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Sample records for previous crystal structure

  1. Crystal structure determination of Efavirenz

    International Nuclear Information System (INIS)

    Popeneciu, Horea; Dumitru, Ristoiu; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria

    2015-01-01

    Needle-shaped single crystals of the title compound, C 14 H 9 ClF 3 NO 2 , were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring

  2. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURES ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    ABSTRACT. Reaction of [VO(acac)2] (acac = acetylacetonate) with ... Single crystal X-ray structural studies indicate that the hydrazone ligands coordinate to ..... Molecular structure of complex (1) at 30% probability displacement. Figure 4.

  3. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

    Preferred Customer

    Reaction of [MoO2(acac)2] (where acac = acetylacetonate) with N'-(2-hydroxy-4- ... Single crystal X-ray structural studies indicate that the hydrazone ligand coordinates .... Molecular structure of the complex at 30% probability displacement.

  4. SYNTHESIS, CHARACTERIZATION, AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

    a

    KEY WORDS: Barium, Crystal structure, 2,6-Pyridinedicarboxylic acid .... The rational design of novel metal-organic frameworks has attracted great ..... Bond, A.D.; Jones, W. Supramolecular Organization and Materials Design, Jones, W.; Rao,.

  5. 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

  6. 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

  7. Crystal structure of cafenstrole

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available The title compound (systematic name: N,N-diethyl-3-mesitylsulfonyl-1H-1,2,4-triazole-1-carboxamide, C16H22N4O3S, is a triazole herbicide. The dihedral angle between the planes of the triazole and benzene ring planes is 88.14 (10°. In the crystal, C—H...O hydrogen bonds and weak C—H...π interactions link adjacent molecules, forming one-dimensional chains along the a axis.

  8. Crystal structure of pseudoguainolide

    Directory of Open Access Journals (Sweden)

    Noureddine Beghidja

    2015-03-01

    Full Text Available The lactone ring in the title molecule, C15H22O3 (systematic name: 3,4a,8-trimethyldodecahydroazuleno[6,5-b]furan-2,5-dione, assumes an envelope conformation with the methine C atom adjacent to the the methine C atom carrying the methyl substituent being the flap atom. The other five-membered ring adopts a twisted conformation with the twist being about the methine–methylene C—C bond. The seven-membered ring is based on a twisted boat conformation. No specific interactions are noted in the the crystal packing.

  9. 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.

  10. Crystal structure of pymetrozine

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

    Full Text Available The title compound, C10H11N5O {systematic name: 6-methyl-4-[(E-(pyridin-3-ylmethylideneamino]-4,5-dihydro-1,2,4-triazin-3(2H-one}, C10H11N5O, is used as an antifeedant in pest control. The asymmetric unit comprises two independent molecules, A and B, in which the dihedral angles between the pyridinyl and triazinyl ring planes [r.m.s. deviations = 0.0132 and 0.0255 ] are 11.60 (6 and 18.06 (4°, respectively. In the crystal, N—H...O, N—H...N, C—H...N and C—H...O hydrogen bonds, together with weak π–π interactions [ring-centroid separations = 3.5456 (9 and 3.9142 (9 Å], link the pyridinyl and triazinyl rings of A molecules, generating a three-dimensional network.

  11. Shear induced structures in crystallizing cocoa butter

    Science.gov (United States)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  12. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus: Purification, Crystallization and Structure Determination

    International Nuclear Information System (INIS)

    Clemons, William M. Jr.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2001-01-01

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 (angstrom) resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 (angstrom) resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  13. Crystal structure and magnetic susceptibility of UOSe single crystals

    International Nuclear Information System (INIS)

    Kaczorowski, D.; Muenster Univ.; Poettgen, R.; Jeitschko, W.; Gajek, Z.; Zygmunt, A.

    1993-01-01

    The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T N =100±2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author)

  14. Crystal structure and magnetic susceptibility of UOSe single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kaczorowski, D. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Poettgen, R.; Jeitschko, W. (Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Gajek, Z.; Zygmunt, A. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research)

    1993-01-01

    The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T[sub N]=100[+-]2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author).

  15. Amine free crystal structure: The crystal structure of d(CGCGCG)2 and methylamine complex crystal

    International Nuclear Information System (INIS)

    Ohishi, Hirofumi; Tsukamoto, Koji; Hiyama, Yoichi; Maezaki, Naoyoshi; Tanaka, Tetsuaki; Ishida, Toshimasa

    2006-01-01

    We succeeded in the crystallization of d(CGCGCG) 2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2F o - F c map was much clear and easily traced. It is First time monoamine co-crystallizes with d(CGCGCG) 2 . However, methylamine was not found from the complex crystal of d(CGCGCG) 2 and methylamine. Five Mg ions were found around d(CGCGCG) 2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg 2+ . DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG) 2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this

  16. What makes a crystal structure report valid?

    NARCIS (Netherlands)

    Spek, Anthony L.|info:eu-repo/dai/nl/156517566

    2018-01-01

    Single crystal X-ray crystallography has developed into a unique, highly automated and accessible tool to obtain detailed information on molecular structures. Proper archival makes that referees, readers and users of the results of reported crystal structures no longer need to depend solely on the

  17. Crystal structure of prethrombin-1

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Zhiwei; Pelc, Leslie A.; Di Cera, Enrico (St. Louis-MED)

    2010-11-15

    Prothrombin is the zymogen precursor of the clotting enzyme thrombin, which is generated by two sequential cleavages at R271 and R320 by the prothrombinase complex. The structure of prothrombin is currently unknown. Prethrombin-1 differs from prothrombin for the absence of 155 residues in the N-terminal domain and is composed of a single polypeptide chain containing fragment 2 (residues 156-271), A chain (residues 272-320), and B chain (residues 321-579). The X-ray crystal structure of prethrombin-1 solved at 2.2-{angstrom} resolution shows an overall conformation significantly different (rmsd = 3.6 {angstrom}) from that of its active form meizothrombin desF1 carrying a cleavage at R320. Fragment 2 is rotated around the y axis by 29{sup o} and makes only few contacts with the B chain. In the B chain, the oxyanion hole is disrupted due to absence of the I16-D194 ion pair and the Na{sup +} binding site and adjacent primary specificity pocket are highly perturbed. A remarkable feature of the structure is that the autolysis loop assumes a helical conformation enabling W148 and W215, located 17 {angstrom} apart in meizothrombin desF1, to come within 3.3 {angstrom} of each other and completely occlude access to the active site. These findings suggest that the zymogen form of thrombin possesses conformational plasticity comparable to that of the mature enzyme and have significant implications for the mechanism of prothrombin activation and the zymogen {yields} protease conversion in trypsin-like proteases.

