Recovery of crystallographic texture in remineralized dental enamel.

Science.gov (United States)

Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

2014-01-01

Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain

The crystallographic growth directions of Sn whiskers

International Nuclear Information System (INIS)

Stein, J.; Welzel, U.; Leineweber, A.; Huegel, W.; Mittemeijer, E.J.

2015-01-01

The growth directions of 55 Sn whiskers, i.e. the crystallographic orientation parallel to the whisker-growth axes, were determined using (i) a focused ion beam microscope for the determination of the physical growth angles of the whiskers with respect to a specimen (reference) coordinate system and (ii) an electron backscatter detector in a scanning electron microscope for the determination of the crystallographic orientation of the whiskers. The Sn whiskers were found to grow preferentially along low-index directions of the β-Sn crystal structure. The experimental findings of this study (and most of the results presented in the literature as well) were explained by applying, in a modified way, the Hartman–Perdok concept of periodic bond chains, i.e. chains of strong bonds running uninterruptedly through the structure, to the Sn whisker-growth phenomenon

Broken symmetry within crystallographic super-spaces: structural and dynamical aspects

International Nuclear Information System (INIS)

Mariette, Celine

2013-01-01

Aperiodic crystals have the property to possess long range order without translational symmetry. These crystals are described within the formalism of super-space crystallography. In this manuscript, we will focus on symmetry breaking which take place in such crystallographic super-space groups, considering the prototype family of n-alkane/urea. Studies performed by X-ray diffraction using synchrotron sources reveal multiple structural solutions implying or not changes of the dimension of the super-space. Once the characterization of the order parameter and of the symmetry breaking is done, we present the critical pre-transitional phenomena associated to phase transitions of group/subgroup types. Coherent neutron scattering and inelastic X-ray scattering allow a dynamical analysis of different kind of excitations in these materials (phonons, phasons). The inclusion compounds with short guest molecules (alkane C n H 2n+2 , n varying from 7 to 13) show at room temperature unidimensional 'liquid-like' phases. The dynamical disorder along the incommensurate direction of these materials generates new structural solutions at low temperature (inter-modulated monoclinic composite, commensurate lock-in). (author) [fr

Recovery of crystallographic texture in remineralized dental enamel.

Directory of Open Access Journals (Sweden)

Samera Siddiqui

Full Text Available Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture and position of the (002 Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected

Characterization of a defective PbWO4 crystal cut along the a-c crystallographic plane: structural assessment and a novel photoelastic stress analysis

Science.gov (United States)

Montalto, L.; Natali, P. P.; Daví, F.; Mengucci., P.; Paone, N.; Rinaldi, D.

2017-12-01

Among scintillators, the PWO is one of the most widely used, for instance in CMS calorimeter at CERN and PANDA project. Crystallographic structure and chemical composition as well as residual stress condition, are indicators of homogeneity and good quality of the crystal. In this paper, structural characterization of a defective PbWO4 (PWO) crystal has been performed by X-ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS) and Photoelasticity in the unusual (a, c) crystallographic plane. XRD and EDS analysis have been used to investigate crystallographic orientation and chemical composition, while stress distribution, which indicates macroscopic inhomogeneities and defects, has been obtained by photoelastic approaches, in Conoscopic and Sphenoscopic configuration. Since the sample is cut along the (a, c) crystallographic plane, a new method is proposed for the interpretation of the fringe pattern. The structural analysis has detected odds from the nominal lattice dimension, which can be attributed to the strong presence of Pb and W. A strong inhomogeneity over the crystal sample has been revealed by the photoelastic inspection. The results give reliability to the proposed procedure which is exploitable in crystals with other structures.

Research on the phenomenon of graphitization. Crystallographic study - Study of bromine sorption

International Nuclear Information System (INIS)

Maire, Jacques

1967-01-01

This research thesis reports the study of the mechanism of graphitization of carbon by using X-ray diffraction analysis and the physical and chemical study of lamellar reactions between carbon and bromine. The author first presents generalities and results of preliminary studies (meaning of graphitization, presentation of the various carbon groups and classes), and then reports the study of the graphitization of compact carbons (soft carbons). More precisely, he reports the crystallographic study of partially graphitized carbons: methods and principles, experimental results and their analysis, discussion of the graphitization mechanism. In the next part, the author reports the study of bromine sorption on carbons: experimental method, isotherms of a natural graphite and of a graphitized carbon, structure of carbon-bromine complexes, isotherms of graphitizable carbons and of all other carbons, distribution of bromine layers in partially graphitized carbons, bromine sorption and Fermi level

Neutron crystallographic studies of amino acids and nucleic acids

International Nuclear Information System (INIS)

Kashiwagi, Tatsuki

2014-01-01

Neutron crystallographic studies of two representative umami materials were executed utilizing iBLX at MLF/J-PARC. The results of them will be summarized in this report. At first, structure analysis of the alpha form crystal of L-glutamic acid was performed in order to assess the usefulness of neutron crystallography at iBIX to our company's R and D. Neutron crystal structure of it was successfully determined at 0.6 A resolution. All hydrogen atoms were clearly observed. Next, the mixed crystal of disodium Inosine-5'-phosphate (IMP · 2Na) and disodium Guanosine-5'-phosphate (GMP · 2Na) was analyzed by neutron crystallography. Neutron crystal structure of the mixed crystal of IMP and GMP (IM/GMP rate = 1.7) was successfully determined at 0.8 A resolution. In the neutron crystal structure of the mixed crystal, the hydrogen atom bonded to the C2 atom of purine base in IMP and the nitrogen atom bonded to the C2 atom of purine base in GMP were clearly observed in the nuclear density map, structurally demonstrating that this crystal is the mixed crystal. (author)

HRTEM study of α-AlMnSi crystals including non-crystallographic projection axes

International Nuclear Information System (INIS)

Song, G.L.; Bursill, L.A.

1997-01-01

The structure of α-AlMnSi is examined by atomic resolution high-resolution transmission electron microscopy (HRTEM) and computer-based image matching techniques. Six distinct zone axes are examined; including both normal crystallographic and non-crystallographic zones axes of the structural motifs, which have m3-bar 5 icosahedral symmetry. The results provide a sound basis for understanding HRTEM images of the quasicrystalline alloy i-AlMnSi; thus it was examined to what extent the requirements for obtaining so-called structure images of complex alloy structures may be met experimentally and define when the images may be reliably interpreted on the basis of computer simulation and image-matching at about 0.17nm resolution. Most difficulty was experienced in obtaining the experimental images, especially for the non-crystallographic zones, which are very sensitive to slight changes in orientation off the desired zone axis or projection, the rate at which the crystal thickness is increasing (wedge-angle) and the orientation of the surfaces of the specimen. Surface amorphous layers due to oxidation and/or electron-induced irradiation damage also limit the efficiency of the HRTEM analysis. For the thin specimens used for HRTEM, both the electron diffraction patterns and the HRTEM images are characteristic of Im3-bar space group symmetry. It is suggested that this Im3-bar symmetry may be an example of a statistical symmetry, where the local symmetry is close to Pm3-bar but the average symmetry is Im3-bar. The transition from Pm3-bar to Im3-bar may be understood in terms of an analysis of small changes in the outer shells of the large icosahedral structural elements which are located at the corners and body-centers of the cubic unit cell. 21 refs., 3 tabs., 10 figs

HRTEM study of {alpha}-AlMnSi crystals including non-crystallographic projection axes

Energy Technology Data Exchange (ETDEWEB)

Song, G.L.; Bursill, L.A.

1997-06-01

The structure of {alpha}-AlMnSi is examined by atomic resolution high-resolution transmission electron microscopy (HRTEM) and computer-based image matching techniques. Six distinct zone axes are examined; including both normal crystallographic and non-crystallographic zones axes of the structural motifs, which have m3-bar 5 icosahedral symmetry. The results provide a sound basis for understanding HRTEM images of the quasicrystalline alloy i-AlMnSi; thus it was examined to what extent the requirements for obtaining so-called structure images of complex alloy structures may be met experimentally and define when the images may be reliably interpreted on the basis of computer simulation and image-matching at about 0.17nm resolution. Most difficulty was experienced in obtaining the experimental images, especially for the non-crystallographic zones, which are very sensitive to slight changes in orientation off the desired zone axis or projection, the rate at which the crystal thickness is increasing (wedge-angle) and the orientation of the surfaces of the specimen. Surface amorphous layers due to oxidation and/or electron-induced irradiation damage also limit the efficiency of the HRTEM analysis. For the thin specimens used for HRTEM, both the electron diffraction patterns and the HRTEM images are characteristic of Im3-bar space group symmetry. It is suggested that this Im3-bar symmetry may be an example of a statistical symmetry, where the local symmetry is close to Pm3-bar but the average symmetry is Im3-bar. The transition from Pm3-bar to Im3-bar may be understood in terms of an analysis of small changes in the outer shells of the large icosahedral structural elements which are located at the corners and body-centers of the cubic unit cell. 21 refs., 3 tabs., 10 figs.

Crystallographic theory of the martensitic transformation

Directory of Open Access Journals (Sweden)

Edwar A. Torres-López

2014-08-01

Full Text Available The martensitic transformation is one of the most researched topics in the materials science during the 20th century. The second half of this century was mainly remembered by the development of several theories related with the kinetics of phase transformation, the mechanisms involved in the nucleation phenomenon, and the way as the crystallographic change is produced. In this paper are described the fundamental concepts that are defined in the crystallographic framework of the martensitic transformation. The study is focused on the application of the most outstanding crystallographic models: the Bain; the Wechsler, Lieberman & Read; and the Bowles & Mackenzie. The topic is presented based upon the particular features of the martensitic transformation, such as its non-diffusional character, type of interface between parent (austenite and product (martensite phases, the formation of substructural defects, and the shape change; all of these features are mathematically described by equations aimed to predict how the transformation will take place rather than to explain the actual movement of the atoms within the structure. This mathematical development is known as the Phenomenological Theory of Martensite Crystallography (PTMC.

Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

Science.gov (United States)

Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

2016-05-01

In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

Science.gov (United States)

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

Science.gov (United States)

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

A crystallographic perspective on sharing data and knowledge

Science.gov (United States)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

Crystallographic features of lath martensite in low-carbon steel

International Nuclear Information System (INIS)

Kitahara, Hiromoto; Ueji, Rintaro; Tsuji, Nobuhiro; Minamino, Yoritoshi

2006-01-01

Electron backscattering diffraction with field-emission scanning electron microscopy was used to analyze crystallographically the lath martensite structure in a 0.20% carbon steel. The crystallographic features of the lath martensite structure, of the order of the prior austenite grain size or larger, were clarified. Although the orientations of the martensite crystals were scattered around the ideal variant orientations, the martensite in this steel maintained the Kurdjumov-Sachs (K-S) orientation relationship. The procedures of the crystallographic analysis of the martensite (ferrite) phase with the K-S orientation relationship were explained in detail. Variant analysis showed that all 24 possible variants did not necessarily appear within a single prior austenite grain and that all six variants did not necessarily appear within each packet. Specific combinations of two variants appeared within local regions (sub-blocks), indicating a strict rule for variant selection. Prior austenite grain boundaries and most of the packet boundaries were clearly recognized. However, it was difficult to determine the block boundaries within the sub-blocks

Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry.

Science.gov (United States)

Neeman, Lior; Ben-Zvi, Regev; Rechav, Katya; Popovitz-Biro, Ronit; Oron, Dan; Joselevich, Ernesto

2017-02-08

The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations.

Crystallization and preliminary crystallographic study of carnosinase CN2 from mice

Energy Technology Data Exchange (ETDEWEB)

Yamashita, Tetsuo; Unno, Hideaki; Ujita, Sayuri; Otani, Hiroto; Okumura, Nobuaki; Hashida-Okumura, Akiko; Nagai, Katsuya; Kusunoki, Masami, E-mail: kusunoki@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871 (Japan)

2006-10-01

Mouse carnosinase was crystallized in complex with Zn{sup 2+} or Mn{sup 2+} and the complexes are undergoing structure determination by the MAD method. Mammalian tissues contain several histidine-containing dipeptides, of which l-carnosine is the best characterized and is found in various tissues including the brain and skeletal muscles. However, the mechanism for its biosynthesis and degradation have not yet been fully elucidated. Crystallographic study of carnosinase CN2 from mouse has been undertaken in order to understand its enzymatic mechanism from a structural viewpoint. CN2 was crystallized by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant. Crystals were obtained in complex with either Mn{sup 2+} or Zn{sup 2+}. Both crystals of CN2 belong to the monoclinic space group P2{sub 1} and have almost identical unit-cell parameters (a = 54.41, b = 199.77, c = 55.49 Å, β = 118.52° for the Zn{sup 2+} complex crystals). Diffraction data were collected to 1.7 and 2.3 Å for Zn{sup 2+} and Mn{sup 2+} complex crystals, respectively, using synchrotron radiation. Structure determination is ongoing using the multiple-wavelength anomalous diffraction (MAD) method.

Crystallization and preliminary crystallographic study of carnosinase CN2 from mice

International Nuclear Information System (INIS)

Yamashita, Tetsuo; Unno, Hideaki; Ujita, Sayuri; Otani, Hiroto; Okumura, Nobuaki; Hashida-Okumura, Akiko; Nagai, Katsuya; Kusunoki, Masami

2006-01-01

Mouse carnosinase was crystallized in complex with Zn 2+ or Mn 2+ and the complexes are undergoing structure determination by the MAD method. Mammalian tissues contain several histidine-containing dipeptides, of which l-carnosine is the best characterized and is found in various tissues including the brain and skeletal muscles. However, the mechanism for its biosynthesis and degradation have not yet been fully elucidated. Crystallographic study of carnosinase CN2 from mouse has been undertaken in order to understand its enzymatic mechanism from a structural viewpoint. CN2 was crystallized by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant. Crystals were obtained in complex with either Mn 2+ or Zn 2+ . Both crystals of CN2 belong to the monoclinic space group P2 1 and have almost identical unit-cell parameters (a = 54.41, b = 199.77, c = 55.49 Å, β = 118.52° for the Zn 2+ complex crystals). Diffraction data were collected to 1.7 and 2.3 Å for Zn 2+ and Mn 2+ complex crystals, respectively, using synchrotron radiation. Structure determination is ongoing using the multiple-wavelength anomalous diffraction (MAD) method

Crystallographic changes in lead zirconate titanate due to neutron irradiation

Directory of Open Access Journals (Sweden)

Alexandra Henriques

2014-11-01

Full Text Available Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method is used to quantify the type and extent of structural changes in PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which the effects of radiation on crystallographic structure may be investigated.

Crystallographic computing system JANA2006: General features

Czech Academy of Sciences Publication Activity Database

Petříček, Václav; Dušek, Michal; Palatinus, Lukáš

2014-01-01

Roč. 229, č. 5 (2014), s. 345-352 ISSN 0044-2968 R&D Projects: GA ČR(CZ) GAP204/11/0809; GA ČR(CZ) GA14-03276S Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : JANA2006 * aperiodic structures * magnetic structures * crystallographic computing Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.310, year: 2014

Crystallographic and oxidation kinetic study of uranium dioxide by high temperature X-ray diffractometry

International Nuclear Information System (INIS)

Teixeira, S.R.

1981-01-01

The structural behavior of UO 2 sintered plates was studied as a function of temperature by X-ray diffractometry. All the experiments were carried out under an inert atmosphere with low oxygen content (approximated 140 ppm). The thermal expansion coefficient of UO 2 05 was found to be 10,5 x 10 - 6 0 C - 1 for temperatures above 165 0 C. Structural transformations during oxidation were observed at 170,235 and 275 0 C. The isothermal oxidation of UO 2 to U 3 O 7 follows a parabolic form and the diffusion of oxygen through the product layer U 4 O 9 is the mechanism controlling the oxidation rate. The phases observed were UO 2 (cubic) - U 4 O 9 (cubic) - U 3 O 7 (tetragonal). Activation energies of oxidation were found for different crystallographic planes (hkl). From this one can conclude that there is a preferential occupation of interstitial oxygen within the UO 2 structure. (Author) [pt

Correlation between Crystallographic and Magnetic Domains at Co/NiO(001) Interfaces

Energy Technology Data Exchange (ETDEWEB)

Ohldag, H.; van der Laan, G.; Arenholz, E.

2008-12-18

Using soft x-ray spectromicroscopy we show that NiO(001) exhibits a crystallographic and magnetic domain structure near the surface identical to that of the bulk. Upon Co deposition a perpendicular coupling between the Ni and Co moments is observed that persists even after formation of uncompensated Ni spins at the interface through annealing. The chemical composition at the interface alters its crystallographic structure and leads to a reorientation of the Ni moments from the <112> to the <110> direction. We show that this reorientation is driven by changes in the magnetocrystalline anisotropy rather than exchange coupling mediated by residual uncompensated spins.

Asymmetric Rolling Process Simulations by Dynamic Explicit Crystallographic Homogenized Finite Element Method

International Nuclear Information System (INIS)

Ngoc Tam, Nguyen; Nakamura, Yasunori; Terao, Toshihiro; Kuramae, Hiroyuki; Nakamachi, Eiji; Sakamoto, Hidetoshi; Morimoto, Hideo

2007-01-01

Recently, the asymmetric rolling (ASR) has been applied to the material processing of aluminum alloy sheet to control micro-crystal structure and texture in order to improve the mechanical properties. Previously, several studies aimed at high formability sheet generation have been carried out experimentally, but finite element simulations to predict the deformation induced texture evolution of the asymmetrically rolled sheet metals have not been investigated rigorously. In this study, crystallographic homogenized finite element (FE) codes are developed and applied to analyze the asymmetrical rolling processes. The textures of sheet metals were measured by electron back scattering diffraction (EBSD), and compared with FE simulations. The results from the dynamic explicit type Crystallographic homogenization FEM code shows that this type of simulation is a comprehensive tool to predict the plastic induced texture evolution

The effect of crystallographic orientation on the active corrosion of pure magnesium

International Nuclear Information System (INIS)

Liu Ming; Qiu Dong; Zhao Mingchun; Song, Guangling; Atrens, Andrej

2008-01-01

An improved method was used to investigate the influence of crystallographic orientation on the corrosion of pure magnesium in 0.1 N HCl. The corrosion depth and orientation of surface features were mapped against crystallographic orientation (obtained by electron backscatter diffraction) for many off-principal magnesium crystals. The grains near (0 0 0 1) orientation are the most corrosion resistant. Most grains exhibited a striated structure of long and narrow hillocks with a unique direction

World directory of crystallographers and of other scientists employing crystallographic methods

CERN Document Server

Filippini, G; Hashizume, H; Torriani, I; Duax, W

1995-01-01

The 9th edition of the World Directory of Crystallographers and of Other Scientists Employing Crystallographic Methods, which contains 7907 entries embracing 72 countries, differs considerably from the 8th edition, published in 1990. The content has been updated, and the methods used to acquire the information presented and to produce this new edition of the Directory have involved the latest advances in technology. The Directory is now also available as a regularly updated electronic database, accessible via e-mail, Telnet, Gopher, World-Wide Web, and Mosaic. Full details are given in an Appendix to the printed edition.

Crystallographic properties of fertilizer compounds

Energy Technology Data Exchange (ETDEWEB)

Frazier, A.W.; Dillard, E.F.; Thrasher, R.D.; Waerstad, K.R.; Hunter, S.R.; Kohler, J.J.; Scheib, R.M.

1991-02-01

This bulletin is a compilation of crystallographic data collected at NFERC on 450 fertilizer-related compounds. In TVA's fertilizer R and D program, petrographic examination, XRD, and infrared spectroscopy are combined with conventional chemical analysis methods in identifying the individual compounds that occur in fertilizer materials. This handbook brings together the results of these characterization studies and supplemental crystallographic data from the literature. It is in one-compound-per-page, loose-leaf format, ordered alphabetically by IUPAC name. Indexes provided include IUPAC name, formula, group, alternate formula, synonyms, x-ray data, optical data. Tables are given for solids, compounds in commercial MAP and DAP, and matrix materials in phosphate rock.

Spectroscopic and crystallographic studies of YAG:Pr4+ single crystals

International Nuclear Information System (INIS)

Pawlak, D.; Frukacz, Z.; Mierczyk, Z.; Suchocki, A.; Zachara, J.

1998-01-01

Y 3 Al 5 O 12 single crystals doped with praseodymium and magnesium ions have been prepared. The reversible color change of this crystal is observed when annealing in oxidizing or reducing atmospheres. The change is ascribed to the formation of Pr 4+ in the as-grown crystal, caused by the second dopant, Mg 2+ . The absorption spectra of YAG:Pr,Mg in the range 200-1100 nm, as grown and annealed in air and H 2 /N 2 atmosphere, are presented and discussed. Additional broad absorption bands are observed for the as-grown crystals and those annealed in oxidizing atmosphere. Crystallographic investigations of the original crystal and after annealing in a reducing atmosphere as described above, show no distinct structural differences. A redox mechanism is proposed to explain the color change during annealing. (orig.)

Crystallographic study of one turn of G/C-rich B-DNA.

Science.gov (United States)

Heinemann, U; Alings, C

1989-11-20

The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the crystal lattice, DNA fragments stack end-to-end along the c-axis to form continuous double helices. The overall helical structure and, notably, the groove dimensions of the decamer are more similar to standard, fiber diffraction-determined B-DNA than A-tract DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of the base-pairs along their long axes leads to a superposition of the base rings with neighboring carbonyl and amino functions. Three-center (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of the decamer. In their common sequence elements, d(CCAGGCCTGG) and the related G.A mismatch decamer d(CCAAGATTGG) show very similar three-dimensional structures, except that d(CCAGGCCTGG) appears to have a less regularly hydrated minor groove. The paucity of minor groove hydration in the center of the decamer may be a general feature of G/C-rich DNA and explain its relative instability in the B-form of DNA.

Crystallographic orientation study of silicon steels using X-ray diffraction, electrons diffraction and the Etch Pit method

International Nuclear Information System (INIS)

Santos, Hamilta de Oliveira

1999-01-01

The aim of the present study is the microstructural and crystallographic orientation of Fe-3%Si steel. The silicon steel shows good electrical properties and it is used in the nuclear and electrical power fields. The studied steel was supplied by Cia. Acos Especiais Itabira S/A - ACESITA. The material was received in the hot compressed condition, in one or two passes. The hot compressing temperatures used were 900, 1000 and 1100 deg C with soaking times ranging from 32 to 470 s. The material preferential crystallographic orientation was evaluated in every grain of the samples. The characterization techniques used were: scanning electron microscopy (SEM) using the etch pit method; X ray diffraction using the Laue back-reflection method; orientation imaging microscopy (OIM). Microstructural characterization in terms of grain size measurement and mean number of grains in the sample were also undertaken. The Laue method was found an easy technique to access crystallographic orientation of this work polycrystalline samples 2.5 mm average grain size. This was due to the inability to focus the X-rays on a single grain of the material. The scanning electron microscopy showed microcavities left by the etch pit method, which allowed the observation of the crystallographic orientation of each grain from the samples. No conclusive grain crystallographic orientation was possible to obtain by the OIM technique due to the non-existing rolling direction. A more extensive work with the OIM technique must be undertaken on the Fe-3%Si with oriented grains and non oriented grains. (author)

Structure of δ-Bi2O3 from density functional theory: A systematic crystallographic analysis

International Nuclear Information System (INIS)

Aidhy, Dilpuneet S.; Sinnott, Susan B.; Wachsman, Eric D.; Phillpot, Simon R.; Nino, Juan C.

2009-01-01

A systematic crystallographic analysis of the and vacancy-ordered structure of cubic δ-Bi 2 O 3 obtained from electronic-structure calculations is presented. The ordering of vacancies leads to a doubling of the unit-cell that results in a 2x2x2 fluorite super-structure, with an associated reduction in its space group symmetry from Fm3-barm to Fm3-bar. The Bi atoms present inside the vacancy-ordered oxygen sublattice have equal Bi-O bond lengths, whereas, those present inside the vacancy-ordered oxygen sublattice have three different pairs of Bi-O bond lengths. The specific ionic displacements and electronic charge configurations also depend on the nature of vacancy ordering in the oxygen sub-lattice. - Graphical abstract: 1/8 of a 2x2x2 δ-Bi 2 O 3 superstructure having Fm3-bar space group. Every oxygen (black) has three possible positions, only one of which is filled either by O1 (red) or O 2 (blue).

Resolution of a protein sequence ambiguity by X-ray crystallographic and mass spectrometric methods

International Nuclear Information System (INIS)

Keefe, L.J.; Lattman, E.E.; Wolkow, C.; Woods, A.; Chevrier, M.; Cotter, R.J.

1992-01-01

Ambiguities in amino acid sequences are a potential problem in X-ray crystallographic studies of proteins. Amino acid side chains often cannot be reliably identified from the electron density. Many protein crystal structures that are now being solved are simple variants of a known wild-type structure. Thus, cloning artifacts or other untoward events can readily lead to cases in which the proposed sequence is not correct. An example is presented showing that mass spectrometry provides an excellent tool for analyzing suspected errors. The X-ray crystal structure of an insertion mutant of Staphylococcal nuclease has been solved to 1.67 A resolution and refined to a crystallographic R value of 0.170. A single residue has been inserted in the C-terminal α helix. The inserted amino acid was believed to be an alanine residue, but the final electron density maps strongly indicated that a glycine had been inserted instead. To confirm the observations from the X-ray data, matrix-assisted laser desorption mass spectrometry was employed to verify the glycine insertion. This mass spectrometric technique has sufficient mass accuracy to detect the methyl group that distinguishes glycine from alanine and can be extended to the more common situation in which crystallographic measurements suggest a problem with the sequence, but cannot pinpoint its location or nature. (orig.)

Resolution of a protein sequence ambiguity by X-ray crystallographic and mass spectrometric methods

Energy Technology Data Exchange (ETDEWEB)

Keefe, L.J.; Lattman, E.E. (Dept. of Biophysics and Biophysical Chemistry, Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)); Wolkow, C.; Woods, A.; Chevrier, M.; Cotter, R.J. (Middle Atlantic Mass Spectrometry Lab., Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))

1992-04-01

Ambiguities in amino acid sequences are a potential problem in X-ray crystallographic studies of proteins. Amino acid side chains often cannot be reliably identified from the electron density. Many protein crystal structures that are now being solved are simple variants of a known wild-type structure. Thus, cloning artifacts or other untoward events can readily lead to cases in which the proposed sequence is not correct. An example is presented showing that mass spectrometry provides an excellent tool for analyzing suspected errors. The X-ray crystal structure of an insertion mutant of Staphylococcal nuclease has been solved to 1.67 A resolution and refined to a crystallographic R value of 0.170. A single residue has been inserted in the C-terminal {alpha} helix. The inserted amino acid was believed to be an alanine residue, but the final electron density maps strongly indicated that a glycine had been inserted instead. To confirm the observations from the X-ray data, matrix-assisted laser desorption mass spectrometry was employed to verify the glycine insertion. This mass spectrometric technique has sufficient mass accuracy to detect the methyl group that distinguishes glycine from alanine and can be extended to the more common situation in which crystallographic measurements suggest a problem with the sequence, but cannot pinpoint its location or nature. (orig.).

The use of Fourier reverse transforms in crystallographic phase refinement

Energy Technology Data Exchange (ETDEWEB)

Ringrose, Sharon [Iowa State Univ., Ames, IA (United States)

1997-10-08

Often a crystallographer obtains an electron density map which shows only part of the structure. In such cases, the phasing of the trial model is poor enough that the electron density map may show peaks in some of the atomic positions, but other atomic positions are not visible. There may also be extraneous peaks present which are not due to atomic positions. A method for determination of crystal structures that have resisted solution through normal crystallographic methods has been developed. PHASER is a series of FORTRAN programs which aids in the structure solution of poorly phased electron density maps by refining the crystallographic phases. It facilitates the refinement of such poorly phased electron density maps for difficult structures which might otherwise not be solvable. The trial model, which serves as the starting point for the phase refinement, may be acquired by several routes such as direct methods or Patterson methods. Modifications are made to the reverse transform process based on several assumptions. First, the starting electron density map is modified based on the fact that physically the electron density map must be non-negative at all points. In practice a small positive cutoff is used. A reverse Fourier transform is computed based on the modified electron density map. Secondly, the authors assume that a better electron density map will result by using the observed magnitudes of the structure factors combined with the phases calculated in the reverse transform. After convergence has been reached, more atomic positions and less extraneous peaks are observed in the refined electron density map. The starting model need not be very large to achieve success with PHASER; successful phase refinement has been achieved with a starting model that consists of only 5% of the total scattering power of the full molecule. The second part of the thesis discusses three crystal structure determinations.

Study of the crystallographic and magnetic properties of cubic manganite spinels NiMn2O4

International Nuclear Information System (INIS)

Boucher, B.

1969-01-01

We study the variation of the crystallographic properties (inversion degree, position parameters and short range order) of the cubic spinel Mn ν Ni 1-ν [Mn 2ν Ni ν ]O 4 , as a function of the thermal treatment applied to the sample. ν lies between 0. 74 and 0. 93; the slower the sample is cooled the more inverse it is. We show, in a molecular field theory, that a system of three magnetic sublattices can afford a 'star' configuration. We establish the conditions of stability of such a structure and its evolution as a function of temperature is foreseen. Neutron diffraction measurements show that the magnetic structure of NiMn 2 O 4 at 4.2 K is a 'star' configuration and that with increasing temperature it becomes a collinear structure in agreement with the theory. Furthermore, we find an anomaly in the value of specific heat at the transition temperature between 'star' and collinear structures. (author) [fr

Dianthraceno[a,e]pentalenes: Synthesis, crystallographic structures and applications in organic field-effect transistors

KAUST Repository

Dai, Gaole

2015-01-01

Two soluble and stable dianthraceno[a,e]pentalenes with two (DAP1) and six (DAP2) phenyl substituents were synthesized. Both compounds possess a small energy band gap and show amphoteric redox behaviour due to intramolecular donor-accepter interactions. X-ray crystallographic analysis revealed that DAP2 has a closely packed structure with multi-dimensional [C-H⋯π] interactions although there are no π-π interactions between the dianthraceno[a,e]pentalene cores. As a result, solution-processed field effect transistors based on DAP2 exhibited an average hole mobility of 0.65 cm2 V-1 s-1. Under similar conditions, DAP1 showed an average field effect hole mobility of 0.001 cm2 V-1 s-1. This journal is

Origin of intragranular crystallographic misorientations in hot-dip Al-Zn-Si coatings

International Nuclear Information System (INIS)

Niederberger, Ch.; Michler, J.; Jacot, A.

2008-01-01

The origin of intragranular variations of the crystallographic orientation in hot-dip Al-Zn-Si coatings is discussed based on new experimental results and modelling. The solidification microstructure in as-received 55Al-43.4Zn-1.6Si (in wt.%) coatings deposited on steel plates in an industrial production line was analyzed by electron backscattered diffraction, glow-discharge optical emission spectroscopy and atomic force microscopy (AFM). The results were compared with those obtained in coatings re-solidified under different cooling and mechanical loading conditions. Continuous variations of the crystallographic orientation as large as 35 deg. were observed within individual grains of Al-Zn-Si, consistent with previous studies. However, the mechanisms previously proposed for the origin of intragranular crystallographic misorientations had to be revisited. The new experimental data acquired during this study indicate that the solidification shrinkage accumulating in the area of the grain envelope is the driving force for the formation of intragranular misorientations. The solidification shrinkage leads to the development of tensile stresses in the oxide film covering the coating while it solidifies. Estimations based on AFM profiles and phase field simulations of the dendritic structure indicate that the stresses applied on the dendrite network are sufficient to deform plastically the dendrite arms during solidification

Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump With a Dual Chromophore

International Nuclear Information System (INIS)

Luecke, H.; Schobert, B.; Stagno, J.; Imasheva, E.S.; Wang, J.M.; Balashov, S.P.; Lanyi, J.K

2008-01-01

Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-(angstrom) resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK a of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as ∼45%, and the 46 o angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer

Study of reticular defects in V3Si (A15 structure)

International Nuclear Information System (INIS)

Ben Lamine, Abdelmottaleb

1980-01-01

The A15 crystal structure is that of superconductive compounds with high critical temperature. This research thesis aims at studying its possible reticular defects. In a first part, the author presents this structure and more particularly its crystallographic properties, reports the indexing of electronic diffraction diagrams (point diagrams and line diagrams of Kikuchi) in the case of V 3 Si. Then, after having described the sample preparation technique, the author reports the study of reticular defects by high voltage electronic microscopy on a raw V 3 Si crystal. The existence of a specific defect is highlighted and the crystallographic study of this defect is reported. It has been performed by means of computer-based simulation of contrast (TWODIS software). Results are then discussed

Crystallographic Study of U-Th bearing minerals in Tranomaro, Anosy Region-Madagascar

International Nuclear Information System (INIS)

Sahoa, F.E.; Rabesiranana, N.; Raoelina Andriambololona; Geckeis, H.; Marquardt, C.; Finck, K.

2011-01-01

As an alternative to conventional fossil fuel, there is a renewed interest in the nuclear fuel to support increasing energy demand. New studies are then undertaken to characterize Madagascar U-Th bearing minerals. This is the case for the urano-thorianite bearing pyroxenites in the south East of Madagascar. In this region, several quarries were abandoned, after being mined by the French Atomic Energy Commission (C.E.A) in the fifties and sixties and are now explored by new mining companies. For this purpose, seven U-Th bearing mineral samples from old abandoned uranium quarries in Tranomaro, Amboasary Sud, Madagascar, have been collected. To determine the mineral microstructure, they were investigated for qualitative and quantitative identification of crystalline compounds using X-ray powder diffraction analytical method (XRD). Results showed that the U and Th compounds, as minor elements, are present in various crystalline structures. This is important to understand their environmental behaviours, in terms of crystallographic dispersion of U-Th minerals and their impacts on human health.

Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri.

Science.gov (United States)

Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro

2008-02-01

In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.

Synthesis, structure and magnetic properties of crystallographically aligned CuCr_2Se_4 thin films

International Nuclear Information System (INIS)

Esters, Marco; Liebig, Andreas; Ditto, Jeffrey J.; Falmbigl, Matthias; Albrecht, Manfred; Johnson, David C.

2016-01-01

We report the low temperature synthesis of highly textured CuCr_2Se_4 thin films using the modulated elemental reactant (MER) method. The structure of CuCr_2Se_4 is determined for the first time in its thin film form and exhibits cell parameters that are smaller than found in bulk CuCr_2Se_4. X-ray diffraction and precession electron diffraction show a strong degree of crystallographic alignment of the crystallites, where the axis is oriented perpendicular to the substrate surface, while being rotationally disordered within the plane. Temperature and field dependent in-plane and out-of-plane magnetization measurements show that the film is ferromagnetic with a Curie temperature of 406 K CuCr_2Se_4 synthesized utilizing the MER method shows stronger magnetic anisotropy (effective anisotropy: 1.82 × 10"6 erg cm"−"3; shape anisotropy: 1.07 × 10"6 erg cm"−"3), with the easy axis lying out of plane, and a larger magnetic moment (6 μ_B/f.u.) than bulk CuCr_2Se_4. - Highlights: • Crystallographically aligned, phase pure CuCr_2Se_4 were synthesized. • The degree of alignment decreases with annealing time. • The films are ferromagnetic with the easy axis along the direction. • The magnetization is larger than bulk CuCr_2Se_4 or other CuCr_2Se_4 films made to date.

Expression, crystallization and preliminary crystallographic study of GluB from Corynebacterium glutamicum

International Nuclear Information System (INIS)

Liu, Qingbo; Li, Defeng; Hu, Yonglin; Wang, Da-Cheng

2013-01-01

GluB, a substrate-binding protein from C. glutamicum, was expressed, purified and crystallized, followed by X-ray diffraction data collection and preliminary crystallographic analysis. GluB is a substrate-binding protein (SBP) which participates in the uptake of glutamic acid in Corynebacterium glutamicum, a Gram-positive bacterium. It is part of an ATP-binding cassette (ABC) transporter system. Together with the transmembrane proteins GluC and GluD and the cytoplasmic protein GluA, which couples the hydrolysis of ATP to the translocation of glutamate, they form a highly active glutamate-uptake system. As part of efforts to study the amino-acid metabolism, especially the metabolism of glutamic acid by C. glutamicum, a bacterium that is widely used in the industrial production of glutamic acid, the GluB protein was expressed, purified and crystallized, an X-ray diffraction data set was collected to a resolution of 1.9 Å and preliminary crystallographic analysis was performed. The crystal belonged to space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 82.50, c = 72.69 Å

Structural studies of metal oxides related to High-Tc superconductors

International Nuclear Information System (INIS)

Hjorth, M.

1990-02-01

The project was started in order to investigate metal oxide structures related in some way to high-T c superconductors, using the crystallographic methods available; and in order to be able to use crystallographic methods in ways that go beyond routine applications in order to contribute to the crystallographic knowledge concerning these oxides. The project goes a step outside the boarders normally defined by using the term ''high-T c superconductors'', thus studying metal oxides from a more general crystallographic viewpoint. The methods used are the expansions of the spherical atom model, and of the thermal probability density function, and combination of X-ray work with high resolution electron microscopy. The use of the expanded diffraction models presents problems such as bad convergence in least squares refinement, physical unreasonable parameters, problems with interpretation of the results and difficulties due to missing or insufficient computer programs. The use of these models is discussed. Dynamical theory is applied when considering electron diffraction results. The theory is presented, focusing on the modifications of the standard theory used for some of the structures considered in the thesis, and in overview on other theoretical topics is given. A presentation is given of the structures which have been considered and of earlier work on related compounds, of the problems and solutions applied to the compound discussed and of the results obtained. The results are discussed. The appendices describe published papers and the work not directly connected to the main topics, e.g. implementation and development of computer programs. (AB) 172 refs

Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study

Science.gov (United States)

Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep; Kumar, Vinay; Madamwar, Datta

2015-01-01

The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. PMID:26249689

Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

Energy Technology Data Exchange (ETDEWEB)

Abdulmalik, Osheiza [The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States); Ghatge, Mohini S.; Musayev, Faik N.; Parikh, Apurvasena [Virginia Commonwealth University, Richmond, VA 23298 (United States); Chen, Qiukan; Yang, Jisheng [The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States); Nnamani, Ijeoma [Duke University Medical Center, Durham, NC 27710 (United States); Danso-Danquah, Richmond [Virginia Commonwealth University, Richmond, VA 23298 (United States); Eseonu, Dorothy N. [Virginia Union University, Richmond, VA 23220 (United States); Asakura, Toshio [Duke University Medical Center, Durham, NC 27710 (United States); Abraham, Donald J.; Venitz, Jurgen; Safo, Martin K., E-mail: msafo@vcu.edu [Virginia Commonwealth University, Richmond, VA 23298 (United States); The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States)

2011-11-01

Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.

Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

International Nuclear Information System (INIS)

Abdulmalik, Osheiza; Ghatge, Mohini S.; Musayev, Faik N.; Parikh, Apurvasena; Chen, Qiukan; Yang, Jisheng; Nnamani, Ijeoma; Danso-Danquah, Richmond; Eseonu, Dorothy N.; Asakura, Toshio; Abraham, Donald J.; Venitz, Jurgen; Safo, Martin K.

2011-01-01

Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization

Crystallographic investigation of grain selection during initial solidification

International Nuclear Information System (INIS)

Esaka, H; Shinozuka, K; Kataoka, Y

2016-01-01

Normally, macroscopic solidified structure consists of chill, columnar and equiaxed zones. In a chill zone, many fine grains nucleate on the mold surface and grow their own preferred growth direction. Only a few of them continue to grow because of grain selection. In order to understand the grain selection process, crystallographic investigation has been carried out in the zone of initial solidification in this study. 10 g of Al-6 wt%Si alloy was melted at 850 °C and poured on the thick copper plate. Longitudinal cross section of the solidified shell was observed by a SEM and analyzed by EBSD. The result of EBSD mapping reveals that crystallographic orientation was random in the range of initial solidification. Further, some grains are elongated along their <100> direction. Columnar grains, whose growth directions are almost parallel to the heat flow direction, develop via grain selection. Here, a dendrite whose growth direction is close to the heat flow direction overgrows the other dendrite whose growth direction is far from the heat flow direction. However, sometimes we observed that dendrite, whose zenith angle is large, overgrew the other dendrite. It can be deduced that the time of nucleation on the mold surface is not constant. (paper)

Automated identification of crystallographic ligands using sparse-density representations

International Nuclear Information System (INIS)

Carolan, C. G.; Lamzin, V. S.

2014-01-01

A novel procedure for identifying ligands in macromolecular crystallographic electron-density maps is introduced. Density clusters in such maps can be rapidly attributed to one of 82 different ligands in an automated manner. A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination

A synthesis, X-ray crystallographic and vibrational studies of guanidinium o-nitrobenzoate hydrate. New NLO crystal in guanidinium nitrobenzoate family

Science.gov (United States)

Drozd, Marek; Daszkiewicz, Marek

2018-06-01

According to literature data the two crystals are known: guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate. Both compounds belong to noncetrosymmetric crystallographic systems are consider as second order generators in nonlinear optic (NLO). For each of these crystals the detailed crystallographic, theoretical calculations and vibrational studies were performed. It is interesting that nitrobenzoic acid create tree variety of compounds ((2) ortho-, (3) meta- and (4) para-) what any data for third member of guanidinium nitrobenzoate crystal were not known. The guanidinium o-nitrobenzoate hydrate crystal was synthesized first time. The performed X-ray crystallographic study shown that crystal belongs to space group without macroscopic symmetry center. Additionally, the vibrational spectra (intensities, frequencies and PED analysis) of investigated compound are presented. These results are compared with theoretical calculations for equilibrium geometry and vibrational properties. Furthermore, the results of the theoretical approach include HOMO and LUMO energies and first order hyperpolarizability were obtained, also. On the basis of these data the crystal was classified as second order generator. All obtained results are compared with previous literature data of guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate compounds. Surprisingly, each of examined crystal belongs to different crystallographic system and shows different vibrational properties.

Effect of PVC on ionic conductivity, crystallographic structural, morphological and thermal characterizations in PMMA-PVC blend-based polymer electrolytes

International Nuclear Information System (INIS)

Ramesh, S.; Liew, Chiam-Wen; Morris, Ezra; Durairaj, R.

2010-01-01

In this paper, temperature dependence of ionic conductivity, crystallographic structural, morphological and thermal characteristics of polymer blends of PMMA and PVC with lithium bis(trifluoromethanesulfonyl) imide (LiTFSI) as a dopant salt are investigated. The study on the temperature dependence of ionic conductivity shows that these polymer blends exhibit Arrhenius behavior. The highest ionic conductivity was achieved when 70 wt% of PMMA was blended with 30 wt% of PVC. X-ray diffraction (XRD) and scanning electron microscopy (SEM) reveal the amorphous nature and surface morphology of polymer electrolytes, respectively. In DSC analysis it was found that the glass transition temperature (T g ) and melting temperature (T m ) decreased, whereas the decomposition temperature (T d ) increased. In contrast, the shift towards higher decomposition temperature and decrease in weight loss of polymer electrolytes, in TGA studies, indicates that the thermal stability of polymer electrolytes improved.

Structure and function of proteins investigated by crystallographic and spectroscopic time-resolved methods

Science.gov (United States)

Purwar, Namrta

Biomolecules play an essential role in performing the necessary functions for life. The goal of this thesis is to contribute to an understanding of how biological systems work on the molecular level. We used two biological systems, beef liver catalase (BLC) and photoactive yellow protein (PYP). BLC is a metalloprotein that protects living cells from the harmful effects of reactive oxygen species by converting H2O2 into water and oxygen. By binding nitric oxide (NO) to the catalase, a complex was generated that mimics the Cat-H2O2 adduct, a crucial intermediate in the reaction promoted by the catalase. The Cat-NO complex is obtained by using a convenient NO generator (1-(N,N-diethylamino)diazen-1-ium-1,2-diolate). Concentrations up to 100˜200 mM are reached by using a specially designed glass cavity. With this glass apparatus and DEANO, sufficient NO occupation is achieved and structure determination of the catalase with NO bound to the heme iron becomes possible. Structural changes upon NO binding are minute. NO has a slightly bent geometry with respect to the heme normal, which results in a substantial overlap of the NO orbitals with the iron-porphyrin molecular orbitals. From the structure of the iron-NO complex, conclusions on the electronic properties of the heme iron can be drawn that ultimately lead to an insight into the catalytic properties of this enzyme. Enzyme kinetics is affected by additional parameters such as temperature and pH. Additionally, in crystallography, the absorbed X-ray dose may impair protein function. To address the effect of these parameters, we performed time-resolved crystallographic experiments on a model system, PYP. By collecting multiple time-series on PYP at increasing X-ray dose levels, we determined a kinetic dose limit up to which kinetically meaningful X-ray data sets can be collected. From this, we conclude that comprehensive time-series spanning up to 12 orders of magnitude in time can be collected from a single PYP

Effect of PVC on ionic conductivity, crystallographic structural, morphological and thermal characterizations in PMMA-PVC blend-based polymer electrolytes

Energy Technology Data Exchange (ETDEWEB)

Ramesh, S., E-mail: rameshtsubra@gmail.com [Centre for Ionics University Malaya, Department of Physics, Faculty of Science, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur (Malaysia); Liew, Chiam-Wen; Morris, Ezra; Durairaj, R. [Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Setapak, 53300 Kuala Lumpur (Malaysia)

2010-11-20

In this paper, temperature dependence of ionic conductivity, crystallographic structural, morphological and thermal characteristics of polymer blends of PMMA and PVC with lithium bis(trifluoromethanesulfonyl) imide (LiTFSI) as a dopant salt are investigated. The study on the temperature dependence of ionic conductivity shows that these polymer blends exhibit Arrhenius behavior. The highest ionic conductivity was achieved when 70 wt% of PMMA was blended with 30 wt% of PVC. X-ray diffraction (XRD) and scanning electron microscopy (SEM) reveal the amorphous nature and surface morphology of polymer electrolytes, respectively. In DSC analysis it was found that the glass transition temperature (T{sub g}) and melting temperature (T{sub m}) decreased, whereas the decomposition temperature (T{sub d}) increased. In contrast, the shift towards higher decomposition temperature and decrease in weight loss of polymer electrolytes, in TGA studies, indicates that the thermal stability of polymer electrolytes improved.

Crystallographic structure and grain size of polycrystalline Cu{sub 2}ZnSnS{sub 4} nanoparticles and thin films studied with XRD and SEM

Energy Technology Data Exchange (ETDEWEB)

Zutz, Folker; Chory, Christine; Riedel, Ingo; Parisi, Juergen [Thin Film Photovoltaics, Energy and Semiconductor Research Laboratory, University of Oldenburg, D-26111 Oldenburg (Germany)

2011-07-01

Cu{sub 2}ZnSnS{sub 4} (CZTS) is a compound semiconductor with an absorption coefficient of >10{sup 4} cm{sup -1} and energy gap of about 1.5 eV. Because CZTS is comprised of abundant and non-toxic precursor elements the semiconductor represents an attractive material for low-cost thin film solar cells. CZTS nanoparticles (NP) were prepared in a low-temperature colloidal synthesis yielding high amounts per synthesis cycle. For thin film deposition the NPs were converted to an ink which can be processed to thin films via printing techniques. Finally, the thin films were annealed in argon atmosphere at different temperatures in order to control the growth of microcrystallites. The photoelectrical quality of the semiconductor sensitively depends on the relative concentrations of the precursor elements (band gap, crystallographic phases) and the average grain size (charge transport). We report on structural investigations (X-ray diffraction, electron microscopy) of CZTS dried powders and thin films processed from inks with varying chemical compositions. Further, the evolution of the grain size was studied as function of the annealing temperature.

Oxide nanoparticles in an Al-alloyed oxide dispersion strengthened steel: crystallographic structure and interface with ferrite matrix

Science.gov (United States)

Zhang, Zhenbo; Pantleon, Wolfgang

2017-07-01

Oxide nanoparticles are quintessential for ensuring the extraordinary properties of oxide dispersion strengthened (ODS) steels. In this study, the crystallographic structure of oxide nanoparticles, and their interface with the ferritic steel matrix in an Al-alloyed ODS steel, i.e. PM2000, were systematically investigated by high-resolution transmission electron microscopy. The majority of oxide nanoparticles were identified to be orthorhombic YAlO3. During hot consolidation and extrusion, they develop a coherent interface and a near cuboid-on-cube orientation relationship with the ferrite matrix in the material. After annealing at 1200 °C for 1 h, however, the orientation relationship between the oxide nanoparticles and the matrix becomes arbitrary, and their interface mostly incoherent. Annealing at 1300 °C leads to considerable coarsening of oxide nanoparticles, and a new orientation relationship of pseudo-cube-on-cube between oxide nanoparticles and ferrite matrix develops. The reason for the developing interfaces and orientation relationships between oxide nanoparticles and ferrite matrix under different conditions is discussed.

Crystallographic cut that maximizes of the birefringence in photorefractive crystals

OpenAIRE

Rueda-Parada, Jorge Enrique

2017-01-01

The electro-optical birefringence effect depends on the crystal type, cut crystal, applied electric field and the incidence direction of light on the principal crystal faces. It is presented a study of maximizing the birefringence in photorefractive crystals of cubic crystallographic symmetry, in terms of these three parameters. General analytical expressions for the birefringence were obtained, from which birefringence can be established for any type of cut. A new crystallographic cut was en...

Crystallographically uniform arrays of ordered (In)GaN nanocolumns

Energy Technology Data Exchange (ETDEWEB)

Gačević, Ž., E-mail: gacevic@isom.upm.es; Bengoechea-Encabo, A.; Albert, S.; Calleja, E. [ETSIT-ISOM, Universidad Politécnica de Madrid, Avda. Complutense s/n, 28040 Madrid (Spain); Torres-Pardo, A.; González-Calbet, J. M. [Dept. Química Inorgánica, Universidad Complutense, 28040 Madrid (Spain); CEI Campus Moncloa, UCM-UPM, Madrid (Spain)

2015-01-21

In this work, through a comparative study of self-assembled (SA) and selective area grown (SAG) (In)GaN nanocolumn (NC) ensembles, we first give a detailed insight into improved crystallographic uniformity (homogeneity of crystallographic tilts and twists) of the latter ones. The study, performed making use of: reflective high energy electron diffraction, X-ray diffraction and scanning electron microscopy, reveals that unlike their SA counterparts, the ensembles of SAG NCs show single epitaxial relationship to both sapphire(0001) and Si(111) underlying substrates. In the second part of the article, making use of X-ray diffraction, we directly show that the selective area growth leads to improved compositional uniformity of InGaN NC ensembles. This further leads to improved spectral purity of their luminescence, as confirmed by comparative macro-photoluminescence measurements performed on SA and SAG InGaN NC ensembles. An improved crystallographic uniformity of NC ensembles facilitates their integration into optoelectronic devices, whereas their improved compositional uniformity allows for their employment in single-color optoelectronic applications.

Multishell structure formation in Ni nanowire under uniaxial strain along <0 0 1> crystallographic direction: A molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Wang Li, E-mail: wanglihxf@sdu.edu.c [School of Mechanical and Electrical Engineering, Shandong University at Weihai, 180 Wenhuaxi Road, Weihai 264209 (China); Peng Chuanxiao [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Gong Jianhong [School of Mechanical and Electrical Engineering, Shandong University at Weihai, 180 Wenhuaxi Road, Weihai 264209 (China)

2010-04-01

Molecular dynamics simulations based upon embedded-atom-method potential are employed to explore the fracture behavior of Ni nanowire along <0 0 1> crystallographic direction at temperature of 300 K. We find the formation of (5,5) multishell structure (MS), which is transformed from (6,5) MS at the necking region of nanowire under the strain rate of 0.02%ps{sup -1}. A reorientation transformation from <0 0 1> to <1 1 0> is first detected before formation of (6,5) MS. The formed (5,5) MS is more stable and can be tensioned longer as lower strain rate is loaded.

Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei

International Nuclear Information System (INIS)

Campos-Acevedo, Adam A.; Garcia-Orozco, Karina D.; Sotelo-Mundo, Rogerio R.; Rudiño-Piñera, Enrique

2013-01-01

Analysis of the different redox states of the catalytic cysteines in four crystallographic structures of thioredoxin 1 from the Pacific whiteleg shrimp L. vannamei highlights their reactivity and corroborates the existence of a structural dimer mediated by an interface of 12 residues which includes a disulfide bridge between the Cys73 residues of each monomer. Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3 2 12, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (V M ) of 2.31 Å 3 Da −1 and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a

Influence of crystallographic orientation on the response of copper crystallites to nanoindentation

Energy Technology Data Exchange (ETDEWEB)

Korchuganov, Aleksandr V., E-mail: avkor@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation); Kryzhevich, Dmitrij S., E-mail: kryzhev@ispms.tsc.ru, E-mail: kost@ispms.tsc.ru; Zolnikov, Konstantin P., E-mail: kryzhev@ispms.tsc.ru, E-mail: kost@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055, Russia and National Research Tomsk State University, Tomsk, 634050 (Russian Federation); Psakhie, Sergey G., E-mail: sp@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055, Russia and National Research Tomsk Polytechnic University, Tomsk, 634050 (Russian Federation)

2014-11-14

Molecular dynamics simulation was performed to study the features of nucleation and development of plastic deformation in copper crystallites in nanoindentation with different crystallographic orientations of their loaded surface: (011), (001), and (111). Atomic interaction was described by a potential constructed in terms of the embedded atom method. It is shown that behavior of the crystallite reaction force correlates well with a change in the fraction of atoms involved in local structural rearrangements. The generation of local structural changes decreases the slope of the crystallite reaction force curve or results in an extremum due to internal stress relaxation. Analysis of structural changes in the material being indented demonstrates that the orientation of its loaded surface greatly affects the features of nucleation and development of plastic deformation.

Crystallographic disorder and magnetism in UPd2-xSn

International Nuclear Information System (INIS)

Suellow, S.; Mattheus, C.C.; Becker, B.; Snel, C.E.; Nieuwenhuys, G.J.; Mydosh, J.A.; Schenck, A.

1997-01-01

The intermetallic compound UPd 2 Sn has been shown in previous investigations to crystallize in an orthorhombic structure (space group Pnma). No indications for magnetic or superconducting transitions were found. However, if the Pd content is reduced, then, similar to UNi 2 Sn, a structural transition occurs. We prepared UPd 1.85 Sn and found it to crystallize as a Heusler compound in the MnCu 2 Al-structure (space group Fm anti 3m). Now the system undergoes a transition into a disordered magnetic state at T mag ≅ 28 K. Here, we present our measurements of the specific heat, susceptibility and muon relaxation of UPd 1.85 Sn, and discuss the nature of the magnetic state in relation to the crystallographic structure. (orig.)

Synthesis, structure and magnetic properties of crystallographically aligned CuCr{sub 2}Se{sub 4} thin films

Energy Technology Data Exchange (ETDEWEB)

Esters, Marco [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States); Liebig, Andreas [Institut für Physik, Universität Augsburg, 86159 Augsburg (Germany); Ditto, Jeffrey J.; Falmbigl, Matthias [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States); Albrecht, Manfred [Institut für Physik, Universität Augsburg, 86159 Augsburg (Germany); Johnson, David C., E-mail: davej@uoregon.edu [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States)

2016-06-25

We report the low temperature synthesis of highly textured CuCr{sub 2}Se{sub 4} thin films using the modulated elemental reactant (MER) method. The structure of CuCr{sub 2}Se{sub 4} is determined for the first time in its thin film form and exhibits cell parameters that are smaller than found in bulk CuCr{sub 2}Se{sub 4}. X-ray diffraction and precession electron diffraction show a strong degree of crystallographic alignment of the crystallites, where the <111> axis is oriented perpendicular to the substrate surface, while being rotationally disordered within the plane. Temperature and field dependent in-plane and out-of-plane magnetization measurements show that the film is ferromagnetic with a Curie temperature of 406 K CuCr{sub 2}Se{sub 4} synthesized utilizing the MER method shows stronger magnetic anisotropy (effective anisotropy: 1.82 × 10{sup 6} erg cm{sup −3}; shape anisotropy: 1.07 × 10{sup 6} erg cm{sup −3}), with the easy axis lying out of plane, and a larger magnetic moment (6 μ{sub B}/f.u.) than bulk CuCr{sub 2}Se{sub 4}. - Highlights: • Crystallographically aligned, phase pure CuCr{sub 2}Se{sub 4} were synthesized. • The degree of alignment decreases with annealing time. • The films are ferromagnetic with the easy axis along the <111> direction. • The magnetization is larger than bulk CuCr{sub 2}Se{sub 4} or other CuCr{sub 2}Se{sub 4} films made to date.

