domain which sequesters Rac and Rho, and a kinase domain, the activity of which is dependent on host actin. Little is known about the targets of the kinase domain and the mechanism of function of YopO remains incomplete. In this work, YopO was crystallized in complex with actin, revealing that YopO binds to actin on subdomain 4, away from the 'hotspot’ between subdomains 1 and 3 which is involved in binding most actin-binding proteins. The structure reveals how recruitment of YopO-bound actin monomers stalls actin polymerization by steric hindrance. The structure also demonstrates how YopO uses actin for self-activation and suggests that actin is being used by YopO as bait for recruitment into actin machineries. Using SILAC mass spectrometry, actin cytoskeletal machineries within macrophages that recruit YopO are identified and these include, amongst others: VASP family proteins, gelsolin family proteins, formins and WASP. Of these, VASP, EVL, diaphanous1, WASP and gelsolin have been identified to be phosphorylated by YopO and were validated by in vitro phosphorylation. This work demonstrates that YopO uses actin as a scaffold for selection of kinase substrates, enabling targeted phosphorylation of the actin machinery and provides insight into the regulation of the actin cytoskeleton by phosphorylation under non-pathogenic conditions.
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Cliffe, Matthew James. "Disorder and defects in functional molecular frameworks." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:cd827bc8-b3dd-4fda-bdb8-f0dc893d66c2.
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This Thesis explores the role of structural defects and disorder and their relationship to experimental data, with a particular emphasis on molecular framework materials. The question of how we can build atomistic models of amorphous materials from experimental data without needing to make system-specific assumptions is addressed. The role of 'structural invariance', i.e. the limited range of distinct local atomic environments within a material, as a restraint within reverse Monte Carlo refinement (RMC) is investigated. The operation of these invariance restraints operate is shown to be system-dependent and the challenges associated with effective refinement, e.g. configurational 'jamming', are also investigated. A generalisation to the 'structural simplicity', i.e. the simplest model, holding all else constant, is most likely to be correct. Three new metrics of structural simplicity are proposed: two intrinsically three-dimensional measures of local geometric invariance and one measure of local symmetry. These metrics are shown to robustly quantify the configurational quality. The ability of these metrics to act as effective restraints for the RMC refinement of amorphous materials is demonstrated by the construction of the first data-driven tetrahedral models of amorphous silicon. The role of defects and disorder within metal–organic frameworks (MOFs) is investigated through the canonical MOF UiO-66(Hf). Through a combination of techniques, including X-ray diffuse scattering, anomalous diffraction, total scattering and electron diffraction measurements, the existence of correlated metal-cluster absences in UiO-66(Hf) is demonstrated. Furthermore the ability to synthetically tune both the interactions and concentration of defects is shown. The thermomechanical properties of defective UiO-66(Hf) are also examined. UiO-66(Hf) is shown to rapidly densify by up to 5% (ΔV/V ) on ligand elimination. The resultant densified phase exhibits colossal (≥100MK-1) volumetric negative thermal expansion (NTE); the largest reported value for any MOF. Finally, the capability to tune the physical properties of MOFs through defect incorporation is demonstrated through the defect-dependence of both the densification and the NTE.