  18. Crystal structure of 2-pentyloxybenzamide

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2014-10-01

    Full Text Available In the title molecule, C12H17NO2, the amide NH2 group is oriented toward the pentyloxy substituent and an intramolecular N—H...O hydrogen bond is formed with the pentyloxy O atom. The benzene ring forms dihedral angles of 2.93 (2 and 5.60 (2° with the amide group and the pentyloxy group mean planes, respectively. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with their molecular planes parallel, but at an offset of 0.45 (1 Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121 and the other in a column approximately parallel to (1-21. The two planes form a dihedral angle of 85.31 (2°, and are linked via C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional framework structure.

  19. Method of fabricating patterned crystal structures

    KAUST Repository

    Yu, Liyang

    2016-12-15

    A method of manufacturing a patterned crystal structure for includes depositing an amorphous material. The amorphous material is modified such that a first portion of the amorphous thin-film layer has a first height/volume and a second portion of the amorphous thin-film layer has a second height/volume greater than the first portion. The amorphous material is annealed to induce crystallization, wherein crystallization is induced in the second portion first due to the greater height/volume of the second portion relative to the first portion to form patterned crystal structures.

  20. Photonic Crystal Laser-Driven Accelerator Structures

    International Nuclear Information System (INIS)

    Cowan, B

    2004-01-01

    The authors discuss simulated photonic crystal structure designs for laser-driven particle acceleration. They focus on three-dimensional planar structures based on the so-called ''woodpile'' lattice, demonstrating guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice. They introduce a candidate geometry and discuss the properties of the accelerating mode. They also discuss the linear beam dynamics in the structure present a novelmethod for focusing the beam. In addition they describe ongoing investigations of photonic crystal fiber-based structures

  1. Crystal structure of actinide metals at high compression

    International Nuclear Information System (INIS)

    Fast, L.; Soederlind, P.

    1995-08-01

    The crystal structures of some light actinide metals are studied theoretically as a function of applied pressure. The first principles electronic structure theory is formulated in the framework of density functional theory, with the gradient corrected local density approximation of the exchange-correlation functional. The light actinide metals are shown to be well described as itinerant (metallic) f-electron metals and generally, they display a crystal structure which have, in agreement with previous theoretical suggestions, increasing degree of symmetry and closed-packing upon compression. The theoretical calculations agree well with available experimental data. At very high compression, the theory predicts closed-packed structures such as the fcc or the hcp structures or the nearly closed-packed bcc structure for the light actinide metals. A simple canonical band picture is presented to explain in which particular closed-packed form these metals will crystallize at ultra-high pressure

  2. Hydrothermal synthesis, crystal structure and luminescence property ...

    Indian Academy of Sciences (India)

    The design and construction of ... dination polymers. It is difficult to design coordination .... The first endotherm at about 180 ... graphic data for coordination polymer 1. ... Sheldrick G M 1997 SHELXS-97: Program for solution of crystal structures ...

  3. imide, crystal structure, thermal and dielectric studies

    Indian Academy of Sciences (India)

    methyl imidazolium methylidene bis(trifluoromethanesulfonyl)imide, crystal structure, thermal and dielectric studies. BOUMEDIENE HADDAD1,2,3,∗, TAQIYEDDINE MOUMENE2, DIDIER VILLEMIN1,. JEAN-FRANÇOIS LOHIER1 and EL-HABIB ...

  4. SYNTHESIS, CRYSTAL STRUCTURE AND MAGNETIC ...

    African Journals Online (AJOL)

    Preferred Customer

    Much of the current effort on such extended hybrid metal organic complexes is ... In this paper, we report the synthesis, single crystal X-ray diffraction analysis and ..... with g = 2.0 (0.37 cm3 mol−1 K), and smoothly increases to a value of 0.45 ...

  5. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...

  6. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    Science.gov (United States)

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions.

  7. Two-dimensional photonic crystal accelerator structures

    Directory of Open Access Journals (Sweden)

    Benjamin M. Cowan

    2003-10-01

    Full Text Available Photonic crystals provide a method of confining a synchronous speed-of-light mode in an all-dielectric structure, likely a necessary feature in any optical accelerator. We explore computationally a class of photonic crystal structures with translational symmetry in a direction transverse to the electron beam. We demonstrate synchronous waveguide modes and discuss relevant parameters of such modes. We then explore how accelerator parameters vary as the geometry of the structure is changed and consider trade-offs inherent in the design of an accelerator of this type.

  8. Crystal structure of enolase from Drosophila melanogaster.

    Science.gov (United States)

    Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

    2017-04-01

    Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

  9. Crystal structure of isomeric boron difluoride acetylnaphtholates

    International Nuclear Information System (INIS)

    Bukvetskij, B.V.; Fedorenko, E.V.; Mirochnik, A.G.; Karasev, V.E.

    2006-01-01

    Crystal structures of luminescent isomeric acetylnaphtholates of boron difluoride are investigated. Full X-ray structural analysis is done at 293 K. Coordinated of atoms, bond angles, bond lengths, interatomic distances are determined. Results of comparative evaluations of the isomers are represented [ru

  10. Crystal structure of levomepromazine maleate

    Directory of Open Access Journals (Sweden)

    Gyula Tamás Gál

    2016-05-01

    Full Text Available The asymmetric unit of the title salt, C19H25N2OS+·C4H3O4− [systematic name: (S-3-(2-methoxyphenothiazin-10-yl-N,N,2-trimethylpropanaminium hydrogen maleate], comprises two (S-levomepromazine cations and two hydrogen maleate anions. The conformations of the two cations are similar. The major difference relates to the orientation of the methoxy substituent at the phenothiazine ring system. The crystal components form a three-dimensional supramolecular network via N—H...O, C—H...O and C—H...π interactions. A comparison of the conformations of the levomepromazine cations with those of the neutral molecule and similar protonated molecules reveals significant conformational flexibility of the phenothiazine ring system and the substituent at the phenothiazine N atom.