Auxeticity of Yukawa Systems with Nanolayers in the (111 Crystallographic Plane

Directory of Open Access Journals (Sweden)

Paweł M. Pigłowski

2017-11-01

Full Text Available Elastic properties of model crystalline systems, in which the particles interact via the hard potential (infinite when any particles overlap and zero otherwise and the hard-core repulsive Yukawa interaction, were determined by Monte Carlo simulations. The influence of structural modifications, in the form of periodic nanolayers being perpendicular to the crystallographic axis [111], on auxetic properties of the crystal was investigated. It has been shown that the hard sphere nanolayers introduced into Yukawa crystals allow one to control the elastic properties of the system. It has been also found that the introduction of the Yukawa monolayers to the hard sphere crystal induces auxeticity in the [ 11 1 ¯ ] [ 112 ] -direction, while maintaining the negative Poisson’s ratio in the [ 110 ] [ 1 1 ¯ 0 ] -direction, thus expanding the partial auxeticity of the system to an additional important crystallographic direction.

Purification, crystallization and preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from Leptospira interrogans

Energy Technology Data Exchange (ETDEWEB)

Li, Xu; Huang, Hua [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Song, Xiaomin [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Wang, Yanli; Xu, Hang [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Teng, Maikun [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Gong, Weimin, E-mail: wgong@sun5.ibp.ac.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2006-12-01

Preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from L. interrogans. 2-Dehydro-3-deoxygalactarate (DDG) aldolase is a member of the class II aldolase family and plays an important role in the pyruvate-metabolism pathway, catalyzing the reversible aldol cleavage of DDG to pyruvate and tartronic semialdehyde. As it is a potential novel antibiotic target, it is necessary to elucidate the catalytic mechanism of DDG aldolase. To determine the crystal structure, crystals of DDG aldolase from Leptospira interrogans were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.2 Å resolution using a Cu Kα rotating-anode X-ray source. The crystal belonged to space group C2, with unit-cell parameters a = 293.5, b = 125.6, c = 87.6 Å, β = 100.9°. The V{sub M} is calculated to be 2.4 Å{sup 3} Da{sup −1}, assuming there to be 12 protein molecules in the asymmetric unit.

Purification, crystallization and preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from Leptospira interrogans

International Nuclear Information System (INIS)

Li, Xu; Huang, Hua; Song, Xiaomin; Wang, Yanli; Xu, Hang; Teng, Maikun; Gong, Weimin

2006-01-01

Preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from L. interrogans. 2-Dehydro-3-deoxygalactarate (DDG) aldolase is a member of the class II aldolase family and plays an important role in the pyruvate-metabolism pathway, catalyzing the reversible aldol cleavage of DDG to pyruvate and tartronic semialdehyde. As it is a potential novel antibiotic target, it is necessary to elucidate the catalytic mechanism of DDG aldolase. To determine the crystal structure, crystals of DDG aldolase from Leptospira interrogans were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.2 Å resolution using a Cu Kα rotating-anode X-ray source. The crystal belonged to space group C2, with unit-cell parameters a = 293.5, b = 125.6, c = 87.6 Å, β = 100.9°. The V M is calculated to be 2.4 Å 3 Da −1 , assuming there to be 12 protein molecules in the asymmetric unit

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

International Nuclear Information System (INIS)

Knight, Jennifer L.; Zhou, Zhiyong; Gallicchio, Emilio; Himmel, Daniel M.; Friesner, Richard A.; Arnold, Eddy; Levy, Ronald M.

2008-01-01

Torsion-angle sampling, as implemented in the Protein Local Optimization Program (PLOP), is used to generate multiple structurally variable single-conformer models which are in good agreement with X-ray data. An ensemble-refinement approach to differentiate between positional uncertainty and conformational heterogeneity is proposed. Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time-intensive nature of manual X-ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0–2.8 Å, it is demonstrated how torsion-angle sampling of backbone and side-chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal-space X-ray target function, can generate multiple structurally variable models which fit the X-ray data well. Torsion-angle sampling as implemented in the Protein Local Optimization Program (PLOP) has been used in this work. Models with the lowest R free values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV-1 protease, calmodulin and SUMO-conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates

Global crystallographic textures obtained by neutron and synchrotron radiation

International Nuclear Information System (INIS)

Brokmeier, Heinz-Guenter

2006-01-01

Global crystallographic textures belong to the main characteristic parameters of engineering materials. The global crystallographic texture is always the average texture of a well-defined sample volume which is representative to solve practical engineering problems. Thus a beam having a high penetration power is needed available as neutron or high energetic X-ray radiation. Texture type and texture sharpness are of great importance for materials properties such as the deep drawing behaviour, one of the basic techniques in many industries. Advantages and disadvantages of both radiations make them complementary for measuring crystallographic textures in a wide range of materials

Structure studies of macromolecular systems

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Dohnálek, Jan; Skálová, Tereza; Dušková, Jarmila; Kolenko, Petr

2006-01-01

Roč. 13, č. 3 (2006), s. 136 ISSN 1211-5894. [Czech and Slovak Crystallographic Colloquium. 22.06.2006-24.06.2006, Grenoble] R&D Projects: GA AV ČR IAA4050811; GA MŠk 1K05008 Keywords : structure * X-ray diffraction * synchrotron Subject RIV: CD - Macromolecular Chemistry http://www. xray .cz/ms/default.htm

A crystallographic and spectroscopic study of crystal sites in the 'spinel' structure; Etude cristallographique et spectroscopique des sites cristallins dans la structure 'spinelle'

Energy Technology Data Exchange (ETDEWEB)

Drifford, M [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1967-06-15

A crystallographic study on magnesium aluminates led to the determination of crystal site average distortion. A spectroscopic study of transition elements doped spinels gave the position of the doping element in tetrahedral (A) or octahedral (B) sites, and the local distortion of the latter. The comparison of average and local parameters points to differences in the behaviour of doping elements and shows the size of (A) sites are independent of the host crystal composition while the average size of (B) sites varies with the composition. (author) [French] Une etude cristallographique des aluminates de magnesium a permis de determiner la deformation moyenne des sites cristallins. Une etude spectroscopique des aluminates de magnesium dopes avec des elements de transition a permis de localiser les dopants entre les sites tetraedriques (A) et octaedriques (B) et d'etudier la deformation locale de ces sites. La comparaison entre les parametres moyens et locaux a caracterise le comportement du dopant et montre que les dimensions des sites (A) sont independantes de la composition de la matrice, alors que les caracteristiques geometriques moyennes des sites (B) varient continument avec la composition. (auteur)

Comparison of the free volume sizes and shapes determined from crystallographic and PALS data

Directory of Open Access Journals (Sweden)

Tydda Maciej

2015-12-01

Full Text Available Two different classes of molecular crystals were investigated. The first group was benzenediols, which are characterized by the same chemical composition but a different organization of their crystallographic structures; all of the compounds from this group have only one kind of free volumes. The second class was represented by olanzapine, which has more complex chemical composition and two kinds of free volumes in the structure. The o-Ps lifetime values determined from positron annihilation lifetime spectroscopy (PALS measurements agree quite well with those calculated for sizes found from crystallographic data for benzenediols (agreement within 10% of the lifetime values. For olanzapine, a good agreement is observed in the case of cuboidal free volumes, while for the other kind of void, the agreement is less satisfactory. Positronium diffusion coefficient determined from o-Ps redistribution in olanzapine agrees with these found for polymers.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

International Nuclear Information System (INIS)

Bennett, Joseph W.; Rabe, Karin M.

2012-01-01

In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb 1/2 Mn 1/2 )O 3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb 2 O 4 ; and (3) ferroelectric semiconductors with formula M 2 P 2 (S,Se) 6 . A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: ► Integration of first-principles methods and database mining. ► Minor structural families with desirable functional properties. ► Survey of polar entries in the Inorganic Crystal Structural Database.

Multi Scale Finite Element Analyses By Using SEM-EBSD Crystallographic Modeling and Parallel Computing

International Nuclear Information System (INIS)

Nakamachi, Eiji

2005-01-01

A crystallographic homogenization procedure is introduced to the conventional static-explicit and dynamic-explicit finite element formulation to develop a multi scale - double scale - analysis code to predict the plastic strain induced texture evolution, yield loci and formability of sheet metal. The double-scale structure consists of a crystal aggregation - micro-structure - and a macroscopic elastic plastic continuum. At first, we measure crystal morphologies by using SEM-EBSD apparatus, and define a unit cell of micro structure, which satisfy the periodicity condition in the real scale of polycrystal. Next, this crystallographic homogenization FE code is applied to 3N pure-iron and 'Benchmark' aluminum A6022 polycrystal sheets. It reveals that the initial crystal orientation distribution - the texture - affects very much to a plastic strain induced texture and anisotropic hardening evolutions and sheet deformation. Since, the multi-scale finite element analysis requires a large computation time, a parallel computing technique by using PC cluster is developed for a quick calculation. In this parallelization scheme, a dynamic workload balancing technique is introduced for quick and efficient calculations

A Journey into Reciprocal Space; A crystallographer's perspective

Science.gov (United States)

Glazer, A. M.

2017-10-01

This book introduces undergraduate and graduate students to a crystallographer's view of real and reciprocal space, a concept that has been of particular use by crystallographers to understand the patterns of spots when x-rays are diffracted by crystals. It then proceeds to develop the concept in a form suitable for physics applications; such as how solid-state physicists use reciprocal space to explain various solid-state properties such as thermal and electrical phenomena.

Crystallographic Analysis of Nucleation at Hardness Indentations in High-Purity Aluminum

DEFF Research Database (Denmark)

Xu, Chaoling; Zhang, Yubin; Lin, Fengxiang

2016-01-01

Nucleation at Vickers hardness indentations has been studied in high-purity aluminum cold-rolled 12 pct. Electron channeling contrast was used to measure the size of the indentations and to detect nuclei, while electron backscattering diffraction was used to determine crystallographic orientations....... It is found that indentations are preferential nucleation sites. The crystallographic orientations of the deformed grains affect the hardness and the nucleation potentials at the indentations. Higher hardness gives increased nucleation probabilities. Orientation relationships between nuclei developed...... they form. Finally, possible nucleation mechanisms are briefly discussed....

Experimental studies on the crystallographic and plastic anisotropies of zircaloy-4 tubes

International Nuclear Information System (INIS)

Costa Viana, C.S. da

1982-01-01

The crystallographic and plastic anisotropies of a zircaloy-4 tubing using direct pole figures and experimental yield loci are analyzed. Tensile and plane-strain compression tests were used to assess the mecahnical behaviour. The results are discussed with respect to the dimensional stability and mechanical behaviour expected for the tube in its use in the core of pressurized water cooled reactors. (Author) [pt

Tungsten heavy metal alloys relations between the crystallographic texture and the internal stress distribution

International Nuclear Information System (INIS)

Nicolas, G.; Voltz, M.

2001-01-01

Quite often the W-Ni-Fe-Co heavy alloys are subjected to a thermomechanical processing of swaging and aging in order to obtain the highest possible level of resistance. Within the framework of this plastic deformation on cylindrical parts, the swaging leads to the distribution of morphological and crystallographic texture as well as specific internal stresses. The resulting mechanical characteristics are correlated to structural and sub-structural variations. (author)

Crystallographic and infrared spectroscopic study of bond distances in Ln[Fe(CN)6].4H2O (Ln=lanthanide)

International Nuclear Information System (INIS)

Zhou Xianju; Wong, W.-T.; Faucher, Michele D.; Tanner, Peter A.

2008-01-01

Along with crystallographic data of Ln[Fe(CN) 6 ].4H 2 O (Ln=lanthanide), the infrared spectra are reassigned to examine bond length trends across the series of Ln. The changes in mean Ln-O, Ln-N, C≡N and Fe-C distances are discussed and the bond natures of Ln-N and Ln-O are studied by bond length linear or quadratic fitting and comparisons with relevant ionic radii. The two different C≡N bond distances have been simulated by the covalo-electrostatic model. - Graphical abstract: Crystallographic and FTIR data for Ln[Fe(CN) 6 ].4H 2 O enable the changes in Ln-O, Ln-N, C≡N and Fe-C distances to be determined and modeled across the lanthanide series

Dependence of Crystallographic Orientation on Pitting Corrosion Behavior of Ni-Fe-Cr Alloy 028

Science.gov (United States)

Zhang, LiNa; Szpunar, Jerzy A.; Dong, JianXin; Ojo, Olanrewaju A.; Wang, Xu

2018-03-01

The influence of crystallographic orientation on the pitting corrosion behavior of Ni-Fe-Cr alloy 028 was studied using a combination of X-ray diffraction (XRD), electron backscatter diffraction (EBSD), potentiodynamic polarization technique, and atomic force microscopy (AFM). The results show that there is anisotropy of pitting corrosion that strongly depends on crystallographic orientation of the surface plane. The distribution of pit density in a standard stereographic triangle indicates that the crystallographic planes close to {100} are more prone to pitting corrosion compared to planes {110} and {111}. The surface energy calculation of (001) and (111) shows that the plane with a high atomic packing density has a low surface energy with concomitant strong resistance to pitting corrosion. A correlation function between crystallographic orientation and pitting corrosion susceptibility suggests a method that not only predicts the pitting resistance of known textured materials, but also could help to improve corrosion resistance by controlling material texture.

A comparative crystallographic analysis of the tetragonal-to-monoclinic transformation in the yttria-zirconia system

Science.gov (United States)

Navruz, N.

2008-06-01

The various requirements for effective transformation toughening cannot be predicted without a detailed understanding of the crystallography of the martensitic transformation. In this connection, a comparative crystallographic analysis for four pairs of lattice-correspondence variants in the yttria-zirconia system has been performed on the basis of infinitesimal-deformation (ID) approach and Wechsler-Lieberman-Read (WLR) crystallographic theory. A comparison of the crystallographic features obtained from these two theories was made. In order to verify the applicability of the two theories to this transformation, the calculated results were also compared with the experimental data available. The present study shows that the predictions of both the ID approach and the WLR crystallographic theory can provide data necessary for the model of transformation toughening and act as a guideline for the experimental work in the yttria-zirconia system.

High resolution neutron diffraction crystallographic investigation of Oxide Dispersion Strengthened steels of interest for fusion technology

International Nuclear Information System (INIS)

Coppola, R.; Rodriguez-Carvajal, J.; Wang, M.; Zhang, G.; Zhou, Z.

2014-01-01

High resolution neutron diffraction measurements have been carried out to characterize the crystallographic phases present in different Oxide Dispersion Strengthened (ODS) steels of interest for fusion technology. The different lattice structures, Im3m for the ferritic ODS and Fm3m for the austenitic ODS, are resolved showing line anisotropy effects possibly correlated with differences in dislocation densities and texture. Many contributions from minority phases are detected well above the background noise; none of the expected crystallographic phases, such as M 23 C 6 and including Y 2 O 3 , fits them, but the TiN phase is identified in accordance with results of other microstructural techniques

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

Directory of Open Access Journals (Sweden)

Kun-Dar Li

2018-02-01

Full Text Available To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, and preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

Science.gov (United States)

Li, Kun-Dar; Miao, Jin-Ru

2018-02-01

To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, and preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

40-Godišnjica institucije Cambridge Crystallographic Data Centre posvećene pohranjivanju podataka o molekularnim i kristalnim strukturama -

Directory of Open Access Journals (Sweden)

Molčanov, K.

2006-06-01

Full Text Available The article is dedicated to 40th anniversary of The Cambridge Crystallographic Data Centre (CCDC, the world-known centre (http://www.ccdc.cam.ac.uk responsible for deposition and control of crystallographic data, including atomic coordinates that define the three-dimensional structures of organic molecules and metal complexes containing organic ligands. Cambride Structural Database (CSD, one among the first established electronic databases, nowadays is the most significant crystallographic database in the world. CSD has about 400,000 deposited structures. The use of the extensive database, which is growing rapidly, needs support of efficient and sophisticated software for searching, analysing and visualising structural data. The seminal role of CSD in the research related to crystallography, chemistry, material sciences, solid state physics and chemistry, life sciences, pharmacology, and in particular in drug design, has been documented in more than 1300 scientific papers. The important issues of CCDC are the accuracy of deposited data and development of software that enables a wide variety of applications. Such demanding project requires higly competent team of experts; thus the article brings into focus the scientific approach of the team based on the long tradition in crystallography, modelling and informatics. The article is not dedicated to 40th anniversary of the centre only, but it also reveals how Cambridge Structural Database can be used in the research and teaching. The use of electronic media and computer graphics makes “data mining" very efficient and useful but also esthetically appealing due to the molecular architecture. At the Rudjer Bošković Institute, Zagreb, Croatia there is The National Affiliated Centre of Cambridge Crystallographic Data Centre responsible for communication and dissemination of CSD in Croatia, Slovenia and Macedonia. The use of CSD is illustrated by two examples performed and published by the presenting

Crystallization and preliminary X-ray crystallographic studies of DnaJ from Streptococcus pneumoniae

International Nuclear Information System (INIS)

Zhao, Shasha; Jin, Li; Niu, Siqiang; Yang, Wei; Zhang, Shaocheng; Guo, Zhen; Zhang, Hongpeng; Huang, Ailong; Yin, Yibing; Wang, Deqiang

2013-01-01

DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported. DnaJ, cooperating with DnaK and GrpE, promotes the folding of unfolded hydrophobic polypeptides, dissociates protein complexes and translocates protein across membranes. Additionally, DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported. The crystals belong to space groups I222 or I2 1 2 1 2 1 and the diffraction resolution is 3.0 Å with unit-cell parameters a = 47.68, b = 104.45, c = 234.57 Å. The crystal most likely contains one molecule in the asymmetric unit, with a V M value of 3.24 Å 3 Da −1 and a solvent content of 62.1%

Magnetic anisotropy induced by crystallographic orientation and morphological alignment in directionally-solidified eutectic Mn-Sb alloy

Energy Technology Data Exchange (ETDEWEB)

Lou, Chang-Sheng [School of Materials Science and Engineering, Shenyang Ligong University, Shenyang 110159 (China); Key Laboratory of Electromagnetic Processing of Materials (Ministry of Education), Northeastern University, Shenyang 110819 (China); Liu, Tie, E-mail: liutie@epm.neu.edu.cn [Key Laboratory of Electromagnetic Processing of Materials (Ministry of Education), Northeastern University, Shenyang 110819 (China); Dong, Meng; Wu, Chun; Shao, Jian-Guo; Wang, Qiang [Key Laboratory of Electromagnetic Processing of Materials (Ministry of Education), Northeastern University, Shenyang 110819 (China)

2017-02-15

The influences of the crystallographic orientation and morphological alignment upon the magnetic anisotropic behavior of polycrystalline materials were investigated. Microstructures obtained in eutectic Mn-Sb alloys via directional solidification simultaneously displayed crystallographic orientation and morphological alignment. Both the crystallographic orientation and the morphological alignment were able to induce magnetic anisotropy in the alloys, wherein the influence of the crystallographic orientation and the morphological alignment upon the magnetic anisotropic behavior of the alloys strongly depended upon their directions and exhibited either mutual promotion or competition. These findings may provide useful guidance for the fabrication design of functional magnetic materials. - Highlights: • We study effects of orientation in crystal and morphology on magnetic anisotropy. • Both orientation in crystal and morphology can induce magnetic anisotropy. • Their effects depend on direction and exhibit either mutual promotion or competition.

Transuranic Hybrid Materials: Crystallographic and Computational Metrics of Supramolecular Assembly

Energy Technology Data Exchange (ETDEWEB)

Surbella, Robert G. [Department; Ducati, Lucas C. [Department; Pellegrini, Kristi L. [Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States; McNamara, Bruce K. [Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States; Autschbach, Jochen [Department; Schwantes, Jon M. [Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States; Cahill, Christopher L. [Department

2017-07-26

A family of twelve supramolecular [AnO2Cl4]2- (An = U, Np, Pu) containing compounds assembled via hydrogen and halogen bonds donated by substituted 4-X-pyridinium cations (X = H, Cl, Br, I) is reported. These materials were prepared from a room-temperature synthesis wherein crystallization of unhydrolyzed and valence pure [An(VI)O2Cl4]2- (An = U, Np, Pu) tectons are the norm. We present a hierarchy of assembly criteria based on crystallographic observations, and subsequently quantify the strengths of the non-covalent interactions using Kohn-Sham density functional calculations. We provide, for the first time, a detailed description of the electrostatic potentials (ESPs) of the actinyl tetrahalide dianions and reconcile crystallographically observed structural motifs and non-covalent interaction (NCI) acceptor-donor pairings. Our findings indicate that the average electrostatic potential across the halogen ligands (the acceptors) changes by only ~2 kJ mol-1 across the AnO22+ series, indicating the magnitude of the potential is independent of the metal center. The role of the cation is therefore critical in directing structural motifs and dictating the resulting hydrogen and halogen bond strengths, the former being stronger due to the positive charge centralized on the pyridyl nitrogen N-H+. Subsequent analyses using the Quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches support this conclusion and highlight the structure directing role of the cations. Whereas one can infer that the 2 Columbic attraction is the driver for assembly, the contribution of the non-covalent interaction is to direct the molecular-level arrangement (or disposition) of the tectons.

CRYSTMET—The NRCC Metals Crystallographic Data File

Science.gov (United States)

Wood, Gordon H.; Rodgers, John R.; Gough, S. Roger; Villars, Pierre

1996-01-01

CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool. PMID:27805157

Ocean acidification reduces the crystallographic control in juvenile mussel shells.

Science.gov (United States)

Fitzer, Susan C; Cusack, Maggie; Phoenix, Vernon R; Kamenos, Nicholas A

2014-10-01

Global climate change threatens the oceans as anthropogenic carbon dioxide causes ocean acidification and reduced carbonate saturation. Future projections indicate under saturation of aragonite, and potentially calcite, in the oceans by 2100. Calcifying organisms are those most at risk from such ocean acidification, as carbonate is vital in the biomineralisation of their calcium carbonate protective shells. This study highlights the importance of multi-generational studies to investigate how marine organisms can potentially adapt to future projected global climate change. Mytilus edulis is an economically important marine calcifier vulnerable to decreasing carbonate saturation as their shells comprise two calcium carbonate polymorphs: aragonite and calcite. M. edulis specimens were cultured under current and projected pCO2 (380, 550, 750 and 1000μatm), following 6months of experimental culture, adults produced second generation juvenile mussels. Juvenile mussel shells were examined for structural and crystallographic orientation of aragonite and calcite. At 1000μatm pCO2, juvenile mussels spawned and grown under this high pCO2 do not produce aragonite which is more vulnerable to carbonate under-saturation than calcite. Calcite and aragonite were produced at 380, 550 and 750μatm pCO2. Electron back scatter diffraction analyses reveal less constraint in crystallographic orientation with increased pCO2. Shell formation is maintained, although the nacre crystals appear corroded and crystals are not so closely layered together. The differences in ultrastructure and crystallography in shells formed by juveniles spawned from adults in high pCO2 conditions may prove instrumental in their ability to survive ocean acidification. Copyright © 2014 Elsevier Inc. All rights reserved.

Crystallographic deterioration of MOVPE InN during the growth

International Nuclear Information System (INIS)

Sugita, K.; Nagai, Y.; Houchin, Y.; Hashimoto, A.; Yamamoto, A.

2007-01-01

This paper reports the crystallographic degradation of MOVPE InN during the growth. Using FWHMs of X-ray rocking curve, tilt ((0002)) and twist ((10-10)) angle distributions are evaluated and effects of the major growth parameters, such as growth temperature, growth time and with/without GaN buffer in the degradation, are revealed. With increasing either thickness of grown InN or growth temperature up to 600 C, the tilt angle distribution is markedly increased, indicating the crystallographic degradation of grown films. The use of a GaN buffer reduces such degradation. Since the twist angle distribution is scarcely changed by such growth parameters, the destruction of InN crystals during growth and annealing is concluded to be anisotropic. The trends of the crystallographic degradation revealed here are in good agreement with those for the electrical and optical degradation previously reported. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Erbium-ion implantation into various crystallographic cuts of Al{sub 2}O{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Nekvindova, P. [Department of Inorganic Chemistry, Institute of Chemical Technology, Technicka 5, 166 28 Prague 6 (Czech Republic); Mackova, A.; Malinsky, P. [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic v.v.i., 250 68 Rez (Czech Republic); Department of Physics, Faculty of Science, J.E. Purkinje University, Ceske mladeze 8, 400 96 Usti nad Labem (Czech Republic); Cajzl, J.; Svecova, B. [Department of Inorganic Chemistry, Institute of Chemical Technology, Technicka 5, 166 28 Prague 6 (Czech Republic); Oswald, J. [Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnicka 10, 162 53 Prague (Czech Republic); Wilhelm, R.A. [Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden (Germany); Technische Universität Dresden, 01062 Dresden (Germany)

2015-12-15

This paper reports on the importance of crystallographic cuts with a different orientation on the luminescent properties and structural changes of Al{sub 2}O{sub 3} implanted with Er{sup +} ions at 190 keV and with a fluence of 1.0 × 10{sup 16} cm{sup −2}. Post-implantation annealing at 1000 °C in oxygen atmosphere was also done. The chemical compositions and erbium concentration-depth profiles of implanted layers were studied by Rutherford Backscattering Spectrometry (RBS) and compared to SRIM simulations. The same value of the maximum erbium concentration (up to 2 at.%) was observed at a depth of about 40 nm for all crystallographic cuts. The structural properties of the prepared layers were characterised by RBS/channelling. The relative amount of disordered atoms of 70–80% was observed in the prepared implanted layers and discussed for various cuts. It has been found that erbium is positioned randomly in the Al{sub 2}O{sub 3} crystalline matrix, and no preferential positions appeared even after the annealing procedure. Erbium luminescence properties were measured in the wavelength range of 1440–1650 nm for all samples. As-implanted Al{sub 2}O{sub 3} samples had a significant luminescence band at 1530 nm. The best luminescence was repeatedly observed in the 〈0 0 0 1〉 cut of Al{sub 2}O{sub 3}. The annealing procedure significantly improved the luminescent properties.

Contribution to the crystallographic study of the uranium-oxygenated system

International Nuclear Information System (INIS)

Perio, P.

1955-04-01

Three uranium oxides, UO 2 , U 3 O 8 and UO 3 are known since a long time. The existence of a fourth, U 2 O 5 , is discussed. The mechanisms of decomposition between UO 3 and U 3 O 8 have even some shadow zones. The aim of this report is the study of the phase relations in an uranium - oxygen system, from the metal until UO 3 . We considered, on the one hand, the equilibrium relations, what should result in a diagram of phases in pressures and temperatures, on the other hand, the transformations bringing one oxide to the other, often by a continuous way and through intermediate of metastable phases. The introduction of the temperature and the consideration of the kinetics effects have permitted to raise the ambiguities. We adopted, to facilitate the presentation of the results, a partition a few arbitrary but convenient, in three chapters,: I - experimental Techniques II - Crystallographic species between U and UO 3 . III - Kinetic of oxidisation of UO 2 . (M.B.) [fr

Synthesis of Cu and Ce co-doped ZnO nanoparticles: crystallographic, optical, molecular, morphological and magnetic studies

Directory of Open Access Journals (Sweden)

Rawat Mohit

2017-07-01

Full Text Available In the present research work, crystallographic, optical, molecular, morphological and magnetic properties of Zn1-xCuxO (ZnCu and Zn1-x-yCeyCuxO (ZnCeCu nanoparticles have been investigated. Polyvinyl alcohol (PVA coated ZnCu and ZnCeCu nanoparticles have been synthesized by chemical sol-gel method and thoroughly studied using various characterization techniques. X-ray diffraction pattern indicates the wurtzite structure of the synthesized ZnCu and ZnCeCu particles. Transmission electron microscopy analysis shows that the synthesized ZnCu and ZnCeCu particles are of spherical shape, having average sizes of 27 nm and 23 nm, respectively. The incorporation of Cu and Ce in the ZnO lattice has been confirmed through Fourier transform infrared spectroscopy. Room temperature photoluminescence spectra of the ZnO doped with Cu and co-doped Ce display two emission bands, predominant ultra-violet near-band edge emission at 409.9 nm (3 eV and a weak green-yellow emission at 432.65 nm (2.27 eV. Room temperature magnetic study confirms the diamagnetic behavior of ZnCu and ferromagnetic behavior of ZnCeCu.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

OpenAIRE

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a prot...

Initial crystallographic studies of a small heat-shock protein from Xylella fastidiosa

International Nuclear Information System (INIS)

Tada, Susely F. S.; Saraiva, Antonio Marcos; Lorite, Gabriela S.; Rosselli-Murai, Luciana K.; Pelloso, Alexandre César; Santos, Marcelo Leite dos; Trivella, Daniela B. B.; Cotta, Mônica A.; Souza, Anete Pereira de; Aparicio, Ricardo

2012-01-01

Initial crystallographic studies of the X. fastidiosa small heat-shock protein HSP17.9 are reported. The ORF XF2234 in the Xylella fastidiosa genome was identified as encoding a small heat-shock protein of 17.9 kDa (HSP17.9). HSP17.9 was found as one of the proteins that are induced during X. fastidiosa proliferation and infection in citrus culture. Recombinant HSP17.9 was crystallized and surface atomic force microscopy experiments were conducted with the aim of better characterizing the HSP17.9 crystals. X-ray diffraction data were collected at 2.7 Å resolution. The crystal belonged to space group P4 3 22, with unit-cell parameters a = 68.90, b = 68.90, c = 72.51 Å, and is the first small heat-shock protein to crystallize in this space group

A crystallographic and spectroscopic study of crystal sites in the 'spinel' structure; Etude cristallographique et spectroscopique des sites cristallins dans la structure 'spinelle'

Energy Technology Data Exchange (ETDEWEB)

Drifford, M. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1967-06-15

A crystallographic study on magnesium aluminates led to the determination of crystal site average distortion. A spectroscopic study of transition elements doped spinels gave the position of the doping element in tetrahedral (A) or octahedral (B) sites, and the local distortion of the latter. The comparison of average and local parameters points to differences in the behaviour of doping elements and shows the size of (A) sites are independent of the host crystal composition while the average size of (B) sites varies with the composition. (author) [French] Une etude cristallographique des aluminates de magnesium a permis de determiner la deformation moyenne des sites cristallins. Une etude spectroscopique des aluminates de magnesium dopes avec des elements de transition a permis de localiser les dopants entre les sites tetraedriques (A) et octaedriques (B) et d'etudier la deformation locale de ces sites. La comparaison entre les parametres moyens et locaux a caracterise le comportement du dopant et montre que les dimensions des sites (A) sont independantes de la composition de la matrice, alors que les caracteristiques geometriques moyennes des sites (B) varient continument avec la composition. (auteur)

Crystallographic Structure Analysis of a Ti-Ta Thin Film Materials Library Fabricated by Combinatorial Magnetron Sputtering.

Science.gov (United States)

Kadletz, Peter M; Motemani, Yahya; Iannotta, Joy; Salomon, Steffen; Khare, Chinmay; Grossmann, Lukas; Maier, Hans Jürgen; Ludwig, Alfred; Schmahl, Wolfgang W

2018-03-12

Ti-Ta thin films exhibit properties that are of interest for applications as microactuators and as biomedical implants. A Ti-Ta thin film materials library was deposited at T = 25 °C by magnetron sputtering employing the combinatorial approach, which led to a compositional range of Ti 87 Ta 13 to Ti 14 Ta 86 . Subsequent high-throughput characterization methods permitted a quick and comprehensive study of the crystallographic, microstructural, and morphological properties, which strongly depend on the chemical composition. SEM investigation revealed a columnar morphology having pyramidal, sharp tips with coarser columns in the Ti-rich and finer columns in the Ta-rich region. By grazing incidence X-ray diffraction four phases were identified, from Ta-lean to Ta-rich: ω phase, α″ martensite, β phase, and a tetragonal Ta-rich phase (Ta (tetr) ). The crystal structure and microstructure were analyzed by Rietveld refinement and clear trends could be determined as a function of Ta-content. The lattice correspondences between β as the parent phase and α″ and ω as derivative phases were expressed in matrix form. The β ⇌ α″ phase transition shows a discontinuity at the composition where the martensitic transformation temperatures fall below room temperature (between 34 and 38 at. % Ta) rendering it first order and confirming its martensitic nature. A short study of the α″ martensite employing the Landau theory is included for a mathematical quantification of the spontaneous lattice strain at room temperature (ϵ̂ max = 22.4(6) % for pure Ti). Martensitic properties of Ti-Ta are beneficial for the development of high-temperature actuators with actuation response at transformation temperatures higher than 100 °C.

Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

Science.gov (United States)

Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

2016-01-01

Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

Busting out of crystallography's Sisyphean prison: from pencil and paper to structure solving at the press of a button: past, present and future of crystallographic software development, maintenance and distribution.

Science.gov (United States)

Cranswick, Lachlan Michael David

2008-01-01

The history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. In practice, this involves practising crystallographers communicating their thoughts to the crystallographic program authors, in the hope that new procedures will be implemented within their software. Against this background, the development of small-molecule single-crystal and powder diffraction software is traced. Starting with the analogue machines and the use of Hollerith tabulators of the late 1930's, it is shown that computing developments have been science led, with new technologies being harnessed to solve pressing crystallographic problems. The development of software is also traced, with a final caution that few of the computations now performed daily are really understood by the program users. Unless a sufficient body of people continues to dismantle and re-build programs, the knowledge encoded in the old programs will become as inaccessible as the knowledge of how to build the Great Pyramid at Giza.

Can Morphing Methods Predict Intermediate Structures?

Science.gov (United States)

Weiss, Dahlia R.; Levitt, Michael

2009-01-01

Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods. PMID:18996395

Study of the crystallographic phase change on copper (I) selenide thin films prepared through chemical bath deposition by varying the pH of the solution

Energy Technology Data Exchange (ETDEWEB)

Sandoval-Paz, M.G., E-mail: myrnasandoval@udec.cl [Departament of Physics, Faculty of Physical Sciences and Mathematics, University of Concepcion, Box 160-C, Concepción (Chile); Rodríguez, C.A. [Department of Materials Engineering, Faculty of Engineering, University of Concepción, Edmundo Larenas 270, Concepción 4070409 (Chile); Porcile-Saavedra, P.F. [Departament of Physics, Faculty of Physical Sciences and Mathematics, University of Concepcion, Box 160-C, Concepción (Chile); Trejo-Cruz, C. [Department of Physics, Faculty of Science, University of Biobío, Avenue Collao 1202, Box 5C, Concepción 4051381 (Chile)

2016-07-15

Copper (I) selenide thin films with orthorhombic and cubic structure were deposited on glass substrates by using the chemical bath deposition technique. The effects of the solution pH on the films growth and subsequently the structural, optical and electrical properties of the films were studied. Films with orthorhombic structure were obtained from baths wherein both metal complex and hydroxide coexist; while films with cubic structure were obtained from baths where the metal hydroxide there is no present. The structural modifications are accompanied by changes in bandgap energy, morphology and electrical resistivity of the films. - Graphical abstract: “Study of the crystallographic phase change on copper (I) selenide thin films prepared through chemical bath deposition by varying the pH of the solution” by M. G. Sandoval-Paz, C. A. Rodríguez, P. F. Porcile-Saavedra, C. Trejo-Cruz. Display Omitted - Highlights: • Copper (I) selenide thin films were obtained by chemical bath deposition. • Orthorhombic to cubic phase change was induced by varying the reaction solution pH. • Orthorhombic phase is obtained mainly from a hydroxides cluster mechanism. • Cubic phase is obtained mainly from an ion by ion mechanism. • Structural, optical and electrical properties are presented as a function of pH.

The crystallographic information file (CIF): A new standard archive file for crystallography

International Nuclear Information System (INIS)

Hall, S.R.; Allen, F.H.; Brown, I.D.

1991-01-01

The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archieve and Retrieval (STAR) procedure. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: It has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF dictionary (core version 1991). The CIF core dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the dictionary will include data items used in more specialized areas of crystallography. (orig.)

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

Science.gov (United States)

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

Science.gov (United States)

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Crystallographic tilt and in-plane anisotropies of an a-plane InGaN/GaN layered structure grown by MOCVD on r-plane sapphire using a ZnO buffer

International Nuclear Information System (INIS)

Liu, H F; Chi, D Z; Liu, W; Guo, S

2016-01-01

High-resolution x-ray diffraction (HRXRD) was used to investigate the crystallographic tilts and structural anisotropies in epitaxial nonpolar a-plane InGaN/GaN grown by metal–organic chemical vapor deposition on r-plane sapphire using a ZnO buffer. The substrate had an unintentional miscut of 0.14° towards its [–4 2 2 3] axis. However, HRXRD revealed a tilt of 0.26° (0.20°) between the ZnO (GaN) (11-20) and the Al 2 O 3 (1-102) atomic planes, with the (11-20) axis of ZnO (GaN) tilted towards its c-axis, which has a difference of 163° in azimuth from that of the substrate’s miscut. Excess broadenings in the GaN/ZnO (11-20) rocking curves (RCs) were observed along its c-axis. Specific analyses revealed that partial dislocations and anisotropic in-plane strains, rather than surface-related effects, wafer curvature or stacking faults, are the dominant factors for the structural anisotropy. The orientation of the partial dislocations is most likely affected by the miscut of the substrate, e.g. via tilting of the misfit dislocation gliding planes created during island coalescences. Their Burgers vector components in the growth direction, in turn, gave rise to crystallographic tilts in the same direction as that of the excess RC-broadenings. (paper)

Crystallographic tilt and in-plane anisotropies of an a-plane InGaN/GaN layered structure grown by MOCVD on r-plane sapphire using a ZnO buffer

Science.gov (United States)

Liu, H. F.; Liu, W.; Guo, S.; Chi, D. Z.

2016-03-01

High-resolution x-ray diffraction (HRXRD) was used to investigate the crystallographic tilts and structural anisotropies in epitaxial nonpolar a-plane InGaN/GaN grown by metal-organic chemical vapor deposition on r-plane sapphire using a ZnO buffer. The substrate had an unintentional miscut of 0.14° towards its [-4 2 2 3] axis. However, HRXRD revealed a tilt of 0.26° (0.20°) between the ZnO (GaN) (11-20) and the Al2O3 (1-102) atomic planes, with the (11-20) axis of ZnO (GaN) tilted towards its c-axis, which has a difference of 163° in azimuth from that of the substrate’s miscut. Excess broadenings in the GaN/ZnO (11-20) rocking curves (RCs) were observed along its c-axis. Specific analyses revealed that partial dislocations and anisotropic in-plane strains, rather than surface-related effects, wafer curvature or stacking faults, are the dominant factors for the structural anisotropy. The orientation of the partial dislocations is most likely affected by the miscut of the substrate, e.g. via tilting of the misfit dislocation gliding planes created during island coalescences. Their Burgers vector components in the growth direction, in turn, gave rise to crystallographic tilts in the same direction as that of the excess RC-broadenings.

Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility

Energy Technology Data Exchange (ETDEWEB)

Serer, María I.; Bonomi, Hernán R. [IIBBA–CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires (Argentina); Guimarães, Beatriz G. [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX (France); Rossi, Rolando C. [Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires (Argentina); Goldbaum, Fernando A.; Klinke, Sebastián, E-mail: sklinke@leloir.org.ar [IIBBA–CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires (Argentina)

2014-05-01

This work reports crystal structures of trimeric riboflavin synthase from the pathogen B. abortus both as the apo protein and in complex with several ligands of interest. It is shown that ligand binding drives the assembly of the unique active site of the trimer, and these findings are complemented by a detailed kinetic study on this enzyme, in which marked inhibition by substrate and product was observed. Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one molecule of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Owing to the absence of this enzyme in animals and the fact that most pathogenic bacteria show a strict dependence on riboflavin biosynthesis, RS has been proposed as a potential target for antimicrobial drug development. Eubacterial, fungal and plant RSs assemble as homotrimers lacking C{sub 3} symmetry. Each monomer can bind two substrate molecules, yet there is only one active site for the whole enzyme, which is located at the interface between two neighbouring chains. This work reports the crystallographic structure of RS from the pathogenic bacterium Brucella abortus (the aetiological agent of the disease brucellosis) in its apo form, in complex with riboflavin and in complex with two different product analogues, being the first time that the structure of an intact RS trimer with bound ligands has been solved. These crystal models support the hypothesis of enhanced flexibility in the particle and also highlight the role of the ligands in assembling the unique active site. Kinetic and binding studies were also performed to complement these findings. The structural and biochemical information generated may be useful for the rational design of novel RS inhibitors with antimicrobial activity.

Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility

International Nuclear Information System (INIS)

Serer, María I.; Bonomi, Hernán R.; Guimarães, Beatriz G.; Rossi, Rolando C.; Goldbaum, Fernando A.; Klinke, Sebastián

2014-01-01

This work reports crystal structures of trimeric riboflavin synthase from the pathogen B. abortus both as the apo protein and in complex with several ligands of interest. It is shown that ligand binding drives the assembly of the unique active site of the trimer, and these findings are complemented by a detailed kinetic study on this enzyme, in which marked inhibition by substrate and product was observed. Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one molecule of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Owing to the absence of this enzyme in animals and the fact that most pathogenic bacteria show a strict dependence on riboflavin biosynthesis, RS has been proposed as a potential target for antimicrobial drug development. Eubacterial, fungal and plant RSs assemble as homotrimers lacking C 3 symmetry. Each monomer can bind two substrate molecules, yet there is only one active site for the whole enzyme, which is located at the interface between two neighbouring chains. This work reports the crystallographic structure of RS from the pathogenic bacterium Brucella abortus (the aetiological agent of the disease brucellosis) in its apo form, in complex with riboflavin and in complex with two different product analogues, being the first time that the structure of an intact RS trimer with bound ligands has been solved. These crystal models support the hypothesis of enhanced flexibility in the particle and also highlight the role of the ligands in assembling the unique active site. Kinetic and binding studies were also performed to complement these findings. The structural and biochemical information generated may be useful for the rational design of novel RS inhibitors with antimicrobial activity

Microstructure, crystallographic texture and mechanical properties of friction stir welded AA2017A

Energy Technology Data Exchange (ETDEWEB)

Ahmed, M.M.Z., E-mail: mohamed_ahmed4@s-petrol.suez.edu.eg [Institute for Microstructural and Mechanical Processing Engineering, University of Sheffield (IMMPETUS), Mappin Street, Sheffield S1 3JD (United Kingdom); Department of Metallurgical and Materials Engineering, Suez Canal University, Suez 43721 (Egypt); Wynne, B.P.; Rainforth, W.M. [Institute for Microstructural and Mechanical Processing Engineering, University of Sheffield (IMMPETUS), Mappin Street, Sheffield S1 3JD (United Kingdom); Threadgill, P.L. [TWI LTD, Granta Park, Great Abington, Cambridge CB21 6AL (United Kingdom)

2012-02-15

In this study a thick section (20 mm) friction stir welded AA2017A-T451 has been characterized in terms of microstructure, crystallographic texture and mechanical properties. For microstructural analysis both optical and scanning electron microscopes have been used. A detailed crystallographic texture analysis has been carried out using the electron back scattering diffraction technique. Crystallographic texture has been examined in both shoulder and probe affected regions of the weld NG. An entirely weak texture is observed at the shoulder affected region which is mainly explained by the effect of the sequential multi pass deformation experienced by both tool probe and tool shoulder. The texture in the probe dominated region at the AS side of the weld is relatively weak but still assembles the simple shear texture of FCC metals with B/B{sup Macron} and C components existing across the whole map. However, the texture is stronger at the RS than at the AS of the weld, mainly dominated byB/B{sup Macron} components and with C component almost absent across the map. An alternating bands between (B) components and (B{sup Macron }) component are observed only at the AS side of the weld. - Highlights: Black-Right-Pointing-Pointer Detailed investigation of microstructure and crystallographic texture. Black-Right-Pointing-Pointer The grain size is varied from the top to the bottom of the NG. Black-Right-Pointing-Pointer An entirely weak texture is observed at the shoulder affected region. Black-Right-Pointing-Pointer The texture in the probe affected region is dominated by simple shear texture.

Crystallographic parameters of magnetic Pr{sub 2}Fe{sub 14−x}Co{sub x}B-type alloys determined using anomalous x-ray diffraction with synchrotron radiation

Energy Technology Data Exchange (ETDEWEB)

Galego, E., E-mail: egalego@ipen.br; Serna, M.M.; Ramanathan, L.V.; Faria, R.N.

2017-02-15

Anomalous x-ray synchrotron diffraction was used to determine the crystallographic parameters of PrFeCoB-based magnetic alloys. The effect of cobalt concentration on the crystallographic parameters of the magnetically hard Pr{sub 2}Fe{sub 14−x}Co{sub x}B phase was studied. The results indicate that addition of cobalt has a marked effect on crystal structure. Variation of the c parameter decreased twice as much as the a parameter with increase in Co content. The positions of inequivalent atoms of the magnetically hard matrix phase ϕ in the Pr-based alloys were determined using Rietveld refinement. This permitted determination of the relative distance of each inequivalent atom from its nearest neighbors. Cobalt occupied the 16k{sub 2} site and Fe had a tendency to occupy the 8j{sub 2} sites located between the Kagomé layers. - Highlights: • Good magnetics properties can be achieved with addition of 4% and 8% Co. • Rietveld refinement is proposed for crystallographic parameters studies. • Co has preference to substitute Fe in 16k{sub 2} site and avoid the 8j{sub 2} site.

Crystallographic orientations in one-directional gray cast solidification

International Nuclear Information System (INIS)

Roviglione, A.; Hermida, J.D.

1991-01-01

The aim of this work is to determine the crystallographic orientations of austenite and the A laminar graphite and the compact, in one-directionally grown samples to decide upon the validity of the mentioned theory. (Author) [es

Algebraic K-theory of crystallographic groups the three-dimensional splitting case

CERN Document Server

Farley, Daniel Scott

2014-01-01

The Farrell-Jones isomorphism conjecture in algebraic K-theory offers a description of the algebraic K-theory of a group using a generalized homology theory. In cases where the conjecture is known to be a theorem, it gives a powerful method for computing the lower algebraic K-theory of a group. This book contains a computation of the lower algebraic K-theory of the split three-dimensional crystallographic groups, a geometrically important class of three-dimensional crystallographic group, representing a third of the total number. The book leads the reader through all aspects of the calculation. The first chapters describe the split crystallographic groups and their classifying spaces. Later chapters assemble the techniques that are needed to apply the isomorphism theorem. The result is a useful starting point for researchers who are interested in the computational side of the Farrell-Jones isomorphism conjecture, and a contribution to the growing literature in the field.

Study of the Adsorption of Atoms and Molecules on Silicon Surfaces: Crystallographics and Electronic Structure

International Nuclear Information System (INIS)

Bengio, Silvina

2003-01-01

This thesis work has been concerned with adsorption properties of silicon surfaces.The atomic and electronic structure of molecules and atoms adsorbed on Si has been investigated by means of photoemission experiments combined with synchrotron radiation.The quantitative atomic structure determination was held applying the photoelectron diffraction technique.This technique is sensible to the local structure of a reference atomic specie and has elemental and chemical-state specificity.This approach has been applied to three quite different systems with different degrees of complexity, Sb/Si(111) √3x √3R30 0 , H 2 O/Si(100)2x1 and NH 3 /Si(111)7x7.Our results show that Sb which forms a ( √3√3)R30 0 phase produces a bulklike-terminated Si(111)1x1 substrate free of stacking faults.Regarding the atomic structure of its interface, this study strongly favours the T4-site milkstool model over the H3 one.An important aspect regarding the H 2 O/Si(100)(2x1) system was establishing the limits of precision with which one can determine not only the location of the adsorbed hydroxyl (OH) species, but also the extent to which this adsorption modifes the asymmetric dimers of the clean surface to which it is bonded.On the Si(111)(7x7) surface the problem is particularly complex because there are several different potentially active sites for NH3 adsorption and fragmentation.The application of the PhD method, however, has shown that the majority of the N atoms are on so-called 'rest atom' sites when deposited at RT.This is consistent with the N in the NH2 chemical state.This investigation represents the first quantitative structural study of any molecular adsorbate on the complex Si(111)(7x7) surface.This atomic structures determination shows the PhD is a powerful tool for the atomic structure determination.The molecular systems interacting with the active sites of the substrate fragments producing a short-range order surface.This long-range disorder is produced by the

A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere.

Science.gov (United States)

Rutenber, E E; McPhee, F; Kaplan, A P; Gallion, S L; Hogan, J C; Craik, C S; Stroud, R M

1996-09-01

The essential role of HIV-1 protease (HIV-1 PR) in the viral life cycle makes it an attractive target for the development of substrate-based inhibitors that may find efficacy as anti-AIDS drugs. However, resistance has arisen to potent peptidomimetic drugs necessitating the further development of novel chemical backbones for diversity based chemistry focused on probing the active site for inhibitor interactions and binding modes that evade protease resistance. AQ148 is a potent inhibitor of HIV-1 PR and represents a new class of transition state analogues incorporating an aminimide peptide isostere. A 3-D crystallographic structure of AQ148, a tetrapeptide isostere, has been determined in complex with its target HIV-1 PR to a resolution of 2.5 A and used to evaluate the specific structural determinants of AQ148 potency and to correlate structure-activity relationships within the class of related compounds. AQ148 is a competitive inhibitor of HIV-1 PR with a Ki value of 137 nM. Twenty-nine derivatives have been synthesized and chemical modifications have been made at the P1, P2, P1', and P2' sites. The atomic resolution structure of AQ148 bound to HIV-1 PR reveals both an inhibitor binding mode that closely resembles that of other peptidomimetic inhibitors and specific protein/inhibitor interactions that correlate with structure-activity relationships. The structure provides the basis for the design, synthesis and evaluation of the next generation of hydroxyethyl aminimide inhibitors. The aminimide peptide isostere is a scaffold with favorable biological properties well suited to both the combinatorial methods of peptidomimesis and the rational design of potent and specific substrate-based analogues.

Monte-Carlo simulation of crystallographical pore growth in III-V-semiconductors

International Nuclear Information System (INIS)

Leisner, Malte; Carstensen, Juergen; Foell, Helmut

2011-01-01

The growth of crystallographical pores in III-V-semiconductors can be understood in the framework of a simple model, which is based on the assumption that the branching of pores is proportional to the current density at the pore tips. The stochastic nature of this model allows its implementation into a three-dimensional Monte-Carlo-simulation of pore growth. The simulation is able to reproduce the experimentally observed crysto pore structures in III-V-semiconductors in full quantitative detail. The different branching probabilities for different semiconductors, as well as doping levels, can be deduced from the specific passivation behavior of the semiconductor-electrolyte-interface at the pore tips.

Crystallographic information of intermediate phases in binary Mg–X (X=Sn, Y, Sc, Ag alloys

Directory of Open Access Journals (Sweden)

Dongyan Liu

2015-09-01

Full Text Available The compositions and structures of thermodynamically stable or metastable precipitations in binary Mg-X (X=Sn, Y, Sc, Ag alloys are predicted using ab-initio evolutionary algorithm. The geometry optimizations of the predicted intermetallic compounds are carried out in the framework of density functional theory (DFT [1]. A complete list of the optimized crystallographic information (in cif format of the predicted intermetallic phases is presented here. The data is related to “Predictions on the compositions, structures, and mechanical properties of intermediate phases in binary Mg–X (X=Sn, Y, Sc, Ag alloys” by Liu et al. [2].

CRYSNET manual. Informal report. [Hardware and software of crystallographic computing network

Energy Technology Data Exchange (ETDEWEB)

None,

1976-07-01

This manual describes the hardware and software which together make up the crystallographic computing network (CRYSNET). The manual is intended as a users' guide and also provides general information for persons without any experience with the system. CRYSNET is a network of intelligent remote graphics terminals that are used to communicate with the CDC Cyber 70/76 computing system at the Brookhaven National Laboratory (BNL) Central Scientific Computing Facility. Terminals are in active use by four research groups in the field of crystallography. A protein data bank has been established at BNL to store in machine-readable form atomic coordinates and other crystallographic data for macromolecules. The bank currently includes data for more than 20 proteins. This structural information can be accessed at BNL directly by the CRYSNET graphics terminals. More than two years of experience has been accumulated with CRYSNET. During this period, it has been demonstrated that the terminals, which provide access to a large, fast third-generation computer, plus stand-alone interactive graphics capability, are useful for computations in crystallography, and in a variety of other applications as well. The terminal hardware, the actual operations of the terminals, and the operations of the BNL Central Facility are described in some detail, and documentation of the terminal and central-site software is given. (RWR)

Direct electron crystallographic determination of zeolite zonal structures

International Nuclear Information System (INIS)

Dorset, Douglas L.; Gilmore, Christopher J.; Jorda, Jose Luis; Nicolopoulos, Stavros

2007-01-01

The prospect for improving the success of ab initio zeolite structure investigations with electron diffraction data is evaluated. First of all, the quality of intensities obtained by precession electron diffraction at small hollow cone illumination angles is evaluated for seven representative materials: ITQ-1, ITQ-7, ITQ-29, ZSM-5, ZSM-10, mordenite, and MCM-68. It is clear that, for most examples, an appreciable fraction of a secondary scattering perturbation is removed by precession at small angles. In one case, ZSM-10, it can also be argued that precession diffraction produces a dramatically improved 'kinematical' data set. There seems to no real support for application of a Lorentz correction to these data and there is no reason to expect for any of these samples that a two-beam dynamical scattering relationship between structure factor amplitude and observed intensity should be valid. Removal of secondary scattering by the precession mode appears to facilitate ab initio structure analysis. Most zeolite structures investigated could be solved by maximum entropy and likelihood phasing via error-correcting codes when precession data were used. Examples include the projected structure of mordenite that could not be determined from selected area data alone. One anomaly is the case of ZSM-5, where the best structure determination in projection is made from selected area diffraction data. In a control study, the zonal structure of SSZ-48 could be determined from selected area diffraction data by either maximum entropy and likelihood or traditional direct methods. While the maximum entropy and likelihood approach enjoys some advantages over traditional direct methods (non-dependence on predicted phase invariant sums), some effort must be made to improve the figures of merit used to identify potential structure solutions

Effect of pre-existing crystallographic preferred orientation on the rheology of Carrara marble

NARCIS (Netherlands)

de Raadt, W.S.; Burlini, L.; Kunze, K.; Spiers, C.J.

2014-01-01

Abstract Localized deformation during high temperature plastic flow is frequently attributed to mechanical weakening caused by grain size reduction and, in some cases, by the development of a crystallographic preferred orientation (CPO). This study aims to investigate experimentally the contribution

Identification of some crystallographic features of martensite in steels by microdiffraction

International Nuclear Information System (INIS)

Sarikaya, M.; Rao, B.V.N.; Thomas, G.

1980-03-01

Considerable attention should be paid to the interpretation of electron diffraction, such as the understanding of the extra reflections and other effects in an SAD pattern obtained from lath martensite by making allowances for spatial resolution limitations in the SAD patterns. These difficulties can be overcome by utilizing the convergent beam electron diffraction (CBED) method which permits the use of different probe sizes to obtain crystallographic information from very small regions. Some crystallographic features of lath martensite in low and medium C steels have been identified and some others verified by using CBED

Crystallographic data processing for free-electron laser sources

International Nuclear Information System (INIS)

White, Thomas A.; Barty, Anton; Stellato, Francesco; Holton, James M.; Kirian, Richard A.; Zatsepin, Nadia A.; Chapman, Henry N.

2013-01-01

A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam

Crystallographic data processing for free-electron laser sources

Energy Technology Data Exchange (ETDEWEB)

White, Thomas A., E-mail: taw@physics.org; Barty, Anton; Stellato, Francesco [DESY, Notkestrasse 85, 22607 Hamburg (Germany); Holton, James M. [University of California, San Francisco, CA 94158 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Kirian, Richard A. [DESY, Notkestrasse 85, 22607 Hamburg (Germany); Arizona State University, Tempe, AZ 85287 (United States); Zatsepin, Nadia A. [Arizona State University, Tempe, AZ 85287 (United States); Chapman, Henry N. [DESY, Notkestrasse 85, 22607 Hamburg (Germany); University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)

2013-07-01

A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.

Crystallographic Structure of Human β-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of GM2 Ganglioside Hydrolysis

Science.gov (United States)

Lemieux, M. Joanne; Mark, Brian L.; Cherney, Maia M.; Withers, Stephen G.; Mahuran, Don J.; James, Michael N. G.

2010-01-01

Lysosomal β-hexosaminidase A (Hex A) is essential for the degradation of GM2 gangliosides in the central and peripheral nervous system. Accumulation of GM2 leads to severely debilitating neurodegeneration associated with Tay-Sachs disease (TSD), Sandoff disease (SD) and AB variant. Here, we present the X-ray crystallographic structure of Hex A to 2.8 Å resolution and the structure of Hex A in complex with NAG-thiazoline, (NGT) to 3.25 Å resolution. NGT, a mechanism-based inhibitor, has been shown to act as a chemical chaperone that, to some extent, prevents misfolding of a Hex A mutant associated with adult onset Tay Sachs disease and, as a result, increases the residual activity of Hex A to a level above the critical threshold for disease. The crystal structure of Hex A reveals an αβ heterodimer, with each subunit having a functional active site. Only the α-subunit active site can hydrolyze GM2 gangliosides due to a flexible loop structure that is removed post-translationally from β, and to the presence of αAsn423 and αArg424. The loop structure is involved in binding the GM2 activator protein, while αArg424 is critical for binding the carboxylate group of the N-acetyl-neuraminic acid residue of GM2. The β-subunit lacks these key residues and has βAsp452 and βLeu453 in their place; the β-subunit therefore cleaves only neutral substrates efficiently. Mutations in the α-subunit, associated with TSD, and those in the β-subunit, associated with SD are discussed. The effect of NGT binding in the active site of a mutant Hex A and its effect on protein function is discussed. PMID:16698036

Crystallographic dependent in-situ CBr4 selective nano-area etching and local regrowth of InP/InGaAs by MOVPE

DEFF Research Database (Denmark)

Kuznetsova, Nadezda; Kulkova, Irina; Semenova, Elizaveta

2014-01-01

Selective area etching and growth in the metalorganic vapor phase epitaxy (MOVPE) reactor on nano-scale structures have been examined. Using different mask orientations, crystallographic dependent etching of InP can be observed when carbon tetrabromide (CBr4) is used as an etchant. Scanning...

Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

Science.gov (United States)

Silva, J. M.; Baêta Júnior, E. S.; Moraes, N. R. D. C.; Botelho, R. A.; Felix, R. A. C.; Brandao, L.

2017-01-01

The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes.

Effect of crystallographic texture on the bulk magnetic properties of non-oriented electrical steels

Energy Technology Data Exchange (ETDEWEB)

Ghosh, Pampa, E-mail: pampaghosh@gmail.com [Department of Mining and Materials Engineering, McGill University, 3610 University Street, Montreal, Quebec, Canada H3A 0C5 (Canada); Chromik, Richard R., E-mail: richard.chromik@mcgill.ca [Department of Mining and Materials Engineering, McGill University, 3610 University Street, Montreal, Quebec, Canada H3A 0C5 (Canada); Vashegi, Babak; Knight, Andrew M. [Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2V4 (Canada)

2014-09-01

Quantitative physical models for non-oriented electrical steels require precise knowledge of chemical and microstructural parameters for the material, with crystallographic texture being one of the most important. Describing the structure–property relationships in these materials is made difficult in that all of the parameters have an effect on magnetic properties. In the present study, a set of non-oriented electrical steel specimens are examined, where chemistry and grain size are kept similar from sample to sample, but texture is varied. A new texture parameter called Magnetic Texture Factor is introduced which is defined as the ratio of the volume fractions of 〈100〉 direction to 〈111〉 direction along magnetization vector. It was found that this Magnetic Texture Factor was a better parameter for identifying trends of magnetic properties with crystallographic texture than the often used Texture Factor, which is described as the ratio of the volume fractions of {100} planes to {111} planes. - Highlights: • Magnetic properties of a set of electrical steels were measured. • The effect of crystallographic texture was isolated from other material parameters. • A new texture factor is introduced called the Magnetic Texture Factor.

Preliminary X-ray crystallographic analysis of the d-xylulose 5-phosphate phosphoketolase from Lactococcus lactis

International Nuclear Information System (INIS)

Petrareanu, Georgiana; Balasu, Mihaela C.; Zander, Ulrich; Scheidig, Axel J.; Szedlacsek, Stefan E.

2010-01-01

The expression, purification, preliminary crystallization and crystallographic analysis of phosphoketolase from L. lactis ssp. lactis (strain IL 1403) are reported. Phosphoketolases are thiamine diphosphate-dependent enzymes which play a central role in the pentose-phosphate pathway of heterofermentative lactic acid bacteria. They belong to the family of aldehyde-lyases and in the presence of phosphate ion cleave the carbon–carbon bond of the specific substrate d-xylulose 5-phosphate (or d-fructose 6-phosphate) to give acetyl phosphate and d-glyceraldehyde 3-phosphate (or d-erythrose 4-phosphate). Structural information about phosphoketolases is particularly important in order to fully understand their mechanism as well as the steric course of phosphoketolase-catalyzed reactions. Here, the purification, preliminary crystallization and crystallographic characterization of d-xylulose 5-phosphate phosphoketolase from Lactococcus lactis are reported. The presence of thiamine diphosphate during purification was essential for the enzymatic activity of the purified protein. The crystals belonged to the monoclinic space group P2 1 . Diffraction data were obtained to a resolution of 2.2 Å

Crystallographic study of grain refinement in aluminum alloys using the edge-to-edge matching model

International Nuclear Information System (INIS)

Zhang, M.-X.; Kelly, P.M.; Easton, M.A.; Taylor, J.A.

2005-01-01

The edge-to-edge matching model for describing the interfacial crystallographic characteristics between two phases that are related by reproducible orientation relationships has been applied to the typical grain refiners in aluminum alloys. Excellent atomic matching between Al 3 Ti nucleating substrates, known to be effective nucleation sites for primary Al, and the Al matrix in both close packed directions and close packed planes containing these directions have been identified. The crystallographic features of the grain refiner and the Al matrix are very consistent with the edge-to-edge matching model. For three other typical grain refiners for Al alloys, TiC (when a = 0.4328 nm), TiB 2 and AlB 2 , the matching only occurs between the close packed directions in both phases and between the second close packed plane of the Al matrix and the second close packed plane of the refiners. According to the model, it is predicted that Al 3 Ti is a more powerful nucleating substrate for Al alloy than TiC, TiB 2 and AlB 2 . This agrees with the previous experimental results. The present work shows that the edge-to-edge matching model has the potential to be a powerful tool in discovering new and more powerful grain refiners for Al alloys

Expression, purification and preliminary crystallographic analysis of sucrose phosphate synthase (SPS) from Halothermothrix orenii

International Nuclear Information System (INIS)

Huynh, Frederick; Tan, Tien-Chye; Swaminathan, Kunchithapadam; Patel, Bharat K. C.

2004-01-01

The first crystallographic study of a sucrose phosphate synthase from H. orenii, an organism that is both thermophilic and halophilic, is reported. The protein crystal diffracts X-rays to 3.01 Å. This is the first report of the crystallization of a sucrose phosphate synthase (SPS; EC 2.4.1.14). It also constitutes the first study of a sucrose phosphate synthase from a non-photosynthetic thermohalophilic anaerobic bacterium, Halothermothrix orenii. The purified recombinant spsA protein has been crystallized in the monoclinic space group C2, with unit-cell parameters a = 154.2, b = 47.9, c = 72.3 Å, β = 103.16°, using the hanging-drop vapour-diffusion method. The crystal diffracts X-rays to a resolution limit of 3.01 Å. Heavy-metal and halide-soaking trials are currently in progress to solve the structure

X-Ray powder diffractometry, crystallographic phase analysis and ...

African Journals Online (AJOL)

Computerized X-Ray diffraction system has been used to determine the composition and lattice parameters of raw and activated kaolinite. The universal diffractometry URD 63 was interfaced with computer via an APX 63 software package for rapid capturing of data on reflected intensity and other crystallographic ...

Study on the crystallographic orientation relationship and formation mechanism of reversed austenite in economical Cr12 super martensitic stainless steel

International Nuclear Information System (INIS)

Ye, Dong; Li, Shaohong; Li, Jun; Jiang, Wen; Su, Jie; Zhao, Kunyu

2015-01-01

Effect of carbides and crystallographic orientation relationship on the formation mechanism of reversed austenite of economical Cr12 super martensitic stainless steel (SMSS) has been investigated mainly by transmission electron microscopy (TEM) and electron backscatter diffraction (EBSD). The results indicate that the M_2_3C_6 precipitation and the formation of the reversed austenite have the interaction effect during tempering process in SMSS. The reversed austenite forms intensively at the sub-block boundary and the lath boundary within a misorientation range of 0–60°. M_2_3C_6 has the same crystallographic orientation relationship with reversed austenite. There are two different kinds of formation modes for reversed austenite. One is a nondiffusional shear reversion; the other is a diffusion transformation. Both are strictly limited by crystallographic orientation relationship. The austenite variants are limited to two kinds within one packet and five kinds within one prior austenite grain. - Highlights: • Reversed austenite forms at martensite boundaries with misorientation of 0–60° • M_2_3C_6 precipitation and reversed austenite formation have the interaction effect. • Two austenite variants with different orientations can be formed inside a packet. • Two reversed austenite formation modes: shear reversion; diffusion transformation

Study on the crystallographic orientation relationship and formation mechanism of reversed austenite in economical Cr12 super martensitic stainless steel

Energy Technology Data Exchange (ETDEWEB)

Ye, Dong; Li, Shaohong; Li, Jun; Jiang, Wen [Faculty of Materials Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China); Su, Jie [Institute for Structural Materials, Central Iron and Steel Research Institute, Beijing 100081 (China); Zhao, Kunyu, E-mail: kyzhaoy@sina.com [Faculty of Materials Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China)

2015-11-15

Effect of carbides and crystallographic orientation relationship on the formation mechanism of reversed austenite of economical Cr12 super martensitic stainless steel (SMSS) has been investigated mainly by transmission electron microscopy (TEM) and electron backscatter diffraction (EBSD). The results indicate that the M{sub 23}C{sub 6} precipitation and the formation of the reversed austenite have the interaction effect during tempering process in SMSS. The reversed austenite forms intensively at the sub-block boundary and the lath boundary within a misorientation range of 0–60°. M{sub 23}C{sub 6} has the same crystallographic orientation relationship with reversed austenite. There are two different kinds of formation modes for reversed austenite. One is a nondiffusional shear reversion; the other is a diffusion transformation. Both are strictly limited by crystallographic orientation relationship. The austenite variants are limited to two kinds within one packet and five kinds within one prior austenite grain. - Highlights: • Reversed austenite forms at martensite boundaries with misorientation of 0–60° • M{sub 23}C{sub 6} precipitation and reversed austenite formation have the interaction effect. • Two austenite variants with different orientations can be formed inside a packet. • Two reversed austenite formation modes: shear reversion; diffusion transformation.

An alternative to the crystallographic reconstruction of austenite in steels

International Nuclear Information System (INIS)

Bernier, Nicolas; Bracke, Lieven; Malet, Loïc; Godet, Stéphane

2014-01-01

An alternative crystallographic austenite reconstruction programme written in Matlab is developed by combining the best features of the existing models: the orientation relationship refinement, the local pixel-by-pixel analysis and the nuclei identification and spreading strategy. This programme can be directly applied to experimental electron backscatter diffraction mappings. Its applicability is demonstrated on both quenching and partitioning and as-quenched lath-martensite steels. - Highlights: • An alternative crystallographic austenite reconstruction program is developed. • The method combines a local analysis and a nuclei identification/spreading strategy. • The validity of the calculated orientation relationship is verified on a Q and P steel. • The accuracy of the reconstructed microtexture is investigated on a martensite steel

The effect of silicon crystallographic orientation on the formation of silicon nanoclusters during anodic electrochemical etching

International Nuclear Information System (INIS)

Timokhov, D. F.; Timokhov, F. P.

2009-01-01

Possible ways for increasing the photoluminescence quantum yield of porous silicon layers have been investigated. The effect of the anodization parameters on the photoluminescence properties for porous silicon layers formed on silicon substrates with different crystallographic orientations was studied. The average diameters for silicon nanoclusters are calculated from the photoluminescence spectra of porous silicon. The influence of the substrate crystallographic orientation on the photoluminescence quantum yield of porous silicon is revealed. A model explaining the effect of the substrate orientation on the photoluminescence properties for the porous silicon layers formed by anode electrochemical etching is proposed.

Calibration of reconstruction parameters in atom probe tomography using a single crystallographic orientation

International Nuclear Information System (INIS)

Suram, Santosh K.; Rajan, Krishna

2013-01-01

The purpose of this work is to develop a methodology to estimate the APT reconstruction parameters when limited crystallographic information is available. Reliable spatial scaling of APT data currently requires identification of multiple crystallographic poles from the field desorption image for estimating the reconstruction parameters. This requirement limits the capacity of accurately reconstructing APT data for certain complex systems, such as highly alloyed systems and nanostructured materials wherein more than one pole is usually not observed within one grain. To overcome this limitation, we develop a quantitative methodology for calibrating the reconstruction parameters in an APT dataset by ensuring accurate inter-planar spacing and optimizing the curvature correction for the atomic planes corresponding to a single crystallographic orientation. We validate our approach on an aluminum dataset and further illustrate its capabilities by computing geometric reconstruction parameters for W and Al–Mg–Sc datasets. - Highlights: ► Quantitative approach is developed to accurately reconstruct APT data. ► Curvature of atomic planes in APT data is used to calibrate the reconstruction. ► APT reconstruction parameters are determined from a single crystallographic axis. ► Quantitative approach is demonstrated on W, Al and Al–Mg–Sc systems. ► Accurate APT reconstruction of complex materials is now possible

Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases.

Science.gov (United States)

McGregor, Nicholas; Yin, Victor; Tung, Ching-Chieh; Van Petegem, Filip; Brumer, Harry

2017-02-01

The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Structural and Functional Studies of A. oryzae Cutinase: Enhanced Thermostability and Hydrolytic Activity of Synthetic Ester and Polyester Degradation

OpenAIRE

Liu, Zhiqiang; Gosser, Yuying; Baker, Peter James; Ravee, Yaniv; Lu, Ziying; Alemu, Girum; Li, Huiguang; Butterfoss, Glenn L.; Kong, Xiang-Peng; Gross, Richard; Montclare, Jin Kim

2009-01-01

Cutinases are responsible for hydrolysis of the protective cutin lipid polyester matrix in plants and thus have been exploited for hydrolysis of small molecule esters and polyesters. Here we explore the reactivity, stability, and structure of Aspergillus oryzae cutinase and compare it to the well-studied enzyme from Fusarium solani. Two critical differences are highlighted in the crystallographic analysis of the A. oryzae structure: (i) an additional disulfide bond and (ii) a topologically fa...

Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

International Nuclear Information System (INIS)

Wikman, Linnea E. K.; Krasotkina, Julya; Kuchumova, Anastasia; Sokolov, Nikolay N.; Papageorgiou, Anastassios C.

2005-01-01

Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2 1 , with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity at physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml −1 purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2 1 space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment

Crystallographic texture control helps improve pipeline steel resistance to hydrogen-induced cracking

Energy Technology Data Exchange (ETDEWEB)

Caleyo, F; Hallen, J M; Herrera, O; Venegas, V [ESIQIE, Instituto Politecnico Nacional, Mexico, (Mexico); Baudin, T [Universite de Paris Sud, Orsay, (France)

2010-07-01

The resistance to HIC of sour service pipeline steels has been improved through several strategies but none have proven to be totally efficient in the preservation of HIC in difficult operating conditions. The crystallographic texture plays a significant role in determining the behavior of HIC in pipeline steels. The present study tried to prove that crystallographic texture control, through warm rolling schedules, helps improve pipeline steel resistance to HIC. Several samples of an API 5L X52 grade pipeline steel were produced using different thermomechanical processes (austenization, controlled rolling and recrystallization). These samples were subjected to cathodic charging. Scanning electron microscopy and automated FEG/EBSD were used to perform metallographic inspections and to collect microstructure data. The results showed that the strong y fiber texture significantly reduces or even prevents the HIC damage. It is possible to improve the HIC resistance of pipeline steels using crystallography texture control and grain boundary engineering.

Overexpression, purification, crystallization and preliminary crystallographic studies of a hyperthermophilic adenylosuccinate synthetase from Pyrococcus horikoshii OT3

International Nuclear Information System (INIS)

Wang, Xiaoying; Akasaka, Ryogo; Takemoto, Chie; Morita, Satoshi; Yamaguchi, Machiko; Terada, Takaho; Shirozu, Mikako; Yokoyama, Shigeyuki; Chen, Shilin; Si, Shuyi; Xie, Yong

2011-01-01

A hyperthermophilic adenylosuccinate synthetase from P. horikoshii OT3, which is 90–120 amino acids shorter than those from the vast majority of organisms, was expressed, purified and crystallized and X-ray diffraction data were collected to 2.5 Å resolution. Adenylosuccinate synthetase (AdSS) is a ubiquitous enzyme that catalyzes the first committed step in the conversion of inosine monophosphate (IMP) to adenosine monophosphate (AMP) in the purine-biosynthetic pathway. Although AdSS from the vast majority of organisms is 430–457 amino acids in length, AdSS sequences isolated from thermophilic archaea are 90–120 amino acids shorter. In this study, crystallographic studies of a short AdSS sequence from Pyrococcus horikoshii OT3 (PhAdSS) were performed in order to reveal the unusual structure of AdSS from thermophilic archaea. Crystals of PhAdSS were obtained by the microbatch-under-oil method and X-ray diffraction data were collected to 2.50 Å resolution. The crystal belonged to the trigonal space group P3 2 12, with unit-cell parameters a = b = 57.2, c = 107.9 Å. There was one molecule per asymmetric unit, giving a Matthews coefficient of 2.17 Å 3 Da −1 and an approximate solvent content of 43%. In contrast, the results of native polyacrylamide gel electrophoresis and analytical ultracentrifugation showed that the recombinant PhAdSS formed a dimer in solution

On the retrieval of crystallographic information from atom probe microscopy data via signal mapping from the detector coordinate space.

Science.gov (United States)

Wallace, Nathan D; Ceguerra, Anna V; Breen, Andrew J; Ringer, Simon P

2018-06-01

Atom probe tomography is a powerful microscopy technique capable of reconstructing the 3D position and chemical identity of millions of atoms within engineering materials, at the atomic level. Crystallographic information contained within the data is particularly valuable for the purposes of reconstruction calibration and grain boundary analysis. Typically, analysing this data is a manual, time-consuming and error prone process. In many cases, the crystallographic signal is so weak that it is difficult to detect at all. In this study, a new automated signal processing methodology is demonstrated. We use the affine properties of the detector coordinate space, or the 'detector stack', as the basis for our calculations. The methodological framework and the visualisation tools are shown to be superior to the standard method of crystallographic pole visualisation directly from field evaporation images and there is no requirement for iterations between a full real-space initial tomographic reconstruction and the detector stack. The mapping approaches are demonstrated for aluminium, tungsten, magnesium and molybdenum. Implications for reconstruction calibration, accuracy of crystallographic measurements, reliability and repeatability are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Crystallographic Analysis and Structural Revision of a ...

African Journals Online (AJOL)

ABSTRACT. Single crystal X-ray analysis of a spiroterpenoid rearrangement product has revealed that its structure is, in fact, isomeric with the structure proposed previously – an observation that has significant mechanistic implications. KEYWORDS. Spiroterpenoid, rearrangement, X-ray crystallography, camphor derivative.

Crystallographic Analysis and Structural Revision of a ...

African Journals Online (AJOL)

Single crystal X-ray analysis of a spiroterpenoid rearrangement product has revealed that its structure is, in fact, isomeric with the structure proposed previously – an observation that has significant mechanistic implications. Keywords: Spiroterpenoid, rearrangement, X-ray crystallography, camphor derivative.

Reactivity of 12-tungstophosphoric acid and its inhibitor potency toward Na+/K+-ATPase: A combined 31P NMR study, ab initio calculations and crystallographic analysis.

Science.gov (United States)

Bošnjaković-Pavlović, Nada; Bajuk-Bogdanović, Danica; Zakrzewska, Joanna; Yan, Zeyin; Holclajtner-Antunović, Ivanka; Gillet, Jean-Michel; Spasojević-de Biré, Anne

2017-11-01

Influence of 12-tungstophosphoric acid (WPA) on conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) in the presence of Na + /K + -ATPase was monitored by 31 P NMR spectroscopy. It was shown that WPA exhibits inhibitory effect on Na + /K + -ATPase activity. In order to study WPA reactivity and intermolecular interactions between WPA oxygen atoms and different proton donor types (D=O, N, C), we have considered data for WPA based compounds from the Cambridge Structural Database (CSD), the Crystallographic Open Database (COD) and the Inorganic Crystal Structure Database (ICSD). Binding properties of Keggin's anion in biological systems are illustrated using Protein Data Bank (PDB). This work constitutes the first determination of theoretical Bader charges on polyoxotungstate compound via the Atom In Molecule theory. An analysis of electrostatic potential maps at the molecular surface and charge of WPA, resulting from DFT calculations, suggests that the preferred protonation site corresponds to WPA bridging oxygen. These results enlightened WPA chemical reactivity and its potential biological applications such as the inhibition of the ATPase activity. Copyright © 2017 Elsevier Inc. All rights reserved.

CRYSTALLOGRAPHIC RELATIONS OF CEMENTITE–AUSTENITE–FERRITE IN THE DIFFUSIVE DECOMPOSITION OF AUSTENITE

Directory of Open Access Journals (Sweden)

BOLSHAKOV V. I.

2016-05-01

Full Text Available Summary. It was made a search for new and more accurate orientation relations between the crystal lattice in the pearlite and bainite austenite decomposition products. Methods. It were used the methods: transmission electron microscopy, the micro-, mathematical matrix and stereographic analysis. The purpose of the research is with theoretical, numerical and experimental methods to set up to a 0.2 degree angular orientation relations between the lattices of ferrite and cementite in the austenite decomposition products in the temperature range 400 ... 700С. Results. It was established a new, refined value for grids in the diffusion decay of γ → α + (α + θ. Practical significance. It was proposed a new oriented dependence and the corresponding double gnomonic projection with poles to planes α and θ phases, which can be used in patterns of crystallographic lattices relations studies at phase transitions, as well as the subsequent modeling of complex physical processes of structure formation in metals and binary systems.

Structural studies of {delta}-endotoxin Cry 1 C from Bacillus thuringiensis

Energy Technology Data Exchange (ETDEWEB)

Guimaraes, B.G.; Garratt, R.C.; Oliva, G. [Sao Paulo Univ., Sao Carlos, SP (Brazil). Inst. de Fisica; Lemos, M.V.F. [UNESP, Jaboticabal, SP (Brazil). Dept. de Biologia Aplicada Agropecuaria; Arantes, O.M.N. [Universidade Estadual de Londrina, PR (Brazil). Dept. de Biologia Geral

1996-12-31

Full text. The {delta}-endotoxins are a family of crystal protein by a soil bacterium, Bacillus thuringiensis. The study of these proteins has been of great interest due to their highly specific activity against insects of the orders Lepidoptera, Diptera and Coleoptera. Thus, the {delta}a-endotoxins have been used for more than two decades as biological insecticides to control agricultural pests and, more recently, insects vectors of some diseases. The knowledge of their three-dimensional structures is very important to understand their mechanism of action and their high specificity. To date, the structure of only three proteins of the {delta}-endotoxins family have been reported: Cry3A, a coleopteran-specific toxin (beetle toxin){sup 1}, Cry1Aa, a lepidopteran-specific toxin (butterfly toxin){sup 2} and CytB, a dipteran-specific toxin (mosquito toxin){sup 3} Our work is aimed at the determination of the crystallographic structure by X-ray diffraction of {delta}-endotoxin Cry1C, also toxic to insects of the Lepidoptera order but towards families other than those affected by Cry1Aa. A comparison between these structures may lead to important conclusions about the reasons for the specificity and would allow the planning of mutants with more efficient activity. The cry1C gene was cloned into an adequate vector and expressed in an acrystalliferous B. thuringiensis strain. After cell culture and sporulation the microcrystals of Cry1C were separated by ultra-centrifugation in sacharose. The protoxin inclusion bodies were activated by commercial trpsin and the protease-resistant core was purified by anion-exchange chromatography. Crystallization experiments are being conducted in order to obtain single crystals suitable for diffraction measurements. We intend to use the Protein Crystallograph Station of the LNLS to collect data as soon as it is available and we have suitable crystals. (author) 3 refs.

Structural studies of δ-endotoxin Cry 1 C from Bacillus thuringiensis

International Nuclear Information System (INIS)

Guimaraes, B.G.; Garratt, R.C.; Oliva, G.; Lemos, M.V.F.; Arantes, O.M.N.

1996-01-01

Full text. The δ-endotoxins are a family of crystal protein by a soil bacterium, Bacillus thuringiensis. The study of these proteins has been of great interest due to their highly specific activity against insects of the orders Lepidoptera, Diptera and Coleoptera. Thus, the δa-endotoxins have been used for more than two decades as biological insecticides to control agricultural pests and, more recently, insects vectors of some diseases. The knowledge of their three-dimensional structures is very important to understand their mechanism of action and their high specificity. To date, the structure of only three proteins of the δ-endotoxins family have been reported: Cry3A, a coleopteran-specific toxin (beetle toxin) 1 , Cry1Aa, a lepidopteran-specific toxin (butterfly toxin) 2 and CytB, a dipteran-specific toxin (mosquito toxin) 3 Our work is aimed at the determination of the crystallographic structure by X-ray diffraction of δ-endotoxin Cry1C, also toxic to insects of the Lepidoptera order but towards families other than those affected by Cry1Aa. A comparison between these structures may lead to important conclusions about the reasons for the specificity and would allow the planning of mutants with more efficient activity. The cry1C gene was cloned into an adequate vector and expressed in an acrystalliferous B. thuringiensis strain. After cell culture and sporulation the microcrystals of Cry1C were separated by ultra-centrifugation in sacharose. The protoxin inclusion bodies were activated by commercial trpsin and the protease-resistant core was purified by anion-exchange chromatography. Crystallization experiments are being conducted in order to obtain single crystals suitable for diffraction measurements. We intend to use the Protein Crystallograph Station of the LNLS to collect data as soon as it is available and we have suitable crystals. (author)

Crystallographic, microstructure and mechanical characteristics of dynamically processed IN718 superalloy

Energy Technology Data Exchange (ETDEWEB)

Sharma, A.D., E-mail: ads.hpu@gmail.com [Department of Physics, Himachal Pradesh University, Shimla 171005 (India); Sharma, A.K. [Terminal Ballistics Research Laboratory, Chandigarh 160030 (India); Thakur, N. [Department of Physics, Himachal Pradesh University, Shimla 171005 (India)

2014-06-01

Highlights: • Measurement of detonation velocity and compaction of powder are achieved together. • A plastic explosive detonation results into dense compacts without grain-growth. • We have studied crystallographic, micromechanical and microstructural features. • The results show no segregation within the compacts. • Density (98%), microhardness (470 ± 3)H{sub v}, microstrain (0.3%), UTS (806 MPa) are obtained. - Abstract: Dynamic consolidation of IN718 superalloy powder without grain-growth and negligible density gradient is accomplished through explosively generated shock wave loading. The compaction of powder and measurement of detonation velocity are achieved successfully in a single-shot experiment by employing instrumented detonics. A plastic explosive having a detonation velocity of the order of 7.1 km/s in a direct proximity with superalloy powder is used for the consolidation process. The compacted specimens are examined for structural, microstructure and mechanical characteristics. X-ray diffraction (XRD) study suggests intact crystalline structure of the compacts. A small micro-strain (0.26%) is observed by using Williamson–Hall method. Wavelength dispersive spectroscopy indicates no segregation within the shock processed superalloy compacted specimens. The monoliths investigated for fractography by using field emission scanning electron microscopy (FE-SEM) show original dendritic structure accompanied by re-solidified molten regions across the interparticle boundaries. Depth-sensing indentations (at 1.96 N) on compacted specimens show excellent micro-hardness of the order of (470 ± 3)H{sub v}. Tensile and compressive strengths of the superalloy monolith are observed to be 806 and 822 MPa, respectively.

Synthetical bone-like and biological hydroxyapatites: a comparative study of crystal structure and morphology

Energy Technology Data Exchange (ETDEWEB)

Markovic, Smilja; Veselinovic, Ljiljana; Lukic, Miodrag J; Ignjatovic, Nenad; Uskokovic, Dragan [Institute of Technical Sciences of the Serbian Academy of Sciences and Arts, Knez Mihailova 35/IV, 11001 Belgrade (Serbia); Karanovic, Ljiljana [Laboratory for Crystallography, Faculty of Mining and Geology, University of Belgrade, Dusina 7, 11000 Belgrade (Serbia); Bracko, Ines, E-mail: dragan.uskokovic@itn.sanu.ac.rs [Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia)

2011-08-15

Phase composition, crystal structure and morphology of biological hydroxyapatite (BHAp) extracted from human mandible bone, and carbonated hydroxyapatite (CHAp), synthesized by the chemical precipitation method, were studied by x-ray powder diffraction (XRD), Fourier transform infrared (FTIR) and Raman (R) spectroscopy techniques, combined with transmission electron microscopy (TEM). Structural and microstructural parameters were determined through Rietveld refinement of recorded XRD data, performed using the FullProf computing program, and TEM. Microstructural analysis shows anisotropic extension along the [0 0 l] crystallographic direction (i.e. elongated crystallites shape) of both investigated samples. The average crystallite sizes of 10 and 8 nm were estimated for BHAp and CHAp, respectively. The FTIR and R spectroscopy studies show that carbonate ions substitute both phosphate and hydroxyl ions in the crystal structure of BHAp as well as in CHAp, indicating that both of them are mixed AB-type of CHAp. The thermal behaviour and carbonate content were analysed using thermogravimetric and differential thermal analysis. The carbonate content of about 1 wt.% and phase transition, at near 790 {sup 0}C, from HAp to {beta}-tricalcium phosphate were determined in both samples. The quality of synthesized CHAp powder, particularly, the particle size distribution and uniformity of morphology, was analysed by a particle size analyser based on laser diffraction and field emission scanning electron microscopy, respectively. These data were used to discuss similarity between natural and synthetic CHAp. Good correlation between the unit cell parameters, average crystallite size, morphology, carbonate content and crystallographic positions of carbonate ions in natural and synthetic HAp samples was found.

Synthetical bone-like and biological hydroxyapatites: a comparative study of crystal structure and morphology

International Nuclear Information System (INIS)

Markovic, Smilja; Veselinovic, Ljiljana; Lukic, Miodrag J; Ignjatovic, Nenad; Uskokovic, Dragan; Karanovic, Ljiljana; Bracko, Ines

2011-01-01

Phase composition, crystal structure and morphology of biological hydroxyapatite (BHAp) extracted from human mandible bone, and carbonated hydroxyapatite (CHAp), synthesized by the chemical precipitation method, were studied by x-ray powder diffraction (XRD), Fourier transform infrared (FTIR) and Raman (R) spectroscopy techniques, combined with transmission electron microscopy (TEM). Structural and microstructural parameters were determined through Rietveld refinement of recorded XRD data, performed using the FullProf computing program, and TEM. Microstructural analysis shows anisotropic extension along the [0 0 l] crystallographic direction (i.e. elongated crystallites shape) of both investigated samples. The average crystallite sizes of 10 and 8 nm were estimated for BHAp and CHAp, respectively. The FTIR and R spectroscopy studies show that carbonate ions substitute both phosphate and hydroxyl ions in the crystal structure of BHAp as well as in CHAp, indicating that both of them are mixed AB-type of CHAp. The thermal behaviour and carbonate content were analysed using thermogravimetric and differential thermal analysis. The carbonate content of about 1 wt.% and phase transition, at near 790 0 C, from HAp to β-tricalcium phosphate were determined in both samples. The quality of synthesized CHAp powder, particularly, the particle size distribution and uniformity of morphology, was analysed by a particle size analyser based on laser diffraction and field emission scanning electron microscopy, respectively. These data were used to discuss similarity between natural and synthetic CHAp. Good correlation between the unit cell parameters, average crystallite size, morphology, carbonate content and crystallographic positions of carbonate ions in natural and synthetic HAp samples was found.

Purification, crystallization and preliminary crystallographic analysis of human cystathionine β-synthase

International Nuclear Information System (INIS)

Oyenarte, Iker; Majtan, Tomas; Ereño, June; Corral-Rodríguez, María Angeles; Kraus, Jan P.; Martínez-Cruz, Luis Alfonso

2012-01-01

This article describes the crystallization and preliminary crystallographic analysis of a protein construct (hCBS 516–525 ) that contains the full-length cystathionine β-synthase from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525. Human cystathionine β-synthase (CBS) is a pyridoxal-5′-phosphate-dependent hemeprotein, whose catalytic activity is regulated by S-adenosylmethionine. CBS catalyzes the β-replacement reaction of homocysteine (Hcy) with serine to yield cystathionine. CBS is a key regulator of plasma levels of the thrombogenic Hcy and deficiency in CBS is the single most common cause of homocystinuria, an inherited metabolic disorder of sulfur amino acids. The properties of CBS enzymes, such as domain organization, oligomerization degree or regulatory mechanisms, are not conserved across the eukaryotes. The current body of knowledge is insufficient to understand these differences and their impact on CBS function and physiology. To overcome this deficiency, we have addressed the crystallization and preliminary crystallographic analysis of a protein construct (hCBS 516–525 ) that contains the full-length CBS from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525, which are located in a disordered loop. The human enzyme yielded crystals belonging to space group I222, with unit-cell parameters a = 124.98, b = 136.33, c = 169.83 Å and diffracting X-rays to a resolution of 3.0 Å. The crystal structure appears to contain two molecules in the asymmetric unit which presumably correspond to a dimeric form of the enzyme

Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

Energy Technology Data Exchange (ETDEWEB)

Wikman, Linnea E. K. [Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521 (Finland); Krasotkina, Julya; Kuchumova, Anastasia; Sokolov, Nikolay N. [Institute for Biomedical Chemistry, Russian Academy of Medical Sciences, 559-B, 10 Pogodinskay St, Moscow 119121 (Russian Federation); Papageorgiou, Anastassios C., E-mail: tassos.papageorgiou@btk.fi [Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521 (Finland)

2005-04-01

Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2{sub 1}, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity at physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2{sub 1} space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment.

Crystallographically-based analysis of the NMR spectra of maghemite

International Nuclear Information System (INIS)

Spiers, K.M.; Cashion, J.D.

2012-01-01

All possible iron environments with respect to nearest neighbour vacancies in vacancy-ordered and vacancy-disordered maghemite have been evaluated and used as the foundation for a crystallographically-based analysis of the published NMR spectra of maghemite. The spectral components have been assigned to particular configurations and excellent agreement obtained in comparing predicted spectra with published spectra taken in applied magnetic fields. The broadness of the published NMR lines has been explained by calculations of the magnetic dipole fields at the various iron sites and consideration of the supertransferred hyperfine fields. - Highlights: ► Analysis of 57 Fe NMR of maghemite based on vacancy ordering and nearest neighbour vacancies. ► Assignment of NMR spectral components based on crystallographic analysis of unique iron sites. ► Strong agreement between predicted spectra and published spectra taken in applied magnetic fields. ► Maghemite NMR spectral broadening due to various iron sites and supertransferred hyperfine field.

Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening.

Science.gov (United States)

Amano, Yasushi; Tanabe, Eiki; Yamaguchi, Tomohiko

2015-05-15

Soluble epoxide hydrolase (sEH) is a potential target for the treatment of inflammation and hypertension. X-ray crystallographic fragment screening was used to identify fragment hits and their binding modes. Eight fragment hits were identified via soaking of sEH crystals with fragment cocktails, and the co-crystal structures of these hits were determined via individual soaking. Based on the binding mode, N-ethylmethylamine was identified as a promising scaffold that forms hydrogen bonds with the catalytic residues of sEH, Asp335, Tyr383, and Tyr466. Compounds containing this scaffold were selected from an in-house chemical library and assayed. Although the starting fragment had a weak inhibitory activity (IC50: 800μM), we identified potent inhibitors including 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol exhibiting the highest inhibitory activity (IC50: 0.51μM). This corresponded to a more than 1500-fold increase in inhibitory activity compared to the starting fragment. Co-crystal structures of the hit compounds demonstrate that the binding of N-ethylmethylamine to catalytic residues is similar to that of the starting fragment. We therefore consider crystallographic fragment screening to be appropriate for the identification of weak but promising fragment hits. Copyright © 2015 Elsevier Ltd. All rights reserved.

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

Science.gov (United States)

Terwilliger, Thomas C; Bricogne, Gerard

2014-10-01

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

Preliminary crystallographic characterization of an RNA helicase from Kunjin virus

International Nuclear Information System (INIS)

Mastrangelo, Eloise; Bollati, Michela; Milani, Mario; Brisbarre, Nadège; Lamballerie, Xavier de; Coutard, Bruno; Canard, Bruno; Khromykh, Alexander; Bolognesi, Martino

2006-01-01

The C-terminal 440 amino acids of the NS3 protein from Kunjin virus (Flaviviridae) code for a helicase. The protein has been overexpressed and crystallized. Characterization of the isolated monoclinic crystal form and diffraction data (at 3.0 Å resolution) are presented, together with a preliminary molecular-replacement solution. Kunjin virus is a member of the Flavivirus genus and is an Australian variant of West Nile virus. The C-terminal domain of the Kunjin virus NS3 protein displays helicase activity. The protein is thought to separate daughter and template RNA strands, assisting the initiation of replication by unwinding RNA secondary structure in the 3′ nontranslated region. Expression, purification and preliminary crystallographic characterization of the NS3 helicase domain are reported. It is shown that Kunjin virus helicase may adopt a dimeric assembly in absence of nucleic acids, oligomerization being a means to provide the helicases with multiple nucleic acid-binding capability, facilitating translocation along the RNA strands. Kunjin virus NS3 helicase domain is an attractive model for studying the molecular mechanisms of flavivirus replication, while simultaneously providing a new basis for the rational development of anti-flaviviral compounds

Response of Seven Crystallographic Orientations of Sapphire Crystals to Shock Stresses of 16 to 86 GPa

OpenAIRE

Kanel, G. I.; Nellis, W. J.; Savinykh, A. S.; Razorenov, S. V.; Rajendran, A. M.

2009-01-01

Shock-wave profiles of sapphire (single-crystal Al2O3) with seven crystallographic orientations were measured with time-resolved VISAR interferometry at shock stresses in the range 16 to 86 GPa. Shock propagation was normal to the surface of each cut. The angle between the c-axis of the hexagonal crystal structure and the direction of shock propagation varied from 0 for c-cut up to 90 degrees for m-cut in the basal plane. Based on published shock-induced transparencies, shock-induced optical ...

X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

Energy Technology Data Exchange (ETDEWEB)

Blagov, A. E.; Dyakova, Yu. A.; Kovalchuk, M. V.; Kohn, V. G.; Marchenkova, M. A.; Pisarevskiy, Yu. V.; Prosekov, P. A., E-mail: prosekov@crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2016-05-15

A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer of the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.

Local and average structures of 0.7Pb(Mg1/3Nb2/3)O3 - 0.3PbZrO3

International Nuclear Information System (INIS)

Krishna, P.S.R.; Shinde, A.B.; Narasimhan, S.L.; Tiwari, V.S.; Singh, G.

2005-01-01

The local and average structure of 0.7Pb(Mg 1/3 Nb 2/3 )O 3 - 0.3PbZrO 3 (PMN-PZ) was studied by neutron diffraction. The Rietveld refinement was carried out to determine the average, long-range crystallographic structure, while the pair density function (PDF) analysis was used in studying the local atomic structure. The local atomic structure determined by the PDF analysis, was found to be significantly different from the average crystallographic structure determined by the Rietveld analysis. These results show that the conflict between the local structural preference and the average structure is not limited to relax or ferroelectric oxides, but may be widely prevalent in mixed-ion ferroelectrics. (author)

On the preferential crystallographic orientation of Au nanoparticles: Effect of electrodeposition time

International Nuclear Information System (INIS)

El-Deab, Mohamed S.

2009-01-01

The crystallographic orientation of Au nanoparticles electrodeposited at glassy carbon (nano-Au/GC) electrodes (prepared by potential step electrolysis) is markedly influenced by the width of the potential step. The oxygen reduction reaction (ORR) and the reductive desorption of cysteine have been studied on nano-Au/GC electrodes. Furthermore, electron backscatter diffraction (EBSD) technique has been used to probe the crystallographic orientation of the electrodeposited Au nanoparticles. That is, Au nanoparticles prepared in short time (5-60 s) have been found rich in the Au(1 1 1) facet orientation and are characterized by a relatively small particle size (ca. 10-50 nm) as well as high particle density (number of particles per unit area) as revealed by SEM images. Whereas Au nanoparticles prepared by longer electrolysis time (>60 s) are found to be much enriched in the Au(1 0 0) and Au(1 1 0) facets and are characterized by a relatively large particle size (>100 nm). EBSD patterns provided definitive information about the crystal orientations mapping of Au nanoparticles prepared at various deposition times.

Magnetic ordering in the monoclinic structure of Nd5Si1.45Ge2.55 and Pr5Si1.5Ge2.5 studied by means of neutron powder diffraction

International Nuclear Information System (INIS)

Magen, C; Ritter, C; Morellon, L; Algarabel, P A; Ibarra, M R

2004-01-01

The compounds Nd 5 Si 1.45 Ge 2.55 and Pr 5 Si 1.5 Ge 2.5 have been investigated by means of magnetization measurements and neutron powder diffraction techniques. These alloys present a room-temperature monoclinic Gd 5 Si 2 Ge 2 -type crystallographic structure and, on cooling, both systems order ferromagnetically, at T C = 56 and 32 K, respectively, from a high-temperature paramagnetic to a low-temperature complex canted ferromagnetic state. The monoclinic crystallographic structure remains unchanged upon cooling down to 4 K, demonstrating the existence of a monoclinic ferromagnetic phase, and the possibility of a full decoupling of magnetic and crystallographic degrees of freedom in the 5:4 lanthanide intermetallic compounds

ZnFe{sub 2}O{sub 4} antiferromagnetic structure redetermination

Energy Technology Data Exchange (ETDEWEB)

Kremenović, Aleksandar, E-mail: akremenovic@rgf.bg.ac.rs [Laboratory for Crystallography, Faculty of Mining and Geology, University of Belgrade, Đušina 7, Belgrade 11000 (Serbia); Antić, Bratislav [Condensed Matter Physics Laboratory, Institute of Nuclear Sciences “Vinča”, University of Belgrade, P.O. Box 522, Belgrade 11001 (Serbia); Vulić, Predrag [Laboratory for Crystallography, Faculty of Mining and Geology, University of Belgrade, Đušina 7, Belgrade 11000 (Serbia); Blanuša, Jovan [Condensed Matter Physics Laboratory, Institute of Nuclear Sciences “Vinča”, University of Belgrade, P.O. Box 522, Belgrade 11001 (Serbia); Tomic, Aleksandra [Condensed Matter Physics Laboratory, Institute of Nuclear Sciences “Vinča”, University of Belgrade, P.O. Box 522, Belgrade 11001 (Serbia); Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027 (United States)

2017-03-15

Magnetic structure of ZnFe{sub 2}O{sub 4} normal spinel is re-examined. Antiferromagnetic structure non-collinear model is established within C{sub a}2 space group having four different crystallographic/magnetic sites for 32 Fe{sup 3+} spins within magnetic unit cell. - Highlights: • Magnetic structure of ZnFe{sub 2}O{sub 4} normal spinel is re-examined. • Antiferromagnetic non-collinear structure model is established within C{sub a}2 space group. • Four different crystallographic/magnetic sites contain 32 Fe{sup 3+} spins within magnetic unit cell.

Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

International Nuclear Information System (INIS)

Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

2008-01-01

A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH 2 -terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH 2 -terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4 1 (or P4 3 ), with unit-cell parameters a = b = 78.6, c = 135.2 Å

Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis

International Nuclear Information System (INIS)

Gaur, Vineet; Sethi, Dhruv K.; Salunke, Dinakar M.

2007-01-01

The purification, identification, crystallization and preliminary crystallographic studies of an allergy-related protein, Pru du amandin, from P. dulcis nuts are reported. Food allergies appear to be one of the foremost causes of hypersensitivity reactions. Nut allergies account for most food allergies and are often permanent. The 360 kDa hexameric protein Pru du amandin, a known allergen, was purified from almonds (Prunus dulcis) by ammonium sulfate fractionation and ion-exchange chromatography. The protein was identified by a BLAST homology search against the nonredundant sequence database. Pru du amandin belongs to the 11S legumin family of seed storage proteins characterized by the presence of a cupin motif. Crystals were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P4 1 (or P4 3 ), with unit-cell parameters a = b = 150.7, c = 164.9 Å

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Bricogne, Gerard

2014-01-01

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

Energy Technology Data Exchange (ETDEWEB)

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

2014-10-01

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

Structure evolution of zinc oxide thin films deposited by unbalance DC magnetron sputtering

Energy Technology Data Exchange (ETDEWEB)

Aryanto, Didik, E-mail: didi027@lipi.go.id [Research Center for Physics, Indonesian Institute of Sciences, Serpong 15314, Tangerang Selatan (Indonesia); Materials Research Group, Physics Department, Universitas Negeri Semarang, Gunungpati, Semarang 50229 Jawa Tengah (Indonesia); Marwoto, Putut; Sugianto [Physics Department, Faculty of Mathematics and Science, Universitas Negeri Semarang, Gunungpati, Semarang 50229 Jawa Tengah (Indonesia); Materials Research Group, Physics Department, Universitas Negeri Semarang, Gunungpati, Semarang 50229 Jawa Tengah (Indonesia); Sudiro, Toto [Research Center for Physics, Indonesian Institute of Sciences, Serpong 15314, Tangerang Selatan (Indonesia); Birowosuto, Muhammad D. [Research Center for Physics, Indonesian Institute of Sciences, Serpong 15314, Tangerang Selatan (Indonesia); CINTRA UMI CNRS/NTU/THALES 3288 Research Techno Plaza, 50 Nanyang Drive, Border X Block, level 6, 637553 (Singapore); Sulhadi [Physics Department, Faculty of Mathematics and Science, Universitas Negeri Semarang, Gunungpati, Semarang 50229 Jawa Tengah (Indonesia)

2016-04-19

Zinc oxide (ZnO) thin films are deposited on corning glass substrates using unbalanced DC magnetron sputtering. The effect of growth temperature on surface morphology and crystallographic orientation of ZnO thin film is studied using atomic force microscopy (AFM) and X-ray diffraction (XRD) techniques. The surface morphology and crystallographic orientation of ZnO thin film are transformed against the increasing of growth temperature. The mean grain size of film and the surface roughness are inversely and directly proportional towards the growth temperature from room temperature to 300 °C, respectively. The smaller grain size and finer roughness of ZnO thin film are obtained at growth temperature of 400 °C. The result of AFM analysis is in good agreement with the result of XRD analysis. ZnO thin films deposited in a series of growth temperatures have hexagonal wurtzite polycrystalline structures and they exhibit transformations in the crystallographic orientation. The results in this study reveal that the growth temperature strongly influences the surface morphology and crystallographic orientation of ZnO thin film.

The crystallographic space groups and Heterotic string theory

International Nuclear Information System (INIS)

El Naschie, M.S.

2009-01-01

While the 17 planar crystallographic groups were shown to correspond to 17 two and three Stein spaces with a total dimension equal to DimE12=5α-bar o ≅685, the present work reveals that the corresponding 219 three dimensional groups leads to a total dimensionality equal to N o ≅8872 which happens to be the exact total number of massless states of the transfinite version of Heterotic super string spectrum.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

Science.gov (United States)

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Shape effect related to crystallographic orientation of deformation behavior in copper crystals

International Nuclear Information System (INIS)

Kim, K.H.; Chang, C.H.; Koo, Y.M.; MacDowell, A.A.

1999-01-01

The deformation behavior of pure copper single crystals has been investigated by scanning electron microscopy and synchrotron radiation using the in situ reflection Laue method. Two types of samples with the same orientation of tensile axes, but with different crystallographic orientations in the directions of the width and thickness of the samples, have been studied. They showed different characteristics of deformation behavior, such as the activated slip systems, the movement of the tensile axis, and the mode of fracture

Birefringent phononic structures

Directory of Open Access Journals (Sweden)

I. E. Psarobas

2014-12-01

Full Text Available Within the framework of elastic anisotropy, caused in a phononic crystal due to low crystallographic symmetry, we adopt a model structure, already introduced in the case of photonic metamaterials, and by analogy, we study the effect of birefringence and acoustical activity in a phononic crystal. In particular, we investigate its low-frequency behavior and comment on the factors which determine chirality by reference to this model.

Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis

Energy Technology Data Exchange (ETDEWEB)

Gaur, Vineet; Sethi, Dhruv K.; Salunke, Dinakar M., E-mail: dinakar@nii.res.in [National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067 (India)

2008-01-01

The purification, identification, crystallization and preliminary crystallographic studies of an allergy-related protein, Pru du amandin, from P. dulcis nuts are reported. Food allergies appear to be one of the foremost causes of hypersensitivity reactions. Nut allergies account for most food allergies and are often permanent. The 360 kDa hexameric protein Pru du amandin, a known allergen, was purified from almonds (Prunus dulcis) by ammonium sulfate fractionation and ion-exchange chromatography. The protein was identified by a BLAST homology search against the nonredundant sequence database. Pru du amandin belongs to the 11S legumin family of seed storage proteins characterized by the presence of a cupin motif. Crystals were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 150.7, c = 164.9 Å.

Magnetic structure of the magnetocaloric compound AlFe{sub 2}B{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Cedervall, Johan, E-mail: johan.cedervall@kemi.uu.se [Department of Chemistry – Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala (Sweden); Andersson, Mikael Svante; Sarkar, Tapati [Department of Engineering Sciences, Uppsala University, Box 534, 751 21 Uppsala (Sweden); Delczeg-Czirjak, Erna K. [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden); Bergqvist, Lars [Department of Materials and Nano Physics and Swedish e-Science Research Centre (SeRC), Royal Institute of Technology (KTH), Electrum 229, SE-164 40 Kista (Sweden); Hansen, Thomas C. [Institut Laue-Langevin, B.P. 156, Grenoble Cedex 9, 38042 France (France); Beran, Premysl [Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, 25068 Czech Republic (Czech Republic); Nordblad, Per [Department of Engineering Sciences, Uppsala University, Box 534, 751 21 Uppsala (Sweden); Sahlberg, Martin [Department of Chemistry – Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala (Sweden)

2016-04-15

The crystal and magnetic structures of AlFe{sub 2}B{sub 2} have been studied with a combination of X-ray and neutron diffraction and electronic structure calculations. The magnetic and magnetocaloric properties have been investigated by magnetisation measurements. The samples have been produced using high temperature synthesis and subsequent heat treatments. The compound crystallises in the orthorhombic crystal system Cmmm and it orders ferromagnetically at 285 K through a second order phase transition. At temperatures below the magnetic transition the magnetic moments align along the crystallographic a-axis. The magnetic entropy change from 0 to 800 kA/m was found to be −1.3 J/K kg at the magnetic transition temperature. - Graphical abstract: The magnetic structure of AlFe{sub 2}B{sub 2} has been investigated using neutron diffraction and the magnetic spins have been found to align ferromagnetically along the crystallographic a-axis. - Highlights: • The crystal and magnetic structures of AlFe{sub 2}B{sub 2} have been studied. • Orders ferromagnetically at 285 K via a second order phase transition. • The magnetic moments are found to be aligned along the crystallographic a-axis. • The magnetic entropy change from 0 to 800 kA/m was found to be −1.3 J/K kg.

Crystallographic preferred orientations of exhumed subduction channel rocks from the Eclogite Zone of the Tauern Window (Eastern Alps, Austria), and implications on rock elastic anisotropies at great depths

Czech Academy of Sciences Publication Activity Database

Keppler, R.; Ullemeyer, K.; Behrmann, J. H.; Stipp, M.; Kurzawski, R. M.; Lokajíček, Tomáš

647/648, April (2015), s. 89-104 ISSN 0040-1951 Institutional support: RVO:67985831 Keywords : crystallographic preferred orientation * eclogite Zone * elastic properties * P-wave anisotropy * retrogression of eclogites * subduction channel Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 2.650, year: 2015

Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis

Energy Technology Data Exchange (ETDEWEB)

Morgunova, Ekaterina [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden); Illarionov, Boris; Saller, Sabine [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Popov, Aleksander [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX 09 (France); Sambaiah, Thota [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Bacher, Adelbert [Chemistry Department, Technical University of Munich, 85747 Garching (Germany); Cushman, Mark [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Fischer, Markus [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Ladenstein, Rudolf, E-mail: rudolf.ladenstein@ki.se [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden)

2010-09-01

Crystallographic studies of lumazine synthase, the penultimate enzyme of the riboflavin-biosynthetic pathway in B. anthracis, provide a structural framework for the design of antibiotic inhibitors, together with calorimetric and kinetic investigations of inhibitor binding. The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R{sub cryst} = 23.7% (R{sub free} = 28.4%) at a resolution of 3.5 Å. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.

Crystallization and preliminary crystallographic studies of the W2 domain of Drosophila melanogaster eukaryotic translation initiation factor 5C domain-containing protein

International Nuclear Information System (INIS)

Zhao, Hui; Wang, Hong; Liu, Huihui; Teng, Maikun; Li, Xu

2012-01-01

The crystallization and preliminary crystallographic studies of the carboxy-terminal domain of D. melanogaster eukaryotic translation initiation factor 5C domain-containing protein are reported. The Drosophila melanogaster eukaryotic translation initiation factor 5C domain-containing protein (ECP) is composed of two independently folded domains which belong to the basic leucine-zipper and W2 domain-containing protein (BZW) family. Based on the sequence similarity between the C-terminal W2 domain of ECP and some eukaryotic translation initiation factors (such as eIF2B∊, eIF4γ, eIF5 etc.), ECP has been speculated to participate in the translation initiation process. Structural information on the C-terminal W2 domain of ECP would be helpful in understanding the specific cellular function of this protein. Here, the W2 domain of ECP was expressed and crystallized. Crystals grown by the hanging-drop vapour-diffusion method diffracted to 2.70 Å resolution and belonged to space group I4, with unit-cell parameters a = b = 81.05, c = 57.44 Å. The Matthews coefficient suggested that there was one molecule per asymmetric unit in the crystal

Crystallization and preliminary X-ray crystallographic studies of VibE, a vibriobactin-specific 2,3-dihydroxybenzoate-AMP ligase from Vibrio cholerae

International Nuclear Information System (INIS)

Liu, Xiuhua; Wang, Zhi; Zhu, Deyu; Wei, Tiandi; Gu, Lichuan; Xu, Sujuan

2011-01-01

This article reports the molecular cloning, protein expression and purification, crystallization and preliminary X-ray crystallographic analysis of the vibriobactin synthetase VibE from V. cholerae. Vibriobactin synthetases (VibABCDEFH) catalyze the biosynthesis of vibriobactin in the pathogenic bacterium Vibrio cholerae. VibE, a vibriobactin-specific 2,3-dihydroxybenzoate-AMP ligase, plays a critical role in the transfer of 2,3-dihydroxybenzoate to the aryl carrier protein domain of holo VibB. Here, the cloning, protein expression and purification, crystallization and preliminary X-ray crystallographic analysis of VibE from V. cholerae are reported. The VibE crystal diffracted to 2.3 Å resolution. The crystal belonged to space group P2 1 , with unit-cell parameters a = 56.471, b = 45.927, c = 77.014 Å, β = 95.895°. There is one protein molecule in the asymmetric unit, with a corresponding Matthews coefficient of 1.63 Å 3 Da −1 and solvent content of 24.41%

Local Atomic Structure and Discommensurations in the Charge Density Wave of CeTe3

International Nuclear Information System (INIS)

Kim, H.J.; Tomic, A.T.; Tessmer, S.H.; Billinge, S.J.L.; Malliakas, C.D.; Kanatzidis, M.G.