  11. PAK4 crystal structures suggest unusual kinase conformational movements.

    Science.gov (United States)

    Zhang, Eric Y; Ha, Byung Hak; Boggon, Titus J

    2018-02-01

    In order for protein kinases to exchange nucleotide they must open and close their catalytic cleft. These motions are associated with rotations of the N-lobe, predominantly around the 'hinge region'. We conducted an analysis of 28 crystal structures of the serine-threonine kinase, p21-activated kinase 4 (PAK4), including three newly determined structures in complex with staurosporine, FRAX486, and fasudil (HA-1077). We find an unusual motion between the N-lobe and C-lobe of PAK4 that manifests as a partial unwinding of helix αC. Principal component analysis of the crystal structures rationalizes these movements into three major states, and analysis of the kinase hydrophobic spines indicates concerted movements that create an accessible back pocket cavity. The conformational changes that we observe for PAK4 differ from previous descriptions of kinase motions, and although we observe these differences in crystal structures there is the possibility that the movements observed may suggest a diversity of kinase conformational changes associated with regulation. Protein kinases are key signaling proteins, and are important drug targets, therefore understanding their regulation is important for both basic research and clinical points of view. In this study, we observe unusual conformational 'hinging' for protein kinases. Hinging, the opening and closing of the kinase sub-domains to allow nucleotide binding and release, is critical for proper kinase regulation and for targeted drug discovery. We determine new crystal structures of PAK4, an important Rho-effector kinase, and conduct analyses of these and previously determined structures. We find that PAK4 crystal structures can be classified into specific conformational groups, and that these groups are associated with previously unobserved hinging motions and an unusual conformation for the kinase hydrophobic core. Our findings therefore indicate that there may be a diversity of kinase hinging motions, and that these may

  12. Crystal structure of new AsS2 compound

    International Nuclear Information System (INIS)

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    2013-01-01

    AsS 2 single crystals have been obtained for the first time from an As 2 S 3 melt at pressures above 6 GPa and temperatures above 800 K in the As 2 S 3 → AsS + AsS 2 reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

  13. Crystal structure of rubidium methyldiazotate

    Directory of Open Access Journals (Sweden)

    Tobias Grassl

    2017-02-01

    Full Text Available The title compound, Rb+·H3CN2O−, has been crystallized in liquid ammonia as a reaction product of the reductive ammonolysis of the natural compound streptozocin. Elemental rubidium was used as reduction agent as it is soluble in liquid ammonia, forming a blue solution. Reductive bond cleavage in biogenic materials under kinetically controlled conditions offers a new approach to gain access to sustainably produced raw materials. The anion is nearly planar [dihedral angle O—N—N—C = −0.4 (2°]. The Rb+ cation has a coordination number of seven, and coordinates to five anions. One anion is bound via both its N atoms, one by both O and N, two anions are bound by only their O atoms, and the last is bound via the N atom adjacent to the methyl group. The diazotate anions are bridged by cations and do not exhibit any direct contacts with each other. The cations form corrugated layers that propagate in the (-101 plane.

  14. Alignment structures in ferroelectric liquid crystals

    Energy Technology Data Exchange (ETDEWEB)

    Islam, N.U

    1998-07-01

    Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S{sub C} phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes

  15. Alignment structures in ferroelectric liquid crystals

    International Nuclear Information System (INIS)

    Islam, N.U.

    1998-01-01

    Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S C phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes an

  16. Information and crystal structure estimation

    International Nuclear Information System (INIS)

    Wilkins, S.W.; Commonwealth Scientific and Industrial Research Organization, Clayton; Varghese, J.N.; Steenstrup, S.

    1984-01-01

    The conceptual foundations of a general information-theoretic based approach to X-ray structure estimation are reexamined with a view to clarifying some of the subtleties inherent in the approach and to enhancing the scope of the method. More particularly, general reasons for choosing the minimum of the Shannon-Kullback measure for information as the criterion for inference are discussed and it is shown that the minimum information (or maximum entropy) principle enters the present treatment of the structure estimation problem in at least to quite separate ways, and that three formally similar but conceptually quite different expressions for relative information appear at different points in the theory. One of these is the general Shannon-Kullback expression, while the second is a derived form pertaining only under the restrictive assumptions of the present stochastic model for allowed structures, and the third is a measure of the additional information involved in accepting a fluctuation relative to an arbitrary mean structure. (orig.)

  17. Structure analysis on synthetic emerald crystals

    Science.gov (United States)

    Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

    2013-05-01

    Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

  18. Synthesis, characterization and crystal structure of a ...

    African Journals Online (AJOL)

    The Mo atom in the complex is in octahedral coordination. Thermal stability of the complex has also been studied. KEY WORDS: Molybdenum complex, Hydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. Bull. Chem. Soc. Ethiop. 2014, 28(3), 409-414. DOI: http://dx.doi.org/10.4314/bcse.v28i3.10 ...

  19. Synthesis, crystal structure, thermal analysis and dielectric ...

    Indian Academy of Sciences (India)

    [13] Perry C H and Lowdes R P 1969 J. Chem. Phys. 51 3648. [14] Sheldrick G M 1997 SHELXS9, Program for the Refinement of Crystal Structures (Germany: University of Gottingen). [15] Loukil M, Kabadou A, Salles Ph and Ben Salah A 2004 Chem. Phys. 300 247. [16] Rolies M M and De Ranter C J 1978 Acta Crystallogr.

  20. Crystal Structure of Human Enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-04-08

    Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the 'pocket factor,' a small molecule that stabilizes the virus, is partly exposed on the floor of the 'canyon.' Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

  1. Modular crystals as modulated structures

    DEFF Research Database (Denmark)

    Elcoro, L.; Perez-Mato, J.M.; Friese, K.