2006-01-01

The local structure of CeTe 3 in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system

Development of dynamic explicit crystallographic homogenization finite element analysis code to assess sheet metal formability

International Nuclear Information System (INIS)

Nakamura, Yasunori; Tam, Nguyen Ngoc; Ohata, Tomiso; Morita, Kiminori; Nakamachi, Eiji

2004-01-01

The crystallographic texture evolution induced by plastic deformation in the sheet metal forming process has a great influence on its formability. In the present study, a dynamic explicit finite element (FE) analysis code is newly developed by introducing a crystallographic homogenization method to estimate the polycrystalline sheet metal formability, such as the extreme thinning and 'earing'. This code can predict the plastic deformation induced texture evolution at the micro scale and the plastic anisotropy at the macro scale, simultaneously. This multi-scale analysis can couple the microscopic crystal plasticity inhomogeneous deformation with the macroscopic continuum deformation. In this homogenization process, the stress at the macro scale is defined by the volume average of those of the corresponding microscopic crystal aggregations in satisfying the equation of motion and compatibility condition in the micro scale 'unit cell', where the periodicity of deformation is satisfied. This homogenization algorithm is implemented in the conventional dynamic explicit finite element code by employing the updated Lagrangian formulation and the rate type elastic/viscoplastic constitutive equation.At first, it has been confirmed through a texture evolution analyses in cases of typical deformation modes that Taylor's 'constant strain homogenization algorithm' yields extreme concentration toward the preferred crystal orientations compared with our homogenization one. Second, we study the plastic anisotropy effects on 'earing' in the hemispherical cup deep drawing process of pure ferrite phase sheet metal. By the comparison of analytical results with those of Taylor's assumption, conclusions are drawn that the present newly developed dynamic explicit crystallographic homogenization FEM shows more reasonable prediction of plastic deformation induced texture evolution and plastic anisotropy at the macro scale

Synthesis and crystal structure of a new Cu3Au-type ternary phase in the Au-In-Pd system: distribution of atoms over crystallographic positions.

Science.gov (United States)

Ptashkina, Evgeniya A; Kabanova, Elizaveta G; Tursina, Anna I; Yatsenko, Alexandr V; Kuznetsov, Victor N

2018-03-01

A new Cu 3 Au-type ternary phase (τ phase) is found in the AuPd-rich part of the Au-In-Pd system. It has a broad homogeneity range based on extensive (Pd,Au) and (In,Au) replacement, with the composition varying between Au 17.7 In 25.3 Pd 57.0 and Au 50.8 In 16.2 Pd 33.0 . The occupancies of the crystallographic positions were studied by single-crystal X-ray diffraction for three samples of different composition. The sites with m-3m symmetry are occupied by atoms with a smaller scattering power than the atoms located on 4/mmm sites. Two extreme structure models were refined. Within the first, the occupation type changes from (Au,In,Pd) 3 (Pd,In) to (Au,Pd) 3 (In,Pd,Au) with an increase in the Au gross content. For the second model, the occupation type (Au,In,Pd) 3 (Pd,Au) remains essentially unchanged for all Au concentrations. Although the diffraction data do not allow the choice of one of these models, the latter model, where Au substitutes In on 4/mmm sites, seems to be preferable, since it agrees with the fact that the homogeneity range of the τ phase is inclined to the Au corner and provides the same occupation type for all the studied samples of different compositions.

Nitrate as a probe of cytochrome c surface: crystallographic identification of crucial "hot spots" for protein-protein recognition.

Science.gov (United States)

De March, Matteo; Demitri, Nicola; De Zorzi, Rita; Casini, Angela; Gabbiani, Chiara; Guerri, Annalisa; Messori, Luigi; Geremia, Silvano

2014-06-01

The electrostatic surface of cytochrome c and its changes with the iron oxidation state are involved in the docking and undocking processes of this protein to its biological partners in the mitochondrial respiratory pathway. To investigate the subtle mechanisms of formation of productive macromolecular complexes and of their breakage following the electron transfer process, the X-ray structures of horse heart ferri-cytochrome c (trigonal form) and ferro-cytochrome c (monoclinic form) were obtained using nitrate ions both as a crystallizing agent and an anionic probe for mapping the electrostatic surface changes. Both crystal forms contain three protein molecules in the asymmetric unit. In addition, a total of 21.5 and 18 crystallographically independent nitrate ions were identified for the trigonal and monoclinic forms, respectively. By matching all the six crystallographically independent protein molecules, 26 different anion-protein interaction sites were identified on the surfaces of cytochrome c, 10 of which were found in both forms, 8 present only in the oxidized and 8 only in the reduced form. The structural analysis of the electron transfer complexes, based on this new information, suggests a specific exit strategy for cytochrome c after formation of productive protein-protein complexes: a directional sliding mechanism for the electron shuttle on the surface of the redox partner is proposed to take place after the electron transfer process has occurred. Copyright © 2014 Elsevier Inc. All rights reserved.

A study of the Nb3Ge system by Ge K-edge extended x-ray absorption fine structure and x-ray absorption near-edge structure spectroscopy

International Nuclear Information System (INIS)

Saini, N L; Filippi, M; Wu Ziyu; Oyanagi, H; Ihara, H; Iyo, A; Agrestini, S; Bianconi, A

2002-01-01

The local structure of Nb 3 Ge intermetallic superconductor has been studied by Ge K-edge absorption spectroscopy. Extended x-ray absorption fine structure (EXAFS) experiments show two Ge-Nb distances. In addition to the crystallographic distance of ∼2.87 A, there exists a second Ge-Nb distance, shorter than the first by ∼0.2 A, assigned to a phase with short-range symmetry related to local displacements in the Nb-Nb chains. The x-ray absorption near-edge structure (XANES) spectrum has been simulated by full multiple-scattering calculations considering the local displacements determined by the EXAFS analysis. The XANES spectrum has been well reproduced by considering a cluster of 99 atoms within a radius of about 7 A from the central Ge atom and introducing determined local displacements

Room temperature phosphorescence study on the structural flexibility of single tryptophan containing proteins

Science.gov (United States)

Kowalska-Baron, Agnieszka; Gałęcki, Krystian; Wysocki, Stanisław

2015-01-01

In this study, we have undertaken efforts to find correlation between phosphorescence lifetimes of single tryptophan containing proteins and some structural indicators of protein flexibility/rigidity, such as the degree of tryptophan burial or its exposure to solvent, protein secondary and tertiary structure of the region of localization of tryptophan as well as B factors for tryptophan residue and its immediate surroundings. Bearing in mind that, apart from effective local viscosity of the protein/solvent matrix, the other factor that concur in determining room temperature tryptophan phosphorescence (RTTP) lifetime in proteins is the extent of intramolecular quenching by His, Cys, Tyr and Trp side chains, the crystallographic structures derived from the Brookhaven Protein Data Bank were also analyzed concentrating on the presence of potentially quenching amino acid side chains in the close proximity of the indole chromophore. The obtained results indicated that, in most cases, the phosphorescence lifetimes of tryptophan containing proteins studied tend to correlate with the above mentioned structural indicators of protein rigidity/flexibility. This correlation is expected to provide guidelines for the future development of phosphorescence lifetime-based method for the prediction of structural flexibility of proteins, which is directly linked to their biological function.

Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

Energy Technology Data Exchange (ETDEWEB)

Silva, J.M.; Baêta Júnior, E.S.; Moraes, N.R.D.C.; Botelho, R.A. [Department of Mechanical and Materials Engineering, Military Institute of Engineering (IME), Praça General Tibúrcio, 80,Urca, Rio de Janeiro/RJ (Brazil); Felix, R.A.C. [Scientific Instrumentation and Mechanical Technology Laboratory, Brazilian Center for Physics Research (CBPF), Rua Dr. Xavier Sigaud, 150-Urca, Rio de Janeiro-RJ (Brazil); Brandao, L., E-mail: brandao@ime.eb.br [Department of Mechanical and Materials Engineering, Military Institute of Engineering (IME), Praça General Tibúrcio, 80,Urca, Rio de Janeiro/RJ (Brazil)

2017-01-01

The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes. - Highlights: • The B{sub 50} of NOG steels was evaluated via texture for different rolling processes. • On comparison to all processes used, the cross-rolling led to highest average B{sub 50}. • Cross-rolling enhances Goss and γ-fiber after annealing. • The better B{sub 50} values were obtained for symmetrical and cross-rolling processes. • For asymmetric rolling process, cylinder diameter ratio changed slightly the texture.

Local Atomic Structure and Discommensurations in the Charge Density Wave of CeTe{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Kim, H J; Tomic, A T; Tessmer, S H; Billinge, S J.L. [Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824 (United States); Malliakas, C D; Kanatzidis, M G [Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 (United States)

2006-06-09

The local structure of CeTe{sub 3} in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system.

Modeling the effects of ion dose and crystallographic symmetry on the morphological evolution of embedded precipitates under thermal annealing

International Nuclear Information System (INIS)

Li, Kun-Dar

2014-01-01

Highlights: •We model the faceted precipitates formation by post-implantation annealing. •The anisotropic interfacial energy and diffusion kinetics play crucial roles. •The evolutions of faceted precipitates, including Ostwald ripening, are revealed. •The mechanism of the nucleation and growth is based on the atomic diffusion. •The effects of ion dose and crystallographic symmetry are also investigated. -- Abstract: Thermal annealing is one of the most common techniques to synthesize embedded precipitates by ion implantation process. In this study, an anisotropic phase field model is presented to investigate the effects of ion dose and crystallographic symmetry on the morphological formation and evolution of embedded precipitates during post-implantation thermal annealing process. This theoretical model provides an efficient numerical approach to understand the phenomenon of faceted precipitates formation by ion implantation. As a theoretical analysis, the interfacial energy and diffusion kinetics play prominent roles in the mechanism of atomic diffusion for the precipitates formation. With a low ion dose, faceted precipitates are developed by virtue of the anisotropic interfacial energy. As an increase of ion dose, connected precipitates with crystallographic characters on the edge are appeared. For a high ion dose, labyrinth-like nanostructures of precipitates are produced and the characteristic morphology of crystallographic symmetry becomes faint. These simulation results for the morphological evolutions of embedded precipitates by ion implantation are corresponded with many experimental observations in the literatures. The quantitative analyses of the simulations are also well described the consequence of precipitates formation under different conditions

Nanocrystalline materials: recent advances in crystallographic characterization techniques

Directory of Open Access Journals (Sweden)

Emilie Ringe

2014-11-01

Full Text Available Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR, the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask `how are nanoshapes created?', `how does the shape relate to the atomic packing and crystallography of the material?', `how can we control and characterize the external shape and crystal structure of such small nanocrystals?'. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed.

Preliminary X-ray crystallographic analysis of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans

International Nuclear Information System (INIS)

Zhang, Yanfei; Cherney, Maia M.; Solomonson, Matthew; Liu, Jianshe; James, Michael N. G.; Weiner, Joel H.

2009-01-01

The sulfide:quinone oxidoreductase from A. ferrooxidans ATCC 23270 was overexpressed in E. coli and purified. Crystallization and preliminarily X-ray crystallographic analysis were performed for the recombinant enzyme. The gene product of open reading frame AFE-1293 from Acidithiobacillus ferrooxidans ATCC 23270 is annotated as encoding a sulfide:quinone oxidoreductase, an enzyme that catalyses electron transfer from sulfide to quinone. Following overexpression in Escherichia coli, the enzyme was purified and crystallized using the hanging-drop vapour-diffusion method. The native crystals belonged to the tetragonal space group P4 2 2 1 2, with unit-cell parameters a = b = 131.7, c = 208.8 Å, and diffracted to 2.3 Å resolution. Preliminary crystallographic analysis indicated the presence of a dimer in the asymmetric unit, with an extreme value of the Matthews coefficient (V M ) of 4.53 Å 3 Da −1 and a solvent content of 72.9%

Crystal structures of β-galactosidase from Penicillium sp. and its complex with galactose

International Nuclear Information System (INIS)

Rojas, A.L.; Nagem, R.A.P.; Garratt, R.C.; Polikarpov, I.; Neustroev, K.N.; Eneyskaya, E.V.; Kulminskaya, A.A.; Golubev, A.M.; Arand, M.; Adamska, M.

2004-01-01

Glycosidase belong to a group of enzymes displaying a great variety of protein folds and substrate specificities. Two critically located acidic residues make up the catalytic machinery of these enzymes, which are responsible for the cleavage of glycosidic bonds. The applications of glycosidase in textile, food, and pulp processing and in catalysts and oligosaccharide synthesis have encouraged the engineering of these proteins to improve their catalytic properties and stability. Furthermore, structural studies broaden our understanding of the catalytic mechanism and the role of glycosidase in the recognition processes of their different substrates. In this work, we describe crystallographic studies of a fungi glycosidase. The crystallographic structures of β-galactosidase from Penicillium sp. and its complex with galactose were solved at 1.90 A and 2.10 A resolution, respectively. The X-ray structure of the enzyme-galactose complex was useful in identifying the residue Glu200 as the proton donor and residue Glu 299 as the nucleophiles involved in catalysis. (author)

Crystal structures of {beta}-galactosidase from Penicillium sp. and its complex with galactose

Energy Technology Data Exchange (ETDEWEB)

Rojas, A.L.; Nagem, R.A.P.; Garratt, R.C.; Polikarpov, I. [Universidade de Sao Paulo, Sao Carlos, SP (Brazil); Neustroev, K.N.; Eneyskaya, E.V.; Kulminskaya, A.A.; Golubev, A.M. [St. Petersburg, Gatchina (Russian Federation); Arand, M.; Adamska, M. [University of Wuerzburg (Germany)

2004-07-01

Glycosidase belong to a group of enzymes displaying a great variety of protein folds and substrate specificities. Two critically located acidic residues make up the catalytic machinery of these enzymes, which are responsible for the cleavage of glycosidic bonds. The applications of glycosidase in textile, food, and pulp processing and in catalysts and oligosaccharide synthesis have encouraged the engineering of these proteins to improve their catalytic properties and stability. Furthermore, structural studies broaden our understanding of the catalytic mechanism and the role of glycosidase in the recognition processes of their different substrates. In this work, we describe crystallographic studies of a fungi glycosidase. The crystallographic structures of {beta}-galactosidase from Penicillium sp. and its complex with galactose were solved at 1.90 A and 2.10 A resolution, respectively. The X-ray structure of the enzyme-galactose complex was useful in identifying the residue Glu200 as the proton donor and residue Glu 299 as the nucleophiles involved in catalysis. (author)

The study of virus structure and function: a personal history

Science.gov (United States)

Rossmann, Michael G.

2014-09-01

I describe my gradually evolving role as a scientist from my birth in Frankfurt (Germany) to my education in the UK, my post-doc years and my experiences as an independent investigator at Purdue University1. I discuss the significance of my post-doctoral work in Minnesota where I had my first encounter with an electronic computer and subsequently in Cambridge where I participated in the first structure determination of proteins. After six years back in England my family moved to Indiana (USA) where my home remains to this day. At Purdue University I first studied the structure of enzymes and in the process I discovered the organization and slow evolution of protein domains, each with a specific function. With this success I started what had been on my mind already for a long time, namely the structural analysis of viruses. Initially we studied plant viruses but then switched to small RNA animal viruses, discovering that some plant and animal RNA viruses have closely similar structures and therefore presumably had a common evolutionary origin. Next I became interested in somewhat larger viruses that had lipid membrane envelopes. In turn that has led to the study of very large dsDNA viruses as big as small bacteria as well as studies of bacterial viruses that require complex molecular motors for different parts of their life cycle. While developing crystallographic techniques for the study of viruses it has become progressively more apparent that electron microscopy is an important new tool that is likely to eclipse x-ray crystallography in the next decade.

Evaluation of crystallographic strain, rotation and defects in functional oxides by the moiré effect in scanning transmission electron microscopy

Science.gov (United States)

Naden, A. B.; O'Shea, K. J.; MacLaren, D. A.

2018-04-01

Moiré patterns in scanning transmission electron microscopy (STEM) images of epitaxial perovskite oxides are used to assess strain and defect densities over fields of view extending over several hundred nanometers. The patterns arise from the geometric overlap of the rastered STEM electron beam and the samples’ crystal periodicities and we explore the emergence and application of these moiré fringes for rapid strain analysis. Using the epitaxial functional oxide perovskites BiFeO3 and Pr1-x Ca x MnO3, we discuss the impact of large degrees of strain on the quantification of STEM moiré patterns, identify defects in the fringe patterns and quantify strain and lattice rotation. Such a wide-area analysis of crystallographic strain and defects is crucial for developing structure-function relations of functional oxides and we find the STEM moiré technique to be an attractive means of structural assessment that can be readily applied to low dose studies of damage sensitive crystalline materials.

Structure studies by electron microscopy and electron diffraction at Physics Department, University of Oslo, 1976-1985

International Nuclear Information System (INIS)

Gjoennes, J.K.; Olsen, A.

1985-08-01

The paper describes the reasearch activities and plans at the electron microscopy laboratorium, Physics Departmen, University of Oslo. Since the first electron microscope was installed in 1968, the research has covered inorganic structures, physical metallurgy, as well as theory of electron scattering and the development of methods in this field. The current plans involve efforts in the development of crystallographic and spectroscopic methods

Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

International Nuclear Information System (INIS)

Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles

2007-01-01

The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°

Deformation-induced crystallographic-preferred orientation of hcp-iron: An experimental study using a deformation-DIA apparatus

Science.gov (United States)

Nishihara, Yu; Ohuchi, Tomohiro; Kawazoe, Takaaki; Seto, Yusuke; Maruyama, Genta; Higo, Yuji; Funakoshi, Ken-ichi; Tange, Yoshinori; Irifune, Tetsuo

2018-05-01

Shear and uniaxial deformation experiments on hexagonal close-packed iron (hcp-Fe) was conducted using a deformation-DIA apparatus at a pressure of 13-17 GPa and a temperature of 723 K to determine its deformation-induced crystallographic-preferred orientation (CPO). Development of the CPO in the deforming sample is determined in-situ based on two-dimensional X-ray diffraction using monochromatic synchrotron X-rays. In the shear deformation geometry, the and axes gradually align to be sub-parallel to the shear plane normal and shear direction, respectively, from the initial random texture. In the uniaxial compression and tensile geometry, the and axes, respectively, gradually align along the direction of the uniaxial deformation axis. These results suggest that basal slip (0001) is the dominant slip system in hcp-Fe under the studied deformation conditions. The P-wave anisotropy for a shear deformed sample was calculated using elastic constants at the inner core condition by recent ab-initio calculations. Strength of the calculated anisotropy was comparable to or higher than axisymmetric anisotropy in Earth's inner core.

Crystallographic features related to a van der Waals coupling in the layered chalcogenide FePS{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Murayama, Chisato; Okabe, Momoko; Fukuda, Koichiro [Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku Nagoya 466-8555 (Japan); Urushihara, Daisuke; Asaka, Toru, E-mail: asaka.toru@nitech.ac.jp [Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku Nagoya 466-8555 (Japan); Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso-cho, Showa-ku Nagoya 466-8555 (Japan); Isobe, Masahiko [Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart (Germany); Yamamoto, Kazuo [Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya 456-8587 (Japan); Matsushita, Yoshitaka [Research Network and Facility Services Division, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan)

2016-10-14

We investigated the crystallographic structure of FePS{sub 3} with a layered structure using transmission electron microscopy and powder X-ray diffraction. We found that FePS{sub 3} forms a rotational twin structure with the common axis along the c*-axis. The high-resolution transmission electron microscopy images revealed that the twin boundaries were positioned at the van der Waals gaps between the layers. The narrow bands of dark contrast were observed in the bright-field transmission electron microscopy images below the antiferromagnetic transition temperature, T{sub N} ≈ 120 K. Low-temperature X-ray diffraction showed a lattice distortion; the a- and b-axes shortened and lengthened, respectively, as the temperature decreased below T{sub N.} We propose that the narrow bands of dark contrast observed in the bright-field transmission electron microscopy images are caused by the directional lattice distortion with respect to each micro-twin variant in the antiferromagnetic phase.

Microstructure and crystallographic texture of pure titanium parts generated by laser additive manufacturing

Science.gov (United States)

Arias-González, Felipe; del Val, Jesús; Comesaña, Rafael; Penide, Joaquín; Lusquiños, Fernando; Quintero, Félix; Riveiro, Antonio; Boutinguiza, Mohamed; Gil, Francisco Javier; Pou, Juan

2018-01-01

In this paper, the microstructure and crystallographic texture of pure Ti thin walls generated by Additive Manufacturing based on Laser Cladding (AMLC) are analyzed in depth. From the results obtained, it is possible to better understand the AMLC process of pure titanium. The microstructure observed in the samples consists of large elongated columnar prior β grains which have grown epitaxially from the substrate to the top, in parallel to the building direction. Within the prior β grains, α-Ti lamellae and lamellar colonies are the result of cooling from above the β-transus temperature. This transformation follows the Burgers relationship and the result is a basket-weave microstructure with a strong crystallographic texture. Finally, a thermal treatment is proposed to transform the microstructure of the as-deposited samples into an equiaxed microstructure of α-Ti grains.

Carbides crystalline structure of AISI M2 high-speed steel

International Nuclear Information System (INIS)

Serna, M.M.; Galego, E.; Rossi, J.L.

2005-01-01

The aim of this study was to identify the crystallographic structure of the extracted carbides of AISI M2 steel spray formed The structure determination of these carbides. The structure determination of these carbides is a very hard work. Since these structures were formed by atom migration it is not possible to reproduce them by a controlled process with a determined chemical composition. The solution of this problem is to obtain the carbide by chemical extraction from the steel. (Author)

Five-parameter crystallographic characteristics of the interfaces formed during ferrite to austenite transformation in a duplex stainless steel

Science.gov (United States)

Haghdadi, N.; Cizek, P.; Hodgson, P. D.; Tari, V.; Rohrer, G. S.; Beladi, H.

2018-05-01

The crystallography of interfaces in a duplex stainless steel having an equiaxed microstructure produced through the ferrite to austenite diffusive phase transformation has been studied. The five-parameter interface character distribution revealed a high anisotropy in habit planes for the austenite-ferrite and austenite-austenite interfaces for different lattice misorientations. The austenite and ferrite habit planes largely terminated on (1 1 1) and (1 1 0) planes, respectively, for the austenite-ferrite interfaces associated with Kurdjumov-Sachs (K-S) and Nishiyama-Wasserman (N-W) orientation relationships. This was mostly attributed to the crystallographic preference associated with the phase transformation. For the austenite-ferrite interfaces with orientation relationships which are neither K-S nor N-W, both austenite and ferrite habit planes had (1 1 1) orientations. Σ3 twin boundaries comprised the majority of austenite-austenite interfaces, mostly showing a pure twist character and terminating on (1 1 1) planes due to the minimum energy configuration. The second highest populated austenite-austenite boundary was Σ9, which tended to have grain boundary planes in the tilt zone due to the geometrical constraints. Furthermore, the intervariant crystallographic plane distribution associated with the K-S orientation relationship displayed a general tendency for the austenite habit planes to terminate with the (1 1 1) orientation, mainly due to the crystallographic preference associated with the phase transformation.

Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels

International Nuclear Information System (INIS)

Adaixo, Ricardo; Morais-Cabral, João Henrique

2010-01-01

The N-terminal PAS domains from the eukaryotic EAG potassium channels are thought to have a regulatory function. Here the expression, purification, crystallization and preliminary crystallographic characterization of two of these domains are described. Per–Arnt–Sim (PAS) domains are ubiquitous in nature; they are ∼130-amino-acid protein domains that adopt a fairly conserved three-dimensional structure despite their low degree of sequence homology. These domains constitute the N-terminus or, less frequently, the C-terminus of a number of proteins, where they exert regulatory functions. PAS-containing proteins generally display two or more copies of this motif. In this work, the crystallization and preliminary analysis of the PAS domains of two eukaryotic potassium channels from the ether-à-go-go (EAG) family are reported

The Almost Periodic Rigidity of Crystallographic Bar-Joint Frameworks

Directory of Open Access Journals (Sweden)

Ghada Badri

2014-04-01

Full Text Available A crystallographic bar-joint framework, C in Rd, is shown to be almost periodically infinitesimally rigid if and only if it is strictly periodically infinitesimally rigid and the rigid unit mode (RUM spectrum, Ω (C, is a singleton. Moreover, the almost periodic infinitesimal flexes of C are characterised in terms of a matrix-valued function, ΦC(z, on the d-torus, Td, determined by a full rank translation symmetry group and an associated motif of joints and bars.

Irradiation and lithium presence influence on the crystallographic nature of zirconia in the framework of PWR zircaloy 4 fuel cladding corrosion study

International Nuclear Information System (INIS)

Gibert, C.

1999-01-01

The-increasing deterioration of the initially protective zirconia layer is one of the hypotheses which can explain the impairment with time of PWR fuel cladding corrosion. This deterioration could be worsened by irradiation or lithium presence in the oxidizing medium. The aim of this thesis was to underline the influence of those two parameters on zirconia crystallographic nature. We first studied the impact of ionic irradiation on pure, powdery, monoclinic zirconia and oxidation formed zirconia, mainly with X-ray diffraction and Raman microscopy. The high or low energy particles used (Kr n+- , Ar n+ ) respectively favored electronic or atomic defaults production. The crystallographic analyses showed that these irradiation have a significant effect on zirconia by inducing nucleation or growth of tetragonal phase. The extent depends on sample nature and particles energy. In all cases, phase transformation is correlated with crystalline parameters, grain size and especially micro-stress changes. The results are consistent with those obtained with 1 to 5 cycles PWR claddings. Therefore, the corrosion acceleration observed in reactor can partly be explained by the stress fields appearance under irradiation, which is particularly detrimental to zirconia layer cohesion. Last, we have underlined that the presence of considerable amounts of lithium in the oxidizing medium ((> 700 ppm) induces the disappearance of the tetragonal zirconia located at the metal/oxide interface and the appearance of a porosity of the dense under layer, which looses its protectiveness. (author)

Nano structured materials studied by coherent X-ray diffraction

International Nuclear Information System (INIS)

Gulden, Johannes

2013-03-01

Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

Nano structured materials studied by coherent X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Gulden, Johannes

2013-03-15

Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

Crystal plasticity study of monocrystalline stochastic honeycombs under in-plane compression

International Nuclear Information System (INIS)

Ma, Duancheng; Eisenlohr, Philip; Epler, Eike; Volkert, Cynthia A.; Shanthraj, Pratheek; Diehl, Martin; Roters, Franz; Raabe, Dierk

2016-01-01

We present a study on the plastic deformation of single crystalline stochastic honeycombs under in-plane compression using a crystal plasticity constitutive description for face-centered cubic (fcc) materials, focusing on the very early stage of plastic deformation, and identifying the interplay between the crystallographic orientation and the cellular structure during plastic deformation. We observe that despite the stochastic structure, surprisingly, the slip system activations in the honeycombs are almost identical to their corresponding bulk single crystals at the early stage of the plastic deformation. On the other hand, however, the yield stresses of the honeycombs are nearly independent of their crystallographic orientations. Similar mechanical response is found in compression testing of nanoporous gold micro-pillars aligned with various crystallographic orientations. The macroscopic stress tensors of the honeycombs show the same anisotropy as their respective bulk single crystals. Locally, however, there is an appreciable fluctuation in the local stresses, which are even larger than for polycrystals. This explains why the Taylor/Schmid factor associated with the crystallographic orientation is less useful to estimate the yield stresses of the honeycombs than the bulk single crystals and polycrystals, and why the plastic deformation occurs at smaller strains in the honeycombs than their corresponding bulk single crystals. Besides these findings, the observations of the crystallographic reorientation suggest that conventional orientation analysis tools, such as inverse pole figure and related tools, would in general fail to study the plastic deformation mechanism of monocrystalline cellular materials.

Crystallographic Analysis of a Japanese Sword by using Bragg Edge Transmission Spectroscopy

Science.gov (United States)

Shiota, Yoshinori; Hasemi, Hiroyuki; Kiyanagi, Yoshiaki

Neutron imaging using a pulsed neutron source can give crystallographic information over wide area of a sample by analysing position dependent transmission spectra. With the use of a Bragg edge imaging method we non-destructively obtained crystallographic information of a Japanese sword, signed by Bishu Osafune Norimitsu, in order to know position dependent crystallographic characteristics and to check usefulness of the method for the Japanese sword investigation. Strong texture appeared on the back side. On the other hand in the middle area almost isotropic feature appeared and edge side showed feature between them. Rather isotropic area in the centre area gradually reduced from the grip side to the tip side. The crystallite size was smaller near the edge and became larger towards the back side. The smaller crystallite size will be due to quenching around the edge and this trend disappeared in the grip (nakago) area. The larger crystallite size will be due to strong hammering. Coarse grains were also observed directly as transmission images with the use of a high spatial resolution detector. The spatial distribution of the grains was not uniform but the reason have not been understood. Furthermore, a white area around a tip area was proved to be a void by looking at the Brag edge transmission spectra. This void may be formed during forging process of two kinds of steel. It is suggested that consideration on differences in the texture and the crystallite size depending on position will give information to clarify the manufacturing process, and Bragg edge analysis will be a profitable tool for research of Japanese sword.

Neutron scattering study on R2PdSi3 (R=Ho,Er,Tm) compounds

International Nuclear Information System (INIS)

Tang, Fei

2010-01-01

Previous studies on the family of inter-metallic rare-earth compounds R 2 PdSi 3 revealed multifaceted magnetic properties, for instance, spin-glass like behavior. Experimental observations include: Signs of a crystallographic superstructure, complicated magnetic structures both in zero field and in applied magnetic fields as well as a generic phase in applied fields for compounds in the series with the heavy rare-earths R=Gd, Tb, Dy, Ho, Er and Tm. This thesis expands the studies on the magnetic properties of R 2 PdSi 3 employing mainly neutron scattering on single crystals with the focus on the compounds with R=Ho, Er and Tm. A detailed analysis of the crystallographic superstructure using modulation wave approach and group theory is presented. The resulting structure implies the existence of two different rare-earth sites with reduced symmetry and an arrangement of the different sites according to sequences as determined by the superstructure. It is shown that the reduced symmetry of the rare-earth sites is explicitly observed in the energy spectra of inelastic neutron scattering. The results on the magnetic structures and excitations are shown and discussed in the framework of the superstructure model. Specifically the generic phase in applied fields is interpreted as a direct consequence of the crystallographic superstructure. It is rather unusual that a crystallographic superstructure is playing such a decisive, and through the field dependence also tunable role in determining the magnetic properties as observed in R 2 PdSi 3 . The mediating interactions between the crystallographic part and the magnetic part of the system are discussed. (orig.)

NMR structure of the protein NP-247299.1: comparison with the crystal structure

International Nuclear Information System (INIS)

Jaudzems, Kristaps; Geralt, Michael; Serrano, Pedro; Mohanty, Biswaranjan; Horst, Reto; Pedrini, Bill; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution. The NMR structure of the protein NP-247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves

Local atomic structure in tetragonal pure ZrO{sub 2} nanopowders

Energy Technology Data Exchange (ETDEWEB)

Acuna, Leandro M.; Lamas, Diego G.; Fuentes, Rodolfo O.; Fabregas, Ismael O. [CITEFA-CONICET, Villa Martelli, Provincia de Buenos Aires (AR). CINSO (Centro de Investigaciones en Solidos); Fantini, Marcia C.A.; Craievich, Aldo F. [Universidade de Sao Paulo (Brazil). Inst. de Fisica; Prado, Rogerio J. [Universidade Federal de Mato Grosso (UFMT), Cuiaba (Brazil). Inst. de Fisica

2010-04-15

The local atomic structures around the Zr atom of pure (undoped) ZrO{sub 2} nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wetchemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO{sub 2} nanopowders can be described by a model consisting of two oxygen subshells (4+4 atoms) with different Zr-O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye-Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4+2+2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. (orig.)

Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction† †Electronic supplementary information (ESI) available: Supplementary figures, crystallographic information, adsorption isotherms and fits, CCDC 1530119–1530126. For ESI and crystallographic data in CIF or other electronic format. See DOI: 10.1039/c7sc00449d Click here for additional data file. Click here for additional data file.

Science.gov (United States)

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; Teat, Simon J.; Gagnon, Kevin J.; Morrison, Gregory Y.; Queen, Wendy L.

2017-01-01

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH4, N2, O2, Ar, and P4 adsorption in Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH4 and Co–Ar interactions observed in Co2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol–1 (for Ar). Moreover, the structures of Co2(dobdc)·3.8N2, Co2(dobdc)·5.9O2, and Co2(dobdc)·2.0Ar reveal the location of secondary (N2, O2, and Ar) and tertiary (O2) binding sites in Co2(dobdc), while high-pressure CO2, CO, CH4, N2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures. PMID:28966783

Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

Science.gov (United States)

Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

2015-05-01

The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples.

Crystal and magnetic structure of the Ca3Mn2O7 Ruddlesden-Popper phase: neutron and synchrotron x-ray diffraction study

International Nuclear Information System (INIS)

Lobanov, Maxim V; Greenblatt, Martha; Caspi, El'ad N; Jorgensen, James D; Sheptyakov, Denis V; Toby, Brian H; Botez, Cristian E; Stephens, Peter W

2004-01-01

The crystallographic and magnetic structures of Ca 3 Mn 2 O 7 Ruddlesden-Popper phase have been determined by a combination of neutron and synchrotron x-ray diffraction. Two-phase behaviour observed at room temperature is attributed to an incomplete structural phase transition. The magnetic structure was solved in the Cm'c2 1 ' Shubnikov group with dominant G-type antiferromagnetic order in the perovskite bilayers. The temperature evolution of the structural and magnetic parameters is presented

Correlation between chemical, crystallographic and spectroscopic parameters in graphite thermometry applied to a contact aureole of La Soledad monzogranite (Venezuelan Andes

Directory of Open Access Journals (Sweden)

K. Reategui

2017-11-01

Full Text Available Graphite samples from a metamorphic contact aureole between phyllites of the Cerro Azul Association (Palaeozoic and La Soledad Monzogranite, in the Venezuelan Andes, were studied by chemical (% inorganic carbon and isotopic distribution, crystallographic (DRX and spectroscopic (Raman techniques in order to assess changes in the graphite in the vicinity of the contact, the correlation between the different parameters, and the determination of the higher temperature reached by the host rock during igneous intrusion. The δ13C reached less negative values near the monzogranite, caused by devolatilization; the graphite present just in contact with the pluton experienced retrograde recrystallization, which causes a shift towards more negative values. The calculated degree of graphitization intervals (GD = 53–80 corresponds to a well-structured mineral with ordered packaging. The peak metamorphic temperature at the contact was calculated from crystallographic (XRD and spectroscopic (Raman parameters with great agreement in both techniques, registering the 528 ± 16 and 526 ± 20 ºC respectively. The metapelitic rocks reached the Cordierite Zone (cordierite + biotite + muscovite in the contact aureole where the graphite is well ordered and in hexagonal microtexture. Factors such as fluid activity and the subsequent retrograde recrystallization have an effect on isotopic redistributions after the intrusive event, as well as on the crystallinity change rate with the temperature, avoiding a clear correlation between the isotopic variations of 13C in graphite and the temperature.

Effect of humidity on the hydration behaviour of prazosin hydrochloride polyhydrate: Thermal, sorption and crystallographic study

International Nuclear Information System (INIS)

Kumar, Lokesh; Bansal, Arvind K.

2011-01-01

Highlights: → Utility of TGA to differentiate between unbound and bound water was demonstrated. → Nature of the lattice arrangement in prazosin hydrochloride polyhydrate was confirmed to be expanded (non-stoichiometric) type hydrate. → Correlation of the DSC, TGA, PXRD and DVS for dehydration of prazosin hydrochloride polyhydrate was delineated. - Abstract: In this study, hydration behaviour of prazosin hydrochloride polyhydrate was assessed using differential scanning calorimetry, thermogravimetric analysis, powder X-ray diffraction and dynamic vapour sorption techniques. Differential scanning calorimetry and thermogravimetric analysis at faster heating rate (20 o C/min) showed single step water loss, attributed to both dihydrate and unbound water. In contrast, thermogravimetric analysis at slower heating rate (1 o C/min) showed unbound and dihydrate lattice water separately, with unbound water being lost initially, followed by loss of dihydrate water. Variable vacuum and variable humidity PXRD study revealed shift in diffraction peaks to higher values on removal of unbound water. Initial PXRD patterns were regained when kept again at ambient conditions. Dynamic vapour sorption depicted type I sorption isotherm with interstitial water, indicating that polyhydrate form show reversible behaviour with change in humidity. Correlation between thermal, sorption and crystallographic data established hydration behaviour to be characteristic of expanded channel type (non-stoichiometric) hydrate.

Homological functor of a torsion free crystallographic group of dimension five with a nonabelian point group

Science.gov (United States)

Ting, Tan Yee; Idrus, Nor'ashiqin Mohd.; Masri, Rohaidah; Sarmin, Nor Haniza; Hassim, Hazzirah Izzati Mat

2014-06-01

Torsion free crystallographic groups, called Bieberbach groups, appear as fundamental groups of compact, connected, flat Riemannian manifolds and have many interesting properties. New properties of the group can be obtained by, not limited to, exploring the groups and by computing their homological functors such as nonabelian tensor squares, the central subgroup of nonabelian tensor squares, the kernel of the mapping of nonabelian tensor squares of a group to the group and many more. In this paper, the homological functor, J(G) of a centerless torsion free crystallographic group of dimension five with a nonabelian point group which is a dihedral point group is computed using commutator calculus.

Structure determination of enterovirus 71

Energy Technology Data Exchange (ETDEWEB)

Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

2013-02-20

Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

Crystallographic and magnetic properties of nanocrystalline perovskite structure SmFeO3 orthoferrite

Science.gov (United States)

Kumar, Ashwini; Shen, Jingdong; Zhao, Huihui; Zhengjian, Qi; Li, Qi

2018-05-01

In this article, we present the structural and magnetic studies of pristine SmFeO3 nanocrystalline ceramic samples as sintered at temperature 850 °C and 1000 °C. X-ray powder diffraction data confirm the existence of single-phase nature with orthorhombic (Pbnm) structure of the samples. The SEM image reveals spherical particles with a size range of 60-130 nm for SFO-850 and SFO-1000 samples. X-ray absorption spectroscopy studies on Fe L3,2 and O K-edges of SmFeO3 sample revealed the homo-valence state of Fe in these materials. From magnetization studies it has been observed the materials exhibit ferromagnetic and antiferromagnetic (canted spin structure) sub-lattices, which results strong magnetic anisotropy in the system.

Structure study of BaCe{sub 0.85}Y{sub 0.15}O{sub 3-Δ} as solid state fuel cell material

Energy Technology Data Exchange (ETDEWEB)

Krezhov, K., E-mail: krezhov@inrne.bas.bg; Malakova, T.; Dimitrov, D. [Institute forNuclear Research and Nuclear Energy, Bulgarian Academy of Sciences, Sofia (Bulgaria); Vladikova, D.; Raikova, G.; Genov, I. [Institute of Electrochemistry and Energy Systems, Bulgarian Academy of Sciences, Sofia (Bulgaria); Svab, E. [Wigner Research Center for Physics, RISSPO, Hungarian Academy of Sciences, Budapest (Hungary); Fabian, M. [Wigner Research Center for Physics, RISSPO, Hungarian Academy of Sciences, Budapest (Hungary); Center for Energy Research, Hungarian Academy of Sciences, Budapest (Hungary)

2016-03-25

The structural details of powder, dense and porous samples of BaCe{sub 0.85}Y{sub 0.15}O{sub 3−δ} (BCY15) used recently in an innovative monolithic design of SOFC were studied from multiple Rietveld analysis of neutron and x-ray diffraction patterns. The 3-layered monolithic assembly built from BCY15 material works as oxide ion conductor in the oxygen space, as proton conductor in the hydrogen area and as mixed conductor in the central membrane. We find that in all the samples of studied BCY15 based materials there are no indications of difference in crystallographic symmetry and the structure refinements did produce best agreement factors in orthorhombic Pnma space group.

Determination of lower bound crystallographic yield loci of zircaloy-4 tubes

International Nuclear Information System (INIS)

Costa Viana, C.S. da

1980-01-01

The use of zircaloy-4 tubing in fuel elements of water cooled reactors is discussed with respect to its mechanisms of deformation and also its resulting anisotropic plastic behaviour. A method for obtaining lower bound crystallographic yield loci of α-Zr is presented and applied to individual crystal orientations and to a real texture described by the main components observed on a direct pole figure. (Author) [pt

The study of changes in structural properties of Cu films under ionizing radiation

Science.gov (United States)

Kaliekperov, M.; Kozlovskiy, A.; Shlimas, D.; Kenzhina, I.; Ivanov, I.; Kozin, S.; Aleksandrenko, V.; Kurakhmedov, A.; Sambaev, E.; Seitbaev, A.; Zdorovets, M.; Kadyrzhanov, K.

2018-05-01

In this paper, we present the results of studies of the irradiation effect with low-energy He+2 ions with an energy of 30 keV (15 keV per charge) on the structural properties of Cu films. Using SEM, EDS, and x-ray diffraction analysis, the surface morphology and structural properties of samples before and after irradiation were studied. As a result of irradiation of initial samples with He+2 ions with a dose of 1·1016 ion cm‑2, a change in the Cu surface morphology of films is observed, and the formation of nanoscale inclusions of hexagonal shape is observed. An increase in the irradiation dose to 1·1017 ion cm‑2 and higher leads to the formation of cracks and amorphous oxide inclusions on the sample surface. It is established that an increase in the irradiation dose leads to a decrease in the degree of crystallinity and a change in the basic crystallographic characteristics. The effect of irradiation on the strength characteristics was estimated.

Deriving Quantitative Crystallographic Information from the Wavelength-Resolved Neutron Transmission Analysis Performed in Imaging Mode

Directory of Open Access Journals (Sweden)

Hirotaka Sato

2017-12-01

Full Text Available Current status of Bragg-edge/dip neutron transmission analysis/imaging methods is presented. The method can visualize real-space distributions of bulk crystallographic information in a crystalline material over a large area (~10 cm with high spatial resolution (~100 μm. Furthermore, by using suitable spectrum analysis methods for wavelength-dependent neutron transmission data, quantitative visualization of the crystallographic information can be achieved. For example, crystallographic texture imaging, crystallite size imaging and crystalline phase imaging with texture/extinction corrections are carried out by the Rietveld-type (wide wavelength bandwidth profile fitting analysis code, RITS (Rietveld Imaging of Transmission Spectra. By using the single Bragg-edge analysis mode of RITS, evaluations of crystal lattice plane spacing (d-spacing relating to macro-strain and d-spacing distribution’s FWHM (full width at half maximum relating to micro-strain can be achieved. Macro-strain tomography is performed by a new conceptual CT (computed tomography image reconstruction algorithm, the tensor CT method. Crystalline grains and their orientations are visualized by a fast determination method of grain orientation for Bragg-dip neutron transmission spectrum. In this paper, these imaging examples with the spectrum analysis methods and the reliabilities evaluated by optical/electron microscope and X-ray/neutron diffraction, are presented. In addition, the status at compact accelerator driven pulsed neutron sources is also presented.

Automated Structure Solution with the PHENIX Suite

Energy Technology Data Exchange (ETDEWEB)

Zwart, Peter H.; Zwart, Peter H.; Afonine, Pavel; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei; Ioerger, Tom R.; McCoy, A.J.; McKee, Eric; Moriarty, Nigel; Read, Randy J.; Sacchettini, James C.; Sauter, Nicholas K.; Storoni, L.C.; Terwilliger, Tomas C.; Adams, Paul D.

2008-06-09

Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

Automated structure solution with the PHENIX suite

Energy Technology Data Exchange (ETDEWEB)

Terwilliger, Thomas C [Los Alamos National Laboratory; Zwart, Peter H [LBNL; Afonine, Pavel V [LBNL; Grosse - Kunstleve, Ralf W [LBNL

2008-01-01

Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

Crystallographic and magnetic properties of (C6D11ND3)CuBr3 and (Zn1-xMnx)3As2

International Nuclear Information System (INIS)

Vries, G.C. de.

1989-08-01

The investigations described concern the crystallographic and magnetic properties of the quasi one-dimensional (1d) ferromagnetic system (C 6 D 11 ND 3 )CuBr 3 (or CHAB) and the II-V type diluted magnetic semiconductor (Zn 1 - x Mn x ) 3 As 2 (or ZMA). Both compounds have been studied with various neutron scattering techniques. The crystallographic properties of CHAB and ZMA have been investigated by neutron diffraction. These diffraction experiments were carried out at the High Flux Reactor (HFR) at Petten, Netherlands. For the investigation of the static and dynamic magnetic properties of CHAB neutron scattering experiments were performed in Petten as well as other European reactor institutes. These investigations comprise a study of the 3d long-rate order and the 1d correlations of the magnetic moments, and a study of the behaviour of the linear spin-wave excitations

Structural comparison of 1{beta}-Methylcarbapenem, Carbapenem and Penem: NMR studies and theoretical calculations

Energy Technology Data Exchange (ETDEWEB)

Sunagawa, M.; Sasaki, A.; Igarashi, J.-E.; Nishimura, T. [Research Center, Sumitomo Pharmaceuticals Co., Ltd., 3-1-98 Kasugadenaka, Konohanaku, Osaka (Japan)

1998-04-01

Structural comparisons of meropenem (1), desmethyl meropenem (2) and the penem analogue (3) which contain the same side chains at both C-2 and C-6 were performed using {sup 1}H NMR measurements together with 3-21G* level of ab initio MO and molecular mechanics calculations. The ab initio MO calculations reproduced the skeletons of these strained {beta}-lactam rings in good agreement with the crystallographic data. {sup 1}H NMR measurements in aqueous solution together with molecular modeling studies indicated that there were conformational differences of the C-2 and C-6 side chains in this series of compounds. These observations suggested that the conformational differences could affect their biological activities. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

Structural comparison of 1β-Methylcarbapenem, Carbapenem and Penem: NMR studies and theoretical calculations

International Nuclear Information System (INIS)

Sunagawa, M.; Sasaki, A.; Igarashi, J.-E.; Nishimura, T.

1998-01-01

Structural comparisons of meropenem (1), desmethyl meropenem (2) and the penem analogue (3) which contain the same side chains at both C-2 and C-6 were performed using 1 H NMR measurements together with 3-21G* level of ab initio MO and molecular mechanics calculations. The ab initio MO calculations reproduced the skeletons of these strained β-lactam rings in good agreement with the crystallographic data. 1 H NMR measurements in aqueous solution together with molecular modeling studies indicated that there were conformational differences of the C-2 and C-6 side chains in this series of compounds. These observations suggested that the conformational differences could affect their biological activities. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

Crystallographic and magnetic structure of the novel compound ErGe 1.83

Science.gov (United States)

Oleksyn, O.; Schobinger-Papamantellos, P.; Ritter, C.; de Groot, C. H.; Buschow, K. H. J.

1997-02-01

The crystal structure and the magnetic ordering of the novel orthorhombic compound ErGe 2-x has been studied by neutron powder diffraction and magnetic measurements. The crystal structure belongs to the DyGe 1.85-type (space group Cmc2 1)·ErGe 2-x ( x = 0.17 (2)) orders antiferromagnetically below TN = 6 K and displays a metamagnetic behaviour. The magnetic cell has the same size as the chemical unit cell ( q = 0 ). The magnetic space group is Cmc2 1 (Sh 36173). At T = 1.5 K the magnetic moments of the two erbium sites have the same ordered magnetic moment values of 7.63 (6) μB/Er and are antiferromagnetically coupled leading to an uniaxial structure along the a direction.

Crystallographic Investigation of Ag (4 mol%) Doped ZnO (SZO) Thin Films by XRD

International Nuclear Information System (INIS)

Lwin Lwin Nwe; Sandar Dwe; Khant Khant Lin; Khin Thuzar; Than Than Win; Ko Ko Kyaw Soe

2008-03-01

Silver doped ZnO(SZO) thin films are prepared by sol-based method. The silver dopant concentration is 4 mol % in this case. XRD analysis carried out to determine, crystallographic properties such as lattice parameters and crystallite size of SZO thin films.

Axial‐type olivine crystallographic preferred orientations: the effect of strain geometry on mantle texture

NARCIS (Netherlands)

Chatzaras, V.; Kruckenberg, Seth C.; Cohen, Shaina M.; Medaris Jr., L. Gordon; Withers, Anthony C.; Bagley, Brian

The effect of finite strain geometry on crystallographic preferred orientation (CPO) is poorly constrained in the upper mantle. Specifically, the relationship between shape preferred orientation (SPO) and CPO in the mantle rocks remains unclear. We analyzed a suite of 40 spinel peridotite xenoliths

Japan: Overview of activities on Neutron Imaging (NI) and Cultural Heritage (CH) studies

International Nuclear Information System (INIS)

Kiyanagi, Yoshiaki

2012-01-01

The pulsed neutron imaging using the time-of-flight method can give structural information on materials by using the characteristic features of the wavelength dependent neutron transmission. The crystal structure (lattice spacing), crystallite size, and preferred orientation in metal materials are investigated by analyzing the Bragg edge shapes and the elements by the resonance absorption peaks. Such information is important for characterizing the steels and other metal products, and only our group has the data analysis code for deducing such information. It is useful to apply the pulsed neutron imaging to the cultural heritages since the method helps to understand smithing and smelting processes of the specimens. The transmission method gives position dependent information and the diffraction gives complemental and more detailed data for the crystal structures and the textures. Therefore, the combined use of these methods is very useful for studying rigorously the crystal structure of cultural heritage samples. We have already collaborated with the Italian group for this direction, since the group has been performing the diffraction study. Therefore, we promote the research collaboratively for comprehensive and rigorous understanding of the crystallographic characteristics of the cultural heritages and archaeological specimens. The main object of this study is to obtain comprehensive crystallographic information of the cultural heritages and archaeological specimens. The main object of this study is to obtain comprehensive crystallographic information of the cultural heritages and the smithing and the smelting. To obtain such outcomes we are planning to perform mainly the pulsed neutron imaging using NOBORU at J-PARC, HUNS at Hokkaido University and INES at ISIS. We are the only group that can obtain the crystallographic images by using the pulsed neutron experiments coupled with the data analysis code we developed. In parallel we improve the Bragg edge analysis

Fundamental piezo-Hall coefficients of single crystal p-type 3C-SiC for arbitrary crystallographic orientation

Science.gov (United States)

Qamar, Afzaal; Dao, Dzung Viet; Phan, Hoang-Phuong; Dinh, Toan; Dimitrijev, Sima

2016-08-01

Piezo-Hall effect in a single crystal p-type 3C-SiC, grown by LPCVD process, has been characterized for various crystallographic orientations. The quantified values of the piezo-Hall effect in heavily doped p-type 3C-SiC(100) and 3C-SiC(111) for different crystallographic orientations were used to obtain the fundamental piezo-Hall coefficients, P 12 = ( 5.3 ± 0.4 ) × 10 - 11 Pa - 1 , P 11 = ( - 2.6 ± 0.6 ) × 10 - 11 Pa - 1 , and P 44 = ( 11.42 ± 0.6 ) × 10 - 11 Pa - 1 . Unlike the piezoresistive effect, the piezo-Hall effect for (100) and (111) planes is found to be independent of the angle of rotation of the device within the crystal plane. The values of fundamental piezo-Hall coefficients obtained in this study can be used to predict the piezo-Hall coefficients in any crystal orientation which is very important for designing of 3C-SiC Hall sensors to minimize the piezo-Hall effect for stable magnetic field sensitivity.

Hydrophilic Pt nanoflowers: synthesis, crystallographic analysis and catalytic performance.

Science.gov (United States)

Mourdikoudis, Stefanos; Altantzis, Thomas; Liz-Marzán, Luis M; Bals, Sara; Pastoriza-Santos, Isabel; Pérez-Juste, Jorge

2016-05-21

Water-soluble Pt nanoflowers (NFs) were prepared by diethylene glycol-mediated reduction of Pt acetylacetonate (Pt(acac) 2 ) in the presence of polyethylenimine. Advanced electron microscopy analysis showed that the NFs consist of multiple branches with a truncated cubic morphology and different crystallographic orientations. We demonstrate that the nature of the solvent strongly influences the resulting morphology. The catalytic performance of the Pt NFs in 4-nitrophenol reduction was found to be superior to that of other nanoparticle-based catalysts. Additionally, the Pt NFs display good catalytic reusability with no loss of activity after five consecutive cycles.

Neutron scattering study on R{sub 2}PdSi{sub 3} (R=Ho,Er,Tm) compounds

Energy Technology Data Exchange (ETDEWEB)

Tang, Fei

2010-12-14

Previous studies on the family of inter-metallic rare-earth compounds R{sub 2}PdSi{sub 3} revealed multifaceted magnetic properties, for instance, spin-glass like behavior. Experimental observations include: Signs of a crystallographic superstructure, complicated magnetic structures both in zero field and in applied magnetic fields as well as a generic phase in applied fields for compounds in the series with the heavy rare-earths R=Gd, Tb, Dy, Ho, Er and Tm. This thesis expands the studies on the magnetic properties of R{sub 2}PdSi{sub 3} employing mainly neutron scattering on single crystals with the focus on the compounds with R=Ho, Er and Tm. A detailed analysis of the crystallographic superstructure using modulation wave approach and group theory is presented. The resulting structure implies the existence of two different rare-earth sites with reduced symmetry and an arrangement of the different sites according to sequences as determined by the superstructure. It is shown that the reduced symmetry of the rare-earth sites is explicitly observed in the energy spectra of inelastic neutron scattering. The results on the magnetic structures and excitations are shown and discussed in the framework of the superstructure model. Specifically the generic phase in applied fields is interpreted as a direct consequence of the crystallographic superstructure. It is rather unusual that a crystallographic superstructure is playing such a decisive, and through the field dependence also tunable role in determining the magnetic properties as observed in R{sub 2}PdSi{sub 3}. The mediating interactions between the crystallographic part and the magnetic part of the system are discussed. (orig.)

Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

Science.gov (United States)

Nagy, Julia; Eilert, Tobias; Michaelis, Jens

2018-03-01

Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Bayesian parameter estimation-based analysis method and software, is an interesting method since it allows for the localization of unknown fluorescent dye molecules attached to macromolecular complexes based on single-molecule Förster resonance energy transfer (smFRET) measurements. However, the precision, accuracy, and reliability of structural models derived from results based on such complex calculation schemes are oftentimes difficult to evaluate. Therefore, we present two proof-of-principle benchmark studies where we use smFRET data to localize supposedly unknown positions on a DNA as well as on a protein-nucleic acid complex. Since we use complexes where structural information is available, we can compare Fast-NPS localization to the existing structural data. In particular, we compare different dye models and discuss how both accuracy and precision can be optimized.

Structural transformations in quenched Fe-Ga alloys

International Nuclear Information System (INIS)

Lograsso, T.A.; Ross, A.R.; Schlagel, D.L.; Clark, A.E.; Wun-Fogle, M.

2003-01-01

It has been speculated that the large increase in magnetostriction in Fe-Ga alloys results from local short-range ordering of the Ga atoms along specific crystallographic directions in the disordered Fe structure. The structural transitions associated with different cooling rates from the high temperature disordered state were investigated with X-ray diffraction of oriented single crystals of Fe-19 at% Ga. Results are presented for long-range ordering during slow cooling and indirect evidence of local short-range ordering of Ga atoms in the disordered state when the alloys are quenched is also presented. In the latter case, the short-range ordering of Ga atoms leads to a tetragonal distortion of the lattice. The dependence of the magnetostrictive response of Fe-Ga alloys on thermal history has been found to be directly related to these structural transformations in Fe-19 at% Ga alloys and experimental support for the proposed magnetostriction model based on Ga-Ga pairing along [100] crystallographic directions is presented

Crystallization and preliminary crystallographic studies of a cysteine protease inhibitor from the human nematode parasite Ascaris lumbricoides

International Nuclear Information System (INIS)

Liu, Sanling; Dong, Jianmei; Mei, Guoqiang; Liu, Guiyun; Xu, Wei; Su, Zhong; Liu, Jinsong

2011-01-01

A recombinant cysteine protease inhibitor from the human nematode parasite A. lumbricoides has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.1 Å resolution. The cysteine protease inhibitor from Ascaris lumbricoides, a roundworm that lives in the human intestine, may be involved in the suppression of human immune responses. Here, the molecular cloning, protein expression and purification, preliminary crystallization and crystallographic characterization of the cysteine protease inhibitor from A. lumbricoides are reported. The rod-shaped crystal belonged to space group C2, with unit-cell parameters a = 99.40, b = 37.52, c = 62.92 Å, β = 118.26°. The crystal diffracted to 2.1 Å resolution and contained two molecules in the asymmetric unit

Solving the RNA polymerase I structural puzzle

Energy Technology Data Exchange (ETDEWEB)

Moreno-Morcillo, María [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Taylor, Nicholas M. I. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Gruene, Tim [Georg-August-University, Tammannstrasse 4, 37077 Göttingen (Germany); Legrand, Pierre [SOLEIL Synchrotron, L’Orme de Merisiers, Saint Aubin, Gif-sur-Yvette (France); Rashid, Umar J. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Ruiz, Federico M. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Steuerwald, Ulrich; Müller, Christoph W. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Fernández-Tornero, Carlos, E-mail: cftornero@cib.csic.es [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)

2014-10-01

Details of the RNA polymerase I crystal structure determination provide a framework for solution of the structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information such as the location of the enzyme active site. Knowing the structure of multi-subunit complexes is critical to understand basic cellular functions. However, when crystals of these complexes can be obtained they rarely diffract beyond 3 Å resolution, which complicates X-ray structure determination and refinement. The crystal structure of RNA polymerase I, an essential cellular machine that synthesizes the precursor of ribosomal RNA in the nucleolus of eukaryotic cells, has recently been solved. Here, the crucial steps that were undertaken to build the atomic model of this multi-subunit enzyme are reported, emphasizing how simple crystallographic experiments can be used to extract relevant biological information. In particular, this report discusses the combination of poor molecular replacement and experimental phases, the application of multi-crystal averaging and the use of anomalous scatterers as sequence markers to guide tracing and to locate the active site. The methods outlined here will likely serve as a reference for future structural determination of large complexes at low resolution.