    2008-01-01

    The use of the superspace formalism is extended to the description and refinement of the homologous series of modular structures with two symmetry-related modules with different orientations. The lillianite homologous series has been taken as a study case. Starting from a commensurate modulated...... composite description with two basic subsystems corresponding to the two different modules, it is shown how a more efficient description can be achieved using so-called zigzag modulation functions. These linear zigzag modulations, newly implemented in the program JANA2006, have very large fixed amplitudes...... and introduce in the starting model the two orientations of the underlying module sublattices. We show that a composite approach with this type of function, which treats the cations and anions as two separate subsystems forming a misfit compound, is the most appropriate and robust method for the refinements....

  2. Photonic Crystal Laser-Driven Accelerator Structures

    International Nuclear Information System (INIS)

    Cowan, Benjamin M.

    2007-01-01

    Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques

  3. Solving crystal structures with the symmetry minimum function

    International Nuclear Information System (INIS)

    Estermann, M.A.

    1995-01-01

    Unravelling the Patterson function (the auto-correlation function of the crystal structure) (A.L. Patterson, Phys. Rev. 46 (1934) 372) can be the only way of solving crystal structures from neutron and incomplete diffraction data (e.g. powder data) when direct methods for phase determination fail. The negative scattering lengths of certain isotopes and the systematic loss of information caused by incomplete diffraction data invalidate the underlying statistical assumptions made in direct methods. In contrast, the Patterson function depends solely on the quality of the available diffraction data. Simpson et al. (P.G. Simpson et al., Acta Crystallogr. 18 (1965) 169) showed that solving a crystal structure with a particular superposition of origin-shifted Patterson functions, the symmetry minimum function, is advantageous over using the Patterson function alone, for single-crystal X-ray data.This paper describes the extension of the Patterson superposition approach to neutron data and powder data by (a) actively using the negative regions in the Patterson map caused by negative scattering lengths and (b) using maximum entropy Patterson maps (W.I.F. David, Nature 346 (1990) 731). Furthermore, prior chemical knowledge such as bond lengths and angles from known fragments have been included. Two successful structure solutions of a known and a previously unknown structure (M. Hofmann, J. Solid State Chem., in press) illustrate the potential of this new development. ((orig.))

  4. Crystal structure of riboflavin synthase

    Energy Technology Data Exchange (ETDEWEB)

    Liao, D.-I.; Wawrzak, Z.; Calabrese, J.C.; Viitanen, P.V.; Jordan, D.B. (DuPont); (NWU)

    2010-03-05

    Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine to yield riboflavin and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine. The homotrimer of 23 kDa subunits has no cofactor requirements for catalysis. The enzyme is nonexistent in humans and is an attractive target for antimicrobial agents of organisms whose pathogenicity depends on their ability to biosynthesize riboflavin. The first three-dimensional structure of the enzyme was determined at 2.0 {angstrom} resolution using the multiwavelength anomalous diffraction (MAD) method on the Escherichia coli protein containing selenomethionine residues. The homotrimer consists of an asymmetric assembly of monomers, each of which comprises two similar {beta} barrels and a C-terminal {alpha} helix. The similar {beta} barrels within the monomer confirm a prediction of pseudo two-fold symmetry that is inferred from the sequence similarity between the two halves of the protein. The {beta} barrels closely resemble folds found in phthalate dioxygenase reductase and other flavoproteins. The three active sites of the trimer are proposed to lie between pairs of monomers in which residues conserved among species reside, including two Asp-His-Ser triads and dyads of Cys-Ser and His-Thr. The proposed active sites are located where FMN (an analog of riboflavin) is modeled from an overlay of the {beta} barrels of phthalate dioxygenase reductase and riboflavin synthase. In the trimer, one active site is formed, and the other two active sites are wide open and exposed to solvent. The nature of the trimer configuration suggests that only one active site can be formed and be catalytically competent at a time.

  5. Nonlinear coherent structures in granular crystals

    Science.gov (United States)

    Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

    2017-10-01

    The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

  6. On the crystal structure of colloidally prepared CsPbBr3 quantum dots.

    Science.gov (United States)

    Cottingham, Patrick; Brutchey, Richard L

    2016-04-18

    Colloidally synthesized quantum dots of CsPbBr3 are highly promising for light-emitting applications. Previous reports based on benchtop diffraction conflict as to the crystal structure of CsPbBr3 quantum dots. We present X-ray diffraction and PDF analysis of X-ray total scattering data that indicate that the crystal structure is unequivocally orthorhombic (Pnma).

  7. Solving crystal structures from neutron diffraction data

    International Nuclear Information System (INIS)

    Wilson, C.C.

    1987-07-01

    In order to pursue crystal structure determination using neutron diffraction data, and given the wide experience available of solving structures using X-ray data, the codes used in X-ray structural analysis should be adapted to the different requirements of a neutron experiment. Modifications have been made to a direct methods program MITHRIL and to a Patterson methods program PATMET to incorporate into these the features of neutron rather than X-ray diffraction. While to date these modifications have been fairly straightforward and many sophistications remain to be exploited, results obtained from the neutron versions of both programs are promising. (author)

  8. Crystal structure of tris(hydroxylammonium orthophosphate

    Directory of Open Access Journals (Sweden)

    Malte Leinemann

    2015-11-01

    Full Text Available The crystal structure of the title salt, ([H3NOH]+3·[PO4]3−, consists of discrete hydroxylammonium cations and orthophosphate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phosphorus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by intermolecular O—H...O and N—H...O hydrogen bonds into a three-dimensional network. Altogether, one very strong O—H...O, two N—H...O hydrogen bonds of medium strength and two weaker bifurcated N—H...O interactions are observed.

  9. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr; Shkurenko, Aleksander; Osior, Agnieszka; Kamieński, Bohdan; Szymański, Sławomir

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  10. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

    Horak, Peter; Dantan, Aurelien Romain; Drewsen, Michael

    2012-01-01

    We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures, such as b......We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures...