Preparation and structural study of LaMnO3 magnetic material

International Nuclear Information System (INIS)

Moreno, L.C.; Valencia, J.S.; Landinez Tellez, D.A.; Arbey Rodriguez M, J.; Martinez, M.L.; Roa-Rojas, J.; Fajardo, F.

2008-01-01

We report the crystallographic parameters of LaMnO 3 obtained from X-ray diffraction data and electronic properties predictions using the density functional theory (DFT). LaMnO 3 was prepared by the citrate precursor method (CPM). The initial solution was 0.1 M of each cation and the citrate nitrate relation was one. The solution was dried at 373 K; the yielded foam was annealed at 873 K and then was characterized by X-ray diffraction. Diffraction peaks show that the space group is R-3c (no. 167) with a=b =5.523 A and c=13.324 A (rhombohedrally distorted perovskite). Structural results of the Rietveld method have a matching of 97% with that obtained from the Structure Prediction Diagnostic Software. DFT calculation reveals a half-metallic character and its magnetic moment is about 2.0 μ B

Effects of side-chain and electron exchange correlation on the band structure of perylene diimide liquid crystals: a density functional study.

Science.gov (United States)

Arantes, J T; Lima, M P; Fazzio, A; Xiang, H; Wei, Su-Huai; Dalpian, G M

2009-04-23

The structural and electronic properties of perylene diimide liquid crystal PPEEB are studied using ab initio methods based on the density functional theory (DFT). Using available experimental crystallographic data as a guide, we propose a detailed structural model for the packing of solid PPEEB. We find that due to the localized nature of the band edge wave function, theoretical approaches beyond the standard method, such as hybrid functional (PBE0), are required to correctly characterize the band structure of this material. Moreover, unlike previous assumptions, we observe the formation of hydrogen bonds between the side chains of different molecules, which leads to a dispersion of the energy levels. This result indicates that the side chains of the molecular crystal not only are responsible for its structural conformation but also can be used for tuning the electronic and optical properties of these materials.

Development of triple scale finite element analyses based on crystallographic homogenization methods

International Nuclear Information System (INIS)

Nakamachi, Eiji

2004-01-01

Crystallographic homogenization procedure is implemented in the piezoelectric and elastic-crystalline plastic finite element (FE) code to assess its macro-continuum properties of piezoelectric ceramics and BCC and FCC sheet metals. Triple scale hierarchical structure consists of an atom cluster, a crystal aggregation and a macro- continuum. In this paper, we focus to discuss a triple scale numerical analysis for piezoelectric material, and apply to assess a macro-continuum material property. At first, we calculate material properties of Perovskite crystal of piezoelectric material, XYO3 (such as BaTiO3 and PbTiO3) by employing ab-initio molecular analysis code CASTEP. Next, measured results of SEM and EBSD observations of crystal orientation distributions, shapes and boundaries of a real material (BaTiO3) are employed to define an inhomogeneity of crystal aggregation, which corresponds to a unit cell of micro-structure, and satisfies the periodicity condition. This procedure is featured as a first scaling up from the molecular to the crystal aggregation. Finally, the conventional homogenization procedure is implemented in FE code to evaluate a macro-continuum property. This final procedure is featured as a second scaling up from the crystal aggregation (unit cell) to macro-continuum. This triple scale analysis is applied to design piezoelectric ceramic and finds an optimum crystal orientation distribution, in which a macroscopic piezoelectric constant d33 has a maximum value

Effects of crystallographic texture on stress-migration resistance in copper thin films

International Nuclear Information System (INIS)

Koike, J.; Wada, M.; Sanada, M.; Maruyama, K.

2002-01-01

The crystallographic texture of heat-treated Cu thin films and its effects on stress-migration resistance were studied as a function of film thickness within a range of 50-900 nm. All as-deposited films had (111) texture. After heat treatment at 723 K, texture transition from (111) to (100) was observed in films of thickness greater than 300 nm. The (111) texture films after heat treatment showed severe stress migration; in contrast, the (100) texture films showed no noticeable stress migration. The observed stress-migration resistance in the (100) texture films can be attributed to the absence of twins and to lower thermal stress as compared with the (111) texture films

The distribution of intervariant crystallographic planes in a lath martensite using five macroscopic parameters

International Nuclear Information System (INIS)

Beladi, Hossein; Rohrer, Gregory S.; Rollett, Anthony D.; Tari, Vahid; Hodgson, Peter D.

2014-01-01

Electron backscatter diffraction analysis was employed to compute the closest orientation relationship and the distribution of intervariant boundary character in a lath martensitic microstructure. The misorientations were close to the Kurdjumov–Sachs orientation relationship. The intervariant crystallographic plane distribution exhibited a relatively high anisotropy with a tendency for the lath interfaces to terminate on (1 1 0) planes. This results from the crystallographic constraints associated with the shear transformation rather than a low energy interface configuration. The lath martensite habit plane was determined to be mostly (1 1 0) or near (1 1 0). The relative populations of boundaries with [1 1 1] and [1 1 0] misorientations were greater than other high index misorientations, mostly characterized as (1 1 0) symmetric tilt and (1 1 0) twist boundary types, respectively. Analysis with homology metrics of the connectivity in the lath martensitic microstructure revealed the connectivity dominated by population of misorientation angle and boundary plane type

XTAL system of crystallographic programs: programmer's manual

International Nuclear Information System (INIS)

Hall, S.R.; Stewart, J.M.; Norden, A.P.; Munn, R.J.; Freer, S.T.

1980-02-01

This document establishes the basis for collaborative writing of transportable computer programs for x-ray crystallography. The concepts and general-purpose utility subroutines described here can be readily adapted to other scientific calculations. The complete system of crystallographic programs and subroutines is called XTAL and replaces the XRAY (6,7,8) system of programs. The coding language for the XTAL system is RATMAC (5). The XTAL system of programs contains routines for controlling execution of application programs. In this sense it forms a suboperating system that presents the same computational environment to the user and programmer irrespective of the operating system in use at a particular installation. These control routines replace all FORTRAN I/O code, supply character reading and writing, supply binary file reading and writing, serve as a support library for applications programs, and provide for interprogram communication

Study on Crystallographic Orientation Effect on Surface Generation of Aluminum in Nano-cutting.

Science.gov (United States)

Xu, Feifei; Fang, Fengzhou; Zhu, Yuanqing; Zhang, Xiaodong

2017-12-01

The material characteristics such as size effect are one of the most important factors that could not be neglected in cutting the material at nanoscale. The effects of anisotropic nature of single crystal materials in nano-cutting are investigated employing the molecular dynamics simulation. Results show that the size effect of the plastic deformation is based on different plastic carriers, such as the twin, stacking faults, and dislocations. The minimum uncut chip thickness is dependent on cutting direction, where even a negative value is obtained when the cutting direction is {110}. It also determines the material deformation and removal mechanism (e.g., shearing, extruding, and rubbing mechanism) with a decrease in uncut chip thickness. When material is deformed by shearing, the primary shearing zone expands from the stagnation point or the tip of stagnation zone. When a material is deformed by extruding and rubbing, the primary deformation zone almost parallels to the cutting direction and expands from the bottom of the cutting edge merging with the tertiary deformation zone. The generated surface quality relates to the crystallographic orientation and the minimum uncut chip thickness. The cutting directions of {110}, {110}, and {111}, whose minimum uncut chip thickness is relatively small, have better surface qualities compared to the other cutting direction.

The distribution function of crystalline orientation's usefulness in crystallographic texture analysis

International Nuclear Information System (INIS)

Hermida, J.D.; Pochettino, A.A.

1982-01-01

The theoretical fundaments of the Distribution Function of Crystalline Orientations (DFCO) are described and this method is compared with the usual description of the crystallographic texture by direct pole figures. Such function is applied to the study of a Zry-4 sample obtained from a tube belonging to a CANDU type fuel element. The DFCO is obtained from the pole figures (0002), (101-bar0) and (101-bar1). The results show the existence of six fundamental components of texture, which are enunciated below, in decreasing order of importance: (2-bar115) ; (3-bar128) ; (1-bar013) ; (2-bar114) ; (0001) ; (0001) . A much more complete view of the crystals' orientation state of such sample can be obtained by analyzing the weight and the distribution of the different components. (M.E.L.) [es

Microstructure and crystallographic texture evolution during TIG welding of zircaloy-2 material

International Nuclear Information System (INIS)

Jha, S.K.; Singh, R.P.; Singh, V.K.; Ramanathan, R.; Samjdar, I.; Srivastava, D.; Tewari, R.; Dey, G.K.

2005-01-01

Zirconium and its alloys are extensively used as structural materials in nuclear reactors, because of better neutron economy, good corrosion resistance in water and good mechanical properties at operating temperature. Zircaloy-2 and zircaloy-4 are widely used in both pressurized water reactors (PWR) and boiling water reactors (BWR) as fuel cladding materials and as calandria tube and pressure tube materials in pressurized heavy water reactors (PHWR). The satisfactory performance and the life of the reactor components depend mainly upon their mechanical properties, corrosion properties and dimensional stability in the reactor condition, which are strong function of metallurgical parameters such as microstructure and texture. Therefore, for best performance of the reactor components these parameters are optimized during their fabrication. The microstructure and texture of the zircaloy-2 components are expected to get modified during the welding of the components. In this study the evolution of the microstructure and texture has been investigated as a function of the welding parameters. Heat input was varied the current and welding time. A variety of analytical techniques have been applied for the study on microstructure and texture of the welds. Optical microscopy and electron microscopy were used to evaluate the detailed microstructure. X-ray diffraction (XRD) was used investigate the crystallographic textures among the base metal, heat affected zone and fusion zone. Particular attention was focused on the determination of microtexture in weld by using electron backscatter diffraction (EBSD) technique. After that, an effort was put to compare the results of X-ray macro-texture and EBS-microtexture. (author)

Crystallographic structure and magnetic properties of pseudobrookite Fe2-xNixTiO5 system (x = 0, 0.1, 0.2, 0.3, 0.5 and 1)

International Nuclear Information System (INIS)

Yosef Sarwanto and Wisnu Ari Adi

2018-01-01

Crystallographic structure and magnetic properties of pseudobrookite Fe 2-x Ni x TiO 5 system (x=0, 0.1, 0.2, 0.3 ,0.5 and 1)have been performed through solid state reaction. Pseudobrookite Fe 2-x Ni x TiO 5 system was synthesized by mixing of Fe 2 O 3 , NiO, and TiO 2 with stoichiometry composition using wet mill. The mixture was milled for 5 hours and sintered in the electric chamber furnace at 1000 °C in the air at atmosphere pressure for 5 hours. The refinement against of X-ray diffraction data shows that the samples with composition of (x = 0) and (x = 0.1) have a single phase with Fe 2 TiO 5 structure. How ever the samples with composition of (x > 0.1) consist of multiple phases, namely Fe 2-x Ni x TiO 5 , FeTiO 3 , Fe 2 NiO 4 and NiO. Particle morphologies of the composition x = 0 and x =0.1 are homogenous and uniform on the sample surface with a polygonal particle shape and particle size varies. At room temperature, the sample with x =0 is paramagnetic and that with x =0.1 is ferromagnetic. Magnetic phase transformation of this study is the caused by the present of Ni substituted Fe in the system. Thus substitution Ni into Fe on the system pseudobrookite Fe 2 TiO 5 only capable of 0.1 at.% without changing the crystal structure of the material. It means that there is an interaction between the magnetic spin Fe 3+ on the 3d 5 configurations and Ni 2 + on the 3d 3 configurations through the mechanism of double exchange. Double exchange mechanism is a magnetic type of exchange that appears between the ions Fe 3+ and Ni 2+ adjacent in different oxidation states. (author)

CIF2Cell: Generating geometries for electronic structure programs

Science.gov (United States)

Björkman, Torbjörn

2011-05-01

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP. Program summaryProgram title: CIF2Cell Catalogue identifier: AEIM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL version 3 No. of lines in distributed program, including test data, etc.: 12 691 No. of bytes in distributed program, including test data, etc.: 74 933 Distribution format: tar.gz Programming language: Python (versions 2.4-2.7) Computer: Any computer that can run Python (versions 2.4-2.7) Operating system: Any operating system that can run Python (versions 2.4-2.7) Classification: 7.3, 7.8, 8 External routines: PyCIFRW [1] Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file. Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF

On the use of distorted fcc structures for describing high-pressure phases

International Nuclear Information System (INIS)

Gerward, L.; Staun Olsen, J.; Benedict, U.

1986-01-01

The paper describes distorted lattices that can be derived from the face-centred cubic Bravais lattice. Crystallographic principles are outlined and it is discussed how various lattices can be identified from the observed splitting of X-ray powder diffraction lines. Examples are taken from recent high-pressure studies of actinide rocksalt structure compounds and cerium metal. (orig.)

The structure of allophycocyanin from Thermosynechococcus elongatus at 3.5 Å resolution

Energy Technology Data Exchange (ETDEWEB)

Murray, James William; Maghlaoui, Karim; Barber, James, E-mail: j.barber@imperial.ac.uk [Division of Molecular Biosciences, Imperial College, Exhibition Road, London SW7 2AZ (United Kingdom)

2007-12-01

The crystal structure of a light-harvesting protein that interacts with photosystem II is reported. Cyanobacteria and red algae use light-harvesting pigments bound by proteins to capture solar radiation and to channel excitation energy into their reaction centres. In most cyanobacteria, a multi-megadalton soluble structure known as the phycobilisome is a major light-harvesting system. Allophycocyanin is the main component of the phycobilisome core, forming a link between the rest of the phycobilisome and the reaction-centre core. The crystal structure of allophycocyanin from Thermosynechococcus elongatus (TeAPC) has been determined and refined at 3.5 Å resolution to a crystallographic R value of 26.0% (R{sub free} = 28.5%). The structure was solved by molecular replacement using the allophycocyanin structure from Spirulina platensis as the search model. The asymmetric unit contains an (αβ) monomer which is expanded by symmetry to a crystallographic trimer.

Crystallographic identification of an unexpected by-product in an Ullman's reaction toward biphenyls: 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

Science.gov (United States)

Manzano, Veronica E; Baggio, Ricardo; Cukiernik, Fabio D

2015-11-01

The synthesis of 3,3'-diacetoxy-4,4'-bis(hexyloxy)biphenyl following the nickel-modified Ullmann reaction yielded a by-product which was identified successfully by crystallographic analysis as 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3. This unexpected nonbiphenyl by-product exhibited IR, (1)H NMR, (13)C NMR and COSY (correlation spectroscopy) spectra fully consistent with the proposed structure. The compound crystallized in the orthorombic Pbca space group, with two independent formula units in the asymmetric unit (one of which was slightly disordered), and showed a supramolecular architecture in which molecules linked by hydroxy-ethanone O-H···O interactions are organized in columns separated by the aliphatic tails.

Electrodeposition of nanocrystalline CdSe thin films from dimethyl sulfoxide solution: Nucleation and growth mechanism, structural and optical studies

International Nuclear Information System (INIS)

Henriquez, R.; Badan, A.; Grez, P.; Munoz, E.; Vera, J.; Dalchiele, E.A.; Marotti, R.E.; Gomez, H.

2011-01-01

Highlights: → Electrodeposition of CdSe nanocrystalline semiconductor thin films. → Polycrystalline wurtzite structure with a slight (1010) preferred orientation. → Absorption edge shifts in the optical properties due to quantum confinement effects. - Abstract: Cadmium selenide (CdSe) nanocrystalline semiconductor thin films have been synthesized by electrodeposition at controlled potential based in the electrochemical reduction process of molecular selenium in dimethyl sulfoxide (DMSO) solution. The nucleation and growth mechanism of this process has been studied. The XRD pattern shows a characteristic polycrystalline hexagonal wurtzite structure with a slight (1 0 1 0) crystallographic preferred orientation. The crystallite size of nanocrystalline CdSe thin films can be simply controlled by the electrodeposition potential. A quantum size effect is deduced from the correlation between the band gap energy and the crystallite size.

Purification, crystallization and preliminary crystallographic studies of haemoglobin from mongoose (Helogale parvula) in two different crystal forms induced by pH variation.

Science.gov (United States)

Mohamed Abubakkar, M; Saraboji, K; Ponnuswamy, M N

2013-02-01

Haemoglobin (Hb) is a respiratory pigment; it is a tetrameric protein that ferries oxygen from the lungs to tissues and transports carbon dioxide on the return journey. The oxygen affinity of haemoglobin is regulated by the concentration of oxygen surrounding it and several efforts have revealed the shapes of Hb in different states and with different functions. However, study of the molecular basis of Hbs from low-oxygen-affinity species is critically needed in order to increase the understanding of the mechanism behind oxygen adaptation. The present study reports the preliminary crystallographic study of low-oxygen-affinity haemoglobin from mongoose, a burrowing mammal. Haemoglobin from mongoose was purified by anion-exchange chromatography, crystallized using the hanging-drop vapour-diffusion method and diffraction data sets were collected from monoclinic (2.3 Å resolution) and orthorhombic (2.9 Å resolution) crystal forms obtained by pH variation. The monoclinic and orthorhombic asymmetric units contained half and a whole biological molecule, respectively.

Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies

Energy Technology Data Exchange (ETDEWEB)

AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio; Egea, Pascal F.

2017-06-01

Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.

Neutron diffraction technique as a method for material studies

International Nuclear Information System (INIS)

Belhorma, B.; Labrim, H.; Gandou, Z.

2010-01-01

The Morocco's first Nuclear Research has been constructed in CNESTEN. The reactor divergence has been tested, and the nominal power of 2MW was successfully achieved. The reactor has 4 beam ports two of them are projected for neutron scattering. Such technique allows studying the crystallographic and magnetic structures of materials using the thermal neutrons produced in the reactor. the powder diffractometer has been designed. Component reception and installation procedures are in progress. The second experiment consists on small angle neutron scattering that allows the study of soft matter and polymers in the range of 1-50 nm. The third technique that can complete the two previous is the 4-circle neutron spectrometry which is designed mainly to study structural properties of the mono-crystalline material and texture.This technique is complementary to the X-ray diffraction already available in CNESTEN. Some applications of this technique are: --to determine the crystallographic and magnetic structure of polycrystalline materials.-- to study the texture in metals and alloys.-- to perform holography measurement

Preliminary crystallographic analysis of two hypothetical ribose-5-phosphate isomerases from Streptococcus mutans

International Nuclear Information System (INIS)

Wang, Chen; Fan, Xuexin; Cao, Xiaofang; Liu, Xiang; Li, Lanfen; Su, Xiaodong

2012-01-01

Two hypothetical ribose-5-phosphate isomerases from S. mutans have been produced in E. coli and crystallized. The crystals diffracted to high resolutions suitable for crystallographic analyses. Study of the enzymes from sugar metabolic pathways may provide a better understanding of the pathogenesis of the human oral pathogen Streptococcus mutans. Bioinformatics, biochemical and crystallization methods were used to characterize and understand the function of two putative ribose-5-phosphate isomerases: SMU1234 and SMU2142. The proteins were cloned and constructed with N-terminal His tags. Protein purification was performed by Ni 2+ -chelating and size-exclusion chromatography. The crystals of SUM1234 diffracted to 1.9 Å resolution and belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 48.97, b = 98.27, c = 101.09 Å, α = β = γ = 90°. The optimized SMU2142 crystals diffracted to 2.7 Å resolution and belonged to space group P1, with unit-cell parameters a = 53.7, b = 54.1, c = 86.5 Å, α = 74.2, β = 73.5, γ = 83.7°. Initial phasing of both proteins was attempted by molecular replacement; the structure of SMU1234 could easily be solved, but no useful results were obtained for SMU2142. Therefore, SeMet-labelled SMU2142 will be prepared for phasing

Crystallization and preliminary crystallographic studies of LipA, a secretory lipase/esterase from Xanthomonas oryzae pv. oryzae

Energy Technology Data Exchange (ETDEWEB)

Aparna, Gudlur; Chatterjee, Avradip; Jha, Gopaljee; Sonti, Ramesh V.; Sankaranarayanan, Rajan, E-mail: sankar@ccmb.res.in [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India)

2007-08-01

The crystallization and preliminary crystallographic studies of LipA, a lipase/esterase secreted by X. oryzae pv. oryzae during its infection of rice plants, are reported. Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight, a serious disease of rice. Several enzymes that are secreted through the type II secretion system of this bacterium play an important role in the plant–microbe interaction, being important for virulence and also being able to induce potent host defence responses. One of these enzymes is a secretory lipase/esterase, LipA, which shows a very weak homology to other bacterial lipases and gives a positive tributyrin plate assay. In this study, LipA was purified from the culture supernatant of an overexpressing clone of X. oryzae pv. oryzae and two types of crystals belonging to space group C2 but with two different unit-cell parameters were obtained using the hanging-drop vapour-diffusion method. Type I crystals diffract to a maximum resolution of 1.89 Å and have unit-cell parameters a = 93.1, b = 62.3, c = 66.1 Å, β = 90.8°. Type II crystals have unit-cell parameters a = 103.6, b = 54.6, c = 66.3 Å, β = 92.6° and diffract to 1.86 Å. Solvent-content analysis shows one monomer in the asymmetric unit in both the crystal forms.

Magnetic structure and lattice deformation in UO/sub 2/

Energy Technology Data Exchange (ETDEWEB)

Aksenov, V L; Frauenheim, T; Sikora, V [Joint Inst. for Nuclear Research, Dubna (USSR)

1981-12-21

The magnetic phase transition in UO/sub 2/ is studied by means of a group theoretical analysis and the admitted symmetry groups in the low temperature phase are determined. With the help of the neutron diffraction data of Faber and Lander a three-arm magnetic and crystallographic structure with two types of translational domains is found and a new interpretation of the experiment of Faber and Lander is given.

Synthesis, crystallographic and magnetic properties of protactinium pnictides

International Nuclear Information System (INIS)

Hery, Yves.

1979-03-01

From a theoretical point of view, protactinium lies in a very important place in the periodic system for it seems to be the first element of the actinide series where the 5f state is occupied. We have studied protactinium pnictides, particularly arsenides and antimonides. PaAs 2 , Pa 3 As 4 , PaSb 2 and Pa 3 Sb 4 were synthetized and their crystallographic properties were determined and discussed. We have measured the magnetic susceptibilities of PaC, PaAs 2 and PaSb 2 . Protactinium exhibits a dual character. In its monocarbide, which is a weakly diamagnet, it behaves as a transition element while in the temperature independent paramagnets PaAs 2 and PaSb 2 , it behaves like a 'f' element. This 'f' element character increases with increasing metal-metal distances. Furthermore the radial expansion of the protactinium 5f orbital seems to be more important than the Uranium one, and consequently the corresponding protactinium 5f electrons are less localized. In addition, some protactinium chalcogenides (βPaS 2 , γPaSe 2 and PaOSe) have been identified [fr

Influence of crystallographic orientation on the fracture toughness of strongly textured Ti--6Al--4V

International Nuclear Information System (INIS)

Bowen, A.W.

1978-01-01

Fracture toughness values for six test piece orientations in a strongly textured 57-mm thick rolled and annealed Ti--6Al--4V bar have been related to their crystallographic orientations. The K/sub Ic/ values, ranging from 46.3 to 93.3 MPa/m, could be divided into two groups. High values (74.7 to 93.3 MPa/m) were obtained when a crystallographic deformation mode ([1010] or [1122] slip) was parallel to the planes of maximum shear stress for plane strain conditions, and the significant fractographic feature for this group was a clearly defined stretch zone. In the second group, where crystallographic deformation modes were not aligned with the planes of maximum shear stress, much lower K/sub Ic/ values were recorded (46.3 to 50.7 MPa/m). In this case there was no stretch zone and, in addition, some test pieces appeared, in effect, to have delaminated in the immediate vicinity of the crack tip. Similar trends were also indicated by the results of Charpy impact tests. The influence of in-plane elastic anisotropy on fracture toughness is discussed, and the importance of test piece geometry highlighted. From the results it could be inferred that high toughness in anisotropic materials is possible only in certain orientations; stretch zone formation and fatigue striation formation are by the same mechanical process; and there will be significantly different critical crack sizes in textured titanium alloy components

Overexpression, purification and crystallographic analysis of a unique adenosine kinase from Mycobacterium tuberculosis

Energy Technology Data Exchange (ETDEWEB)

Wang, Yimin; Long, Mary C.; Ranganathan, Senthil; Escuyer, Vincent; Parker, William B.; Li, Rongbao, E-mail: li@sri.org [Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama 35205 (United States)

2005-06-01

Adenosine kinase from M. tuberculosis has been overexpressed, purified and crystallized in the presence of adenosine. Structure determination using molecular replacement with diffraction data collected at 2.2 Å reveals a dimeric structure. Adenosine kinase from Mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. The enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against M. tuberculosis. The mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine analogs) may prove to be a novel therapeutic intervention for this disease. The M. tuberculosis adenosine kinase was overexpressed in Escherichia coli and the enzyme was purified with activity comparable to that reported previously. The protein was crystallized in the presence of adenosine using the vapour-diffusion method. The crystals diffracted X-rays to high resolution and a complete data set was collected to 2.2 Å using synchrotron radiation. The crystal belonged to space group P3{sub 1}21, with unit-cell parameters a = 70.2, c = 111.6 Å, and contained a single protein molecule in the asymmetric unit. An initial structural model of the protein was obtained by the molecular-replacement method, which revealed a dimeric structure. The monomers of the dimer were related by twofold crystallographic symmetry. An understanding of how the M. tuberculosis adenosine kinase differs from the human homolog should aid in the design of more potent and selective antimycobacterial agents that are selectively activated by this enzyme.

Overexpression, purification and crystallographic analysis of a unique adenosine kinase from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Wang, Yimin; Long, Mary C.; Ranganathan, Senthil; Escuyer, Vincent; Parker, William B.; Li, Rongbao

2005-01-01

Adenosine kinase from M. tuberculosis has been overexpressed, purified and crystallized in the presence of adenosine. Structure determination using molecular replacement with diffraction data collected at 2.2 Å reveals a dimeric structure. Adenosine kinase from Mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. The enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against M. tuberculosis. The mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine analogs) may prove to be a novel therapeutic intervention for this disease. The M. tuberculosis adenosine kinase was overexpressed in Escherichia coli and the enzyme was purified with activity comparable to that reported previously. The protein was crystallized in the presence of adenosine using the vapour-diffusion method. The crystals diffracted X-rays to high resolution and a complete data set was collected to 2.2 Å using synchrotron radiation. The crystal belonged to space group P3 1 21, with unit-cell parameters a = 70.2, c = 111.6 Å, and contained a single protein molecule in the asymmetric unit. An initial structural model of the protein was obtained by the molecular-replacement method, which revealed a dimeric structure. The monomers of the dimer were related by twofold crystallographic symmetry. An understanding of how the M. tuberculosis adenosine kinase differs from the human homolog should aid in the design of more potent and selective antimycobacterial agents that are selectively activated by this enzyme

Realization of highly crystallographic three-dimensional nanosheets by a stress-induced oriented-diffusion method

Energy Technology Data Exchange (ETDEWEB)

Gharooni, M.; Hosseini, M.; Mohajerzadeh, S., E-mail: mohajer@ut.ac.ir; Taghinejad, M.; Taghinejad, H. [Thin Film and Nanoelectronics Lab, Nanoelectronics Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Tehran 143957131 (Iran, Islamic Republic of); Abdi, Y. [Nano-Physics Research Lab, Department of Physics, University of Tehran, Tehran 1439955961 (Iran, Islamic Republic of)

2014-07-28

Morphologically controlled nanostructures have been increasingly important because of their strongly shape dependent physical and chemical properties. Formation of nanoscale silicon based structures that employ high levels of strain, intentional, and unintentional twins or grain boundaries can be dramatically different from the commonly conceived bulk processes. We report, realization of highly crystallographic 3D nanosheets with unique morphology and ultra-thin thickness by a stress-induced oriented-diffusion method, based on plasma processing of metal layer deposited on Si substrate and its post deep reactive ion etching. Annealing in plasma ambient creates rod-like metal alloy precursors which induce stress at its interface with Si substrate due to the mismatch of lattice constants. This stress opens facilitated gateways for orientated-diffusion of metal atoms in 〈110〉 directions and leads to formation of NSs (nanosheets) with [111] crystalline essence. Nanosheets are mainly triangular, hexagonal, or pseudo hexagonal in shape and their thicknesses are well controlled from several to tens of nanometers. The structural and morphological evolution of features were investigated in detail using transmission electron microscope, atomic force microscope, scanning electron microscope and possible mechanism is proposed to explain the formation of the thermodynamically unfavorable morphology of nanosheets. Significant photoemission capability of NSs was also demonstrated by photoluminescence spectroscopy.

Influences of crystallographic orientations on deformation mechanism and grain refinement of Al single crystals subjected to one-pass equal-channel angular pressing

International Nuclear Information System (INIS)

Han, W.Z.; Zhang, Z.F.; Wu, S.D.; Li, S.X.

2007-01-01

The influences of crystallographic orientations on the evolution of dislocation structures and the refinement process of sub-grains in Al single crystals processed by one-pass equal-channel angular pressing (ECAP) were systematically investigated by means of scanning electron microscopy, electron backscatter diffraction and transmission electron microscopy. Three single crystals with different orientations, denoted as crystal I, crystal II and crystal III, were specially designed according to the shape of the ECAP die. For crystal I, its insert direction is parallel to [1 1 0] and its extrusion direction is parallel to [1-bar11]. For crystal II, the (1-bar11) plane is located parallel to the intersection plane of the ECAP die, and the [1 1 0] direction is along the general shear direction on the intersection plane. For crystal III, the (1-bar11) plane is laid on the plane perpendicular to the intersection of the ECAP die, and the [1 1 0] direction is vertical to the general shear direction. For crystal I, abundant cell block structures with multi-slip characters were formed, and they should be induced by four symmetric slip systems, while for crystal II, there are two sets of sub-grain structures with higher misorientation, making an angle of ∼70 deg., which can be attributed to the interactions of the two asymmetric primary slip planes, whereas for crystal III, only one set of ribbon structures was parallel to the traces of (1-bar11) with the lowest misorientation angle among the three single crystals, which should result from the homogeneous slip on the primary slip plane. The different microstructural features of the three single crystals provide clear experimental evidence that the microstructures and misorientation evolution are strongly affected by the crystallographic orientation or by the interaction between shear deformation imposed by the ECAP die and the intrinsic slip deformation of the single crystals. Based on the experimental results and the

X-ray diffraction studies of the structure and orientations of thiophene and fluorenone based molecule

International Nuclear Information System (INIS)

Porzio, William; Pasini, Mariacecilia; Destri, Silvia; Giovanella, Umberto; Fontaine, Philippe

2006-01-01

The crystal structure of a conjugated molecule containing thiophene and fluorenone residues has been determined from powder X-ray diffraction (XRD). Thin films ( -5 Pa) onto oxidized silicon substrates, are oriented along with different crystallographic directions. A comparison of XRD in both Grazing Incidence and Bragg-Brentano geometries allowed to perform a quantitative analysis of the various orientations. This approach is generally applicable in the case of multi-oriented films. The results fully account for the poor performance of this molecule in p-type field effect transistor devices

Study of the optical properties and structure of ZnSe/ZnO thin films grown by MOCVD with varying thicknesses

Energy Technology Data Exchange (ETDEWEB)

Jabri, S., E-mail: slaheddine.jabri@fst.rnu.tn [Unité des nanomatériaux et photoniques, Faculté des Sciences de Tunis, Campus Universitaire Ferhat Hachad, El Manar, 2092 Tunis (Tunisia); Amiri, G.; Sallet, V. [Groupe d’Etude de la Matière Condensée, CNRS-Université de Versailles St Quentin, Université Paris-Saclay, 45 avenue des Etats Unis, 78035 Versailles Cedex (France); Souissi, A. [Laboratoire de Photovoltaïque, Centre de Recherches et des Technologies de l’Energie, Technopole Borj Cedria, B.P. 95, Hammammlif 2050 (Tunisia); Meftah, A. [Unité des nanomatériaux et photoniques, Faculté des Sciences de Tunis, Campus Universitaire Ferhat Hachad, El Manar, 2092 Tunis (Tunisia); Galtier, P. [Groupe d’Etude de la Matière Condensée, CNRS-Université de Versailles St Quentin, Université Paris-Saclay, 45 avenue des Etats Unis, 78035 Versailles Cedex (France); Oueslati, M. [Unité des nanomatériaux et photoniques, Faculté des Sciences de Tunis, Campus Universitaire Ferhat Hachad, El Manar, 2092 Tunis (Tunisia)

2016-05-15

ZnSe layers were grown on ZnO substrates by the metal organic chemical vapor deposition technique. A new structure appeared at lower thicknesses films. The structural properties of the thin films were studied by the X-ray diffraction (XRD) and Raman spectroscopy methods. First, Raman selection rules are explicitly put forward from a theoretical viewpoint. Second, experimentally-retrieved-intensities of the Raman signal as a function of polarization angle of incident light are fitted to the obtained theoretical dependencies in order to confirm the crystallographic planes of zinc blend ZnSe thin film, and correlate with DRX measurements. Raman spectroscopy has been used to characterize the interfacial disorder that affects energy transport phenomena at ZnSe/ZnO interfaces and the Photoluminescence (PL) near the band edge of ZnSe thin films.

Geochemical and Crystallographic Study of Turbo Torquatus (Mollusca: Gastropoda) From Southwestern Australia

Science.gov (United States)

Roger, L. M.; George, A. D.; Shaw, J.; Hart, R. D.; Roberts, M. P.; Becker, T.; Evans, N. J.; McDonald, B. J.

2018-01-01

Shells of the marine gastropod Turbo torquatus were sampled from three different locations along the Western Australian coastline, namely Marmion Lagoon (31°S), Rottnest Island (32°S), and Hamelin Bay (34°S). Marmion Lagoon and Rottnest Island have similar sea surface temperature ranges that are ˜1°C warmer than Hamelin Bay, with all sites influenced by the warm southward flowing Leeuwin Current. The shells were characterized using crystallographic, spectroscopic, and geochemical analyses. Shell mineral composition varies between the three sites suggesting the influence of sea surface temperature, oxygen consumption, and/or bedrock composition on shell mineralogy and preferential incorporation and/or elemental discrimination of Mg, P, and S. Furthermore, T. torquatus was found to exert control over the incorporation of most, if not all, the elements measured here, suggesting strong biological regulation. At all levels of testing, the concentrations of Li varied significantly, which indicates that this trace element may not be a suitable environmental proxy. Variation in Sr concentration between sites and between specimens reflects combined environmental and biological controls suggesting that Sr/Ca ratios in T. torquatus cannot be used to estimate sea surface temperature without experimentally accounting for metabolic and growth effects. The mineral composition and microstructure of T. torquatus shells may help identify sea surface temperature variations on geological time scales. These findings support the previously hypothesized involvement of an active selective pathway across the calcifying mantle of T. torquatus for most, if not all, the elements measured here.

Structural and dielectric studies on Ag doped nano ZnSnO3

Science.gov (United States)

Deepa, K.; Angel, S. Lilly; Rajamanickam, N.; Jayakumar, K.; Ramachandran, K.

2018-04-01

Undoped and Ag-doped nano Zinc Stannate (ZSO) ternary oxide were prepared by co-precipitation method. The crystallographic, morphological and optical properties of the synthesized nanoparticles were studied using X-ray diffraction (XRD) and UV-Visible spectroscopy (UV-Vis) and Scanning electron microscopy (SEM). The electrical properties of the synthesized samples were studied by dielectric measurements. Higher concentration Ag doped ZSO nanoparticles exhibit higher dielectric constant at low frequency.

Hydrogen-induced crack interaction and coalescence: the role of local crystallographic texture

Energy Technology Data Exchange (ETDEWEB)

Caleyo, F.; Hallen, J. M.; Venegas, V. [ESIQIE, Instituto Politecnico Nacional, Mexico, (Mexico); Baudin, T. [Universite de Paris Sud, Orsay, (France)

2010-07-01

Hydrogen induced cracking (HIC) is a big concern in pipeline industry specialized in sour service. The strategies to improve HIC resistance of pipeline steel have not been completely efficient. This study investigated the role of grain orientation in the interaction and coalescence of non-coplanar HIC cracks through experimental analysis. HIC samples of pipeline steels (API 5L X46 and ASME-A106) were studied using automated electron backscatter diffraction (EBSD) and orientation imaging microscopy (OIM). The results showed that the microtexture can play a significant role in the coalescence of closely spaced non-coplanar HIC cracks. It was also found that the presence of cleavage planes and slip systems correctly oriented to the mixed-mode stresses can activate low-resistance transgranular paths along in which cracks can merge. It is demonstrated that crystallographic texture must be considered in developing predictive models for the study of the stepwise propagation of HIC cracking in pipeline steels.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

Energy Technology Data Exchange (ETDEWEB)

Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy); Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Luchinat, Claudio, E-mail: garib@mrc-lmb.cam.ac.uk [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy)

2014-04-01

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

International Nuclear Information System (INIS)

Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo; Murshudov, Garib N.; Luchinat, Claudio

2014-01-01

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state

Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene

International Nuclear Information System (INIS)

Ciaccafava, Alexandre; Lartigue, Audrey; Mansuelle, Pascal; Jeudy, Sandra; Abergel, Chantal

2011-01-01

The mimivirus L544 gene product was expressed in E. coli and crystallized; preliminary phasing of a MAD data set was performed using the selenium signal present in a crystal of recombinant selenomethionine-substituted protein. Mimivirus is the prototype of a new family (the Mimiviridae) of nucleocytoplasmic large DNA viruses (NCLDVs), which already include the Poxviridae, Iridoviridae, Phycodnaviridae and Asfarviridae. Mimivirus specifically replicates in cells from the genus Acanthamoeba. Proteomic analysis of purified mimivirus particles revealed the presence of many subunits of the DNA-directed RNA polymerase II complex. A fully functional pre-transcriptional complex appears to be loaded in the virions, allowing mimivirus to initiate transcription within the host cytoplasm immediately upon infection independently of the host nuclear apparatus. To fully understand this process, a systematic study of mimivirus proteins that are predicted (by bioinformatics) or suspected (by proteomic analysis) to be involved in transcription was initiated by cloning and expressing them in Escherichia coli in order to determine their three-dimensional structures. Here, preliminary crystallographic analysis of the recombinant L544 protein is reported. The crystals belonged to the orthorhombic space group C222 1 with one monomer per asymmetric unit. A MAD data set was used for preliminary phasing using the selenium signal present in a selenomethionine-substituted protein crystal

Relationship between local deformation behavior and crystallographic features of as-quenched lath martensite during uniaxial tensile deformation

International Nuclear Information System (INIS)

Michiuchi, M.; Nambu, S.; Ishimoto, Y.; Inoue, J.; Koseki, T.

2009-01-01

Electron backscattering diffraction patterns were used to investigate the relationship between local deformation behavior and the crystallographic features of as-quenched lath martensite of low-carbon steel during uniform elongation in tensile tests. The slip system operating during the deformation up to a strain of 20% was estimated by comparing the crystal rotation of each martensite block after deformation of 20% strain with predictions by the Taylor and Sachs models. The results indicate that the in-lath-plane slip system was preferentially activated compared to the out-of-lath-plane system up to this strain level. Further detailed analysis of crystal rotation at intervals of approximately 5% strain confirmed that the constraint on the operative slip system by the lath structure begins at a strain of 8% and that the local strain hardening of the primary slip systems occurred at approximately 15% strain.

Electrochemical performance of mixed crystallographic phase nanotubes and nanosheets of titania and titania-carbon/silver composites for lithium-ion batteries

International Nuclear Information System (INIS)

Das, Shyamal K.; Bhattacharyya, Aninda J.

2011-01-01

Highlights: → Carbon wired TiO 2 nanotubes as anode for lithium ion batteries. → Mixed phase nanotubes show higher energy and power density than titania nanosheets. → Lithium storage and phase stabilization influenced by morphology of carbon coating. - Abstract: The role of homogeneity in ex situ grown conductive coatings and dimensionality in the lithium storage properties of TiO 2 is discussed here. TiO 2 nanotube and nanosheet comprising of mixed crystallographic phases of anatase and TiO 2 (B) have been synthesized by an optimized hydrothermal method. Surface modifications of TiO 2 nanotube are realized via coating the nanotube with Ag nanoparticles and amorphous carbon. The first discharge cycle capacity (at current rate = 10 mA g -1 ) for TiO 2 nanotube and nanosheet were 355 mAh g -1 and 225 mAh g -1 , respectively. The conductive surface coating stabilized the titania crystallographic structure during lithium insertion-deinsertion processes via reduction in the accessibility of lithium ions to the trapping sites. The irreversible capacity is beneficially minimized from 110 mAh g -1 for TiO 2 nanotubes to 96 mAh g -1 and 57 mAh g -1 respectively for Ag and carbon modified TiO 2 nanotubes. The homogeneously coated amorphous carbon over TiO 2 renders better lithium battery performance than randomly distributed Ag nanoparticles coated TiO 2 due to efficient hopping of electrons.

Local dynamics of proteins and DNA evaluated from crystallographic B factors

International Nuclear Information System (INIS)

Schneider, Bohdan; Gelly, Jean-Christophe; Brevern, Alexandre G. de; Černý, Jiří

2014-01-01

surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Energy Technology Data Exchange (ETDEWEB)

Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic); Gelly, Jean-Christophe; Brevern, Alexandre G. de [INSERM, U1134, DSIMB, 75739 Paris (France); Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris (France); Institut National de la Transfusion Sanguine (INTS), 75739 Paris (France); Laboratoire d’Excellence GR-Ex, 75739 Paris (France); Černý, Jiří [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic)

2014-09-01

surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.

Effect of sputtering parameters and substrate composition on the structure of tantalum thin films

Energy Technology Data Exchange (ETDEWEB)

Hallmann, Lubica, E-mail: lubica.hallmann@zzm.uzh.c [Clinic of Fixed and Removable Prosthodontics and Dental Material Science, Center of Dental Medicine, University of Zürich (Switzerland); Ulmer, Peter [Institute of Geochemistry and Petrology, ETH Zürich (Switzerland)

2013-10-01

The crystallographic properties of tantalum films deposited as a bioactive coating on Co–Cr–Mo and Ti–Al–Nb alloys have been investigated. The desired tough and ductile alpha phase of tantalum has been obtained by DC magnetron sputtering on Co–Cr–Mo and Ti–Al–Nb substrates. The thickness of the tantalum layer was between 20 and 600 nm. The crystallographic structure of tantalum thin film was dependent on the sputtering parameters such as DC power, bias voltage and gas impurities. Oxygen is an important factor for the stabilization of the tantalum alpha phase on Co–Cr–Mo substrate. The crystallographic structure and texture of tantalum thin films was found to be additionally dependent on the substrate composition. For Ti–Al–Nb substrate, oxygen content was not an important factor for the stabilization of the alpha phase. The observed shift of X-ray diffraction peaks to lower 2(θ) is an indication of stress evolving during the sputtering process and was dependent on bias voltage and oxygen content of the carrier gas.

Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins.

Science.gov (United States)

Merlino, Antonello; Vitagliano, Luigi; Howes, Barry D; Verde, Cinzia; di Prisco, Guido; Smulevich, Giulietta; Sica, Filomena; Vergara, Alessandro

2009-12-01

Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air-exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis-histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 A resolution. The analysis of the electron density of the heme pocket shows, for both the alpha and the beta iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein.

Al-doped ZnO seed layer-dependent crystallographic control of ZnO nanorods by using electrochemical deposition

Energy Technology Data Exchange (ETDEWEB)

Son, Hyo-Soo; Choi, Nak-Jung [Department of Nano-Optical Engineering, Korea Polytechnic University, Siheung 429-793 (Korea, Republic of); Kim, Kyoung-Bo [Department of Metallurgical and Materials Engineering, Inha Technical College, Incheon 402-752 (Korea, Republic of); Kim, Moojin [Department of Renewable Energy, Jungwon University, Goesan-gun, Chungbuk 367-805 (Korea, Republic of); Lee, Sung-Nam, E-mail: snlee@kpu.ac.kr [Department of Nano-Optical Engineering, Korea Polytechnic University, Siheung 429-793 (Korea, Republic of)

2016-10-15

Highlights: • Polar and semipolar ZnO NRs were successfully achieved by hydrothermal synthesis. • Semipolar and polar ZnO NRs were grown on ZnO and AZO/m-sapphire, respectively. • Al % of AZO/m-sapphire enhanced the lateral growth rate of polar ZnO NRs. - Abstract: We investigated the effect of an Al-doped ZnO film on the crystallographic direction of ZnO nanorods (NRs) using electrochemical deposition. From high-solution X-ray diffraction measurements, the crystallographic plane of ZnO NRs grown on (1 0 0) ZnO/m-plane sapphire was (1 0 1). The surface grain size of the (100) Al-doped ZnO (AZO) film decreased with increasing Al content in the ZnO seed layer, implying that the Al dopant accelerated the three-dimensional (3D) growth of the AZO film. In addition, it was found that with increasing Al doping concentration of the AZO seed layer, the crystal orientation of the ZnO NRs grown on the AZO seed layer changed from [1 0 1] to [0 0 1]. With increasing Al content of the nonpolar (1 0 0) AZO seed layer, the small surface grains with a few crystallographic planes of the AZO film changed from semipolar (1 0 1) ZnO NRs to polar (0 0 1) ZnO NRs due to the increase of the vertical [0 0 1] growth rate of the ZnO NRs owing to excellent electrical properties.

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

NARCIS (Netherlands)

Joosten, R.P.; Joosten, K.; Cohen, S.X.; Vriend, G.; Perrakis, A.

2011-01-01

MOTIVATION: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better

Expression, purification, crystallization and preliminary crystallographic analysis of PA3885 (TpbA) from Pseudomonas aeruginosa PAO1

International Nuclear Information System (INIS)

Yang, Wen; Li, Kan; Bai, Yuwei; Zhou, Ruimin; Zhou, Weihong; Bartlam, Mark

2010-01-01

PA3885 (TpbA), a tyrosine phosphatase, may function as a balancing factor between biofilm formation and motility in the opportunistic pathogen P. aeruginosa. Here, the expression, purification, crystallization and preliminary crystallographic analysis of PA3885 from P. aeruginosa PAO1 are reported. Biofilms are important in cell communication and growth in most bacteria and are also responsible for most human clinical infections and diseases. Quorum-sensing systems have been identified to be crucial for biofilm formation and regulation. PA3885 (TpbA), a tyrosine phosphatase, is reported to convert extracellular quorum-sensing signals into internal gene-cascade reactions that result in reduced biofilm formation in the opportunistic pathogen Pseudomonas aeruginosa. Here, PA3885 from P. aeruginosa PAO1 was expressed, purified and crystallized. Single crystals were studied by X-ray crystallography and native diffraction data were collected to 2.8 Å resolution. These crystals were determined to belong to space group C2. It was not possible to conclusively determine the number of proteins in the asymmetric unit from the preliminary X-ray diffraction data analysis alone and attempts to determine the crystal structure of PA3885 are currently under way

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

Science.gov (United States)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

Fiftieth Anniversary of the Cambridge Structural Database and Thirty Years of Its Use in Croatia

Directory of Open Access Journals (Sweden)

Kojić-Prodić B.

2015-07-01

Full Text Available This article is dedicated to the memory of Dr. F. H. Allen and the 50th anniversary of the Cambridge Crystallographic Data Centre (CCDC; the world-renowned centre for deposition and control of crystallographic data including atomic coordinates that define the three-dimensional structures of organic molecules and metal complexes containing organic ligands. The mission exposed at the web site (http://www.ccdc.cam.ac.uk is clearly stated: “The Cambridge Crystallographic Data Centre (CCDC is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high quality information, software and services.” The Cambridge Structural Database (CSD, one among the first established electronic databases, nowadays is one of the most significant crystallographic databases in the world. In the International Year of Crystallography 2014, the CSD announced in December over 750,000 deposited structures. The use of the extensive and rapidly growing database needs support of sophisticated and efficient software for checking, searching, analysing, and visualising structural data. The seminal role of the CSD in researches related to crystallography, chemistry, materials science, solid state physics and chemistry, (biotechnology, life sciences, and pharmacology is widely known. The important issues of the CCDC are the accuracy of deposited data and development of software for checking the data. Therefore, the Crystallographic Information File (CIF is introduced as the standard text file format for representing crystallographic information. Among the most important software for users is ConQuest, which enables searching all the CSD information fields, and the web implementation WebCSD software. Mercury is available for visualisation of crystal structures and crystal morphology including intra- and intermolecular interactions with graph-set notations of hydrogen bonds, and analysis of geometrical parameters. The CCDC gives even

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide

International Nuclear Information System (INIS)

Feng, Youjun; Qi, Jianxun; Zhang, Huimin; Wang, Jinzi; Liu, Jinhua; Jiang, Fan; Gao, Feng

2005-01-01

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide. Simian immunodeficiency virus (SIV) in the rhesus macaque is regarded as a classic animal model, playing a crucial role in HIV vaccine strategies and therapeutics by characterizing various cytotoxic T-lymphocyte (CTL) responses in macaque monkeys. However, the availability of well documented structural reports focusing on rhesus macaque major histocompatibility complex class I (MHC I) molecules remains extremely limited. Here, a complex of the rhesus macaque MHC I molecule (Mamu-A*02) with human β 2 m and an immunodominant SIV-Gag nonapeptide, GESNLKSLY (GY9), has been crystallized. The crystal diffracts X-rays to 2.7 Å resolution and belongs to space group C2, with unit-cell parameters a = 124.11, b = 110.45, c = 100.06 Å, and contains two molecules in the asymmetric unit. The availability of the structure, which is being solved by molecular replacement, will provide new insights into rhesus macaque MHC I (Mamu-A*02) presenting pathogenic SIV peptides

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide

Energy Technology Data Exchange (ETDEWEB)

Feng, Youjun [Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080 (China); Graduate School, Chinese Academy of Sciences, Beijing (China); Qi, Jianxun [Graduate School, Chinese Academy of Sciences, Beijing (China); Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Zhang, Huimin; Wang, Jinzi [Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080 (China); Liu, Jinhua [College of Veterinary Medicine, China Agricultural University, Beijing 100094 (China); Jiang, Fan [Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Gao, Feng, E-mail: gaofeng@im.ac.cn [Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080 (China); College of Veterinary Medicine, China Agricultural University, Beijing 100094 (China)

2006-01-01

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide. Simian immunodeficiency virus (SIV) in the rhesus macaque is regarded as a classic animal model, playing a crucial role in HIV vaccine strategies and therapeutics by characterizing various cytotoxic T-lymphocyte (CTL) responses in macaque monkeys. However, the availability of well documented structural reports focusing on rhesus macaque major histocompatibility complex class I (MHC I) molecules remains extremely limited. Here, a complex of the rhesus macaque MHC I molecule (Mamu-A*02) with human β{sub 2}m and an immunodominant SIV-Gag nonapeptide, GESNLKSLY (GY9), has been crystallized. The crystal diffracts X-rays to 2.7 Å resolution and belongs to space group C2, with unit-cell parameters a = 124.11, b = 110.45, c = 100.06 Å, and contains two molecules in the asymmetric unit. The availability of the structure, which is being solved by molecular replacement, will provide new insights into rhesus macaque MHC I (Mamu-A*02) presenting pathogenic SIV peptides.

New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

Directory of Open Access Journals (Sweden)

Assem Barakat

2015-11-01

Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

Magnetic structure of holmium-yttrium superlattices

DEFF Research Database (Denmark)

Jehan, D.A.; McMorrow, D.F.; Cowley, R.A.

1993-01-01

We present the results of a study of the chemical and magnetic structures of a series of holmium-yttrium superlattices and a 5000 angstrom film of holmium, all grown by molecular-beam epitaxy. By combining the results of high-resolution x-ray diffraction with detailed modeling, we show...... that the superlattices have high crystallographic integrity: the structural coherence length parallel to the growth direction is typically almost-equal-to 2000 angstrom, while the interfaces between the two elements are well defined and extend over approximately four lattice planes. The magnetic structures were...... determined using neutron-scattering techniques. The moments on the Ho3+ ions in the superlattices form a basal-plane helix. From an analysis of the superlattice structure factors of the primary magnetic satellites, we are able to determine separately the contributions made by the holmium and yttrium...

(S-2-(4-Chlorobenzoyl-1,2,3,4-tetrahydrobenzo[e]pyrazino[1,2-a][1,4]diazepine-6,12(11H,12aH-dione—Synthesis and Crystallographic Studies

Directory of Open Access Journals (Sweden)

Adam Mieczkowski

2017-10-01

Full Text Available (S-2-(4-Chlorobenzoyl-1,2,3,4-tetrahydrobenzo[e]pyrazino[1,2-a][1,4]diazepine-6,12(11H,12aH-dione was obtained in a three-step, one-pot synthesis, starting from optically pure (S-2-piperazine carboxylic acid dihydrochloride. Selective acylation of the β-nitrogen atom followed by condensation with isatoic anhydride and cyclization with HATU/DIPEA to a seven-member benzodiazepine ring, led to the tricyclic benzodiazepine derivative. Crystallographic studies and initial biological screening were performed for the title compound.

Correlating Atom Probe Crystallographic Measurements with Transmission Kikuchi Diffraction Data.

Science.gov (United States)

Breen, Andrew J; Babinsky, Katharina; Day, Alec C; Eder, K; Oakman, Connor J; Trimby, Patrick W; Primig, Sophie; Cairney, Julie M; Ringer, Simon P

2017-04-01

Correlative microscopy approaches offer synergistic solutions to many research problems. One such combination, that has been studied in limited detail, is the use of atom probe tomography (APT) and transmission Kikuchi diffraction (TKD) on the same tip specimen. By combining these two powerful microscopy techniques, the microstructure of important engineering alloys can be studied in greater detail. For the first time, the accuracy of crystallographic measurements made using APT will be independently verified using TKD. Experimental data from two atom probe tips, one a nanocrystalline Al-0.5Ag alloy specimen collected on a straight flight-path atom probe and the other a high purity Mo specimen collected on a reflectron-fitted instrument, will be compared. We find that the average minimum misorientation angle, calculated from calibrated atom probe reconstructions with two different pole combinations, deviate 0.7° and 1.4°, respectively, from the TKD results. The type of atom probe and experimental conditions appear to have some impact on this accuracy and the reconstruction and measurement procedures are likely to contribute further to degradation in angular resolution. The challenges and implications of this correlative approach will also be discussed.

A search for the ground state structure and the phase stability of tantalum pentoxide

International Nuclear Information System (INIS)

Pérez-Walton, S; Valencia-Balvín, C; Padilha, A C M; Dalpian, G M; Osorio-Guillén, J M

2016-01-01

Tantalum pentoxide (Ta 2 O 5 ) is a wide-gap semiconductor that presents good catalytic and dielectric properties, conferring to this compound promising prospective use in a variety of technological applications. However, there is a lack of understanding regarding the relations among its crystalline phases, as some of them are not even completely characterized and there is currently no agreement about which models better explain the crystallographic data. Additionally, its phase diagram is unknown. In this work we performed first-principles density functional theory calculations to study the structural properties of the different phases and models of Ta 2 O 5 , the equation of state and the zone-centered vibrational frequencies. From our results, we conclude that the phases that are built up from only distorted octahedra instead of combinations with pentagonal and/or hexagonal bipyramids are energetically more favorable and dynamically stable. More importantly, this study establishes that, given the pressure range considered, the B-phase is the most favorable structure and there is no a crystallographic phase transition to another phase at high-pressure. Additionally, for the equilibrium volume of the B-phase and the λ-model, the description of the electronic structure and optical properties were performed using semi-local and hybrid functionals. (paper)

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

Energy Technology Data Exchange (ETDEWEB)

Blankenship, Elise; Vukoti, Krishna [Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Miyagi, Masaru, E-mail: mxm356@cwru.edu [Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Lodowski, David T., E-mail: mxm356@cwru.edu [Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States)

2014-03-01

This work reports the first sub-angstrom resolution structure of S. erythraeus trypsin. The detailed model of a prototypical serine protease at a catalytically relevant pH with an unoccupied active site is presented and is compared with other high-resolution serine protease structures. With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

International Nuclear Information System (INIS)

Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T.

2014-01-01

This work reports the first sub-angstrom resolution structure of S. erythraeus trypsin. The detailed model of a prototypical serine protease at a catalytically relevant pH with an unoccupied active site is presented and is compared with other high-resolution serine protease structures. With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity

Band structure of Heusler compounds studied by photoemission and tunneling spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Arbelo Jorge, Elena

2011-07-01

Heusler compounds are key materials for spintronic applications. They have attracted a lot of interest due to their half-metallic properties predicted by band structure calculations. The aim of this work is to evaluate experimentally the validity of the predictions of half metallicity by band structure calculations for two specific Heusler compounds, Co{sub 2}FeAl{sub 0.3}Si{sub 0.7} and Co{sub 2}MnGa. Two different spectroscopy methods for the analysis of the electronic properties were used: Angular Resolved Ultraviolet Photoemission Spectroscopy (ARUPS) and Tunneling Spectroscopy. Heusler compounds are prepared as thin films by RF-sputtering in an ultra high vacuum system. For the characterization of the samples, bulk and surface crystallographic and magnetic properties of Co{sub 2}FeAl{sub 0.3}Si{sub 0.7} and Co{sub 2}MnGa are studied. X-ray and electron diffraction reveal a bulk and surface crossover between two different types of sublattice order (from B2 to L2{sub 1}) with increasing annealing temperature. X-ray magnetic circular dichroism results show that the magnetic properties in the surface and bulk are identical, although the magnetic moments obtained are 5 % below from the theoretically predicted. By ARUPS evidence for the validity of the predicted total bulk density of states (DOS) was demonstrated for both Heusler compounds. Additional ARUPS intensity contributions close to the Fermi energy indicates the presence of a specific surface DOS. Moreover, it is demonstrated that the crystallographic order, controlled by annealing, plays an important role on broadening effects of DOS features. Improving order resulted in better defined ARUPS features. Tunneling magnetoresistance measurements of Co{sub 2}FeAl{sub 0.3}Si{sub 0.7} and Co{sub 2}MnGa based MTJ's result in a Co{sub 2}FeAl{sub 0.3}Si{sub 0.7} spin polarization of 44 %, which is the highest experimentally obtained value for this compound, although it is lower than the 100 % predicted. For Co

Crystallization and preliminary crystallographic analysis of human LR11 Vps10p domain

International Nuclear Information System (INIS)

Nakata, Zenzaburo; Nagae, Masamichi; Yasui, Norihisa; Bujo, Hideaki; Nogi, Terukazu; Takagi, Junichi

2010-01-01

LR11/sorLA contains in its extracellular region a large (∼700-residue) Vps10p domain that is implicated in its intracellular protein-trafficking function. Here, the expression, purification, crystallization and preliminary crystallographic characterization of this domain are described. Low-density lipoprotein receptor (LDLR) relative with 11 binding repeats (LR11; also known as sorLA) is genetically associated with late-onset Alzheimer’s disease and is thought to be involved in neurodegenerative processes. LR11 contains a vacuolar protein-sorting 10 protein (Vps10p) domain. As this domain has been implicated in protein–protein interaction in other receptors, its structure and function are of great biological interest. Human LR11 Vps10p domain was expressed in mammalian cells and the purified protein was crystallized using the hanging-drop vapour-diffusion method. Enzymatic deglycosylation of the sample was critical to obtaining diffraction-quality crystals. Deglycosylated LR11 Vps10p-domain crystals belonged to the hexagonal space group P6 1 22. A diffraction data set was collected to 2.4 Å resolution and a clear molecular-replacement solution was obtained

Biominerals at the nanoscale: transmission electron microscopy methods for studying the special properties of biominerals

DEFF Research Database (Denmark)

Posfai, Mihaly; Kasama, Takeshi; Dunin-Borkowski, Rafal E.

2013-01-01

Biominerals have important functions in living organisms: apatite crystals are responsible for the strength of our bones and the hardness of our teeth, calcite and aragonite are used by many organisms for making shells, and magnetite and greigite help bacteria and birds to navigate in magnetic...... fields. In order to fulfill their roles in organisms, biominerals have strictly controlled physical and chemical properties. Transmission electron microscopy (TEM) is ideally suited for the study of the structures, arrangements, compositions, morphologies, crystallographic orientations, crystallographic...... minerals that form in the cells of magnetotactic bacteria....

Production, purification, crystallization and structure determination of H-1 Parvovirus

International Nuclear Information System (INIS)

Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

2012-01-01

The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

Crystal structure of the high-affinity Na+,K+-ATPase–ouabain complex with Mg2+ bound in the cation binding site

DEFF Research Database (Denmark)

Laursen, Mette; Yatime, Laure; Nissen, Poul

2013-01-01

of ouabain and the side chains of αM1, αM2, and αM6. Furthermore, the structure reveals that cation transport site II is occupied by Mg2+, and crystallographic studies indicate that Rb+ and Mn2+, but not Na+, bind to this site. Comparison with the low-affinity [K2]E2–MgFx–ouabain structure [Ogawa et al...

Cloning, expression, purification and initial crystallographic studies of UbiG: a methyltransferase involved in ubiquinone biosynthesis in Escherichia coli

International Nuclear Information System (INIS)

Costa, M.A.F.; Magalhaes, R.D.; Nagem, R.A.P.; Ferreira-Junior, J.R.; Barros, M.H.

2012-01-01

Full text: Ubiquinone is a molecule that functions as an electron carrier in the respiratory chain in living organisms. Some clinical phenotypes, including, encephalomyopathy, has been associated with ubiquinone deficiency, raising the interest in the biosynthetic pathway of this molecule. This pathway was proposed mainly from the results of the genetic analysis of mutants of E. coli. UbiG is a methyltransferase involved in ubiquinone biosynthesis in E. coli. In this work we have cloned, expressed, purified and made initial crystallographic assessments of UbiG for later determination of its three-dimensional structure. The gene encoding UbiG was amplified from E. coli genomic DNA by polymerase chain reaction. The 753 bases pairs amplicon was inserted into the expression plasmid pMCSG7 by ligation independent cloning system and transformed into BL21(DE3) E. coli strain. The expression of UbiG, verified by SDS polyacrylamide gel, showed a protein of approximately 29kDa after IPTG induction. The recombinant UbiG, in the soluble fraction of the cellular lysate, was purified by affinity chromatography and the molecular weight of recombinant UbiG of approximately 29 kDa was confirmed by mass spectrometry. After removal of His-tag by TEV protease, another affinity chromatography was performed and UbiG, without His-tag, was observed in flow-through fraction. In Size-Exclusion Chromatography (SEC), the recombinant UbiG showed a unique peak with correct molecular weight of a monomer. Analysis of CD indicated that recombinant UbiG has 31,80% of alpha helix at 20 deg C and DLS showed that 70.9% of the sample is still monomeric in solution even five days after purification. Initial crystallization studies were performed with Crystal Screen 1 and Crystal Screen 2 from Hampton Research. Needle-shaped microcrystals of UbiG were obtained using a precipitant solution consisting of 0,1M lithium sulfate, 0,1M Tris pH 7,5 and 30% w/v polyethylene glycol 4,000. (author)

Cloning, expression, purification and initial crystallographic studies of UbiG: a methyltransferase involved in ubiquinone biosynthesis in Escherichia coli

Energy Technology Data Exchange (ETDEWEB)

Costa, M.A.F.; Magalhaes, R.D.; Nagem, R.A.P. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil); Ferreira-Junior, J.R.; Barros, M.H. [Universidade de Sao Paulo (USP), SP (Brazil)

2012-07-01

Full text: Ubiquinone is a molecule that functions as an electron carrier in the respiratory chain in living organisms. Some clinical phenotypes, including, encephalomyopathy, has been associated with ubiquinone deficiency, raising the interest in the biosynthetic pathway of this molecule. This pathway was proposed mainly from the results of the genetic analysis of mutants of E. coli. UbiG is a methyltransferase involved in ubiquinone biosynthesis in E. coli. In this work we have cloned, expressed, purified and made initial crystallographic assessments of UbiG for later determination of its three-dimensional structure. The gene encoding UbiG was amplified from E. coli genomic DNA by polymerase chain reaction. The 753 bases pairs amplicon was inserted into the expression plasmid pMCSG7 by ligation independent cloning system and transformed into BL21(DE3) E. coli strain. The expression of UbiG, verified by SDS polyacrylamide gel, showed a protein of approximately 29kDa after IPTG induction. The recombinant UbiG, in the soluble fraction of the cellular lysate, was purified by affinity chromatography and the molecular weight of recombinant UbiG of approximately 29 kDa was confirmed by mass spectrometry. After removal of His-tag by TEV protease, another affinity chromatography was performed and UbiG, without His-tag, was observed in flow-through fraction. In Size-Exclusion Chromatography (SEC), the recombinant UbiG showed a unique peak with correct molecular weight of a monomer. Analysis of CD indicated that recombinant UbiG has 31,80% of alpha helix at 20 deg C and DLS showed that 70.9% of the sample is still monomeric in solution even five days after purification. Initial crystallization studies were performed with Crystal Screen 1 and Crystal Screen 2 from Hampton Research. Needle-shaped microcrystals of UbiG were obtained using a precipitant solution consisting of 0,1M lithium sulfate, 0,1M Tris pH 7,5 and 30% w/v polyethylene glycol 4,000. (author)

Preparation and chemical crystallographic study of new hydrides and hydro-fluorides of ionic character; Preparation et etude cristallochimique de nouveaux hydrures et fluorohydrures a caractere ionique

Energy Technology Data Exchange (ETDEWEB)

Park, Hyung-Ho

1988-07-22

Within the context of a growing interest in the study of reversible hydrides with the perspective of their application in hydrogen storage, this research thesis more particularly addressed the case of ternary hydrides and fluorides, and of hydro-fluorides. The author reports the development of a method of preparation of alkaline hydrides, of alkaline earth hydrides and of europium hydride, and then the elaboration of ternary hydrides. He addresses the preparation of caesium fluorides and of calcium or nickel fluorides, of Europium fluorides, and of ternary fluorides. Then, he addresses the preparation of hydro-fluorides (caesium, calcium, europium fluorides, and caesium and nickel fluorides). The author presents the various experimental techniques: chemical analysis, radio-crystallographic analysis, volumetric mass density measurement, magnetic measurements, ionic conductivity measurements, Moessbauer spectroscopy, and nuclear magnetic resonance. He reports the crystallographic study of some ternary alkaline and alkaline-earth hydrides (KH-MgH{sub 2}, RbH-CaH{sub 2}, CsH-CaH{sub 2}, RbH-MgH{sub 2} and CsH-MgH{sub 2}) and of some hydro-fluorides (CsCaF{sub 2}H, EuF{sub 2}H, CsNiF{sub 2}H) [French] Dans une premiere partie, de nouveaux hydrures ternaires ont ete prepares et caracterises. Les systemes etudies sont AH-MH 2 (A = K, Rb, Cs et M = Mg, Ca). Dans les systemes AH-MgH 2 l'evolution structurale a ete discutee en fonction du caractere iono-covalent de la liaison magnesium-hydrogene. Dans une deuxieme partie, plusieurs nouveaux fluorohydrures ont ete mis en evidence. L'effet de la substitution de l'hydrogene au fluor dans ces phases a ete etudiee en utilisant la RMN, la spectroscopie Moessbauer, la conductivite ionique et les mesures magnetiques.

Unexpected ferromagnetic interaction in a new tetranuclear copper(II) complex: synthesis, crystal structure, magnetic properties, and theoretical studies.

Science.gov (United States)

Fondo, Matilde; García-Deibe, Ana M; Corbella, Monstserrat; Ruiz, Eliseo; Tercero, Javier; Sanmartín, Jesús; Bermejo, Manuel R

2005-07-11

The new tetranuclear carbonate complex [Cu2L)2(CO3)] x 8H2O (1 x 8H2O) (H3L = (2-(2-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) has been obtained by two different synthetic routes and fully characterized. Recrystallization of 1 x 8H2O in methanol yields single crystals of {[(Cu2L)2(CO3)]}2 x 12H2O (1 x 6H2O), suitable for X-ray diffraction studies. The crystal structure of 1 x 6H2O shows two crystallographically different tetranuclear molecules in the asymmetric unit, 1a and 1b. Both molecules can be understood as self-assembled from two dinuclear [Cu2L]+ cations, joined by a mu4-eta(2):eta(1):eta(1) carbonate ligand. The copper atoms of each crystallographically different [(Cu2L)2(CO3)] molecule present miscellaneous coordination polyhedra: in both 1a and 1b, two metal centers are in square pyramidal environments, one displays a square planar chromophore and the other one has a geometry that can be considered as an intermediate between square pyramid and trigonal bipyramid. Magnetic studies reveal net intramolecular ferromagnetic coupling between the metal atoms. Density functional calculations allow the assignment of the different magnetic coupling constants and explain the unexpected ferromagnetic behavior, because of the presence of an unusual NCN bridging moiety and countercomplementarity of the phenoxo (or carbonate) and NCN bridges.

Y-TZP zirconia regeneration firing: Microstructural and crystallographic changes after grinding.

Science.gov (United States)

Ryan, Daniel Patrick Obelenis; Fais, Laiza Maria Grassi; Antonio, Selma Gutierrez; Hatanaka, Gabriel Rodrigues; Candido, Lucas Miguel; Pinelli, Ligia Antunes Pereira

2017-07-26

This study evaluated microstructural and crystallographic phase changes after grinding (G) and regeneration firing/anneling (R) of Y-TZP ceramics. Thirty five bars (Lava TM and Ice Zirkon) were divided: Y-TZP pre-sintered, control (C), regeneration firing (R), dry grinding (DG), dry grinding+regeneration firing (DGR), wet grinding (WG) and wet grinding+regeneration firing (WGR). Grinding was conducted using a diamond bur and annealing at 1,000°C. The microstructure was analyzed by SEM and the crystalline phases by X-ray diffraction (XRD). XRD showed that pre-sintered specimens contained tetragonal and monoclinic phases, while groups C and R showed tetragonal, cubic and monoclinic phases. After grinding, the cubic phase was eliminated in all groups. Annealing (DGR and WGR) resulted in only tetragonal phase. SEM showed semi-circular cracks after grinding and homogenization of particles after annealing. After grinding, surfaces show tetragonal and monoclinic phases and R can be assumed to be necessary prior to porcelain layering when grinding is performed.

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ... Crystallographic Structure Of Mycobacterium Tuberculosis ... Hemoglobin O pdb|1NGK|K Chain K..., Crystallographic ... Structure Of Mycobacterium Tuberculosis Hemoglobin ...O ... pdb|1NGK|J Chain J, Crystallographic Structure Of ... Mycobacterium Tuberculosis Hemoglo...bin O pdb|1NGK|I Chain ... I, Crystallographic Structure Of Mycobacterium ... Tuberculosis Hem...oglobin O pdb|1NGK|H Chain H, ... Crystallographic Structure Of Mycobacterium Tuberculosis

ORF Alignment: NC_000962 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ... Crystallographic Structure Of Mycobacterium Tuberculosis ... Hemoglobin O pdb|1NGK|K Chain K..., Crystallographic ... Structure Of Mycobacterium Tuberculosis Hemoglobin ...O ... pdb|1NGK|J Chain J, Crystallographic Structure Of ... Mycobacterium Tuberculosis Hemoglo...bin O pdb|1NGK|I Chain ... I, Crystallographic Structure Of Mycobacterium ... Tuberculosis Hem...oglobin O pdb|1NGK|H Chain H, ... Crystallographic Structure Of Mycobacterium Tuberculosis

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ... Crystallographic Structure Of Mycobacterium Tuberculosis ... Hemoglobin O pdb|1NGK|K Chain K..., Crystallographic ... Structure Of Mycobacterium Tuberculosis Hemoglobin ...O ... pdb|1NGK|J Chain J, Crystallographic Structure Of ... Mycobacterium Tuberculosis Hemoglo...bin O pdb|1NGK|I Chain ... I, Crystallographic Structure Of Mycobacterium ... Tuberculosis Hem...oglobin O pdb|1NGK|H Chain H, ... Crystallographic Structure Of Mycobacterium Tuberculosis

Proof of the Structure of the Stemodia chilensis Tetracyclic Diterpenoid (+)-19-Acetoxystemodan-12-ol by Synthesis from (+)-Podocarpic Acid: X-ray Structure Determination of a Key Intermediate.

Science.gov (United States)

Leonelli, Francesca; Mostarda, Azzurra; De Angelis, Luca; Lamba, Doriano; Demitri, Nicola; La Bella, Angela; Ceccacci, Francesca; Migneco, Luisa M; Marini Bettolo, Rinaldo

2016-04-22

The first synthesis of (+)-19-acetoxystemodan-12-ol (1), a stemodane diterpenoid isolated from Stemodia chilensis, is described. The structure was supported by an X-ray crystallographic analysis of intermediate (+)-9a, which confirmed the proposed structure and excluded the structure of (-)-19-hydroxystemod-12-ene as a possible candidate for the Chilean Calceolaria diterpenoid to which the (-)-19-hydroxystemar-13-ene structure (9b) had been erroneously assigned.

Adsorption of xylene para- and meta- isomers in NaX and BaX zeolites. Study of properties-structure relations; Adsorption des isomeres para- et meta- du xylene dans les zeolithes NaX et BaX. Etude des relations proprietes-structure

Energy Technology Data Exchange (ETDEWEB)

Descours, A.

1997-02-14

The separation of para-xylene from C8 aromatics is performed industrially bu adsorption process on zeolitic molecular sieves. The sorption properties of these zeolites are strongly linked to their structure, and their comprehension require an accurate knowledge of the interactions between sorbate molecules and zeolitic structure. The aim of this work is to characterise from a structural point of view the adsorption of para- and meta-xylenes in BaX and NaX zeolites. The former is selective for para-xylene, and the latter has not selective properties for para- and meta-isomers of xylene. For each zeolite, the adsorption of pure para-xylene and meta-xylene or a mixture of the two isomers, is investigated as a function of coverage. Powder neutron diffraction is used to determine the crystalline structure of these zeolites and the different crystallographic adsorption sites of the molecules. The influence of coverage on sorbate-sorbent and sorbate-sorbate interactions is investigated. Infrared spectroscopy allows to determine the chemical environment of the sorbate molecules at low coverage or when the coverage increases, and is particularly effective for the study of the binary mixture of xylenes. This study is performed by sorbing a mixture of xylene isomers, or by sorbing these isomers successively. Infrared studies and crystallographic analysis are compared in order to get a consistent description of adsorption mechanism of xylene isomers for both zeolites as a function of coverage. The role of coverage, of cation type, an the presence of the two xylene isomers is the super-cages is essential. For both zeolites, the increase of coverage actually leads to steric hindrances between sorbed molecules and molecular rearrangements. These reorganizations are connected to the cationic distribution of NaX and BaX zeolites. The sorbed molecules are connected to the cationic distribution of NaX and BaX zeolites. The sorbed molecules are particularly confined in BaX zeolite

Synthesis, structure, theoretical studies and luminescent properties of a ternary erbium(III) complex with acetylacetone and bathophenanthroline ligands

Energy Technology Data Exchange (ETDEWEB)

Martín-Ramos, Pablo [CEMDRX, Department of Physics, Universidade de Coimbra, Rua Larga, P-3004-516 Coimbra (Portugal); Advanced Materials Laboratory, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia (Spain); Silva, Pedro S. Pereira, E-mail: psidonio@pollux.fis.uc.pt [CEMDRX, Department of Physics, Universidade de Coimbra, Rua Larga, P-3004-516 Coimbra (Portugal); Chamorro-Posada, Pedro [Higher Technical School of Telecommunications Engineering, Universidad de Valladolid, Campus Miguel Delibes, Paseo Belén 15, 47011 Valladolid (Spain); Silva, Manuela Ramos [CEMDRX, Department of Physics, Universidade de Coimbra, Rua Larga, P-3004-516 Coimbra (Portugal); Milne, Bruce F. [Centre for Computational Physics, Department of Physics, Universidade de Coimbra, P-3004-516 Coimbra (Portugal); Donostia International Physics Centre, Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Nogueira, Fernando [Centre for Computational Physics, Department of Physics, Universidade de Coimbra, P-3004-516 Coimbra (Portugal); Martín-Gil, Jesús [Advanced Materials Laboratory, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia (Spain)

2015-06-15

A novel erbium(III) complex with acetylacetone (Hacac) and bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, bath) ligands, formulated as [Er(acac){sub 3}(bath)], has been characterized by elemental analysis, X-ray diffraction, thermogravimetric analysis, Fourier transform infrared spectroscopy, Raman spectroscopy, absorption and emission spectroscopies. In the theoretical part of this study, semi-empirical quantum chemistry methods using AM1, PM3, PM6 and PM7 models have been employed to predict the structure of the complex, calculate the geometric and crystallographic parameters, and make comparisons with spectroscopic data using INDO/S-CI calculations. Real-time time-dependent density-functional theory (TDDFT) has also been used to calculate the optical absorption spectrum of the complex in the gas phase. - Highlights: • Synthesis and structure of a new erbium(III) β-diketonate complex. • TDDFT used for the first time to calculate the optical absorption spectrum. • Complex show strong near-infrared luminescence at 1.53 µm due to antenna effect.

Synthesis, structure, theoretical studies and luminescent properties of a ternary erbium(III) complex with acetylacetone and bathophenanthroline ligands

International Nuclear Information System (INIS)

Martín-Ramos, Pablo; Silva, Pedro S. Pereira; Chamorro-Posada, Pedro; Silva, Manuela Ramos; Milne, Bruce F.; Nogueira, Fernando; Martín-Gil, Jesús

2015-01-01

A novel erbium(III) complex with acetylacetone (Hacac) and bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, bath) ligands, formulated as [Er(acac) 3 (bath)], has been characterized by elemental analysis, X-ray diffraction, thermogravimetric analysis, Fourier transform infrared spectroscopy, Raman spectroscopy, absorption and emission spectroscopies. In the theoretical part of this study, semi-empirical quantum chemistry methods using AM1, PM3, PM6 and PM7 models have been employed to predict the structure of the complex, calculate the geometric and crystallographic parameters, and make comparisons with spectroscopic data using INDO/S-CI calculations. Real-time time-dependent density-functional theory (TDDFT) has also been used to calculate the optical absorption spectrum of the complex in the gas phase. - Highlights: • Synthesis and structure of a new erbium(III) β-diketonate complex. • TDDFT used for the first time to calculate the optical absorption spectrum. • Complex show strong near-infrared luminescence at 1.53 µm due to antenna effect

Rearrangement of crystallographic domains driven by magnetic field in ferromagnetic Ni2MnGa and antiferromagnetic CoO

International Nuclear Information System (INIS)

Terai, Tomoyuki; Yasui, Motoyoshi; Yamamoto, Masataka; Kakeshita, Tomoyuki

2009-01-01

We have investigated the rearrangement of crystallographic domains (martensite variants) in Ni 2 MnGa ferromagnetic shape memory alloy and CoO antiferromagnetic oxide by applying magnetic field up to 8.0 MA/m. From the result of optical microscope observation of Ni 2 MnGa single crystal, when a magnetic field is applied along [001] p (p represents a parent phase), the rearrangement of crystallographic domains occurs and the single domain state is obtained below T Ms = 202 K. The same rearrangement occurs but partially when a magnetic field is applied along [110] p . On the other hand, when a magnetic field is applied along [111] p , the rearrangement does not occur. In case of the CoO single crystal, when a magnetic field is applied along [001] p below T Ms = 293 K, the rearrangement occurs at 170 K ≤ T ≤ 293 K, but does not occur at T p and [111] p , the rearrangement does not occur below T Ms . In order to explain the rearrangement in the alloy and the oxide, we have evaluated the magnetic shear stress, τ mag , which is derived from the difference in magnetic energy among crystallographic domains and have compared it with the shear stress required for the twinning plane movement, τ req . As a result, we have found that the rearrangement occurs when the value of τ mag is larger than or equal to the value of τ req for the present alloy and oxide.

Solution structure of the isolated Pelle death domain.

Science.gov (United States)

Moncrieffe, Martin C; Stott, Katherine M; Gay, Nicholas J

2005-07-18

The interaction between the death domains (DDs) of Tube and the protein kinase Pelle is an important component of the Toll pathway. Published crystallographic data suggests that the Pelle-Tube DD interface is plastic and implies that in addition to the two predominant Pelle-Tube interfaces, a third interaction is possible. We present the NMR solution structure of the isolated death domain of Pelle and a study of the interaction between the DDs of Pelle and Tube. Our data suggests the solution structure of the isolated Pelle DD is similar to that of Pelle DD in complex with Tube. Additionally, they suggest that the plasticity observed in the crystal structure may not be relevant in the functioning death domain complex.

Purification, crystallization and preliminary crystallographic analysis of the CBS pair of the human metal transporter CNNM4

International Nuclear Information System (INIS)

Gómez García, Inmaculada; Oyenarte, Iker; Martínez-Cruz, Luis Alfonso

2011-01-01

This work describes the purification and preliminary crystallographic analysis of the CBS-pair regulatory domain of the human ancient domain protein 4 (ACDP4), also known as CNNM4. This work describes the purification and preliminary crystallographic analysis of the CBS-pair regulatory domain of the human ancient domain protein 4 (ACDP4), also known as CNNM4. ACDP proteins represent the least-studied members of the eight different types of magnesium transporters that have been identified in mammals to date. In humans the ACDP family includes four members: CNNM1–4. CNNM1 acts as a cytosolic copper chaperone and has been associated with urofacial syndrome, whereas CNNM2 and CNNM4 have been identified as magnesium transporters. Interestingly, mutations in the CNNM4 gene have clinical consequences that are limited to retinal function and biomineralization and are considered to be the cause of Jalili syndrome, which consists of autosomal recessive cone-rod dystrophy and amelogenesis imperfecta. The truncated protein was overexpressed, purified and crystallized in the orthorhombic space group C222. The crystals diffracted X-rays to 3.6 Å resolution using synchrotron radiation. Matthews volume calculations suggested the presence of two molecules in the asymmetric unit, which were likely to correspond to a CBS module of the CBS pair of CNNM4

Comparative Structural Analysis of ERa and ERb Bound to Selective Estrogen Agonists and Antagonists

National Research Council Canada - National Science Library

Greene, Geoffrey

2001-01-01

...) complexed with receptor-selective estrogens and antiestrogens (SERMs) The crystallographic structures of ERalpha and ERbeta ligand binding domains complexed with cis-R,R-diethyl-tetrahydrochrysene-2,8-diol (R,R-THC...

Comparative Structural Analysis of ERa and ERb Bound to Selective Estrogen Agonists and Antagonists

National Research Council Canada - National Science Library

Greene, Geoggrey

2000-01-01

...) complexed with receptor-selective estrogens and antiestrogens (SERMs). The crystallographic structures of ERalpha and ERbeta ligand binding domains complexed with cis- R,R-diethyl-tetrahydrochrysene-2, 8 -diol (R,R-THC...

Brillouin-zone database on the Bilbao Crystallographic Server.

Science.gov (United States)

Aroyo, Mois I; Orobengoa, Danel; de la Flor, Gemma; Tasci, Emre S; Perez-Mato, J Manuel; Wondratschek, Hans

2014-03-01

The Brillouin-zone database of the Bilbao Crystallographic Server (http://www.cryst.ehu.es) offers k-vector tables and figures which form the background of a classification of the irreducible representations of all 230 space groups. The symmetry properties of the wavevectors are described by the so-called reciprocal-space groups and this classification scheme is compared with the classification of Cracknell et al. [Kronecker Product Tables, Vol. 1, General Introduction and Tables of Irreducible Representations of Space Groups (1979). New York: IFI/Plenum]. The compilation provides a solution to the problems of uniqueness and completeness of space-group representations by specifying the independent parameter ranges of general and special k vectors. Guides to the k-vector tables and figures explain the content and arrangement of the data. Recent improvements and modifications of the Brillouin-zone database, including new tables and figures for the trigonal, hexagonal and monoclinic space groups, are discussed in detail and illustrated by several examples.

Multi-structure docking analysis of BACE1 crystal structures and non-peptidic ligands.

Science.gov (United States)

Haghighijoo, Zahra; Hemmateenejad, Bahram; Edraki, Najmeh; Miri, Ramin; Emami, Saeed

2017-09-01

In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis. It was found that using one crystal structure for docking did not result in high accuracy for predicting activity of the BACE1 inhibitors. Instead, using of the multi-structural docking scores, post-processed by chemometrics methods arrived to highly accurate predictive models. In this regards, the PDB accession codes of 4B70, 4DVF and 2WEZ could discriminate between active and inactive compounds, with higher accuracy. Clustering of the BACE1 structures based on principal component analysis of the crystallographic structures the revealed that the discriminant structures are in the center of the clusters. Thus, these structures can be selected as predominant crystal structures for docking studies of non-peptidic BACE1 inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Cation distribution and crystallographic characterization of the spinel oxides MgCr{sub x}Fe{sub 2−x}O{sub 4} by neutron diffraction

Energy Technology Data Exchange (ETDEWEB)

Zakaria, A.K.M., E-mail: zakaria6403@yahoo.com [Institute of Nuclear Science & Technology, Bangladesh Atomic Energy Commission, Dhaka (Bangladesh); Nesa, Faizun [Department of Natural Science, Daffodil International University, Dhaka (Bangladesh); Department of Physics, Jahangirnagar University, Savar, Dhaka (Bangladesh); Saeed Khan, M.A. [Department of Physics, Jahangirnagar University, Savar, Dhaka (Bangladesh); Datta, T.K.; Aktar, Sanjida; Liba, Samia Islam; Hossain, Shahzad; Das, A.K.; Kamal, I.; Yunus, S.M. [Institute of Nuclear Science & Technology, Bangladesh Atomic Energy Commission, Dhaka (Bangladesh); Eriksson, S.-G. [Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg (Sweden)

2015-06-05

Highlights: • MgCr{sub x}Fe{sub 2−x}O{sub 4} ferrites crystallize at 1300 °C and possess cubic symmetry. • Cation distribution and crystallographic parameters have been determined precisely. • Cell parameter decreases with increasing Cr content in the system. • Ferrimagnetic ordering was found at room temperature for all the samples. - Abstract: The spinel system MgCr{sub x}Fe{sub 2−x}O{sub 4} (x = 0.0, 0.2, 0.4, 0.6, 0.8 and 1.0) has been prepared by solid state sintering method in air at 1573 K. X-ray and neutron powder diffraction experiments have been performed on the samples at room temperature for structural characterization. Rietveld refinement of the neutron diffraction data reveals that all the samples of the series possess cubic symmetry corresponding to the space group F d-3m. The distribution of the three cations Mg, Fe and Cr over the two sublattices and other crystallographic parameters has been determined precisely. The results reveal that Cr has been substituted for Fe selectively. Cr ions invariably occupy the octahedral (B) site for all values of x. Mg and Fe ions are distributed over both A and B sites for all x values. With increasing x the occupation of Mg increases in the A site and decreases in the B site for all the samples, while the Fe ions gradually decreases in both the sites for all values of x. The lattice constant decreases with increasing Cr content in the system. The magnetic structure at room temperature was ferrimagnetic for all the samples.

Crystallographic isomorphism in the structural type of α-HgI{sub 2} by example of KHgI{sub 3} · H{sub 2}O, β-Ag{sub 2}HgI{sub 4}, and β-Cu{sub 2}HgI{sub 4}

Energy Technology Data Exchange (ETDEWEB)

Borisov, S. V., E-mail: borisov@niic.nsc.ru; Magarill, S. A.; Pervukhina, N. V. [Russian Academy of Sciences, Nikolaev Institute of Inorganic Chemistry, Siberian Branch (Russian Federation)

2017-03-15

The structure of KHgI{sub 3} · H{sub 2}O is assigned to the family of crystal structures having the three-layer cubic packing of iodine anions with cations in the tetrahedral voids (the structures of α-HgI{sub 2}, β-Ag{sub 2}HgI{sub 4}, and β-Cu{sub 2}HgI{sub 4} among them). Crystallographic analysis shows that the nodes of the three-layer close packing are populated by iodine anions and K cations in the ratio 3/4: 1/4. Transformation of the structure of α-HgI{sub 2} into the structure of KHgI{sub 3} · H{sub 2}O can be formally represented as the replacement of (HgI){sub n}{sup +} fragments by (KH{sub 2}O){sub n}{sup +} fragments: (Hg{sub 2}I{sub 4})–(HgI){sup +} + (KH{sub 2}O){sub n}{sup +} = KHgI{sub 3} · H{sub 2}O. Perforated layers of vertex-sharing HgI{sub 4} tetrahedra break down into parallel isolated chains. Channels formed in place of I–Hg–I–Hg–fragments are occupied by–H{sub 2}O–K–-H{sub 2}-O-K-H{sub 2}O-chains weakly bound to neighbors.

Enhancing nanoscale SEM image segmentation and reconstruction with crystallographic orientation data and machine learning

International Nuclear Information System (INIS)

Converse, Matthew I.; Fullwood, David T.

2013-01-01

Current methods of image segmentation and reconstructions from scanning electron micrographs can be inadequate for resolving nanoscale gaps in composite materials (1–20 nm). Such information is critical to both accurate material characterizations and models of piezoresistive response. The current work proposes the use of crystallographic orientation data and machine learning for enhancing this process. It is first shown how a machine learning algorithm can be used to predict the connectivity of nanoscale grains in a Nickel nanostrand/epoxy composite. This results in 71.9% accuracy for a 2D algorithm and 62.4% accuracy in 3D. Finally, it is demonstrated how these algorithms can be used to predict the location of gaps between distinct nanostrands — gaps which would otherwise not be detected with the sole use of a scanning electron microscope. - Highlights: • A method is proposed for enhancing the segmentation/reconstruction of SEM images. • 3D crystallographic orientation data from a nickel nanocomposite is collected. • A machine learning algorithm is used to detect trends in adjacent grains. • This algorithm is then applied to predict likely regions of nanoscale gaps. • These gaps would otherwise be unresolved with the sole use of an SEM

Evidence for a strong sulfur-aromatic interaction derived from crystallographic data.

Science.gov (United States)

Zauhar, R J; Colbert, C L; Morgan, R S; Welsh, W J

2000-03-01

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS

Effect of lone-electron-pair cations on the orientation of crystallographic shear planes in anion-deficient perovskites.

Science.gov (United States)

Batuk, Dmitry; Batuk, Maria; Abakumov, Artem M; Tsirlin, Alexander A; McCammon, Catherine; Dubrovinsky, Leonid; Hadermann, Joke

2013-09-03

Factors affecting the structure and orientation of the crystallographic shear (CS) planes in anion-deficient perovskites were investigated using the (Pb(1-z)Sr(z))(1-x)Fe(1+x)O(3-y) perovskites as a model system. The isovalent substitution of Sr(2+) for Pb(2+) highlights the influence of the A cation electronic structure because these cations exhibit very close ionic radii. Two compositional ranges have been identified in the system: 0.05 ≤ z ≤ 0.2, where the CS plane orientation gradually varies but stays close to (203)p, and 0.3 ≤ z ≤ 0.45 with (101)p CS planes. The incommensurately modulated structure of Pb0.792Sr0.168Fe1.040O2.529 was refined from neutron powder diffraction data using the (3 + 1)D approach (space group X2/m(α0γ), X = (1/2, 1/2, 1/2, 1/2), a = 3.9512(1) Å, b = 3.9483(1) Å, c = 3.9165(1) Å, β = 93.268(2)°, q = 0.0879(1)a* + 0.1276(1)c*, RF = 0.023, RP = 0.029, and T = 900 K). A comparison of the compounds with different CS planes indicates that the orientation of the CS planes is governed mainly by the stereochemical activity of the lone-electron-pair cations inside the perovskite blocks.

X-ray structure determination and deuteration of nattokinase

International Nuclear Information System (INIS)

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-01-01

X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D 2 O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D 2 O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis

Routine phasing of coiled-coil protein crystal structures with AMPLE

Directory of Open Access Journals (Sweden)

Jens M. H. Thomas

2015-03-01

Full Text Available Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

Crystal structures of wild-type Trichoderma reesei Cel7A catalytic domain in open and closed states

Energy Technology Data Exchange (ETDEWEB)

Bodenheimer, Annette M. [Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh NC USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, TN USA; Meilleur, Flora [Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh NC USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, TN USA

2016-11-07

Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

Electrical properties of NiAs-type MnTe films with preferred crystallographic plane of (110)

Energy Technology Data Exchange (ETDEWEB)

Yang, L.; Wang, Z. H., E-mail: zhwang@imr.ac.cn; Zhang, Z. D. [Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016 (China)

2016-01-28

NiAs-type manganese telluride (MnTe) films with preferred crystallographic plane of (110) were prepared on Si/SiO{sub 2} substrates by pulsed laser deposition. X-ray diffraction (XRD) of the films was studied at different temperatures. The XRD peak of MnTe (110) films shifts to higher angle with decreasing temperature, showing the decrease of the lattice parameter. Resistivity of the films was studied in the temperature range of 2–350 K. The bump between 150 and 250 K was observed in the films, which may be related to the special s-d and p-d overlaps induced by the compressed lattice. The magnon drag effect near its Néel temperature T{sub N} and enlarged magnetic-elastic coupling below 100 K were observed and analyzed in details.

Magnetic and crystallographic properties of Gd(Cu/sub 1-x/Ni/sub x/)2 and Gd(Cu/sub 1-x/Al/sub x/)2 intermetallic compounds

International Nuclear Information System (INIS)

Borombaev, M.K.; Levitin, R.Z.; Markosyan, A.S.; Snegirev, V.V.

1986-01-01

Magnetization, paramagnetic susceptibility, and temperature dependence of lattice parameters of Gd(Cu/sub 1-x/Ni/sub x/) 2 (0 2 (0 2 -type structure have been studied in a wide range of temperatures. Below the ordering temperature anomalies in thermal expansion along the crystallographic axes a, b, and c enabled to distinguish between various types of magnetic arrangements. The Gd(Cu/sub 1-x/Ni/sub x/) 2 system has two types of antiferromagnetic phases: AF1 (0 = 0.13 the system orders ferromagnetically. In the Gd(Cu/sub 1-x/Al/sub x/) 2 system two magnetic phases AF1 and AF3 occur in the concentration regions 0 <= x <= 0.035 and 0.04 <= x <= 0.07, respectively. The obtained results are discussed in terms of the RKKY model via the changing conduction electron concentration. (author)

Photo-crystallography: from the structure towards the electron density of metastable states

Energy Technology Data Exchange (ETDEWEB)

Legrand, V [Laboratoire de Cristallographie et de Modelisation des Materiaux Mineraux et Biologiques, CNRS UMR 7036, UHP Nancy 1, Faculte des sciences, Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-les-Nancy Cedex (France); Carbonera, C [Institut de Chimie de la Matiere Condensee de Bordeaux, UPR CNRS 9048, Universite de Bordeaux 1, Groupe de Sciences Moleculaires, 87 Avenue du Docteur Schweitzer, 33608 Pessac cedex (France); Pillet, S [Laboratoire de Cristallographie et de Modelisation des Materiaux Mineraux et Biologiques, CNRS UMR 7036, UHP Nancy 1, Faculte des sciences, Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-les-Nancy Cedex (France); Souhassou, M [Laboratoire de Cristallographie et de Modelisation des Materiaux Mineraux et Biologiques, CNRS UMR 7036, UHP Nancy 1, Faculte des sciences, Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-les-Nancy Cedex (France); Letard, J F [Institut de Chimie de la Matiere Condensee de Bordeaux, UPR CNRS 9048, Universite de Bordeaux 1, Groupe de Sciences Moleculaires, 87 Avenue du Docteur Schweitzer, 33608 Pessac cedex (France); Guionneau, P [Institut de Chimie de la Matiere Condensee de Bordeaux, UPR CNRS 9048, Universite de Bordeaux 1, Groupe de Sciences Moleculaires, 87 Avenue du Docteur Schweitzer, 33608 Pessac cedex (France); Lecomte, C [Laboratoire de Cristallographie et de Modelisation des Materiaux Mineraux et Biologiques, CNRS UMR 7036, UHP Nancy 1, Faculte des sciences, Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-les-Nancy Cedex (France)

2005-01-01

A photo-crystallographic study of Fe(btr){sub 2}(NCS){sub 2}{center_dot}H{sub 2}O was performed in order to describe the modification of structures and charge densities on going from the ground low spin (LS) state to the metastable high spin (HS) state during the LIESST phenomenon at 15 K. Related photo-magnetic and spectroscopic measurements are also described. We show that at 15 K, the thermally quenched and photo-induced structures of the metastable HS state are identical. For comparison, we also derived the structure of the HS and LS states at 130 K in the hysteresis loop; the thermal spin transition and the LIESST spin transition exhibit similar structural behaviours.

Structural study of piracetam polymorphs and cocrystals: crystallography redetermination and quantum mechanics calculations.

Science.gov (United States)

Tilborg, Anaëlle; Jacquemin, Denis; Norberg, Bernadette; Perpète, Eric; Michaux, Catherine; Wouters, Johan

2011-12-01

Pharmaceutical compounds are mostly developed as solid dosage forms containing a single-crystal form. It means that the selection of a particular crystal state for a given molecule is an important step for further clinical outlooks. In this context, piracetam, a pharmaceutical molecule known since the sixties for its nootropic properties, is considered in the present work. This molecule is analyzed using several experimental and theoretical approaches. First, the conformational space of the molecule has been systematically explored by performing a quantum mechanics scan of the two most relevant dihedral angles of the lateral chain. The predicted stable conformations have been compared to all the reported experimental geometries retrieved from the Cambridge Structural Database (CSD) covering polymorphs and cocrystals structures. In parallel, different batches of powders have been recrystallized. Under specific conditions, single crystals of polymorph (III) of piracetam have been obtained, an outcome confirmed by crystallographic analysis. © 2011 International Union of Crystallography. Printed in Singapore – all rights reserved.

Transfer of olivine crystallographic orientation through a cycle of serpentinisation and dehydration

Science.gov (United States)

Dunkel, Kristina G.; Austrheim, Håkon; Ildefonse, Benoit; Jamtveit, Bjørn

2017-08-01

Our ability to decipher the mechanisms behind metamorphic transformation processes depends in a major way on the extent to which crystallographic and microstructural information is transferred from one stage to another. Within the Leka Ophiolite Complex in the Central Norwegian Caledonides, prograde olivine veins that formed by dehydration of serpentinite veins in dunites exhibit a characteristic distribution of microstructures: The outer part of the veins comprises coarse-grained olivine that forms an unusual, brick-like microstructure. The inner part of the veins, surrounding a central fault, is composed of fine-grained olivine. Where the fault movement included a dilational component, optically clear, equant olivine occurs in the centre. Electron backscatter diffraction mapping reveals that the vein olivine has inherited its crystallographic preferred orientation (CPO) from the olivine in the porphyroclastic host rock; however, misorientation is weaker and associated to different rotation axes. We propose that prograde olivine grew epitaxially on relics of mantle olivine and thereby acquired its CPO. Growth towards pre-existing microfractures along which serpentinisation had occurred led to straight grain boundaries and a brick-like microstructure in the veins. When dehydration embrittlement induced slip, a strong strain localisation on discrete fault planes prevented distortion of the CPO due to cataclastic deformation; grain size reduction did not significantly modify the olivine CPO. This illustrates how a CPO can be preserved though an entire metamorphic cycle, including hydration, dehydration, and deformation processes, and that the CPO and the microstructures (e.g. grain shape) of one phase do not necessarily record the same event.

Correlation between atomic structure and magnetic properties of La0.7Ca0.3MnO3 thin films grown on SrTiO3 (1 0 0)

International Nuclear Information System (INIS)

Rubio-Zuazo, J.; Andres, A. de; Taboada, S.; Prieto, C.; Martinez, J.L.; Castro, G.R.

2005-01-01

The crystallographic structure of La 0.7 Ca 0.3 MnO 3 (LCMO) ultra-thin films grown on SrTiO 3 (0 0 1) has been investigated by surface X-ray diffraction (SXD) and the correlation between their transport and magnetic properties and crystallographic structure is discussed. LCMO thin films in a thickness range between 2.4 and 27 nm were grown by DC-sputtering on SrTiO 3 (0 0 1). We distinguish two different crystallographic structures associated to the 2.4 and 27 nm thin films, respectively. The 27 nm film structure corresponds to a tetragonal perovskite (space group Pbnm), as has been reported for bulk LCMO. For the 2.4 nm film the La/Ca ions are located at the regular position of an ideal perovskite and the MnO 6 octahedrons are aligned along the c-axis. The MnO 2 stacking layer (basal plane) is distorted and coplanar to the a-b crystallographic axis with an anti-correlation between octahedron layers. This observed distortion is not compatible with the Pbnm space group. The new phase, which cannot be excluded to coexist at the interface of thicker films, can be described, as an example, through an I4/mcm or Pbcn space group. Based on the observed structure, plausible models to explain their transport and magnetic behaviour are proposed. For the 2.4 nm film, an octahedron in-plane (basal plane) distortion induced by the substrate is observed. Thicker films behave structurally and magnetically as bulk-like materials

Investigation of the crystallographic structure of hydrogenated (Ga,Mn)As

Energy Technology Data Exchange (ETDEWEB)

Bihler, Christoph; Huebl, Hans; Galler, Bastian; Brandt, Martin [Walter Schottky Institut, TU Muenchen, Am Coulombwall 3, 85748 Garching (Germany); Martinez-Criado, Gema; Ciatto, Gianluca [ESRF, 6 rue J. Horowitz, Boite Postale 220, 38043 Grenoble (France); Bonapasta, Aldo Amore; Filippone, Francesco [ISM, Via Salaria, CP 10, 00016 Monterotondo Stazione (Italy); Schoch, Wladimir; Limmer, Wolfgang [Institut fuer Halbleiterphysik, Universitaet Ulm, 89069 Ulm (Germany)

2007-07-01

The lattice expansion of (Ga,Mn)As samples after deuteration {lambda}V{sub D}/V{sub Mn-As}structure (EXAFS) {chi} function corresponding to the first coordination shell of deuterated samples, as well as the comparison of the corresponding X-ray absorption near edge structure (XANES) with simulations of the different complexes strongly suggests that the BC complex predicted by theoretical calculations can be excluded in the deuterated samples. Rather, both EXAFS and XANES spectra can be explained by the formation of AB complexes or complexes in which the D atom is not bound to a nearest As neighbor, but a more distant As atom.

Microstructural and crystallographic characteristics of modulated martensite, non-modulated martensite, and pre-martensitic tweed austenite in Ni-Mn-Ga alloys

International Nuclear Information System (INIS)

Zhou, Le; Schneider, Matthew M.; Giri, Anit; Cho, Kyu; Sohn, Yongho

2017-01-01

A combinatorial approach using diffusion couples and TEM analyses was carried out to investigate the composition-dependent martensitic transformation in NiMnGa alloys. The compositions cover a large portion of the off-stoichiometric Ni 2 MnGa compositions and some Mn-rich compositions. Crystallographic variations of the martensitic phase, including non-modulated (NM) martensite, modulated (5M or 7M) martensite, and austenitic phase were identified in the diffusion couples and investigated with respect to their microstructure and crystallography. The 5M and 7M martensitic structures were only found near the interphase boundary between austenite and martensite, while the NM martensitic structures were found mostly away from the interphase boundary. The tetragonality ratio (c/a) for NM martensite generally increases with e/a ratio, but was also dependent on the composition. The habit plane and martensitic microstructure that consists of twinned variants with differing orientations were documented using electron diffraction. The pre-martensitic state was observed in the austenitic phase that was located near the interphase boundary between austenite and martensite, with distinctive tweed microstructure and a strain field originating from the local lattice distortions. The combinatorial approach proves to be efficient and systematic in studying the composition-dependent martensitic transformation in NiMnGa alloys and can be potentially applied to other shape memory alloys.

Programmatic conversion of crystal structures into 3D printable files using Jmol

OpenAIRE

Scalfani, Vincent F.; Williams, Antony J.; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M.; Liddie, Jahred M.; Bara, Jason E.

2016-01-01

Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from...

Timely deposition of macromolecular structures is necessary for peer review

International Nuclear Information System (INIS)

Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

2013-01-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature

Timely deposition of macromolecular structures is necessary for peer review

Energy Technology Data Exchange (ETDEWEB)

Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

2013-12-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor.

Directory of Open Access Journals (Sweden)

Cyril F Reboul

Full Text Available BACKGROUND: The C-terminal domain of MotB (MotB-C shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. METHODOLOGY/PRINCIPAL FINDINGS: We determined the structure of a new crystalline form (Form B of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the β-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. CONCLUSION/SIGNIFICANCE: Our structural analysis provides a new insight into the mechanism by which MotB inserts into the peptidoglycan mesh, thus anchoring the power-generating complex to the cell wall.

Structural studies of precursor and partially oxidized conducting complexes. 19. Synthesis and crystal structure of Cs2[Pt(CN)4]Cl/sub 0.30, the first anhydrous one-dimensional tetracyanoplatinate chloride complex

International Nuclear Information System (INIS)

Brown, R.K.; Williams, J.M.

1978-01-01

The preparation and single-crystal x-ray structural characterization of a new, partially oxidized tetracyanoplatinate (POTCP), Cs 2 [Pt(CN) 4 ]Cl/sub 0.30/, CsCP(Cl), has been carried out. This one-dimensional conducting salt crystallizes with four formula units in the tetragonal unit cell I4/mcm, with cell constants a = 13.176 (2) A, c = 5.718 (1) A, and V = 992.7 A 3 . A total of 3112 observed data were averaged to yield 427 independent reflections. The structure was solved by standard heavy-atom methods and was refined by full-matrix least squares to a final R(F 0 2 ) = 0.045 and R/sub w/(F 0 2 ) = 0.059. Pertinent structural features include perfectly linear chains of Pt atoms with Pt-Pt separations crystallographically constrained to a value of (c/2) = 2.859 (2) A and interchain Pt-Pt distances of 9.317 A. Separations between the Cs + and Cl - ions are significantly shorter than the sum of the ionic radii. A discussion of these unusually short interionic distances and the absence of hydration as determined from the structural study and themogravimetric analyses is given. 2 figures, 2 tables

Crystallographic Orientation Determination of Hexagonal Structure Crystals by Laser Ultrasonic Technique

International Nuclear Information System (INIS)

Li, W; Coulson, J; Marrow, P; Smith, R J; Clark, M; Sharples, S D; Lainé, S J

2016-01-01

Spatially resolved acoustic spectroscopy (SRAS) is a laser ultrasonic technique that shows qualitative contrast between grains of different orientation, illustrating the sensitivity of acoustic waves to the material structure. The technique has been improved significantly on determining the full orientation of multigrain cubic metals, by comparing the measured surface acoustic wave (SAW) velocity to a pre-calculated model. In this paper we demonstrate the ability of this technique to determine the orientation of hexagonal structure crystals, such as magnesium and titanium based alloys. Because of the isotropy of the SAW velocity on the basal plane (0001) of hexagonal crystals, the slowness surface is shown as a circle. As the plane moves from (0001) towards (112-bar0) or towards (101-bar0), the slowness surface gradually turns into an oval. These acoustic properties increase the difficulty in orientation determination. The orientation results of a grade 1 commercially pure titanium by SRAS is presented, with comparison with electron backscattered diffraction (EBSD) results. Due to the nature of SAWs on hexagonal structure crystals, only the results of Euler angles 1 and 2 are discussed. The error between SRAS and EBSD is also investigated. (paper)

Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: II, application to decayed human teeth.

Science.gov (United States)

Adachi, Tetsuya; Pezzotti, Giuseppe; Yamamoto, Toshiro; Ichioka, Hiroaki; Boffelli, Marco; Zhu, Wenliang; Kanamura, Narisato

2015-05-01

A systematic investigation, based on highly spectrally resolved Raman spectroscopy, was undertaken to research the efficacy of vibrational assessments in locating chemical and crystallographic fingerprints for the characterization of dental caries and the early detection of non-cavitated carious lesions. Raman results published by other authors have indicated possible approaches for this method. However, they conspicuously lacked physical insight at the molecular scale and, thus, the rigor necessary to prove the efficacy of this spectroscopy method. After solving basic physical challenges in a companion paper, we apply them here in the form of newly developed Raman algorithms for practical dental research. Relevant differences in mineral crystallite (average) orientation and texture distribution were revealed for diseased enamel at different stages compared with healthy mineralized enamel. Clear spectroscopy features could be directly translated in terms of a rigorous and quantitative classification of crystallography and chemical characteristics of diseased enamel structures. The Raman procedure enabled us to trace back otherwise invisible characteristics in early caries, in the translucent zone (i.e., the advancing front of the disease) and in the body of lesion of cavitated caries.

Crystal structure and magnetism of Fe2(OH)[B2O4(OH)

DEFF Research Database (Denmark)

Kurayoshi, Yotaro; Hara, Shigeo; Sato, Hirohiko

2014-01-01

The structure and magnetism of Fe2(OH)[B2O4(OH)] are reported. Powder x-ray diffraction reveals a characteristic structure containing two crystallographically independent zigzag-ladder chains of magnetic Fe2+ ions. Magnetization measurements reveal a phase transition at 85 K, below which a weak...... spontaneous magnetization (approximate to 0.15 μB/Fe) appears. Below 85 K, magnetization increases with decreasing temperature down to 70 K, below which it decreases and approaches a constant value at low temperature. The Mossbauer spectrum at room temperature is composed of two paramagnetic doublets...... corresponding to the two crystallographic Fe2+ sites. Below 85 K, each doublet undergoes further splitting because of the magnetic hyperfine fields. The temperature dependence of the hyperfine field is qualitatively different for the two distinguishable Fe2+ sites. This is responsible for the anomalous...

Development of Microstructure and Crystallographic Texture in a Double-Sided Friction Stir Welded Microalloyed Steel

Science.gov (United States)

Rahimi, S.; Wynne, B. P.; Baker, T. N.

2017-01-01

The evolution of microstructure and crystallographic texture has been investigated in double-sided friction stir welded microalloyed steel, using electron backscatter diffraction (EBSD). The microstructure analyses show that the center of stirred zone reached a temperature between Ac1 and Ac3 during FSW, resulting in a dual-phase austenitic/ ferritic microstructure. The temperatures in the thermo-mechanically affected zone and the overlapped area between the first and second weld pass did not exceed the Ac1. The shear generated by the rotation probe occurs in austenitic/ferritic phase field where the austenite portion of the microstructure is transformed to a bainitic ferrite, on cooling. Analysis of crystallographic textures with regard to shear flow lines generated by the probe tool shows the dominance of simple shear components across the whole weld. The austenite texture at Ac1 - Ac3 is dominated by the B { {1bar{1}2} }D2 { {11bar{2}} }< 111rangle simple shear texture components. The formation of ultrafine equiaxed ferrite with submicron grain size has been observed in the overlapped area between the first and second weld pass. This is due to continuous dynamic strain-induced recrystallization as a result of simultaneous severe shear deformation and drastic undercooling.

Crystal structure of 3,4a,7,7,10a-pentamethyl-3-vinyldodecahydro-1H-benzo[f]chromen-9-ol isolated from Sideritis perfoliata

Directory of Open Access Journals (Sweden)

Ísmail Çelik

2016-10-01

Full Text Available The asymmetric unit of the title compound, C20H34O2, contains two crystallographically independent molecules (1 and 2 with similar conformations. In both molecules, the cyclohexane rings adopt a chair conformation, while the oxane rings are also puckered. In the crystal, O—H...O hydrogen bonds connect adjacent molecules, forming C(6 helical chains located around a 21 screw axis and running along the crystallographic a axis. The packing of these chains is governed only by van der Waals interactions. Semi-empirical PM3 quantum chemical calculations are in a satisfactory agreement with the structural results of the X-ray structure analysis. The absolute structure was indeterminate in the present experiment.