  11. Crystal structure of natural phaeosphaeride A

    Directory of Open Access Journals (Sweden)

    Victoria V. Abzianidze

    2015-08-01

    Full Text Available The asymmetric unit of the title compound, C15H23NO5, contains two independent molecules. Phaeosphaeride A contains two primary sections, an alkyl chain consisting of five C atoms and a cyclic system consisting of fused five- and six-membered rings with attached substituents. In the crystal, the molecules form layered structures. Nearly planar sheets, parallel to the (001 plane, form bilayers of two-dimensional hydrogen-bonded networks with the hydroxy groups located on the interior of the bilayer sheets. The network is constructed primarily of four O—H...O hydrogen bonds, which form a zigzag pattern in the (001 plane. The butyl chains interdigitate with the butyl chains on adjacent sheets. The crystal was twinned by a twofold rotation about the c axis, with refined major–minor occupancy fractions of 0.718 (6:0.282 (6.

  12. Crystal structure of Cryptosporidium parvum pyruvate kinase.

    Directory of Open Access Journals (Sweden)

    William J Cook

    Full Text Available Pyruvate kinase plays a critical role in cellular metabolism of glucose by serving as a major regulator of glycolysis. This tetrameric enzyme is allosterically regulated by different effector molecules, mainly phosphosugars. In response to binding of effector molecules and substrates, significant structural changes have been identified in various pyruvate kinase structures. Pyruvate kinase of Cryptosporidium parvum is exceptional among known enzymes of protozoan origin in that it exhibits no allosteric property in the presence of commonly known effector molecules. The crystal structure of pyruvate kinase from C. parvum has been solved by molecular replacement techniques and refined to 2.5 Å resolution. In the active site a glycerol molecule is located near the γ-phosphate site of ATP, and the protein structure displays a partially closed active site. However, unlike other structures where the active site is closed, the α6' helix in C. parvum pyruvate kinase unwinds and assumes an extended conformation. In the crystal structure a sulfate ion is found at a site that is occupied by a phosphate of the effector molecule in many pyruvate kinase structures. A new feature of the C. parvum pyruvate kinase structure is the presence of a disulfide bond cross-linking the two monomers in the asymmetric unit. The disulfide bond is formed between cysteine residue 26 in the short N-helix of one monomer with cysteine residue 312 in a long helix (residues 303-320 of the second monomer at the interface of these monomers. Both cysteine residues are unique to C. parvum, and the disulfide bond remained intact in a reduced environment. However, the significance of this bond, if any, remains unknown at this time.

  13. Crystal structure of MboIIA methyltransferase.

    Science.gov (United States)

    Osipiuk, Jerzy; Walsh, Martin A; Joachimiak, Andrzej

    2003-09-15

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 A resolution the crystal structure of a beta-class DNA MTase MboIIA (M.MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M.MboIIA methylates the 3' adenine of the pentanucleotide sequence 5'-GAAGA-3'. The protein crystallizes with two molecules in the asymmetric unit which we propose to resemble the dimer when M.MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M.RsrI. However, the cofactor-binding pocket in M.MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases.

  14. Accuracy of crystal structure error estimates

    International Nuclear Information System (INIS)

    Taylor, R.; Kennard, O.

    1986-01-01

    A statistical analysis of 100 crystal structures retrieved from the Cambridge Structural Database is reported. Each structure has been determined independently by two different research groups. Comparison of the independent results leads to the following conclusions: (a) The e.s.d.'s of non-hydrogen-atom positional parameters are almost invariably too small. Typically, they are underestimated by a factor of 1.4-1.45. (b) The extent to which e.s.d.'s are underestimated varies significantly from structure to structure and from atom to atom within a structure. (c) Errors in the positional parameters of atoms belonging to the same chemical residue tend to be positively correlated. (d) The e.s.d.'s of heavy-atom positions are less reliable than those of light-atom positions. (e) Experimental errors in atomic positional parameters are normally, or approximately normally, distributed. (f) The e.s.d.'s of cell parameters are grossly underestimated, by an average factor of about 5 for cell lengths and 2.5 for cell angles. There is marginal evidence that the accuracy of atomic-coordinate e.s.d.'s also depends on diffractometer geometry, refinement procedure, whether or not the structure has a centre of symmetry, and the degree of precision attained in the structure determination. (orig.)

  15. The Crystal Structures of Potentially Tautomeric Compounds

    Science.gov (United States)

    Furmanova, Nina G.

    1981-08-01

    Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

  16. Novel Crystal Structure C60 Nanowire

    Science.gov (United States)

    Mickelson, William; Aloni, Shaul; Han, Weiqiang; Cumings, John; Zettl, Alex

    2003-03-01

    We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride (BN) nanotubes. For small-diameter BN tubes, the wire consists of a linear chain of C60's. With increasing BN tube inner diameter, novel C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) which are unknown for bulk or thin film forms of C60. C60 in BN nanotubes presents a model system for studying the properties of new dimensionally-constrained "silo" crystal structures.

  17. Crystal structure of MboIIA methyltransferase

    OpenAIRE

    Osipiuk, Jerzy; Walsh, Martin A.; Joachimiak, Andrzej

    2003-01-01

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-l-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 Å resolution the crystal structure of a β-class DNA MTase MboIIA (M·MboIIA) from the bacterium Moraxella bovis,...