Influence of crystallographic texture in X70 pipeline steels on toughness anisotropy and delamination

Science.gov (United States)

Al-Jabr, Haytham M.

The effects of microstructure and crystallographic texture in four commercially-produced API X70 pipeline steels and their relation to planar anisotropy of toughness and delamination were evaluated. The experimental steels were processed through either a hot strip mill, a Steckel mill, or a compact strip mill. Different processing routes were selected to obtain plates with potential variations in the microstructure and anisotropic characteristics. Tensile and Charpy impact testing were used to evaluate the mechanical properties in three orientations: longitudinal (L), transverse (T) and diagonal (D) with respect to the rolling direction to evaluate mechanical property anisotropy. The yield and tensile strengths were higher in the T orientation and toughness was lower in the D orientation for all plates. Delamination was observed in some of the ductile fracture surfaces of the impact samples. To further study the splitting behavior and effects on impact toughness, a modified impact test (MCVN) specimen with side grooves was designed to intensify induced stresses parallel to the notch root and thus facilitate evaluation of delamination. Scanning electron microscopy combined with electron backscattered diffraction (EBSD) were used to evaluate the grain size, microstructural constituents, and crystallographic texture to determine the factors leading to delamination and the anisotropy in toughness. The ferrite grain size is mainly responsible for the differences in DBTTs between the L and T orientations. The higher DBTT in the D orientation observed in pipeline steels is attributed to crystallographic texture. The higher DBTT in the D direction is due to the higher volume fraction of grains having their {100} planes parallel or close to the primary fracture plane for the D orientation. An equation based on a new "brittleness parameter," based on an assessment of grain orientations based on EBSD data, was developed to predict the changes in DBTTs with respect to sample

Crystallographic and electronic structure of the Ca2TiMnO6 double perovskite

International Nuclear Information System (INIS)

López, J.P. Garzón; Cardona, R.; Santos, A. Sarmiento; Téllez, D.A. Landínez; Roa-Rojas, J.

2014-01-01

In this work, we report synthesis and crystalline structure study of the Ca 2 TiMnO 6 complex perovskite, by X-ray diffraction experiments and through the application of the Rietveld refinement using the GSAS code. Results revealed the crystallization of the system in a tetragonal perovskite with the characteristic structure given by I4/m (#87) space group and lattice parameters a=5.339(4) Å and c=7.736(6) Å. Ab initio calculations of density of states (DOS) and electronic structure were carried out for this perovskite-like system, by the Density Functional Theory (DFT) and using the Full-potential Linearized Augmented Plane Waves (FP-LAPW) method. The exchange-correlation potential was treated using the Generalized Gradient Approximation (GGA). All calculations were carried-out using spin polarization. For the up spin orientation the compound has a semiconducting behavior and for down spin polarization it behaves like a conductor. The calculated effective magnetic moment in cell was 4.02 μ B , which is close to the expected value calculated from Hund's rules

Crystallographic features of poly(vinylidene fluoride) film upon an attractive substrate of KBr.

Science.gov (United States)

Huang, Rui; Wang, Gang; Guo, Shuo; Wang, Ke; Fu, Qiang

2017-10-18

Among all the polymorphs of poly(vinylidene fluoride) (PVDF), the polar γ-form possesses the highest melting point and electrical breakdown strength as well as the strongest solvent and irradiation resistance, which are beneficial for the durability of PVDF products. Since the γ-form is neither kinetically favorable nor the most thermodynamically stable, it is still difficult to attain the exclusive γ-polymorph, particularly in the case of neat PVDF. In this study, the melt isothermal crystallization of PVDF films was carried out between two KBr wafers. Owing to the characteristics of KBr wafer, including no IR absorbance and high optical transmittance, the crystallographic features originating from the KBr substrate can be conveniently elucidated through the in situ inspected techniques of FTIR and PLM. The KBr wafers significantly accelerated the crystallization kinetics of α-crystals, and then readily triggered the solid-state α- to γ-transformation of the pre-formed α-spherulites, resulting in a 10 μm-thick, neat PVDF film with an absolute crystallinity of 35% and a relative γ fraction as high as 94%. When the film thickness was increased to 40 μm, the crystallization rate of the α-form was still rapid, but the solid-state transformation was not appreciable. These interesting crystallographic phenomena are attributed to the existence of ion-dipole interaction between the -CF 2 or -CH 2 of PVDF chains and the surface of KBr wafer. Unlike most traditional substrate-dominated crystallizations that prevail in a surface epitaxy manner, in which the target films are of ultra-thin thickness (of the order of 10 nm), the ion-dipole interaction promotes the effective thickness to a ten micron level, which enables its production and application at scalable level. Moreover, the triggering of α- to γ-transformation via external fields could be an alternative for achieving the γ-dominant PVDF products, particularly when the introduction of external additives is

Crystallographic structures of absorbates and neutron diffraction

International Nuclear Information System (INIS)

Marti, C.; Thorel, P.

1975-01-01

The advantage of neutron diffraction is that it is possible to work at any pressure and therefore to study an adsorbant-adsorbate couple within a wide pressure and temperature range and at thermodynamic equilibrium. Nitrogen adsorbed on graphite and CF 4 adsorbed on graphite were measured [fr

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

International Nuclear Information System (INIS)

Makino, Debora Lika; Conti, Elena

2013-01-01

The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented

Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase.

Science.gov (United States)

Daughtry, Kelly D; Xiao, Youli; Stoner-Ma, Deborah; Cho, Eunsun; Orville, Allen M; Liu, Pinghua; Allen, Karen N

2012-02-08

Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 Å resolution) and in the product complex (at 2.2 Å resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.

X-ray structure determination and deuteration of nattokinase

Energy Technology Data Exchange (ETDEWEB)

Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

2013-11-01

X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

Synthesis, crystal structure and DFT studies of N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide

Science.gov (United States)

Gautam, P.; Gautam, D.; Chaudhary, R. P.

2013-12-01

The title compound N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide ( III) was obtained from the reaction of 2-(propan-2-ylidene)hydrazinecarbothioamide ( II) with acetic anhydride instead of formation of the desired thiosemcarbazide derivative of Meldrum acid. The structures of II and III were established by elemental analysis, IR, NMR, Mass and X-ray crystallographic studies. II crystallizes in triclinic system, sp. gr. Z = 2; III crystallizes in the monoclinic system, sp. gr. P21/ c, Z = 8. Density functional theory (DFT) calculations have been carried out for III. 1H and 13C NMR of III has been calculated and correlated with experimental results.

Synthesis, crystal structure and DFT studies of N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide

International Nuclear Information System (INIS)

Gautam, P.; Gautam, D.; Chaudhary, R. P.

2013-01-01

The title compound N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide (III) was obtained from the reaction of 2-(propan-2-ylidene)hydrazinecarbothioamide (II) with acetic anhydride instead of formation of the desired thiosemcarbazide derivative of Meldrum acid. The structures of II and III were established by elemental analysis, IR, NMR, Mass and X-ray crystallographic studies. II crystallizes in triclinic system, sp. gr. P-bar1 Z = 2; III crystallizes in the monoclinic system, sp. gr. P2 1 /c, Z = 8. Density functional theory (DFT) calculations have been carried out for III. 1 H and 13 C NMR of III has been calculated and correlated with experimental results

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Science.gov (United States)

Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

2014-05-01

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Lithium insertion in the two crystallographic forms of the binary-phase Mo15Se19

Science.gov (United States)

Tarascon, J. M.; Murphy, D. W.

1986-02-01

Compounds which can undergo topotactic insertion of lithium are of potential technological importance in secondary lithium batteries. In this paper we present the chemical and electrochemical insertion of lithium into the binary-phase Mo15Se19, which can exist in two crystallographic forms, denoted AA and BB, when prepared from In3Mo15Se19 and In2Mo15Se19, respectively. We show that both forms can reversibly accommodate up to eight lithium atoms, yielding two new series of compounds of formula LixMo15Se19. This behavior is consistent with the electronic structure of the host material predicted from band-structure calculations. The room-temperature phase diagram of both LixMo15Se19 systems as a function of x has been established using electrochemical test cells (based on Mo15Se19 as the cathode), and in situ x-ray measurements as the cells discharge. Both LixMo15Se19 systems contain three single-phase domains as a function of x: two hexagonal phases and an orthorhombic phase. The nature of the transitions between these single phases and the variation of the lattice parameters within a single-phase domain are reported. While the mechanism of intercalation of lithium is similar for both Mo15Se19 forms, there is a drastic difference in Li intercalation behavior for the parent indium phases In2Mo15Se19 and In3Mo15Se19. We found that In2Mo15Se19 can reversibly incorporate 6.4 lithium atoms while In3Mo15Se19 does not react. This behavior is explained on the basis of structural considerations.

The structural and optical properties of metal ion-implanted GaN

Energy Technology Data Exchange (ETDEWEB)

Macková, A.; Malinský, P. [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v.v.i., 250 68 Řež (Czech Republic); Department of Physics, Faculty of Science, J.E. Purkinje University, České Mládeže 8, 400 96 Ústí nad Labem (Czech Republic); Sofer, Z.; Šimek, P.; Sedmidubský, D. [Department of Inorganic Chemistry, Institute of Chemical Technology, 166 28 Prague (Czech Republic); Veselý, M. [Dept. of Organic Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6 (Czech Republic); Böttger, R. [Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden – Rossendorf, 01328 Dresden (Germany)

2016-03-15

The practical development of novel optoelectronic materials with appropriate optical properties is strongly connected to the structural properties of the prepared doped structures. We present GaN layers oriented along the (0 0 0 1) crystallographic direction that have been grown by low-pressure metal–organic vapour-phase epitaxy (MOVPE) on sapphire substrates implanted with 200 keV Co{sup +}, Fe{sup +} and Ni{sup +} ions. The structural properties of the ion-implanted layers have been characterised by RBS-channelling and Raman spectroscopy to obtain a comprehensive insight into the structural modification of implanted GaN layers and to study the subsequent influence of annealing on crystalline-matrix recovery. Photoluminescence was measured to control the desired optical properties. The post-implantation annealing induced the structural recovery of the modified GaN layer depending on the introduced disorder level, e.g. depending on the ion implantation fluence, which was followed by structural characterisation and by the study of the surface morphology by AFM.

Structure of valinomycin and its complexes

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Makrlík, E.; Dušek, Michal; Císařová, I.; Dohnálek, Jan; Dušková, Jarmila; Skálová, Tereza

2009-01-01

Roč. 16, 2a (2009), s. 30-31 ISSN 1211-5894. [Struktura - Colloquium of Czech and Slovak Crystallographic Association. Hluboká nad Vltavou, 22.06.2009-25.06.2009] R&D Projects: GA ČR GA305/07/1073; GA AV ČR IAA500500701 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z10100521 Keywords : valinomycin * complex * structure 8 hydration Subject RIV: CD - Macromolecular Chemistry

Spectroscopy, crystal structure, valance molecular orbital energy level diagram and DFT study of cis-[Cr(2,2'-bipy) 2Cl 2](Cl) 0.38(PF 6) 0.62

Science.gov (United States)

Kar, Tapas; Liao, Meng-Sheng; Biswas, Susobhan; Sarkar, Saikat; Dey, Kamalendu; Yap, Glenn P. A.; Kreisel, Kevin

2006-11-01

A new octahedral chromium(III) complex having 2,2'-bipyridine as ligand system was synthesized in methanol. Single crystal X-ray diffraction analysis shows that it possesses non-stoichiometry in its anionic primary covalency. It has also been studied by elemental analyses, optical spectroscopy (UV-vis, IR) and magnetic susceptibility data. DFT calculations (with B3LYP functional and double-ξ quality LANLDZ(D95V) basis set) were carried out to interpret the electronic and infrared spectra of the complex. The DFT optimized geometric structure for the complex is compared with the X-ray crystallographic data; the theory-experiment agreement is satisfactory.

Experimental and theoretical evidence of a supercritical-like transition in an organic semiconductor presenting colossal uniaxial negative thermal expansion† †Electronic supplementary information (ESI) available: Diffraction and crystallography, Cambridge Structural Database survey, DFT computational details, UV spectroscopy, differential scanning calorimetry, and optical microscopy. CCDC 1810678–1810688. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c8sc00159f

Science.gov (United States)

Roche, Gilles H.; Wantz, Guillaume; Moreau, Joël J. E.; Dautel, Olivier J.; Filhol, Jean-Sébastien

2018-01-01

Thermal expansion coefficients of most materials are usually small, typically up to 50 parts per million per kelvin, and positive, i.e. materials expand when heated. Some materials show an atypical shrinking behavior in one or more crystallographic directions when heated. Here we show that a high mobility thiophene-based organic semiconductor, BHH-BTBT, has an exceptionally large negative expansion between 95 and 295 K (–216 BTBT, a much studied organic semiconductor with a closely related molecular formula and 3D crystallographic structure. Complete theoretical characterization of BHH-BTBT using ab initio molecular dynamics shows that below ∼200 K two different α and β domains exist of which one is dominant but which dynamically exchange around and above 210 K. A supercritical-like transition from an α dominated phase to a β dominated phase is observed using DSC measurements, UV-VIS spectroscopy, and X-ray diffraction. The origin of the extreme negative and positive thermal expansion is related to steric hindrance between adjacent tilted thiophene units and strongly enhanced by attractive S···S and S···C interactions within the highly anharmonic mixed-domain phase. This material could trigger the tailoring of optoelectronic devices highly sensitive to strain and temperature. PMID:29780527

Crystallographic study and self irradiation damage on plutonium at low temperature; Etude cristallographique et effets de l'auto-irradiation sur le plutonium a basse temperature

Energy Technology Data Exchange (ETDEWEB)

Solente, P [Commissariat a l' Energie Atomique, Fontenay-aux-Roses (France). Centre d' Etudes Nucleaires

1965-05-01

We have studied the variation of the parameters of {alpha} plutonium and aluminium stabilised {delta} alloys at low temperature, in order to verify the existence of an antiferromagnetic transition at low temperature. The effects of {alpha} particles on the length of a polycrystal of {alpha} plutonium at 4,2 deg. K are also presented at 18 deg. K a plutonium shows no crystallographic change from its structure at room temperature. The thermal expansion coefficients along the 3 axis seem to be positive at this temperature. Therefore a magnetic contribution on thermal expansion coefficients must be small. A dilatation anomaly of {delta}Pu has been observed at 100 deg. K, together with an anomaly of the diffraction lines intensity. No sur-structure line has been observed at 20 deg. K. The length of {alpha} plutonium Increases with time at a rate of about 5 x 10{sup -6} per hour when held in liquid helium. This effect is attributed to the creation of Frenkel pairs. (author) [French] On presente une etude cristallographique a basse temperature du plutonium {alpha} et stabilise {delta} par des additions d'aluminium en vue de verifier l'existence d'une transformation antiferromagnetique a basse temperature. L'effet des particules {alpha} a 4,2 deg. K sur la longueur d'un polycristal de plutonium {alpha} a egalement ete etudie. Il a ete determine que le plutonium {alpha} ne mange pas de phase allotropique Jusqu'a 18 deg. K, les coefficients de dilatation des trois axes de la maille semblent rester positifs. Une eventuelle contribution magnetique sur les coefficients de dilatation devrait donc etre faible. Une legere anomalie de dilatation de Pu {delta} a ete observee a 100 deg. K ainsi qu'une anomalie d'intensite des raies de diffraction. Aucune raie de surstructure n'a ete observee. Le plutonium {alpha} s'allonge lorsqu'il est plonge dans l'helium liquide d'un taux de l'ordre de 5 x 10{sup -6}/heure. Cet effet a ete attribuee a la creation de paires de Frenkel. (auteur)

Crystallographic and Electronic Structure of the Sr3Sb2CoO9 Triple Perovskite

International Nuclear Information System (INIS)

González, W; Téllez, D A Landínez; Roa-Rojas, J; Cardona, R

2014-01-01

Compounds The perovskites are materials with physical and chemical characteristics that make them optimal for application in the technological and scientist. When the ideal formula of perovskite ABO 3 is modified by introducing a special structural arrangement can get to get triple perovskites, which correspond to the formula A 3 B 2 B'O 9 . In this work we report the synthesis process and the study of electronic structure and crystal Sr 3 Sb 2 CoO 9 new triple perovskite. From the experiments of X-ray Diffraction and the application of the Rietveld refinement method was revealed that the system crystallizes in a perovskite structure with a characteristic triple given by the space group Immm (#71) and lattice parameters a=9.791(9) Å, b=5.656(7) Å and c=16.957(8) Å. Ab initio calculations of density of states (DOS) and electronic structure were carried out for this perovskite-like system by using the Quantum EXPRESSO code. The exchange-correlation potential was treated using the Generalized Gradient Approximation (GGA). All calculations were carried-out using spin polarization.

Quantitative DMS mapping for automated RNA secondary structure inference

OpenAIRE

Cordero, Pablo; Kladwang, Wipapat; VanLang, Christopher C.; Das, Rhiju

2012-01-01

For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using a pseudo-energy framework developed for 2'-OH acylation (SHAPE) mapping. On six non-coding RNAs with crystallographic models, DMS- guided modeling achieves overall false negative and false discovery rates of 9.5% and 11.6%, comparable or better than SHAPE-guided modeling; and non-parametric bootstrappin...

Purification, crystallization and preliminary X-ray crystallographic analysis of the ATPase domain of human TAP in nucleotide-free and ADP-, vanadate- and azide-complexed forms

International Nuclear Information System (INIS)

Meena, Sita R.; Gangwar, Shanti P.; Saxena, Ajay K.

2012-01-01

The ATPase domain of human TAP in nucleotide free, ADP, vanadate and azide complexed forms were purified and crystallized. The X-ray diffraction data sets were collected for all crystals in the resolution range of 2.8–3.0 Å. The human transporter associated with antigen processing (TAP) protein belongs to the ATP-binding cassette (ABC) transporter superfamily and is formed by the heterodimerization of TAP1 and TAP2 subunits. TAP selectively pumps cytosolic peptides into the lumen of the endoplasmic reticulum in an ATP-dependent manner. The catalytic cycle of the ATPase domain of TAP is not understood at the molecular level. The structures of catalytic intermediates of the ATPase domain of TAP will contribute to the understanding of the chemical mechanism of ATP hydrolysis. In order to understand this mechanism, the ATPase domain of human TAP1 (NBD1) was expressed and purified, crystallized in nucleotide-free and transition-state complex forms and X-ray crystallographic studies were performed. The NBD1 protein was crystallized (i) in the nucleotide-free apo form; (ii) in complex with ADP–Mg 2+ , mimicking the product-bound state; (iii) in complex with vanadate–ADP–Mg 2+ , mimicking the ATP-bound state; and (iv) in complex with azide–ADP–Mg 2+ , also mimicking the ATP-bound state. X-ray diffraction data sets were collected for apo and complexed NBD1 using an in-house X-ray diffraction facility at a wavelength of 1.5418 Å. The apo and complexed NBD1 crystals belonged to the primitive hexagonal space group P6 2 , with one monomer in the asymmetric unit. Here, the crystallization, data collection and preliminary crystallographic analysis of apo and complexed NBD1 are reported

Crystal Structure and Substrate Specificity of PTPN12

Directory of Open Access Journals (Sweden)

Hui Li

2016-05-01

Full Text Available PTPN12 is an important tumor suppressor that plays critical roles in various physiological processes. However, the molecular basis underlying the substrate specificity of PTPN12 remains uncertain. Here, enzymological and crystallographic studies have enabled us to identify two distinct structural features that are crucial determinants of PTPN12 substrate specificity: the pY+1 site binding pocket and specific basic charged residues along its surface loops. Key structurally plastic regions and specific residues in PTPN12 enabled recognition of different HER2 phosphorylation sites and regulated specific PTPN12 functions. In addition, the structure of PTPN12 revealed a CDK2 phosphorylation site in a specific PTPN12 loop. Taken together, our results not only provide the working mechanisms of PTPN12 for desphosphorylation of its substrates but will also help in designing specific inhibitors of PTPN12.

Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment.

Directory of Open Access Journals (Sweden)

Alison C Pitts

Full Text Available Bacterial microcompartments form a protective proteinaceous barrier around metabolic enzymes that process unstable or toxic chemical intermediates. The genome of the virulent, multidrug-resistant Clostridium difficile 630 strain contains an operon, eut, encoding a bacterial microcompartment with genes for the breakdown of ethanolamine and its utilisation as a source of reduced nitrogen and carbon. The C. difficile eut operon displays regulatory genetic elements and protein encoding regions in common with homologous loci found in the genomes of other bacteria, including the enteric pathogens Salmonella enterica and Enterococcus faecalis. The crystal structures of two microcompartment shell proteins, CD1908 and CD1918, and an uncharacterised protein with potential enzymatic activity, CD1925, were determined by X-ray crystallography. CD1908 and CD1918 display the same protein fold, though the order of secondary structure elements is permuted in CD1908 and this protein displays an N-terminal β-strand extension. These proteins form hexamers with molecules related by crystallographic and non-crystallographic symmetry. The structure of CD1925 has a cupin β-barrel fold and a putative active site that is distinct from the metal-ion dependent catalytic cupins. Thin-section transmission electron microscopy of Escherichia coli over-expressing eut proteins indicates that CD1918 is capable of self-association into arrays, suggesting an organisational role for CD1918 in the formation of this microcompartment. The work presented provides the basis for further study of the architecture and function of the C. difficile eut microcompartment, its role in metabolism and the wider consequences of intestinal colonisation and virulence in this pathogen.

Synthesis and structural characterisation of mixed An(IV)-An(III) actinide oxalates used as precursors for dedicated fuel or target

International Nuclear Information System (INIS)

Tamain, Christelle; Grandjean, Stephane; Arab Chapelet, Benedicte; Abraham, Francis

2010-01-01

Oxalic co-conversion process plays an important role by producing mixed-actinide compounds used as starting materials as they are particularly suitable precursors of actinide oxide solid solutions. In these oxalate compounds, a mixed crystallographic site which accommodates both elements in spite of their different oxidation states has been established. The charge compensation is ensured by monovalent cations present in the acidic solution. This communication reviews the various mixed-actinide oxalates obtained by crystallization from acidic solution. First, crystallographic structures determined by X-ray diffraction from single crystals are described. Then completing data obtained by powder X-ray diffraction are presented on various systems. The different supramolecular arrangements underline the complexity of An(IV)-An(III)/Ln(III) oxalate system and the need to pursue studies on single crystals. (authors)

Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited.

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Roman Šink

Full Text Available The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.

The mimivirus R355 gene product: preliminary crystallographic analysis of a putative ubiquitin-like protein-specific protease

International Nuclear Information System (INIS)

Jeudy, Sandra; Lartigue, Audrey; Mansuelle, Pascal; Ogata, Yuki; Abergel, Chantal

2010-01-01

The genome sequence of mimivirus, the largest known double-stranded DNA virus, encodes a putative protease: the R355 gene product. Its expression in E. coli, its crystallization and the preliminary phasing of a MAD data set using the selenium signal present in a crystal of recombinant selenomethionine-substituted protein are reported. The complete genome sequence of the largest known double-stranded DNA virus, mimivirus, reveals the presence of a gene (denoted R355) that potentially encodes a cysteine protease that is expressed late (after 6 h) in the infectious cycle of the virus. In order to verify a sequence-based functional prediction and understand its role during the infectious process, the R355 protein was produced to assay its proteolytic activity and solve its three-dimensional structure. Here, the preliminary crystallographic analysis of the recombinant viral protein is reported. The crystals belonged to the orthorhombic space group P2 1 2 1 2 1 , with a monomer in the asymmetric unit. A MAD data set was used for preliminary phasing using the selenium signal from a selenomethionine-substituted protein crystal

A transmission Kikuchi diffraction study of cementite in a quenched and tempered steel

Energy Technology Data Exchange (ETDEWEB)

Saleh, Ahmed A., E-mail: asaleh@uow.edu.au [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, NSW 2522 (Australia); Casillas, Gilberto [Electron Microscopy Centre, University of Wollongong, NSW 2500 (Australia); Pereloma, Elena V. [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, NSW 2522 (Australia); Electron Microscopy Centre, University of Wollongong, NSW 2500 (Australia); Carpenter, Kristin R. [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, NSW 2522 (Australia); Plate Mill: Manufacturing, BlueScope Steel Ltd., Port Kembla, NSW 2505 (Australia); Killmore, Christopher R. [Research & Development: Sales & Marketing, BlueScope Steel Ltd., Port Kembla, NSW 2505 (Australia); Gazder, Azdiar A. [Electron Microscopy Centre, University of Wollongong, NSW 2500 (Australia)

2016-04-15

This is the first transmission Kikuchi diffraction (TKD) study to report the indexing of nano-sized cementite as distinct structures and its orientation relationship with the body-centered cubic matrix in a quenched and tempered steel. Crystallographic analysis via TKD and selected area diffraction returned the well-known Bagaryatskii and Isaichev orientation relationships. However, the indexing of nano-sized cementite via TKD was sensitive to the thickness of the electron transparent region such that TEM remains the most precise method to characterise such precipitates. - Highlights: • Nano-sized cementite in a QT steel has been investigated by TKD and TEM. • Cementite has been indexed as distinct structures via TKD. • Crystallographic analysis returned the Bagaryatskii and Isaichev ORs. • Success of TKD is sensitive to the thickness of the electron transparent region. • TEM remains the most precise technique to characterise nano-sized precipitates.

A transmission Kikuchi diffraction study of cementite in a quenched and tempered steel

International Nuclear Information System (INIS)

Saleh, Ahmed A.; Casillas, Gilberto; Pereloma, Elena V.; Carpenter, Kristin R.; Killmore, Christopher R.; Gazder, Azdiar A.

2016-01-01

This is the first transmission Kikuchi diffraction (TKD) study to report the indexing of nano-sized cementite as distinct structures and its orientation relationship with the body-centered cubic matrix in a quenched and tempered steel. Crystallographic analysis via TKD and selected area diffraction returned the well-known Bagaryatskii and Isaichev orientation relationships. However, the indexing of nano-sized cementite via TKD was sensitive to the thickness of the electron transparent region such that TEM remains the most precise method to characterise such precipitates. - Highlights: • Nano-sized cementite in a QT steel has been investigated by TKD and TEM. • Cementite has been indexed as distinct structures via TKD. • Crystallographic analysis returned the Bagaryatskii and Isaichev ORs. • Success of TKD is sensitive to the thickness of the electron transparent region. • TEM remains the most precise technique to characterise nano-sized precipitates.

Structures and Spectroscopy Studies of Two M(II-Phosphonate Coordination Polymers Based on Alkaline Earth Metals (M = Ba, Mg

Directory of Open Access Journals (Sweden)

Kui-Rong Ma

2013-01-01

Full Text Available The two examples of alkaline-earth M(II-phosphonate coordination polymers, [Ba2(L(H2O9]·3H2O (1 and [Mg1.5(H2O9]·(L-H21.5·6H2O (2 (H4L = H2O3PCH2N(C4H8NCH2PO3H2, N,N′-piperazinebis(methylenephosphonic acid, (L-H2 = O3PH2CHN(C4H8NHCH2PO3 have been hydrothermally synthesized and characterized by elemental analysis, FT-IR, PXRD, TG-DSC, and single-crystal X-ray diffraction. Compound 1 possesses a 2D inorganic-organic alternate arrangement layer structure built from 1D inorganic chains through the piperazine bridge, in which the ligand L−4 shows two types of coordination modes reported rarely at the same time. In 1, both crystallographic distinct Ba(1 and Ba(2 ions adopt 8-coordination two caps and 9-coordination three caps triangular prism geometry structures, respectively. Compound 2 possesses a zero-dimensional mononuclear structure with two crystallographic distinct Mg(II ions. Free metal cations   [MgO6]n2+ and uncoordinated anions (L-H2n2- are joined together by static electric force. Results of photoluminescent measurement indicate three main emission bands centered at 300 nm, 378.5 nm, and 433 nm for 1 and 302 nm, 378 nm, and 434.5 nm for 2 (λex=235 nm, respectively. The high energy emissions could be derived from the intraligand π∗-n transition stations of H4L (310 nm and 382 nm, λex=235 nm, while the low energy emission (>400 nm of 1-2 may be due to the coordination effect with metal(II ions.

High pressure study of the intermetallic compound UFe2Al10

International Nuclear Information System (INIS)

Halevy, I.; Zenou, V.Y.; Salhov, S.; Caspi, E.N.; Schaefer, W.; Yaar, I.

2006-01-01

The crystallographic and electronic structure of UFe 2 Al 10 was studied as a function of pressure by combining X-ray diffraction results with the full potential linearized augmented plane wave (LAPW) calculations method. The volume-pressure reduction measured at 23.5 GPa is V/V 0 = 0.87, with a B 0 value of 132 ± 8 GPa. The uranium 5f electrons in this compound are located in a narrow and well-defined band above E Fermi , having a very weak interaction with the iron 3d band located below E Fermi . Consequently, the DOS at E Fermi is close to zero, indicating a close to zero-magnetic moment of the uranium atom at low temperature up to a pressure of 23.5 GPa, as expected from the layered crystallographic structure of this compound. The above assumption is supported by preliminary neutron diffraction data, where no long-range magnetic order was detected down to 3 K

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the mannose 6-phosphate isomerase from Salmonella typhimurium

Energy Technology Data Exchange (ETDEWEB)

Gowda, Giri; Sagurthi, Someswar Rao [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India); Savithri, H. S. [Department of Biochemistry, Indian Institute of Science, Bangalore 560 012 (India); Murthy, M. R. N., E-mail: mrn@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India)

2008-02-01

The cloning, expression, purification, crystallization and preliminary X-ray crystallographic studies of mannose 6-phosphate isomerase from S. typhimurium are reported. Mannose 6-phosphate isomerase (MPI; EC 5.3.1.8) catalyzes the reversible isomerization of d-mannose 6-phosphate (M6P) and d-fructose 6-phosphate (F6P). In the eukaryotes and prokaryotes investigated to date, the enzyme has been reported to play a crucial role in d-mannose metabolism and supply of the activated mannose donor guanosine diphosphate d-mannose (GDP-d-mannose). In the present study, MPI was cloned from Salmonella typhimurium, overexpressed in Escherichia coli and purified using Ni–NTA affinity column chromatography. Purified MPI crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 36.03, b = 92.2, c = 111.01 Å. A data set extending to 1.66 Å resolution was collected with 98.8% completeness using an image-plate detector system mounted on a rotating-anode X-ray generator. The asymmetric unit of the crystal cell was compatible with the presence of a monomer of MPI. A preliminary structure solution of the enzyme has been obtained by molecular replacement using Candida albicans MPI as the phasing model and the program Phaser. Further refinement and model building are in progress.

Methods for estimating the enthalpy of formation of inorganic compounds; thermochemical and crystallographic investigations of uranyl salts of group VI elements

International Nuclear Information System (INIS)

Brandenburg, N.P.

1978-01-01

The first part of this thesis is concerned with parameter methods for estimating the standard enthalpy of formation, ΔH 0 sub(f), of inorganic compounds. In this type of method the estimate is a function of parameters, assigned to cation and anion, respectively. The usefulness of a new estimation method is illustrated in the case of uranyl sulphide. In the second part of this thesis crystallographic and thermochemical properties of uranyl salts of group VI elements are described. Crystal structures are given for β-UO 2 SO 4 , UO 2 SeO 3 , and α-UO 2 SeO 4 . Thermochemical measurements have been restricted to the determination of ΔH 0 sub(f)(UO 2 SO 3 ) and ΔH 0 sub(f)(UO 2 TeO 3 ) by means of isoperibol solution calorimetry. (Auth.)

Structural and Moessbauer Effect Studies of 0.5Bi0.95Dy0.05FeO3-0.5Pb(Fe2/3W1/3)O3 Multiferroic

International Nuclear Information System (INIS)

Stoch, A.; Zachariasz, P.; Stoch, P.; Kulawik, J.; Maurin, J.

2011-01-01

A polycrystalline ceramic of 0.5Bi 0.95 Dy 0.05 FeO 3 -0.5Pb(Fe 2/3 W 1/3 )O 3 was synthesized from a solid-state reaction method. At room temperature material exhibits both magnetic and electric dipolar properties simultaneously. Detailed X-ray diffraction analysis and Moessbauer effect studies have been done to determine the crystallographic structure and magnetic properties of 0.5Bi 0.95 Dy 0.05 FeO 3 -0.5Pb(Fe 2/3 W 1/3 )O 3 . T N temperature was estimated at around 600 K. (authors)

X-ray crystallographic studies on novel natural products from marine animals

International Nuclear Information System (INIS)

Choudhary, M.I.; Clardy, J.C.

1991-01-01

This chapter starts with an analysis to illustrate the utility of X-ray diffraction. The X-ray diffraction experiment is particularly suitable for structure elucidation of naturally occurring compounds, especially those that are structurally novel or have a great deal of stereochemistry. Marine plants and animals constitute a prodigious source of new and structurally complex secondary metabolites. Their unique structural features also provide strong incentives for further structural, synthetic and biosynthetic investigations. Organic compounds isolated from various marine animals in relatively small quantities, where structural work by conventional spectroscopic techniques did not lead to ambiguous structures, are investigated and the structures were finally determined through single-crystal X-ray diffraction measurements. (A.S.) 20 refs.; 5 figs

Anisotropic chemical etching of semipolar {101-bar 1-bar}/{101-bar +1} ZnO crystallographic planes: polarity versus dangling bonds

International Nuclear Information System (INIS)

Palacios-Lidon, E; Perez-GarcIa, B; Colchero, J; Vennegues, P; Zuniga-Perez, J; Munoz-Sanjose, V

2009-01-01

ZnO thin films grown by metal-organic vapor phase epitaxy along the nonpolar [112-bar] direction and exhibiting semipolar {101-bar 1-bar}/{101-bar +1} facets have been chemically etched with HCl. In order to get an insight into the influence of the ZnO wurtzite structure in the chemical reactivity of the material, Kelvin probe microscopy and convergent beam electron diffraction have been employed to unambiguously determine the absolute polarity of the facets, showing that {101-bar +1} facets are unstable upon etching in an HCl solution and transform into (000+1)/{101-bar 1-bar} planes. In contrast, {101-bar 1-bar} undergo homogeneous chemical etching perpendicular to the initial crystallographic plane. The observed etching behavior has been explained in terms of surface oxygen dangling bond density, suggesting that the macroscopic polarity plays a secondary role in the etching process.

Crystallographic relations between face- and body-centred cubic crystals formed under near-equilibrium conditions: Observations from the Gibeon meteorite

International Nuclear Information System (INIS)

He Youliang; Godet, Stephane; Jacques, Pascal J.; Jonas, John J.

2006-01-01

The orientations of the kamacite lamellae formed from a single prior-taenite grain were measured by analysing the electron backscatter diffraction patterns obtained using scanning electron microscopy. These are shown to be close to the Kurdjumov-Sachs and Nishiyama-Wassermann relations and their intermediate, i.e., the Greninger-Troiano relation. The orientations of the α grains in the plessite regions were also measured and these were found to be continuously distributed around the Bain circles formed by the variants of the common correspondence relationships, including the Pitsch one in this case. The local misorientations between individual face- and body-centred cubic crystals along their common interfaces were measured. These can be characterized by the orientation relationships mentioned above as long as a certain amount of tolerance is allowed. Orientation variations within individual kamacite lamellae were also analysed. The crystallographic data support the view that somewhat different mechanisms are involved in the formation of Widmanstaetten structures and of the plessite in meteorites

Strong morphological and crystallographic texture and resulting yield strength anisotropy in selective laser melted tantalum

International Nuclear Information System (INIS)

Thijs, Lore; Montero Sistiaga, Maria Luz; Wauthle, Ruben; Xie, Qingge; Kruth, Jean-Pierre; Van Humbeeck, Jan

2013-01-01

Selective laser melting (SLM) makes use of a high energy density laser beam to melt successive layers of metallic powders in order to create functional parts. The energy density of the laser is high enough to melt refractory metals like Ta and produce mechanically sound parts. Furthermore, the localized heat input causes a strong directional cooling and solidification. Epitaxial growth due to partial remelting of the previous layer, competitive growth mechanism and a specific global direction of heat flow during SLM of Ta result in the formation of long columnar grains with a 〈1 1 1〉 preferential crystal orientation along the building direction. The microstructure was visualized using both optical and scanning electron microscopy equipped with electron backscattered diffraction and the global crystallographic texture was measured using X-ray diffraction. The thermal profile around the melt pool was modeled using a pragmatic model for SLM. Furthermore, rotation of the scanning direction between different layers was seen to promote the competitive growth. As a result, the texture strength increased to as large as 4.7 for rotating the scanning direction 90° every layer. By comparison of the yield strength measured by compression tests in different orientations and the averaged Taylor factor calculated using the viscoplastic self-consistent model, it was found that both the morphological and crystallographic texture observed in SLM Ta contribute to yield strength anisotropy

Crystal structure and magnetic properties of Mn substituted ludwigite Co 3O 2BO 3

Science.gov (United States)

Knyazev, Yu. V.; Ivanova, N. B.; Kazak, N. V.; Platunov, M. S.; Bezmaternykh, L. N.; Velikanov, D. А.; Vasiliev, А. D.; Ovchinnikov, S. G.; Yurkin, G. Yu.

2012-03-01

The needle shape single crystals Co3-x MnxO2BO3 with ludwigite structure have been prepared. According to the X-ray diffraction data the preferable character of distinct crystallographic positions occupation by Mn ions is established. Magnetization field and temperature dependencies are measured. Paramagnetic Curie temperature value Θ=-100 K points out the predominance of antiferromagnetic interactions. Spin-glass magnetic ordering takes the onset at TN=41 K. The crystallographic and magnetic properties of Co3O2BO3:Mn are compared with the same for the isostructural analogs Co3O2BO3 and CoO2BO3:Fe.

Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating

Science.gov (United States)

Kim, Dorothy M.; Nimigean, Crina M.

2016-01-01

Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K+ channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K+ channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data. PMID:27141052

Recombinant ACHT1 from Arabidopsis thaliana: crystallization and X-ray crystallographic analysis.

Science.gov (United States)

Pan, Weimin; Wang, Junchao; Yang, Ye; Liu, Lin; Zhang, Min

2017-07-01

Thioredoxins (Trxs) play important roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. They execute their function by regulating the oxidation and reduction of disulfide bonds. ACHT1 (atypical cysteine/histidine-rich Trx1) is a thylakoid-associated thioredoxin-type protein found in the Arabidopsis thaliana chloroplast. Recombinant ACHT1 protein was overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal diffracted to 1.7 Å resolution and a complete X-ray data set was collected. Preliminary crystallographic analysis suggested that the crystals belonged to space group C222 1 , with unit-cell parameters a = 102.7, b = 100.6, c = 92.8 Å.

Estimation of the crystallographic strain limit during the reversible β ⇄ α″ martensitic transformation in titanium shape memory alloys

Science.gov (United States)

Zhukova, Yu. S.; Petrzhik, M. I.; Prokoshkin, S. D.

2010-11-01

Three methods are described to calculate the crystallographic strain limit that is determined by the maximum deformation of the crystal lattice in the reversible βbcc ⇄ α″orth martensitic transformation and ensures pseudoelastic deformation accumulation and shape recovery in Ti-Nb-Ta alloys.

Influence of chemical composition in crystallographic texture Fe-Cr-Mo alloys

International Nuclear Information System (INIS)

Moura, L.B.; Guimaraes, R.F.

2010-01-01

The use of steels with higher contents of Mo in the oil industry has been an alternative to reduce the effect of naphthenic corrosion in refining units. The addition of Mo in Fe-Cr alloys in the same manner that increases resistance to corrosion naphthenic causes some difficulties such as difficulty of forming, welding and embrittlement. In this work, experimental ingots of Fe-Cr-Mo alloys (Cr - 9, 15 and 17%, Mo - 5, 7 and 9%) were melted in vacuum induction furnace and hot and cold rolled in a laboratory rolling mill. The influence of chemical composition on crystallographic texture of samples subjected to the same thermo-mechanical treatment was analyzed by x-ray diffraction. The results indicate that fiber (111) becomes more intense with increasing Mo and/or Cr contents. (author)

Novel Fluorinated Indanone, Tetralone and Naphthone Derivatives: Synthesis and Unique Structural Features

Directory of Open Access Journals (Sweden)

Joseph C. Sloop

2012-02-01

Full Text Available Several fluorinated and trifluoromethylated indanone, tetralone and naphthone derivatives have been prepared via Claisen condensations and selective fluorinations in yields ranging from 22–60%. In addition, we report the synthesis of new, selectively fluorinated bindones in yields ranging from 72–92%. Of particular interest is the fluorination and trifluoroacetylation regiochemistry observed in these fluorinated products. We also note unusual transformations including a novel one pot, dual trifluoroacetylation, trifluoroacetylnaphthone synthesis via a deacetylation as well as an acetyl-trifluoroacetyl group exchange. Solid-state structural features exhibited by these compounds were investigated using crystallographic methods. Crystallographic results, supported by spectroscopic data, show that trifluoroacetylated ketones prefer a chelated cis-enol form whereas fluorinated bindone products exist primarily as the cross-conjugated triketo form.

Protein crystal structure analysis using synchrotron radiation at atomic resolution

International Nuclear Information System (INIS)

Nonaka, Takamasa

1999-01-01

We can now obtain a detailed picture of protein, allowing the identification of individual atoms, by interpreting the diffraction of X-rays from a protein crystal at atomic resolution, 1.2 A or better. As of this writing, about 45 unique protein structures beyond 1.2 A resolution have been deposited in the Protein Data Bank. This review provides a simplified overview of how protein crystallographers use such diffraction data to solve, refine, and validate protein structures. (author)

Structural, magnetic, and electronic transport properties of pyrochlore iridate Pr2Ir2O7

Science.gov (United States)

Kumar, Harish; Chaurasia, Rachna; Kumari, Pratibha; Paramanik, A. K.

2018-04-01

We have studied the structural, magnetic, and electronic transport properties of pyrochlore iridate Pr2Ir2O7. Structural investigation has been done using x-ray powder diffraction and Rietveld analysis. Pr2Ir2O7 crystallize in cubic crystallographic phase with Fd-3m space group. Temperature dependent magnetization data does not show magnetic bifurcation down to 2 K. Electrical resistivity data of Pr2Ir2O7 exhibits metallic behavior throughout temperature range. Below 50 K, a small rise in resistivity data of Pr2Ir2O7 is observed down to 12 K.

Lithium insertion in the two crystallographic forms of the binary-phase Mo15Se19

International Nuclear Information System (INIS)

Tarascon, J.M.; Murphy, D.W.

1986-01-01

Compounds which can undergo topotactic insertion of lithium are of potential technological importance in secondary lithium batteries. In this paper we present the chemical and electrochemical insertion of lithium into the binary-phase Mo 15 Se 19 , which can exist in two crystallographic forms, denoted AA and BB, when prepared from In 3 Mo 15 Se 19 and In 2 Mo 15 Se 19 , respectively. We show that both forms can reversibly accommodate up to eight lithium atoms, yielding two new series of compounds of formula Li/sub x/Mo 15 Se 19 . This behavior is consistent with the electronic structure of the host material predicted from band-structure calculations. The room-temperature phase diagram of both Li/sub x/Mo 15 Se 19 systems as a function of x has been established using electrochemical test cells (based on Mo 15 Se 19 as the cathode), and in situ x-ray measurements as the cells discharge. Both Li/sub x/Mo 15 Se 19 systems contain three single-phase domains as a function of x: two hexagonal phases and an orthorhombic phase. The nature of the transitions between these single phases and the variation of the lattice parameters within a single-phase domain are reported. While the mechanism of intercalation of lithium is similar for both Mo 15 Se 19 forms, there is a drastic difference in Li intercalation behavior for the parent indium phases In''Mo 15 Se 19 and In 3 Mo 15 Se 19 . We found that In 2 Mo 15 Se 19 can reversibly incorporate 6.4 lithium atoms while In 3 Mo 15 Se 19 does not react. This behavior is explained on the basis of structural considerations

Detection and correction of underassigned rotational symmetry prior to structure deposition

International Nuclear Information System (INIS)

Poon, Billy K.; Grosse-Kunstleve, Ralf W.; Zwart, Peter H.; Sauter, Nicholas K.

2010-01-01

An X-ray structural model can be reassigned to a higher symmetry space group using the presented framework if its noncrystallographic symmetry operators are close to being exact crystallographic relationships. About 2% of structures in the Protein Data Bank can be reclassified in this way. Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit

Effect of defects, magnetocrystalline anisotropy, and shape anisotropy on magnetic structure of iron thin films by magnetic force microscopy

Directory of Open Access Journals (Sweden)

Ke Xu

2017-05-01

Full Text Available Microstructures of magnetic materials, including defects and crystallographic orientations, are known to strongly influence magnetic domain structures. Measurement techniques such as magnetic force microscopy (MFM thus allow study of correlations between microstructural and magnetic properties. The present work probes effects of anisotropy and artificial defects on the evolution of domain structure with applied field. Single crystal iron thin films on MgO substrates were milled by Focused Ion Beam (FIB to create different magnetically isolated squares and rectangles in [110] crystallographic orientations, having their easy axis 45° from the sample edge. To investigate domain wall response on encountering non-magnetic defects, a 150 nm diameter hole was created in the center of some samples. By simultaneously varying crystal orientation and shape, both magnetocrystalline anisotropy and shape anisotropy, as well as their interaction, could be studied. Shape anisotropy was found to be important primarily for the longer edge of rectangular samples, which exaggerated the FIB edge effects and provided nucleation sites for spike domains in non-easy axis oriented samples. Center holes acted as pinning sites for domain walls until large applied magnetic fields. The present studies are aimed at deepening the understanding of the propagation of different types of domain walls in the presence of defects and different crystal orientations.

Crystallographic and 119Sn and 155Gd Moessbauer analyses of Gd5Ge2(Si1-xSnx)2 (x = 0.23 and x = 0.40)

International Nuclear Information System (INIS)

Campoy, J. C. P.; Santos, A. O. dos; Cardoso, L. P.; Paesano, A.; Raposo, M. T.; Fabris, J. D.

2010-01-01

We report the structural characterization of Gd 5 Ge 2 (Si 1-x Sn x ) 2 (x = 0.23 and x = 0.40) compounds by means of 100 and 298 K-X-ray diffractometry (XRD) and 4 K- 155 Gd and 298 K- 119 Sn Moessbauer spectroscopy. These compounds order ferromagnetically at 218.4 and 172.7 K, respectively. At ∼100 K, it was identified the Gd 5 Si 4 -orthorhombic phase (type I) for both samples. At ∼298 K, it was identified a Gd 5 Si 2 Ge 2 -monoclinic phase, for x = 0.23 and a Sm 5 Sn 4 -orthorhombic phase (type II), for x 0.40. The Rietveld analysis of XRD data suggests a first order magneto-structural transition at Curie temperature for both compositions. Moessbauer results are well consistent with the proposed crystallographic models for these systems.

Crystallographic computing system Jana2006: solution and refinement of twinned structures

Czech Academy of Sciences Publication Activity Database

Petříček, Václav; Dušek, Michal; Plášil, Jakub

2016-01-01

Roč. 231, č. 10 (2016), s. 583-599 ISSN 2194-4946 R&D Projects: GA ČR GA15-12653S; GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : crystal structure analysis * Jana2006 * twinning Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.179, year: 2016

Synthesis, crystal structure and DFT studies of N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide

Energy Technology Data Exchange (ETDEWEB)

Gautam, P.; Gautam, D.; Chaudhary, R. P., E-mail: rpchaudhary65@gmail.com [Sant Longowal Institute of Engineering and Technology, Department of Chemistry (India)

2013-12-15

The title compound N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide (III) was obtained from the reaction of 2-(propan-2-ylidene)hydrazinecarbothioamide (II) with acetic anhydride instead of formation of the desired thiosemcarbazide derivative of Meldrum acid. The structures of II and III were established by elemental analysis, IR, NMR, Mass and X-ray crystallographic studies. II crystallizes in triclinic system, sp. gr. P-bar1 Z = 2; III crystallizes in the monoclinic system, sp. gr. P2{sub 1}/c, Z = 8. Density functional theory (DFT) calculations have been carried out for III. {sup 1}H and {sup 13}C NMR of III has been calculated and correlated with experimental results.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Energy Technology Data Exchange (ETDEWEB)

Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I. [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States); Merz, Kenneth M. Jr [University of Florida, Gainesville, Florida (United States); Westerhoff, Lance M., E-mail: lance@quantumbioinc.com [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States)

2014-05-01

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Synchrotron Topographic and Diffractometer Studies of Buried Layered Structures Obtained by Implantation with Swift Heavy Ions in Silicon Single Crystals

International Nuclear Information System (INIS)

Wierzchowski, W.; Wieteska, K.; Zymierska, D.; Graeff, W.; Czosnyka, T.; Choinski, J.

2006-01-01

A distribution of crystallographic defects and deformation in silicon crystals subjected to deep implantation (20-50 μm) with ions of the energy of a few MeV/amu is studied. Three different buried layered structures (single layer, binary buried structure and triple buried structure) were obtained by implantation of silicon single crystals with 184 MeV argon ions, 29.7 MeV boron ions, and 140 MeV argon ions, each implantation at a fluency of 1x10 14 ions cm -2 . The implanted samples were examined by means of white beam X-ray section and projection topography, monochromatic beam topography and by recording local rocking curves with the beam restricted to 50 x 50 μm 2 . The experiment pointed to a very low level of implantation-induced strain (below 10 -5 ). The white beam Bragg case section experiment revealed a layer producing district black contrast located at a depth of the expected mean ion range. The presence of these buried layered structures in studied silicon crystals strongly affected the fringe pattern caused by curvature of the samples. In case of white beam projection and monochromatic beam topographs the implanted areas were revealed as darker regions with a very tiny grain like structure. One may interpret these results as the effect of considerable heating causing annihilation of point defects and formation of dislocation loops connected with point defect clusters. (author)

Photoinduced domain structures in monocrystalline films of yttrium-iron garnets

International Nuclear Information System (INIS)

Doroshenko, R.A.; Vladimirov, I.V.; Setchenkov, M.S.

1988-01-01

Results of investigating the domain structure in Y 3 Fe 5 O 12 epitaxial films under polarized light effect are presented. The domain structure was observed using Faraday effect at 80 K, crystallographic directions were determined by X-ray method. The sample structure is shown to consist of macrodomains, which parallel boundaries are oriented on (011), (110), (101) and are reoriented under the light effect, therewith easiest magnetization axes are brought about perpendicular to vector E of the affecting light. When explaining such changes in domain structure elastic stresses and induced anisotropy of elastic nature must be taken accout of

Reversal of the Lattice Structure in SrCoOx Epitaxial Thin Films Studied by Real-Time Optical Spectroscopy and First-Principles Calculations

Science.gov (United States)

Choi, Woo Seok; Jeen, Hyoungjeen; Lee, Jun Hee; Seo, S. S. Ambrose; Cooper, Valentino R.; Rabe, Karin M.; Lee, Ho Nyung

2013-08-01

Using real-time spectroscopic ellipsometry, we directly observed a reversible lattice and electronic structure evolution in SrCoOx (x=2.5-3) epitaxial thin films. Drastically different electronic ground states, which are extremely susceptible to the oxygen content x, are found in the two topotactic phases: i.e., the brownmillerite SrCoO2.5 and the perovskite SrCoO3. First-principles calculations confirmed substantial differences in the electronic structure, including a metal-insulator transition, which originate from the modification in the Co valence states and crystallographic structures. More interestingly, the two phases can be reversibly controlled by changing the ambient pressure at greatly reduced temperatures. Our finding provides an important pathway to understanding the novel oxygen-content-dependent phase transition uniquely found in multivalent transition metal oxides.

Comparative study on inorganic composition and crystallographic properties of cortical and cancellous bone.

Science.gov (United States)

Wang, Xiao-Yan; Zuo, Yi; Huang, Di; Hou, Xian-Deng; Li, Yu-Bao

2010-12-01

To comparatively investigate the inorganic composition and crystallographic properties of cortical and cancellous bone via thermal treatment under 700 °C. Thermogravimetric measurement, infrared spectrometer, X-ray diffraction, chemical analysis and X-ray photo-electron spectrometer were used to test the physical and chemical properties of cortical and cancellous bone at room temperature 250 °C, 450 °C, and 650 °C, respectively. The process of heat treatment induced an extension in the a-lattice parameter and changes of the c-lattice parameter, and an increase in the crystallinity reflecting lattice rearrangement after release of lattice carbonate and possible lattice water. The mineral content in cortical and cancellous bone was 73.2wt% and 71.5wt%, respectively. For cortical bone, the weight loss was 6.7% at the temperature from 60 °C to 250 °C, 17.4% from 250 °C to 450 °C, and 2.7% from 450 °C to 700 °C. While the weight loss for the cancellous bone was 5.8%, 19.9%, and 2.8 % at each temperature range, the Ca/P ratio of cortical bone was 1.69 which is higher than the 1.67 of stoichiometric HA due to the B-type CO₃²⁻ substitution in apatite lattice. The Ca/P ratio of cancellous bone was lower than 1.67, suggesting the presence of more calcium deficient apatite. The collagen fibers of cortical bone were arrayed more orderly than those of cancellous bone, while their mineralized fibers ollkded similar. The minerals in both cortical and cancellous bone are composed of poorly crystallized nano-size apatite crystals with lattice carbonate and possible lattice water. The process of heat treatment induces a change of the lattice parameter, resulting in lattice rearrangement after the release of lattice carbonate and lattice water and causing an increase in crystal size and crystallinity. This finding is helpful for future biomaterial design, preparation and application. Copyright © 2010 The Editorial Board of Biomedical and Environmental Sciences

Dynamical X-ray scattering from the relaxed structures

International Nuclear Information System (INIS)

Benediktovitch, A.; Feranchuk, I.; Ulyanenkov, A.

2009-01-01

High-resolution X-ray diffraction is now widely used analytical tool for investigation of nano scale multilayered structures in semiconductor and optical technologies. The HRXRD method delivers unique information on the crystallographic lattice of the samples, concentration of solid solutions, lattice mismatches, layer thicknesses, defect distribution, and relaxation degree of the epitaxial layers. The evaluation of the experimental results, however, requires a robust and precise theory due to complex dynamical scattering of X-rays from near perfect crystallographic structure of the samples. Usually, the Takagi-Taupin approach [1] or the recurrent matrix methods [2] are used for the simulation of the X-ray diffraction profiles from the epitaxial multilayered structures. The use of these theories, however, becomes essentially difficult, when the lateral lattice mismatches are present in multilayers, for example, in the case of partially or fully relaxed epitaxially grown samples. In the present work, the general solution of this problem is found analytically. The angular divergence of the incident beam is also considered and the algorithm for the diffracted profile mapping in the reciprocal space is developed. The experimental reciprocal space mapping of typical AlGaN/GaN/AlN samples with partially relaxed layers is compared to the simulated maps, which describe well the location and character of the diffraction spots caused by different layers. (author)

Extended x-ray absorption fine structure study of phase transitions in the piezoelectric perovskite K0.5Na0.5NbO3

Science.gov (United States)

Kodre, A.; Tellier, J.; Arčon, I.; Malič, B.; Kosec, M.

2009-06-01

Following an x-ray diffraction study of phase transitions of the piezoelectric perovskite K0.5Na0.5NbO3 the structural changes of the material are studied using extended x-ray absorption fine structure analysis, whereby the neighborhood of Nb atom is determined in the temperature range of monoclinic, tetragonal, and cubic phases. Within the entire range Nb atom is displaced from the center of the octahedron of its immediate oxygen neighbors, as witnessed by the splitting of Nb-O distance. The model shows high prevalence of the displacement in the (111) crystallographic direction of the simple perovskite cell. The corresponding splitting of the Nb-Nb distance is negligible. There is no observable disalignment of the linear Nb-O-Nb bonds from the ideal cubic arrangement, judging from the intensity of the focusing of the photoelectron wave on the Nb-Nb scattering path by the interposed oxygen atom. As a general result, the phase transitions are found as an effect of the long-range order, while the placement of the atoms in the immediate vicinity remains largely unaffected.

Structure of a Wear-Resistant Medium-Carbon Steel After Hot Deformation in Hammer Dies and Heat Treatment

Science.gov (United States)

Knyazyuk, T. V.; Petrov, S. N.; Ryabov, V. V.; Khlusova, E. I.