  18. Crystal and molecular structure of 2-thiouridine

    Energy Technology Data Exchange (ETDEWEB)

    Hawkinson, S W

    1977-01-01

    The ''minor'' nucleoside 2-thiouridine, C/sub 9/H/sub 12/O/sub 5/N/sub 2/S, crystallizes in a monoclinic cell, space group P2/sub 1/ with a = 5.049 (2), b = 7.526 (2), c = 14.050 (3) A, ..beta.. = 90.17 (2)/sup 0/, and d = 1.619 g cm/sup -3/ (for Z = 2) at 22 +- 2/sup 0/C. The structure was derived from 1334 unique intensities measured with an Oak Ridge computer-controlled diffractometer to a limit of sin theta/lambda = 0.65 A/sup -1/ with Nb-filtered Mo K..cap alpha.. radiation. Atomic parameters were obtained by a combination of Patterson and Fourier techniques and refined by full-matrix least squares to a final R(F) value of 0.023 for all data. The bond lengths and angles in the molecule agree well with those of other thiopyrimidines (C(2) - S = 1.677 A). The conformation of the sugar ring relative to the base is anti with a torsion angle chi(O(1')--C(1') ..-->.. N(1)--C(6)) of 17/sup 0/. The sugar exists in the 3'-endo conformation. The O(5')--C(5') bond is gauche to C(4) - O(1') and trans to C(4')--C(3') (torsion angles of 74 and -169/sup 0/ respectively). The molecules are linked together in the crystal by hydrogen bonds in an intricate network which is identical to that inferred by Kojic-Prodic, Liminga, Sljukic and Ruzic-Toros (Acta Cryst. (1974), B30, 1550-1555) for the crystal structure of 5,6-dihydro-2-thiouridine. 2 figures; 6 tables.

  19. Syntheses and Crystal Structures of Ferrocenoindenes

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2013-02-01

    Full Text Available Ferrocenoindenes display planar chirality and thus represent valuable ligands for asymmetric catalysis. Here, we report on the synthesis of novel 3-(1,1-dibromomethyleneferroceno[1,2-a]indene, (Z-3-(1-bromomethylene-6-iodoferroceno[1,2-a]indene, and benzo[5,6-f]ferroceno[2,3,a]inden-1-one. Any application-oriented design of chiral catalysts requires fundamental knowledge about the ligands involved, not only in terms of atom-connectivity, but also in terms of their three-dimensional structure and steric demand. Therefore, the crystal structures of 2-ferrocenylbenzoic acid, ferroceno[1,2-a]indene, and (Z-3-(1-bromomethylene-6-iodoferroceno[1,2-a]indene have been determined. The bond-lengths that can be retrieved therefrom also allow for an estimation of the reactivity of the aryl-iodo, bromo-methylidene and dibromomethylidene moieties.

  20. The crystal structure of scandium dyhydrate triglycolate

    International Nuclear Information System (INIS)

    Dukareva, L.M.; Antishkina, A.S.; Porai-Koshits, M.A.; Ostrikova, V.N.; Arkhangel'skij, I.V.; Amanov, A.Z.

    1978-01-01

    The structure of colorless crystals of scandium glycolate dehydrate Sc(CH 2 OHCOO) 3 x2H 2 O, synthesized at the chemical department of MSU has been investigated. Parameters of the monoclinic lattice are determined according to roentgenograms of swing and Kforograms and are specified using the DRON-1 diffractor: a=14.624-+0.005 A; b=13.052-+0.003 A; c=5.730+-0.003 A; γ=96.26 deg+-0.01 deg; rhosub(exper.)=1.09 g/cm 3 ; Z=4; Sp.=P 2/b. Experimental photographic data are obtained using the KFOR chamber. Scannings of the layer lines h anti Ko-h anti K4, containing 742 independent reflexes are taken. Deciphering of the structure is carried out by means of analysis of the Paterson functions distribution and conventional and differential electron densities. Description of the system is presented

  1. Structure, thermodynamics, and crystallization of amorphous hafnia

    International Nuclear Information System (INIS)

    Luo, Xuhui; Demkov, Alexander A.

    2015-01-01

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO 2 . The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia

  2. Fortuitous structure determination of ‘as-isolated’ Escherichia coli bacterioferritin in a novel crystal form

    International Nuclear Information System (INIS)

    Eerde, André van; Wolterink-van Loo, Suzanne; Oost, John van der; Dijkstra, Bauke W.

    2006-01-01

    E. coli bacterioferritin was crystallized in a novel crystal form from different conditions and the structure was solved. The crystals belonged to space group P2 1 3 and diffracted to a resolution of 2.5 Å. Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 Å resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on ‘as-isolated’ E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins

  3. The Crystal Structures of Two Novel Cadmium-Picolinic Acid ...

    African Journals Online (AJOL)

    The crystal structures of two novel cadmium-picolinic acid complexes grown in aqueous solutions at selected pH values are reported. The structures are compared to expected solution species under the same conditions. The crystal structure of complex 1 exhibits a seven coordinate structure which contains a protonated ...

  4. Structural Transitions in Cholesteric Liquid Crystal Droplets

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Ye; Bukusoglu, Emre; Martínez-González, José A.; Rahimi, Mohammad; Roberts, Tyler F.; Zhang, Rui; Wang, Xiaoguang; Abbott, Nicholas L.; de Pablo, Juan J.

    2016-07-26

    Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates.

  5. Crystal structure of pure ZrO2 nanopowders

    International Nuclear Information System (INIS)

    Lamas, D.G.; Rosso, A.M.; Anzorena, M. Suarez; Fernandez, A.; Bellino, M.G.; Cabezas, M.D.; Walsoee de Reca, N.E.; Craievich, A.F.

    2006-01-01

    The crystal structure of pure (undoped) zirconia nanopowders synthesized by different wet-chemical routes has been investigated by synchrotron X-ray diffraction. Whereas some previous authors reported the retention of the cubic phase in similar materials, we demonstrate here that pure zirconia nanopowders with average crystallite sizes ranging from 5 to 10 nm exhibit the tetragonal phase. In addition, our results suggest that a tetragonal-to-cubic transition for decreasing crystallite size could eventually occur at a very small critical crystallite size

  6. Crystal structure of strontium dinickel iron orthophosphate

    Directory of Open Access Journals (Sweden)

    Said Ouaatta

    2015-10-01

    Full Text Available The title compound, SrNi2Fe(PO43, synthesized by solid-state reaction, crystallizes in an ordered variant of the α-CrPO4 structure. In the asymmetric unit, two O atoms are in general positions, whereas all others atoms are in special positions of the space group Imma: the Sr cation and one P atom occupy the Wyckoff position 4e (mm2, Fe is on 4b (2/m, Ni and the other P atom are on 8g (2, one O atom is on 8h (m and the other on 8i (m. The three-dimensional framework of the crystal structure is built up by [PO4] tetrahedra, [FeO6] octahedra and [Ni2O10] dimers of edge-sharing octahedra, linked through common corners or edges. This structure comprises two types of layers stacked alternately along the [100] direction. The first layer is formed by edge-sharing octahedra ([Ni2O10] dimer linked to [PO4] tetrahedra via common edges while the second layer is built up from a strontium row followed by infinite chains of alternating [PO4] tetrahedra and FeO6 octahedra sharing apices. The layers are held together through vertices of [PO4] tetrahedra and [FeO6] octahedra, leading to the appearance of two types of tunnels parallel to the a- and b-axis directions in which the Sr cations are located. Each Sr cation is surrounded by eight O atoms.