2018-01-01

The structure of model specimens and articles fabricated from medium-carbon high-strength steels is studied for developing modes of forming of working members of tilling machines with cutting edges thinned without the expensive operation of electromachining. The effect of the temperature of heating of billets on the grain size of austenite is determined. The kinetics of recrystallization is studied in the temperature, rate and strain ranges typical for hot forming. A quantitative crystallographic analysis of the microstructure is performed by the EBSD technique. The degrees of distortion of the crystal lattices of structural components and the mean sizes of martensite blocks are determined.

Relationship between strain stored by compressive deformation and crystallographic orientation in a pure aluminum

International Nuclear Information System (INIS)

Takayama, Y; Watanabe, H; Yoshimura, T

2015-01-01

In order to investigate relationship between stored strain and crystallographic orientation, 99.99% purity aluminum cubes were compressed with uniaxial or with plane strain state up to a nominal strain of 30%. The aluminum cubes were examined on the same surface before and after compression by SEM/EBSD technique. Stored strain was estimated by Kernel Average Misorientation (KAM) derived from the EBSD analysis, and Taylor factor (TF) was measured before the compressive deformation. The analysis revealed that KAM value or the stored strain decreases until a certain value of TF and then increases with increment of TF. (paper)

Crystallographic, DFT and docking (cathepsin B) studies on an organotellurium(IV) compound

International Nuclear Information System (INIS)

Caracelli, Ignez; Maganhi, Stella H.; Zukerman-Schpector, Julio; Sousa Madureira, Lucas; Stefani, Helio A.; Guadagnin, Rafael C.; Tiekink, Edward R.T.

2016-01-01

Some biologically active organotellurium compounds exhibit inhibitory potency against cathepsin B. In this study, an alkyl derivative, viz. [CH 3 (CH 2 ) 2 C(I)=C(H)](nBu)TeI 2 , 1, has been structurally characterised by X-ray crystallography and shown to be coordinated within a C 2 I 2 donor set. When the stereochemically active lone pair of electrons is taken into account, a distorted trigonal bipyramidal geometry results with the iodide atoms in axial positions. Both intra- and inter-molecular Te..I interactions are also noted. If all interactions are considered, the coordination geometry is based on a Ψ-pentagonal bipyramidal geometry. An unusual feature of the structure is the curving of the functionalised C 5 chain. This feature has been explored by DFT methods and shown to arise as a result of close C-H..I interactions. A docking study (cathepsin B) was performed to understand the inhibition mechanism and to compare the new results with previous observations. Notably, 1 has the same pose exhibited by analogous biologically active compounds with aryl groups. Thus, the present study suggests that (alkyl) 2 TeX 2 compounds should also be evaluated for biological activity.

Structural and magnetic properties of Mn{sub 50}Fe{sub 50−x}Sn{sub x} (x=10, 15 and 20) alloys

Energy Technology Data Exchange (ETDEWEB)

Ghosh, Tanmoy [LCMP, S.N. Bose National Centre for Basic Sciences, Kolkata 700106 (India); Agarwal, Sandeep [Haldia Institute of Technology, Haldia 721657 (India); Mukhopadhyay, P.K., E-mail: pkm@bose.res.in [LCMP, S.N. Bose National Centre for Basic Sciences, Kolkata 700106 (India)

2016-11-15

In this work we report measurements and comparisons of the structural, magnetic and transport properties of a series of Mn{sub 50}Fe{sub 50−x}Sn{sub x} alloys (x=10, 15 and 20). We found that while the lower Sn composition sample stabilized in β-Mn-type crystallographic phase, the higher Sn composition alloys contained both β-Mn-type as well as Mn{sub 3}Sn-type hexagonal DO{sub 19} phases. Through d.c. and a.c. magnetic property measurements we have established the existence of a ferromagnetic transition near room temperature followed by a spin reorientation at lower temperature in the Mn{sub 3}Sn-type crystallographic phase of the alloys. Our resistivity study also revealed an interesting behavior with negative temperature coefficient (TCR) in these alloys. - Highlights: • Mn{sub 50}Fe{sub 50-x}Sn{sub x} alloys were studied over a limited concentration range. • Lower Sn alloys behaved similar to ß-Mn alloys both structurally and magnetically. • Higher Sn alloys showed magnetic transitions similar to Mn{sub 3}Sn and Fe{sub 3}Sn. • Resistivity showed bad metallic behavior with negetive temperature coefficient.

Expression, purification, crystallization and preliminary crystallographic analysis of the proliferation-associated protein Ebp1

International Nuclear Information System (INIS)

Kowalinski, Eva; Bange, Gert; Wild, Klemens; Sinning, Irmgard

2007-01-01

Preliminary X-ray analysis of the proliferation-associated protein Ebp1 from Homo sapiens is provided. ErbB-3-binding protein 1 (Ebp1) is a member of the family of proliferation-associated 2G4 proteins (PA2G4s) and plays a role in cellular growth and differentiation. Ligand-induced activation of the transmembrane receptor ErbB3 leads to dissociation of Ebp1 from the receptor in a phosphorylation-dependent manner. The non-associated protein is involved in transcriptional and translational regulation in the cell. Here, the overexpression, purification, crystallization and preliminary crystallographic studies of Ebp1 from Homo sapiens are reported. Initially observed crystals were improved by serial seeding to single crystals suitable for data collection. The optimized crystals belong to the tetragonal space group P4 1 2 1 2 or P4 3 2 1 2 and diffracted to a resolution of 1.6 Å

Expression, purification, crystallization and preliminary crystallographic analysis of the proliferation-associated protein Ebp1

Energy Technology Data Exchange (ETDEWEB)

Kowalinski, Eva; Bange, Gert; Wild, Klemens; Sinning, Irmgard, E-mail: irmi.sinning@bzh.uni-heidelberg.de [Heidelberg University Biochemistry Center, INF 328, D-69120 Heidelberg (Germany)

2007-09-01

Preliminary X-ray analysis of the proliferation-associated protein Ebp1 from Homo sapiens is provided. ErbB-3-binding protein 1 (Ebp1) is a member of the family of proliferation-associated 2G4 proteins (PA2G4s) and plays a role in cellular growth and differentiation. Ligand-induced activation of the transmembrane receptor ErbB3 leads to dissociation of Ebp1 from the receptor in a phosphorylation-dependent manner. The non-associated protein is involved in transcriptional and translational regulation in the cell. Here, the overexpression, purification, crystallization and preliminary crystallographic studies of Ebp1 from Homo sapiens are reported. Initially observed crystals were improved by serial seeding to single crystals suitable for data collection. The optimized crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2 and diffracted to a resolution of 1.6 Å.

Purification, crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from Acinetobacter baumannii

International Nuclear Information System (INIS)

Park, Jeong Soon; Lee, Woo Cheol; Song, Jung Hyun; Kim, Seung Il; Lee, Je Chul; Cheong, Chaejoon; Kim, Hye-Yeon

2012-01-01

The crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from A. baumannii are reported. The meso isomer of diaminopimelate (meso-DAP) is a biosynthetic precursor of l-lysine in bacteria and plants, and is a key component of the peptidoglycan layer in the cell walls of Gram-negative and some Gram-positive bacteria. Diaminopimelate epimerase (DapF) is a pyridoxal-5′-phosphate-independent racemase which catalyses the interconversion of (6S,2S)-2,6-diaminopimelic acid (ll-DAP) and meso-DAP. In this study, DapF from Acinetobacter baumannii was overexpressed in Escherichia coli strain SoluBL21, purified and crystallized using a vapour-diffusion method. A native crystal diffracted to a resolution of 1.9 Å and belonged to space group P3 1 or P3 2 , with unit-cell parameters a = b = 74.91, c = 113.35 Å, α = β = 90, γ = 120°. There were two molecules in the asymmetric unit

Reversal of the lattice structure in SrCoO(x) epitaxial thin films studied by real-time optical spectroscopy and first-principles calculations.

Science.gov (United States)

Choi, Woo Seok; Jeen, Hyoungjeen; Lee, Jun Hee; Seo, S S Ambrose; Cooper, Valentino R; Rabe, Karin M; Lee, Ho Nyung

2013-08-30

Using real-time spectroscopic ellipsometry, we directly observed a reversible lattice and electronic structure evolution in SrCoO(x) (x=2.5-3) epitaxial thin films. Drastically different electronic ground states, which are extremely susceptible to the oxygen content x, are found in the two topotactic phases: i.e., the brownmillerite SrCoO2.5 and the perovskite SrCoO3. First-principles calculations confirmed substantial differences in the electronic structure, including a metal-insulator transition, which originate from the modification in the Co valence states and crystallographic structures. More interestingly, the two phases can be reversibly controlled by changing the ambient pressure at greatly reduced temperatures. Our finding provides an important pathway to understanding the novel oxygen-content-dependent phase transition uniquely found in multivalent transition metal oxides.

Study of the crystallographic and magnetic properties of cubic manganite spinels NiMn{sub 2}O{sub 4}; Etude des proprietes cristallographiques et magnetiques des manganites spinelles cubiques NiMn{sub 2}O{sub 4}

Energy Technology Data Exchange (ETDEWEB)

Boucher, B [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1969-07-01

We study the variation of the crystallographic properties (inversion degree, position parameters and short range order) of the cubic spinel Mn{sub {nu}}Ni{sub 1-{nu}}[Mn{sub 2{nu}}Ni{sub {nu}}]O{sub 4}, as a function of the thermal treatment applied to the sample. {nu} lies between 0. 74 and 0. 93; the slower the sample is cooled the more inverse it is. We show, in a molecular field theory, that a system of three magnetic sublattices can afford a 'star' configuration. We establish the conditions of stability of such a structure and its evolution as a function of temperature is foreseen. Neutron diffraction measurements show that the magnetic structure of NiMn{sub 2}O{sub 4} at 4.2 K is a 'star' configuration and that with increasing temperature it becomes a collinear structure in agreement with the theory. Furthermore, we find an anomaly in the value of specific heat at the transition temperature between 'star' and collinear structures. (author) [French] On etudie la variation des proprietes cristallographiques (inversion, parametre de position, ordre a courte distance) du spinelle cubique Mn{sub {nu}}Ni{sub 1-{nu}}[Mn{sub 2{nu}}Ni{sub {nu}}]O{sub 4}, en fonction du traitement thermique que subit l'echantillon, {nu} est compris entre 0,74 et 0,93; plus le corps est refroidi lentement, plus il est inverse. On montre, dans le cadre d'une theorie de champ moleculaire, qu'un systeme a trois sous-reseaux magnetiques peut presenter une configuration en ''etoile''. On etablit les conditions de stabilite d'une telle structure et on prevoit son evolution en fonction de la temperature. Les mesures de diffraction de neutrons montrent que la structure magnetique de NiMn{sub 2}O{sub 4} a 4,2 K est du type ''en etoile'' et qu'elle evolue en fonction de la temperature vers une structure colineaire comme le prevoit la theorie. De plus on observe une anomalie de chaleur specifique a la temperature de la transition entre la structure ''en etoile'' et la structure colineaire. (auteur)

Macromolecular crystallographic results obtained using a 2048x2048 CCD detector at CHESS

International Nuclear Information System (INIS)

Thiel, D.J.; Ealick, S.E.; Tate, M.W.; Gruner, S.M.; Eikenberry, E.F.

1996-01-01

We present results of macromolecular crystallographic experiments performed at the Cornell High Energy Synchrotron Source (CHESS) with a new CCD-based detector. This detector, installed in January 1995, complements a 1024x1024 CCD detector that has been in continuous operation at CHESS since December 1993. The new detector is based on a 4-port, 2048x2048 pixel CCD that is directly coupled to a Gd 2 O 2 S:Tb phosphor by a 3:1 tapered fiber optic. The active area of the phosphor is a square 82 mm on an edge. The readout time is 7 seconds. In the standard mode of operation, the pixel size at the active area is 41 μm on the edge leading to the capability of resolving approximately 200 orders of diffraction across the detector face. The detector also operates in a 1024x1024 mode in which the pixel size is electronically increased by a factor of 4 in area resulting in smaller data files and faster detector readout but at the expense of spatial resolution. Most of the data that has been collected by this detector has been collected in this mode. Dozens of data sets have been collected by many experimenters using this detector at CHESS during the four month period from its installation until the start of the six-month down period of the storage ring. The capabilities of the detector will be illustrated with results from various crystallographic measurements including experiments in which the recorded diffraction patterns extend in resolution as far as 1 A. The results demonstrate that this detector is capable of collecting data of quality at least equal to that of imaging plates but, in many circumstances, with much greater beamline efficiency. copyright 1996 American Institute of Physics

Analysis of Crystallographic Structure of a Japanese Sword by the Pulsed Neutron Transmission Method

Science.gov (United States)

Kino, K.; Ayukawa, N.; Kiyanagi, Y.; Uchida, T.; Uno, S.; Grazzi, F.; Scherillo, A.

We measured two-dimensional transmission spectra of pulsed neutron beams for a Japanese sword sample. Atom density, crystalline size, and preferred orientation of crystals were obtained using the RITS code. The position dependence of the atomic density is consistent with the shape of the sample. The crystalline size is very small and shows position dependence, which is understood by the unique structure of Japanese swords. The preferred orientation has strong position dependence. Our study shows the usefulness of the pulsed neutron transmission method for cultural metal artifacts.

X-ray Crystallographic, Multifrequency Electron Paramagnetic Resonance, and Density Functional Theory Characterization of the Ni(P(Cy)2N(tBu)2)2(n+) Hydrogen Oxidation Catalyst in the Ni(I) Oxidation State.

Science.gov (United States)

Niklas, Jens; Westwood, Mark; Mardis, Kristy L; Brown, Tiara L; Pitts-McCoy, Anthony M; Hopkins, Michael D; Poluektov, Oleg G

2015-07-06

The Ni(I) hydrogen oxidation catalyst [Ni(P(Cy)2N(tBu)2)2](+) (1(+); P(Cy)2N(tBu)2 = 1,5-di(tert-butyl)-3,7-dicyclohexyl-1,5-diaza-3,7-diphosphacyclooctane) has been studied using a combination of electron paramagnetic resonance (EPR) techniques (X-, Q-, and D-band, electron-nuclear double resonance, hyperfine sublevel correlation spectroscopy), X-ray crystallography, and density functional theory (DFT) calculations. Crystallographic and DFT studies indicate that the molecular structure of 1(+) is highly symmetrical. EPR spectroscopy has allowed determination of the electronic g tensor and the spin density distribution on the ligands, and revealed that the Ni(I) center does not interact strongly with the potentially coordinating solvents acetonitrile and butyronitrile. The EPR spectra and magnetic parameters of 1(+) are found to be distinctly different from those for the related compound [Ni(P(Ph)2N(Ph)2)2](+) (4(+)). One significant contributor to these differences is that the molecular structure of 4(+) is unsymmetrical, unlike that of 1(+). DFT calculations on derivatives in which the R and R' groups are systematically varied have allowed elucidation of structure/substituent relationships and their corresponding influence on the magnetic resonance parameters.

pH-tuneable binding of 2′-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study

Energy Technology Data Exchange (ETDEWEB)

Ciulli, Alessio [University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Lobley, Carina M. C. [Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (United Kingdom); Tuck, Kellie L. [University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Smith, Alison G. [Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA (United Kingdom); Blundell, Tom L. [Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (United Kingdom); Abell, Chris, E-mail: ca26@cam.ac.uk [University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

2007-02-01

A combined crystallographic, calorimetric and mutagenic study has been used to show how changes in pH give rise to two distinct binding modes of 2′-phospho-ADP-ribose to ketopantoate reductase. The crystal structure of Escherichia coli ketopantoate reductase in complex with 2′-monophosphoadenosine 5′-diphosphoribose, a fragment of NADP{sup +} that lacks the nicotinamide ring, is reported. The ligand is bound at the enzyme active site in the opposite orientation to that observed for NADP{sup +}, with the adenine ring occupying the lipophilic nicotinamide pocket. Isothermal titration calorimetry with R31A and N98A mutants of the enzyme is used to show that the unusual ‘reversed binding mode’ observed in the crystal is triggered by changes in the protonation of binding groups at low pH. This research has important implications for fragment-based approaches to drug design, namely that the crystallization conditions and the chemical modification of ligands can have unexpected effects on the binding modes.

pH-tuneable binding of 2′-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study

International Nuclear Information System (INIS)

Ciulli, Alessio; Lobley, Carina M. C.; Tuck, Kellie L.; Smith, Alison G.; Blundell, Tom L.; Abell, Chris

2007-01-01

A combined crystallographic, calorimetric and mutagenic study has been used to show how changes in pH give rise to two distinct binding modes of 2′-phospho-ADP-ribose to ketopantoate reductase. The crystal structure of Escherichia coli ketopantoate reductase in complex with 2′-monophosphoadenosine 5′-diphosphoribose, a fragment of NADP + that lacks the nicotinamide ring, is reported. The ligand is bound at the enzyme active site in the opposite orientation to that observed for NADP + , with the adenine ring occupying the lipophilic nicotinamide pocket. Isothermal titration calorimetry with R31A and N98A mutants of the enzyme is used to show that the unusual ‘reversed binding mode’ observed in the crystal is triggered by changes in the protonation of binding groups at low pH. This research has important implications for fragment-based approaches to drug design, namely that the crystallization conditions and the chemical modification of ligands can have unexpected effects on the binding modes

Composition and structure of an iron-bearing, layered double hydroxide (LDH) - Green rust sodium sulphate

DEFF Research Database (Denmark)

Christiansen, B. C.; Balic-Zunic, T.; Petit, P. O.

2009-01-01

with Fe(II) and Fe(III) in an ordered distribution. The interlayers contain sulphate, water and sodium in an arrangement characteristic for the nikischerite group. The crystal structure is highly disordered by slacking faults. The composition, formula and crystallographic parameters are: NaFe(II)(6)Fe...

Crystal structure refinement with SHELXL

Energy Technology Data Exchange (ETDEWEB)

Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

2015-01-01

New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

Crystallographic, DFT and docking (cathepsin B) studies on an organotellurium(IV) compound

Energy Technology Data Exchange (ETDEWEB)

Caracelli, Ignez; Maganhi, Stella H. [Univ. Federal de Sao Carlos (Brazil). BioMat; Zukerman-Schpector, Julio; Sousa Madureira, Lucas [Univ. Federal de Sao Carlos (Brazil). Lab. de Cristalografia, Estereodinamica e Modelagem Molecular; Stefani, Helio A. [Sao Paulo Univ. (Brazil). Dept. de Farmacia; Guadagnin, Rafael C. [Univ. Federal de Sao Paulo, Diadema (Brazil). Inst. e Ciencias Mabientais, Quimicas e Farmaceuticas; Tiekink, Edward R.T. [Sunway Univ., Selangor Darul Ehsan (Malaysia). Centre for Crystalline Materials

2016-08-01

Some biologically active organotellurium compounds exhibit inhibitory potency against cathepsin B. In this study, an alkyl derivative, viz. [CH{sub 3}(CH{sub 2}){sub 2}C(I)=C(H)](nBu)TeI{sub 2}, 1, has been structurally characterised by X-ray crystallography and shown to be coordinated within a C{sub 2}I{sub 2} donor set. When the stereochemically active lone pair of electrons is taken into account, a distorted trigonal bipyramidal geometry results with the iodide atoms in axial positions. Both intra- and inter-molecular Te..I interactions are also noted. If all interactions are considered, the coordination geometry is based on a Ψ-pentagonal bipyramidal geometry. An unusual feature of the structure is the curving of the functionalised C{sub 5} chain. This feature has been explored by DFT methods and shown to arise as a result of close C-H..I interactions. A docking study (cathepsin B) was performed to understand the inhibition mechanism and to compare the new results with previous observations. Notably, 1 has the same pose exhibited by analogous biologically active compounds with aryl groups. Thus, the present study suggests that (alkyl){sub 2}TeX{sub 2} compounds should also be evaluated for biological activity.

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

Energy Technology Data Exchange (ETDEWEB)

Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

2014-06-01

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

Taking MAD to the extreme: ultrafast protein structure determination

International Nuclear Information System (INIS)

Walsh, M.A.; Dementieva, I.; Evans, G.; Sanishvili, R.; Joachimiak, A.

1999-01-01

Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl-substituted protein, producing experimental phases to 2.25 (angstrom) resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

Science.gov (United States)

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the

Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success

International Nuclear Information System (INIS)

Choi, Ryan; Kelley, Angela; Leibly, David; Nakazawa Hewitt, Stephen; Napuli, Alberto; Van Voorhis, Wesley

2011-01-01

An overview of the methods used for high-throughput cloning and protein-expression screening of SSGCID hexahistidine recombinant proteins is provided. It is demonstrated that screening for recombinant proteins that are highly recoverable from immobilized metal-affinity chromatography improves the likelihood that a protein will produce a structure. The recombinant expression of soluble proteins in Escherichia coli continues to be a major bottleneck in structural genomics. The establishment of reliable protocols for the performance of small-scale expression and solubility testing is an essential component of structural genomic pipelines. The SSGCID Protein Production Group at the University of Washington (UW-PPG) has developed a high-throughput screening (HTS) protocol for the measurement of protein recovery from immobilized metal-affinity chromatography (IMAC) which predicts successful purification of hexahistidine-tagged proteins. The protocol is based on manual transfer of samples using multichannel pipettors and 96-well plates and does not depend on the use of robotic platforms. This protocol has been applied to evaluate the expression and solubility of more than 4000 proteins expressed in E. coli. The UW-PPG also screens large-scale preparations for recovery from IMAC prior to purification. Analysis of these results show that our low-cost non-automated approach is a reliable method for the HTS demands typical of large structural genomic projects. This paper provides a detailed description of these protocols and statistical analysis of the SSGCID screening results. The results demonstrate that screening for proteins that yield high recovery after IMAC, both after small-scale and large-scale expression, improves the selection of proteins that can be successfully purified and will yield a crystal structure

Structural investigation of chemically synthesized ferrite magnetic nanomaterials

Science.gov (United States)

Uyanga, E.; Sangaa, D.; Hirazawa, H.; Tsogbadrakh, N.; Jargalan, N.; Bobrikov, I. A.; Balagurov, A. M.

2018-05-01

In recent times, interest in ferrite magnetic nanomaterials has considerably grown, mainly due to their highly promising medical and biological applications. Spinel ferrite powder samples, with high heat generation abilities in AC magnetic fields, were studied for their application to the hyperthermia treatment of cancer tumors. These properties of ferrites strongly depend on their chemical composition, ion distribution between crystallographic positions, magnetic structure and method of preparation. In this study, crystal and magnetic structures of several magnetic spinels were investigated by neutron diffraction. The explanation of the mechanism triggering the heat generation ability in the magnetic materials, and the electronic and magnetic states of ferrite-spinel type structures, were theoretically defined by a first-principles method. Ferrites with the composition of CuxMg1-xFe2O4 have been investigated as a heat generating magnetic nanomaterial. Atomic fraction of copper in ferrite was varied between 0 and 100% (that is, x between 0 and 1.0 with 0.2 steps), with the copper dope limit corresponding to appear a tetragonal phase.

Neutron diffraction stress determination in W-laminates for structural divertor applications

Directory of Open Access Journals (Sweden)

R. Coppola

2015-07-01

Full Text Available Neutron diffraction measurements have been carried out to develop a non-destructive experimental tool for characterizing the crystallographic structure and the internal stress field in W foil laminates for structural divertor applications in future fusion reactors. The model sample selected for this study had been prepared by brazing, at 1085 °C, 13 W foils with 12 Cu foils. A complete strain distribution measurement through the brazed multilayered specimen and determination of the corresponding stresses has been obtained, assuming zero stress in the through-thickness direction. The average stress determined from the technique across the specimen (over both ‘phases’ of W and Cu is close to zero at −17 ± 32 MPa, in accordance with the expectations.

Hydrostatic pressure study of the structural phase transitions and superconductivity in single crystals of (Ba1-xKx)Fe2As2 (x=0 and 0.45) and CaFe2As2

International Nuclear Information System (INIS)

Torikachvili, M.S.; Bud'ko, S.L.; Ni Ni; Canfield, P.C.

2009-01-01

We studied the effect of hydrostatic pressure (P) on the structural phase transitions and superconductivity in the ternary and pseudo-ternary iron arsenides CaFe 2 As 2 , BaFe 2 As 2 , and (Ba 0.55 K 0.45 )Fe 2 As 2 , by means of measurements of electrical resistivity (ρ) in the 1.8-300 K temperature (T) range, pressures up to 20 kbar, and magnetic fields up to 9 T. CaFe 2 As 2 and BaFe 2 As 2 (lightly doped with Sn) display structural phase transitions near 170 and 85 K, respectively, and do not exhibit superconductivity in ambient pressure, while K-doped (Ba 0.55 K 0.45 )Fe 2 As 2 is superconducting for T 2 As 2 is to shift the onset of the crystallographic transformation down in temperature at the rate of ∼-1.04 K/kbar, while shifting the whole ρ(T) curves downward, whereas its effect on superconducting (Ba 0.55 K 0.45 )Fe 2 As 2 is to shift the onset of superconductivity to lower temperatures at the rate of ∼-0.21 K/kbar. The effect of pressure on CaFe 2 As 2 is first to suppress the crystallographic transformation and induce superconductivity with onset near 12 K very rapidly, i.e., for P c2 ) data in (Ba 0.55 K 0.45 )Fe 2 As 2 and CaFe 2 As 2 are discussed.

Structure of glutaredoxin Grx1p C30S mutant from yeast

DEFF Research Database (Denmark)

Håkansson, Kjell O; Winther, Jakob R

2007-01-01

-bound protein and the glutaredoxin domain in the fusion protein are similar. The covalent disulfide bond between the glutathione and protein is broken upon exposure to synchrotron radiation. The structure and the glutathione-binding mode are described and compared with existing crystallographic and nuclear...... replacement using the known rxYFP structure as a search model. The structure of the Grx1p moiety was built and the structure was refined against 2.7 A synchrotron data to an R(free) of 25.7%. There are no specific contacts between the two domains, indicating that the observed enhanced exchange of reduction...

X-ray crystallographic studies on acetylcholinesterase and on its interaction with anticholinesterase agents. Midterm report, 30 April 1993-29 April 1994

Energy Technology Data Exchange (ETDEWEB)

Silman, I.; Sussman, J.L.

1994-11-24

The EMBL-DESY synchrotron facility at Hamburg was employed to collect a complete 2.3 A data set for a crystal of native Torpedo AChE, as well as for complexes with reversible ligands, including edrophonium, d-tubocurarine and huperzine A, diffracting to similar resolution. The X26c Laue beam line at the NSLS synchrotron facility at Brookhaven National Laboratory (BNL) was used to obtain a Laue diffraction pattern for a crystal of native Torpedo AChE, diffracting out to 2.8 A. This is a first step towards our long-range objective of performing time-resolved X-ray crystallographic measurements on AChE. A complete 2.8 A data set was collected on a covalent adduct of Torpedo AChE with the transition-state analog, m -(N,N,N-trimethylammonio) trifluoroacetophenone, which serves as a powerful, quasi-irreversible inhibitor. This permitted detailed analysis of the multiple ligand-AChE interactions.

Molecular dynamics study on threshold displacement energies in Fe-Cr alloys

Science.gov (United States)

Fu, Jiawei; Ding, Wenyi; Zheng, Mingjie; Mao, Xiaodong

2018-03-01

The threshold displacement energies (Ed) of Fe and Cr atoms in Fe-Cr alloys with Cr contents ranging from 0% to 21% have been obtained with molecular dynamics (MD) method. The values of Ed have been calculated along the three high-symmetry crystallographic directions [0 0 1], [0 1 1] and [1 1 1], a slightly 2° tilt from these directions, and a high-index crystallographic directions [1 3 5]. The results showed that [0 1 1] crystallographic direction had the highest Ed among the three high-symmetry directions in each Cr content alloy. Fe-9Cr had higher weighted average Ed than the other Cr content alloys for both Fe and Cr PKA due to its statistically high Ed along the [0 1 1] crystallographic direction up to 44.3 eV. And the statistical analysis on the primary damage configuration demonstrated that 〈1 1 0〉Fe-Fe dumbbells were the dominant defect structures after relaxation. These data can enrich the database of Ed in Fe-Cr alloys and have potential applications in guiding the optimization design of radiation-resistant RAFM steels.

Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand

Science.gov (United States)

Naseem, Saira; Khalid, Muhammad; Tahir, Muhammad Nawaz; Halim, Mohammad A.; Braga, Ataualpa A. C.; Naseer, Muhammad Moazzam; Shafiq, Zahid

2017-09-01

Herein, we present the synthesis of novel xanthene-based hydrazone (1). The chemical structure of 1 was resolved using spectroscopic techniques such as NMR, FT-IR, UV-VIS and X-ray crystallographic approaches. X-ray diffraction analysis shows that the compound (1) crystallizes in triclinic crystal lattice with the Pbar1 space group and diffused to form multi-layered structure due to non-covalent interactions such as intramolecular hydrogen bonding (H.B). In addition to experimental investigation, density functional theory (DFT) calculation with M06-2X/6-31G(d,p) and B3LYP/6-31G(d,p) level of theories was performed on compound (1) to obtain optimized geometry, spectroscopic and electronic properties. DFT optimized geometry shows good agreement with the experimental XRD structure. The hyper conjugative interactions and hydrogen bonding network are responsible for the stability of compound (1) as revealed by natural bond orbital (NBO) calculation. Moreover, hydrogen bonding network in the dimer is confirmed by FT-IR and thermodynamic studies showing excellent agreement with XRD and NBO findings. TD-DFT/UV-VIS analysis provides insight that maximum excitation is found in 1 which shows good agreement with experimental UV-VIS result. The global reactivity parameters are calculated using the energies of frontier molecular orbitals also disclosed that the compound is more stable might be due to hydrogen bonding network. Experimental and molecular docking studies indicated that this compound has anti-bacterial and anti-diabetic properties. The binding affinity of this compound against the multidrug efflux pump subunit AcrB OS=Escherichia coli (strain K12) and Human Pancreatic Alpha-Amylase is -9.2 and -10.00 kcal/mol which are higher than the control drugs. Pi-Pi, Pi-anaion, amide-pi and pi-alkyl bonds play key role in drug-protein complexes.

Structural, hyperfine and Raman properties of RE2FeSbO7 compounds

International Nuclear Information System (INIS)

Berndt, G.; Silva, K.L.; Ivashita, F.F.; Paesano, A.; Blanco, M.C.; Miner, E.V.P.; Carbonio, R.E.; Dantas, S.M.; Ayala, A.P.; Isnard, O.

2015-01-01

Highlights: • We prepared monophasic RE 2 FeSbO 7 pyrochlores. • RE 2 FeSbO 7 compounds were characterized regarding crystallographic, vibrational and hyperfine properties. • We find out that a site disorder takes place for the RE’s of larger ionic radii. • Lattice parameters, Raman bands and quadrupole splittings were shown to depend correlatedly on the RE ionic radius. - Abstract: Pyrochlores of the RE 2 FeSbO 7 type were synthesized by ball-milling followed by annealing in free atmosphere at high temperatures. The samples prepared were characterized by X-ray diffraction, Raman spectroscopy and 57 Fe Mössbauer spectroscopy, at room temperature. The results showed that RE 2 FeSbO 7 compounds have a cubic structure, i.e., Fd-3m (#227) space group, and that a site disorder takes place for the RE’s of larger ionic radii. Lattice parameters, Raman bands and quadrupole splittings were shown to depend correlatedly on the RE ionic radius. This behavior is discussed in terms of the pyrochlore crystallographic structure

Investigation of electronic lattice structure by positron annihilation in some insulators

International Nuclear Information System (INIS)

Coussot, Gerard

1970-01-01

The angular distribution of gamma quanta resulting from positron annihilation in single insulator crystals was measured with long slit geometry apparatus for intense positron sources ( 64 Cu ≅ 1 Ci). Two new phenomena were observed in the angular correlation curves. In the f. c. c. MgO, UO 2 , CaF 2 crystals, modulations appeared at angles corresponding to the limit of the first Brillouin zone in relation to the crystallographic direction studied. In SiO 2 , F 2 Mg, F 2 Mn crystals, a narrow peak at 0 mrad and a fine structure superimposed on the broad distribution, were resolved. The fine structure which is correlated with the narrow component is characterized by modulations appearing at angles corresponding to the projection of reciprocal lattice vectors along the crystallographic direction investigated. The narrow peak at p ≅ 0 suggests the formation of a bound state (positron-electron). If this bound state is described by a Bloch wave, the modulations observed correspond to the Fourier components which contribute to every reciprocal lattice vector p = G ('Umklapp' process). This model predicts that the 'Umklapp' process in polycrystals must produce a change in slope which can be experimentally observed. A systematic research of optimal observation conditions shows that the intensity of the narrow component is closely correlated with the purity and the perfection of the crystal where p-Ps is presumably formed as suggested by magnetic experiments. (author) [fr

Preparation, structure study and electrochemistry of layered H₂V₃O₈ materials

DEFF Research Database (Denmark)

Sarkar, Sudeep; Bhowmik, Arghya; Pan, Jaysree

2016-01-01

The present study explores H2V3O8 as high capacity cathode material for lithium-ion batteries (LIB's). Despite having high discharge capacity, H2V3O8 material suffers from poor electrochemical stability for prolonged cycle life. Ultra-long H2V3O8 nanobelts with ordered crystallographic patterns...

Electron backscatter diffraction characterization of laser-induced periodic surface structures on nickel surface

Energy Technology Data Exchange (ETDEWEB)

Sedao, Xxx, E-mail: sedao.xxx@gmail.com [Laboratoire Hubert Curien, Université Jean Monnet, 42000 St-Etienne (France); Maurice, Claire [Laboratoire Georges Friedel, Ecole Nationale Supérieure des Mines, 42023 St-Etienne (France); Garrelie, Florence; Colombier, Jean-Philippe; Reynaud, Stéphanie [Laboratoire Hubert Curien, Université Jean Monnet, 42000 St-Etienne (France); Quey, Romain; Blanc, Gilles [Laboratoire Georges Friedel, Ecole Nationale Supérieure des Mines, 42023 St-Etienne (France); Pigeon, Florent [Laboratoire Hubert Curien, Université Jean Monnet, 42000 St-Etienne (France)

2014-05-01

Graphical abstract: -- Highlight: •Lattice rotation and its distribution in laser-induced periodic surface structures (LIPSS) and the subsurface region on a nickel substrate are revealed using electron backscatter diffraction (EBSD). -- Abstract: We report on the structural investigation of laser-induced periodic surface structures (LIPSS) generated in polycrystalline nickel target after multi-shot irradiation by femtosecond laser pulses. Electron backscatter diffraction (EBSD) is used to reveal lattice rotation caused by dislocation storage during LIPSS formation. Localized crystallographic damages in the LIPSS are detected from both surface and cross-sectional EBSD studies. A surface region (up to 200 nm) with 1–3° grain disorientation is observed in localized areas from the cross-section of the LIPSS. The distribution of the local disorientation is inhomogeneous across the LIPSS and the subsurface region.

Solution and crystallographic structures of the central region of the phosphoprotein from human metapneumovirus.

Directory of Open Access Journals (Sweden)

Cedric Leyrat

Full Text Available Human metapneumovirus (HMPV of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs. We located the central region of HMPV P (P(ced which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of P(ced using small angle X-ray scattering (SAXS and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS and ensemble optimization were employed to select correct models and capture the dynamic character of P(ced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (P(core, that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales P(ced structures suggests that P(ced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes.

Structural Transformation of LiFePO4 during Ultrafast Delithiation.

Science.gov (United States)

Kuss, Christian; Trinh, Ngoc Duc; Andjelic, Stefan; Saulnier, Mathieu; Dufresne, Eric M; Liang, Guoxian; Schougaard, Steen B

2017-12-21

The prolific lithium battery electrode material lithium iron phosphate (LiFePO 4 ) stores and releases lithium ions by undergoing a crystallographic phase change. Nevertheless, it performs unexpectedly well at high rate and exhibits good cycling stability. We investigate here the ultrafast charging reaction to resolve the underlying mechanism while avoiding the limitations of prevailing electrochemical methods by using a gaseous oxidant to deintercalate lithium from the LiFePO 4 structure. Oxidizing LiFePO 4 with nitrogen dioxide gas reveals structural changes through in situ synchrotron X-ray diffraction and electronic changes through in situ UV/vis reflectance spectroscopy. This study clearly shows that ultrahigh rates reaching 100% state of charge in 10 s does not lead to a particle-wide union of the olivine and heterosite structures. An extensive solid solution phase is therefore not a prerequisite for ultrafast charge/discharge.

Preliminary X-ray crystallographic analysis of the glycosyltransferase from a marine Streptomyces species

International Nuclear Information System (INIS)

Gong, Liping; Xiao, Yi; Liu, Qiang; Li, Sumei; Zhang, Changsheng; Liu, Jinsong

2010-01-01

The recombinant glycosyltransferase ElaGT from the elaiophylin-producing marine Streptomyces sp. SCSIO 01934 has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.9 Å resolution. ElaGT is a glycosyltransferase from a marine Streptomyces species that is involved in the biosynthesis of elaiophylin. Here, the molecular cloning, protein expression and purification, preliminary crystallization and crystallographic characterization of ElaGT are reported. The rod-shaped crystals belonged to space group P2 1 22, with unit-cell parameters a = 66.7, b = 131.7, c = 224.6 Å, α = 90, β = 90, γ = 90°. Data were collected to 2.9 Å resolution. A preliminary molecular-replacement solution implied the presence of two ElaGT molecules in the asymmetric unit

Crystal chemistry of germanates: Characteristic structural features of Li,Ge-germanates

International Nuclear Information System (INIS)

Ilyushin, G.D.; Dem'yanets, L.N.

2000-01-01

Crystallochemical classification of eleven compounds from the Li-germanate family is suggested. Depending on the set of the primary building units (PBU) (M-octahedra of the composition [GeO 6 ] and T-tetrahedra of the composition [GeO 4 ]) and the type of their 'condensation', these germanates are divided into three crystallochemical groups: framework MT-structures (four phases), condensed MT-structures (two phases), and tetrahedral T-condensed structures (five phases). The structural characteristics of the framework Li,Ge-germanates are considered, i.e., their symmetry, crystallographically independent sets of the primary building units, framework architecture, and the types of chains and layers of the (Ge,O)-radicals

Prediction of molecular crystal structures

International Nuclear Information System (INIS)

Beyer, Theresa

2001-01-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Prediction of molecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Beyer, Theresa

2001-07-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

synthesis and structures

Indian Academy of Sciences (India)

Priya Saxena

2017-08-29

Aug 29, 2017 ... to a single crystal X-ray diffraction study for 1, 2 and 4-7. Keywords. Sterically .... 2.2b Mono-Schiff base 2: A suspension of I (1.00 g,. 2.27 mmol) and ...... bridge Crystallographic Data Centre, CCDC, 12 Union. Road, Cambridge .... H-C 2014 Rational design and synthesis of porous poly- mer networks: ...

Edge separation using diffraction anomalous fine structure

International Nuclear Information System (INIS)

Ravel, B.; Bouldin, C.E.; Renevier, H.; Hodeau, J.L.; Berar, J.F.

1999-01-01

We exploit the crystallographic sensitivity of the Diffraction Anomalous Fine-Structure (DAFS) measurement to separate the fine structure contributions of different atomic species with closely spaced resonant energies. In BaTiO 3 the Ti K edge and Ba Lm edges are separated by 281 eV, or about 8.2 Angstrom -1 ), thus severely limiting the information content of the Ti K edge signal. Using the site selectivity of DAFS we can separate the two fine structure spectra using an iterative Kramers-Kronig method, thus extending the range of the Ti K edge spectrum. This technique has application to many rare earth/transition metal compounds, including many magnetic materials of technological significance for which K and L edges overlap in energy. (au)

The breakage behaviour of Aspirin under quasi-static indentation and single particle impact loading: effect of crystallographic anisotropy.

Science.gov (United States)

Olusanmi, D; Roberts, K J; Ghadiri, M; Ding, Y

2011-06-15

The influence of crystallographic structural anisotropy on the breakage behaviour of Aspirin under impact loading is highlighted. Under both quasi-static testing conditions, using nano-indentation, and dynamic impact tests, Aspirin demonstrates clear anisotropy in its slip and fracture behaviour. During nano-indentation on the (100) and (001) faces, cracks were propagated along the [010] direction. While the hardness was found to be comparatively similar for both these faces, it was observed that slip due to plastic deformation occurred more readily on the (100) than the (001) crystal planes suggesting the former as the preferred slip plane. Furthermore, the fracture toughness on the (001) planes was found to be distinctly lower than that of the (100) planes, indicating the former as the preferred cleavage plane. Observations of the crystal morphology of damaged particles after dynamic impact testing showed that both the chipping and fragmentation of Aspirin mostly occurred via cleavage in a manner consistent with the observed fracture behaviour following nano-indentation. This work highlights the importance of cleavage as a dominant factor underpinning the fracture mechanism of Aspirin under both quasi-static and impact loading conditions. Copyright © 2011 Elsevier B.V. All rights reserved.

Impact of AlN seeding layer growth rate in MOVPE growth of semi-polar gallium nitride structures on high index silicon

Energy Technology Data Exchange (ETDEWEB)

Ravash, Roghaiyeh; Blaesing, Juergen; Hempel, Thomas; Noltemeyer, Martin; Dadgar, Armin; Christen, Juergen; Krost, Alois [Otto-von-Guericke-University Magdeburg, FNW/IEP/AHE, Postfach 4120, 39016 Magdeburg (Germany)

2011-03-15

We present metal organic vapor phase epitaxy growth of semi-polar GaN structures on high index silicon surfaces. The crystallographic structure of GaN grown on Si(112), (115), and (117) substrates is investigated by X-ray analysis and scanning electron microscopy. X-ray diffraction was performed in Bragg Brentano geometry as well as pole figure measurements. The results demonstrate that the orientation of GaN crystallites on Si is significantly dependent on thickness of the AlN seeding layer and TMAl-flow rate. We observe that the crystallographic structures of GaN by applying thin AlN seeding layers grown with high TMAl-flow rate depend on Si surface direction while they are independent for thicker layers. By applying such seeding layer we obtain single crystalline semi-polar GaN on Si(112), while GaN structures grown with the same growth parameters on Si(117) show four components of GaN(0002). (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Crystallographic and electronic structure of the Ca{sub 2}TiMnO{sub 6} double perovskite

Energy Technology Data Exchange (ETDEWEB)

López, J.P. Garzón [Grupo de Física de Nuevos Materiales, Departamento de Física, Universidad Nacional de Colombia, AA 5997 Bogotá DC (Colombia); Grupo de Estudios de Materiales – GEMA, Departamento de Física, Universidad Nacional de Colombia, AA 5997 Bogotá DC (Colombia); Cardona, R. [Grupo de Estudios de Materiales – GEMA, Departamento de Física, Universidad Nacional de Colombia, AA 5997 Bogotá DC (Colombia); Santos, A. Sarmiento [Grupo de Superficies, Electroquímica y Corrosión, Universidad Pedagógica y Tecnológica de Colombia, Tunja (Colombia); Téllez, D.A. Landínez [Grupo de Física de Nuevos Materiales, Departamento de Física, Universidad Nacional de Colombia, AA 5997 Bogotá DC (Colombia); Roa-Rojas, J., E-mail: jroar@unal.edu.co [Grupo de Física de Nuevos Materiales, Departamento de Física, Universidad Nacional de Colombia, AA 5997 Bogotá DC (Colombia)

2014-12-15

In this work, we report synthesis and crystalline structure study of the Ca{sub 2}TiMnO{sub 6} complex perovskite, by X-ray diffraction experiments and through the application of the Rietveld refinement using the GSAS code. Results revealed the crystallization of the system in a tetragonal perovskite with the characteristic structure given by I4/m (#87) space group and lattice parameters a=5.339(4) Å and c=7.736(6) Å. Ab initio calculations of density of states (DOS) and electronic structure were carried out for this perovskite-like system, by the Density Functional Theory (DFT) and using the Full-potential Linearized Augmented Plane Waves (FP-LAPW) method. The exchange-correlation potential was treated using the Generalized Gradient Approximation (GGA). All calculations were carried-out using spin polarization. For the up spin orientation the compound has a semiconducting behavior and for down spin polarization it behaves like a conductor. The calculated effective magnetic moment in cell was 4.02 μ{sub B}, which is close to the expected value calculated from Hund's rules.

Analysis of ADU structure obtained under different precipitation conditions

International Nuclear Information System (INIS)

Ramella, Jose L.; Esteban, Adolfo; Mendez De Leo, Lucia P.; Sassone, Ariel; Novara, Oscar E.; Boero, Norma L.; Leyva, Ana G.

1999-01-01

ADU is the nominal name for ammonium poly uranate. It is a very complex compound of polymeric structure, which may have, according to precipitation conditions, different chemical composition and crystallographic structure. ADU is used as uranium oxide precursor in the manufacture of fuel elements. In former papers it was proved that if ultrasound is applied during precipitation and digestion the characteristics of the final product (U 3 O 8 UO 2 ) improve. By studying ADU thermal decomposition obtained by ultrasonic application, it was intended to obtain its composition. Therefore, differential thermal gravimetric and differential thermal analyses were performed. Samples were taken from special points and analyzed by X-ray diffraction, infra-red spectroscopy and scanning. An experiment was also designed to identify the products released during heating. Results and conclusions obtained are presented in this work. (author)

Dependence of Fracture Toughness on Crystallographic Orientation in Single-Crystalline Cubic (β) Silicon Carbide

Energy Technology Data Exchange (ETDEWEB)

Pharr, M.; Katoh, Y.; Bei, H.

2006-01-01

Along with other desirable properties, the ability of silicon carbide (SiC) to retain high strength after elevated temperature exposures to neutron irradiation renders it potentially applicable in fusion and advanced fission reactors. However, properties of the material such as room temperature fracture toughness must be thoroughly characterized prior to such practical applications. The objective of this work is to investigate the dependence of fracture toughness on crystallographic orientation for single-crystalline β-SiC. X-ray diffraction was first performed on the samples to determine the orientation of the crystal. Nanoindentation was used to determine a hardness of 39.1 and 35.2 GPa and elastic modulus of 474 and 446 GPa for the single-crystalline and polycrystalline samples, respectively. Additionally, crack lengths and indentation diagonals were measured via a Vickers micro-hardness indenter under a load of 100 gf for different crystallographic orientations with indentation diagonals aligned along fundamental cleavage planes. Upon examination of propagation direction of cracks, the cracks usually did not initiate and propagate from the corners of the indentation where the stresses are concentrated but instead from the indentation sides. Such cracks clearly moved along the {1 1 0} family of planes (previously determined to be preferred cleavage plane), demonstrating that the fracture toughness of SiC is comparatively so much lower along this set of planes that the lower energy required to cleave along this plane overpowers the stress-concentration at indentation corners. Additionally, fracture toughness in the <1 1 0> direction was 1.84 MPa·m1/2, lower than the 3.46 MPa·m1/2 measured for polycrystalline SiC (which can serve as an average of a spectrum of orientations), further demonstrating that single-crystalline β-SiC has a strong fracture toughness anisotropy.

Elastic, thermal and high pressure structural properties of heavy rare earth antimonides

International Nuclear Information System (INIS)

Soni, P.; Pagare, G.; Sanyal, S.P.

2009-01-01

Pressure induced structural phase transition of two heavy rare earth antimonides (RESb; RE=Ho, Er) have been studied theoretically by using an inter-ionic potential theory. This method has been found quite satisfactory in the case of pnictides of rare earth and describes the crystal properties in the framework of rigid-ion modal. The long-range Coulomb interaction, short-range repulsive interaction and van der Waals (vdW) interactions are properly incorporated in this theory. These compounds exhibit first order crystallographic phase transition from their NaCl-type structure to CsCl-type structure at 27 GPa and 33.2 GPa, respectively. The bulk moduli of RESb compounds are compared with the experimental values of elastic constants. We have also calculated the Debye temperature by incorporating the elastic constants for both the rare earth antimonides. (author)

Determination of Basic Structure-Property Relations for Processing and Modeling in Advanced Nuclear Fuel: Microstructure Evolution and Mechanical Properties

International Nuclear Information System (INIS)

Wheeler, Kirk; Parra, Manuel; Peralta, Pedro

2009-01-01

The project objective is to study structure-property relations in solid solutions of nitrides and oxides with surrogate elements to simulate the behavior of fuels of inert matrix fuels of interest to the Advanced Fuel Cycle Initiative (AFCI), with emphasis in zirconium-based materials. Work with actual fuels will be carried out in parallel in collaboration with Los Alamos National Laboratory (LANL). Three key aspects will be explored: microstructure characterization through measurement of global texture evolution and local crystallographic variations using Electron Backscattering Diffraction (EBSD); determination of mechanical properties, including fracture toughness, quasi-static compression strength, and hardness, as functions of load and temperature, and, finally, development of structure-property relations to describe mechanical behavior of the fuels based on experimental data. Materials tested will be characterized to identify the mechanisms of deformation and fracture and their relationship to microstructure and its evolution. New aspects of this research are the inclusion of crystallographic information into the evaluation of fuel performance and the incorporation of statistical variations of microstructural variables into simplified models of mechanical behavior of fuels that account explicitly for these variations. The work is expected to provide insight into processing conditions leading to better fuel performance and structural reliability during manufacturing and service, as well as providing a simplified testing model for future fuel production

Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of membrane-type 1 matrix metalloproteinase (MT1-MMP)

International Nuclear Information System (INIS)

Terawaki, Shin-ichi; Kitano, Ken; Aoyama, Miki; Hakoshima, Toshio

2008-01-01

The radixin FERM domain was shown to bind the MT1-MMP cytoplasmic peptide and crystals of the complex were obtained. ERM proteins play a role in the cross-linking found between plasma membranes and actin filaments. The N-terminal FERM domains of ERM proteins are responsible for membrane association through direct interaction with the cytoplasmic tails of integral membrane proteins. During cell migration and movement, membrane-type 1 matrix metalloproteinase (MT1-MMP) on plasma membranes sheds adhesion molecule CD44 in addition to degrading the extracellular matrix. Here, the interaction between the radixin FERM domain and the MT1-MMP cytoplasmic tail is reported and preliminary crystallographic characterization of crystals of the radixin FERM domain bound to the cytoplasmic tail of MT1-MMP is presented. The crystals belong to space group P6 1 22, with unit-cell parameters a = b = 122.7, c = 128.3 Å, and contain one complex in the crystallographic asymmetric unit. The diffraction data were collected to a resolution of 2.4 Å

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

Science.gov (United States)

Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B; Belcher-Dufrisne, Meagan; Wiriyasermkul, Pattama; Giese, M Hunter; Leal-Pinto, Edgar; Kloss, Brian; Tabuso, Shantelle; Love, James; Punta, Marco; Banerjee, Surajit; Rajashankar, Kanagalaghatta R; Rost, Burkhard; Logothetis, Diomedes; Quick, Matthias; Hendrickson, Wayne A

2018-01-01

Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO42- at the molecular level is limited. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues. PMID:29792261

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

International Nuclear Information System (INIS)

Masuda, Tetsuya; Ohta, Keisuke; Tani, Fumito; Mikami, Bunzo; Kitabatake, Naofumi

2011-01-01

Highlights: → X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. → The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the Cα atom of G96 in thaumatin II was observed. → The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. → The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the Cα atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

Energy Technology Data Exchange (ETDEWEB)

Masuda, Tetsuya, E-mail: t2masuda@kais.kyoto-u.ac.jp [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011 (Japan); Ohta, Keisuke; Tani, Fumito [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011 (Japan); Mikami, Bunzo [Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Kitabatake, Naofumi [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011 (Japan)

2011-07-08

Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

Structure of the first PDZ domain of human PSD-93

DEFF Research Database (Denmark)

Fiorentini, Monica; Nielsen, Ann Kallehauge; Kristensen, Ole

2009-01-01

The crystal structure of the PDZ1 domain of human PSD-93 has been determined to 2.0 A resolution. The PDZ1 domain forms a crystallographic trimer that is also predicted to be stable in solution. The main contributions to the stabilization of the trimer seem to arise from interactions involving...... the PDZ1-PDZ2 linker region at the extreme C-terminus of PDZ1, implying that the oligomerization that is observed is not of biological significance in full-length PSD-93. Comparison of the structures of the binding cleft of PSD-93 PDZ1 with the previously reported structures of PSD-93 PDZ2 and PDZ3...

Towards Prediction Of Crystal Structure Of Al-Rich Intermetallides Formed In Al-T-A Systems

International Nuclear Information System (INIS)

Bram, Avraham I.; Meshic, Louisa; Ilse Katz institute for nanotechnology, Ben Gurion University of the Negev; Venkert, Arie

2014-01-01

Crystal structure of the material has a significant contribution on its properties. However, there is no universal model that can predict precisely the crystallographic structure of a stable material at specific composition and temperature. Since the 1950's, various prediction approaches were developed and yielded many different methods of computer simulation and innovative theories which are summarized in the review of Woodley et al. These methods are based on complicated calculations of quantum sizes

Role of tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase.

Science.gov (United States)

Pennacchio, Angela; Esposito, Luciana; Zagari, Adriana; Rossi, Mosè; Raia, Carlo A

2009-09-01

A mutant of the thermostable NAD(+)-dependent (S)-stereospecific alcohol dehydrogenase from Sulfolobus solfataricus (SsADH) which has a single substitution, Trp95Leu, located at the substrate binding pocket, was fully characterized to ascertain the role of Trp95 in discriminating between chiral secondary alcohols suggested by the wild-type SsADH crystallographic structure. The Trp95Leu mutant displays no apparent activity with short-chain primary and secondary alcohols and poor activity with aromatic substrates and coenzyme. Moreover, the Trp --> Leu substitution affects the structural stability of the archaeal ADH, decreasing its thermal stability without relevant changes in secondary structure. The double mutant Trp95Leu/Asn249Tyr was also purified to assist in crystallographic analysis. This mutant exhibits higher activity but decreased affinity toward aliphatic alcohols, aldehydes as well as NAD(+) and NADH compared to the wild-type enzyme. The crystal structure of the Trp95Leu/Asn249Tyr mutant apo form, determined at 2.0 A resolution, reveals a large local rearrangement of the substrate site with dramatic consequences. The Leu95 side-chain conformation points away from the catalytic metal center and the widening of the substrate site is partially counteracted by a concomitant change of Trp117 side chain conformation. Structural changes at the active site are consistent with the reduced activity on substrates and decreased coenzyme binding.

The structure and dynamics of patterns of Benard convection cells

International Nuclear Information System (INIS)

Rivier, N.; Imperial Coll. of Science and Technology, London; Lausanne Univ.

1990-08-01

Benard-Marangoni convection, in containers with large aspect ratio, exhibits space-filling cellular structures, highly deformable, but crystallized. They contain dislocations and grain boundaries generated and moved by elementary topological transformations, and are subjected to a weak shear stress due to the earth's rotation. The cellular structure and its fluctuations are analyzed from a crystallographic viewpoint, by using two complementary approaches. One is a global analysis of cellular structures in cylindrical symmetry. Their structural stability and defect pattern are obtained as topological mode-locking of a continuous structural parameter. The other, a local, molecular dynamics of the cells, gives a realistic parametrization of the forces and the transformations by generalizing the Voronoi cell construction in one extra dimension. 23 refs., 8 figs

A Computational Study of the Growth of Hexagonal Ice

Science.gov (United States)

Fulford, Maxwell; Salvalaglio, Matteo; Parrinello, Michele; Molteni, Carla

Hexagonal ice (Ih) has two distinct crystallographic surfaces; a basal and prism surface. At low vapour pressures, Ih forms thin plates and elongated prisms, depending on the temperature. The macroscopic shape depends on the relative rate of growth of the basal and prism surfaces. The aim of our research is to estimate the relative rate of growth of the two surfaces for a range of temperatures and ultimately predict the shape of Ih, using computer simulations. Our simulations show the well-know phenomenon that the surface of ice lowers its interfacial free energy by forming a stable quasi-liquid layer (QLL). The QLL mediates crystal growth and has a thickness which varies with temperature and crystallographic surface. We use a combination of Molecular Dynamics and Metadynamics to study how the interfacial structure at the ice/quasi-liquid and quasi-liquid/vapour interfaces influence the adsorption potential, surface transport properties and growth shape..

Moessbauer determination of magnetic structure of Fe3BO6 crystal