  7. Evaluation of a rapid dipstick (Crystal VC for the diagnosis of cholera in Zanzibar and a comparison with previous studies.

    Directory of Open Access Journals (Sweden)

    Benedikt Ley

    Full Text Available The gold standard for the diagnosis of cholera is stool culture, but this requires laboratory facilities and takes at least 24 hours. A rapid diagnostic test (RDT that can be used by minimally trained staff at treatment centers could potentially improve the reporting and management of cholera outbreaks.We evaluated the Crystal VC™ RDT under field conditions in Zanzibar in 2009. Patients presenting to treatment centers with watery diarrhea provided a stool sample for rapid diagnostic testing. Results were compared to stool culture performed in a reference laboratory. We assessed the overall performance of the RDT and evaluated whether previous intake of antibiotics, intravenous fluids, location of testing, and skill level of the technician affected the RDT results.We included stool samples from 624 patients. Compared to culture, the overall sensitivity of the RDT was 93.1% (95%CI: 88.7 to 96.2%, specificity was 49.2% (95%CI: 44.3 to 54.1%, the positive predictive value was 47.0% (95%CI: 42.1 to 52.0% and the negative predictive value was 93.6% (95%CI: 89.6 to 96.5%. The overall false positivity rate was 50.8% (213/419; fieldworkers frequently misread very faint test lines as positive.The observed sensitivity of the Crystal VC RDT evaluated was similar compared to earlier versions, while specificity was poorer. The current version of the RDT could potentially be used as a screening tool in the field. Because of the high proportion of false positive results when field workers test stool specimens, positive results will need to be confirmed with stool culture.

  8. Crystal structure of a snake venom cardiotoxin

    International Nuclear Information System (INIS)

    Rees, B.; Samama, J.P.; Thierry, J.C.; Gilibert, M.; Fischer, J.; Schweitz, H.; Lazdunski, M.; Moras, D.

    1987-01-01

    Cardiotoxin V/sup II/4 from Naja mossambica crystallizes in space group P6 1 (a = b = 73.9 A; c = 59.0 A) with two molecules of toxin (molecular mass = 6715 Da) in the asymmetric unit. The structure was solved by using a combination of multiple isomorphous replacement and density modification methods. Model building and least-squares refinement led to an agreement factor of 27% for a data set to 3-A resolution prior to any inclusion of solvent molecules. The topology of the molecule is similar to that found in short and long snake neurotoxins, which block the nicotinic acetylcholine receptor. Major differences occur in the conformation of the central loop, resulting in a change in the concavity of the molecule. Hydrophobic residues are clustered in two distinct areas. The existence of stable dimeric entities in the crystalline state, with the formation of a six-stranded antiparallel β sheet, may be functionally relevant

  9. Electronic structure of single crystal C60

    International Nuclear Information System (INIS)

    Wu, J.; Shen, Z.X.; Dessau, D.S.; Cao, R.; Marshall, D.S.; Pianetta, P.; Lindau, I.; Yang, X.; Terry, J.; King, D.M.; Wells, B.O.; Elloway, D.; Wendt, H.R.; Brown, C.A.; Hunziker, H.; Vries, M.S. de

    1992-01-01

    We report angle-resolved photoemission data from single crystals of C 60 cleaved in UHV. Unlike the other forms of pure carbon, the valence band spectrum of C 60 consists of many sharp features that can be essentially accounted for by the quantum chemical calculations describing individual molecules. This suggests that the electronic structure of solid C 60 is mainly determined by the bonding interactions within the individual molecules. We also observe remarkable intensity modulations of the photoemission features as a function of photon energy, suggesting strong final state effects. Finally, we address the issue of the band width of the HOMO state of C 60 . We assert that the width of the photoemission peak of C 60 does not reflect the intrinsic band width because it is broadened by the non 0-0 transitions via the Franck-Condon principle. Our view point provides a possible reconciliation between these photoemission data and those measured by other techniques. (orig.)

  10. Formamidinium iodide: crystal structure and phase transitions

    Directory of Open Access Journals (Sweden)

    Andrey A. Petrov

    2017-04-01

    Full Text Available At a temperature of 100 K, CH5N2+·I− (I, crystallizes in the monoclinic space group P21/c. The formamidinium cation adopts a planar symmetrical structure [the r.m.s. deviation is 0.002 Å, and the C—N bond lengths are 1.301 (7 and 1.309 (8 Å]. The iodide anion does not lie within the cation plane, but deviates from it by 0.643 (10 Å. The cation and anion of I form a tight ionic pair by a strong N—H...I hydrogen bond. In the crystal of I, the tight ionic pairs form hydrogen-bonded zigzag-like chains propagating toward [20-1] via strong N—H...I hydrogen bonds. The hydrogen-bonded chains are further packed in stacks along [100]. The thermal behaviour of I was studied by different physicochemical methods (thermogravimetry, differential scanning calorimetry and powder diffraction. Differential scanning calorimetry revealed three narrow endothermic peaks at 346, 387 and 525 K, and one broad endothermic peak at ∼605 K. The first and second peaks are related to solid–solid phase transitions, while the third and fourth peaks are attributed to the melting and decomposition of I. The enthalpies of the phase transitions at 346 and 387 K are estimated as 2.60 and 2.75 kJ mol−1, respectively. The X-ray powder diffraction data collected at different temperatures indicate the existence of I as the monoclinic (100–346 K, orthorhombic (346–387 K and cubic (387–525 K polymorphic modifications.

  11. CCDC 1408042: Experimental Crystal Structure Determination : 6,13-dimesitylpentacene

    KAUST Repository

    Shi, Xueliang

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  12. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  13. Redetermination of the Crystal Structure of Al2Br6

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Poulsen, Finn W.; Nielsen, Kurt

    1997-01-01

    . In accordance with previous results, the structure belongs to the monoclinic space group P2(1)/a, no. 14, C-2h(5), with a = 10.301(4), b = 7.095(2), c = 7.525(3) Angstrom, and beta = 96.44(3)degrees, and with two Al2Br6 molecules per unit cell. The single crystal was refined to R = 0.0746. Rather similar......The structure of aluminium bromide has been reinvestigated by X-ray diffraction in three different ways: (a) on a single crystal grown in a glass capillary, (b) on powder in a Debye-Scherrer glass capillary and (c) on an area of powder placed in a protective container for Bragg-Brentano geometry...... structural results were obtained from full-profile Rietveld refinements of powder data [goodness of fit = 1.38 and 2.54 for (b) and (c), respectively]. The Al2Br6 molecule consists of two edge-sharing, almost regular AlBr4 tetrahedra. The Al-Br bond distances are in the range 2.21-2.42 Angstrom...

  14. Analysis of the crystal structure of an active MCM hexamer.

    Science.gov (United States)

    Miller, Justin M; Arachea, Buenafe T; Epling, Leslie B; Enemark, Eric J

    2014-09-29

    In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis.

  15. Crystal structure of Clostridium difficile toxin A

    Energy Technology Data Exchange (ETDEWEB)

    Chumbler, Nicole M.; Rutherford, Stacey A.; Zhang, Zhifen; Farrow, Melissa A.; Lisher, John P.; Farquhar, Erik; Giedroc, David P.; Spiller, Benjamin W.; Melnyk, Roman A.; Lacy, D. Borden

    2016-01-11

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics.

  16. Navigation and Comprehension of Digital Expository Texts: Hypertext Structure, Previous Domain Knowledge, and Working Memory Capacity

    Science.gov (United States)

    Burin, Debora I.; Barreyro, Juan P.; Saux, Gastón; Irrazábal, Natalia C.

    2015-01-01

    Introduction: In contemporary information societies, reading digital text has become pervasive. One of the most distinctive features of digital texts is their internal connections via hyperlinks, resulting in non-linear hypertexts. Hypertext structure and previous knowledge affect navigation and comprehension of digital expository texts. From the…

  17. Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form

    Directory of Open Access Journals (Sweden)

    Boguslaw Stec

    2007-10-01

    Full Text Available We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCOfrom the red algae Galdieria Sulphuraria. The protein crystallized in two different crystalforms, the I422 crystal form being obtained from high salt and the P21 crystal form beingobtained from lower concentration of salt and PEG. We report here the crystallization,preliminary stages of structure determination and the detection of the structural phasetransition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzymebelongs to the hexadecameric class (L8S8 with an approximate molecular weight 0.6MDa.The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a singlehexadecamer per asymmetric unit. The preservation of diffraction power in a phasetransition for such a large macromolecule is rare.

  18. Band structures in fractal grading porous phononic crystals

    Science.gov (United States)

    Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

    2018-05-01

    In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

  19. Structural Color Patterns by Electrohydrodynamic Jet Printed Photonic Crystals.

    Science.gov (United States)

    Ding, Haibo; Zhu, Cun; Tian, Lei; Liu, Cihui; Fu, Guangbin; Shang, Luoran; Gu, Zhongze

    2017-04-05

    In this work, we demonstrate the fabrication of photonic crystal patterns with controllable morphologies and structural colors utilizing electrohydrodynamic jet (E-jet) printing with colloidal crystal inks. The final shape of photonic crystal units is controlled by the applied voltage signal and wettability of the substrate. Optical properties of the structural color patterns are tuned by the self-assembly of the silica nanoparticle building blocks. Using this direct printing technique, it is feasible to print customized functional patterns composed of photonic crystal dots or photonic crystal lines according to relevant printing mode and predesigned tracks. This is the first report for E-jet printing with colloidal crystal inks. Our results exhibit promising applications in displays, biosensors, and other functional devices.

  20. Physicochemical and crystal structure analyses of the antidiabetic agent troglitazone.

    Science.gov (United States)

    Kobayashi, Katsuhiro; Fukuhara, Hiroshi; Hata, Tadashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2003-07-01

    The antidiabetic agent troglitazone has two asymmetric carbons located at the chroman ring and the thiazolidine ring and is produced as a mixture of equal amounts of four optical isomers, 2R-5S, 2S-5R, 2R-5R, and 2S-5S. The crystalline powdered drug substance consists of two diastereomer pairs, 2R-5R/2S-5S and 2R-5S/2S-5R. There are many types of crystals obtained from various crystallization conditions. The X-ray structure analysis and the physicochemical analyses of troglitazone were performed. The solvated crystals of the 2R-5R/2S-5S pair were crystallized from several solutions: methanol, ethanol, acetonitrile, and dichloromethane. The ratio of solvent and troglitazone was 1 : 2 (L1/2-form). The monohydrate crystals were obtained from aqueous acetone solution (L1-form). On the other hand, only an anhydrate crystal of the 2R-5S/2S-5R pair was crystallized from various solutions (H0-form). The dihydrous mixed crystal (MA2-form) was obtained from a mixture of the two diastereomer pairs of 2R-5R/2S-5S and 2R-5S/2S-5R in equal amounts by the slow evaporation of aqueous acetone solution. The crystal structure of the MA2-form is similar to the H0-form. When the MA2 crystal was kept under low humidity, it was converted into the dehydrated form (MA0-form) with retention of the single crystal form. The structure of the MA0-form is isomorphous to the H0-form. The MA2-form was converted into the MA0-form and vice versa with retention of the single crystal under low and high humidity, respectively. The crystallization and storage conditions of the drug substances were successfully analyzed.

  1. Facile synthesis and structure characterization of hexagonal tungsten bronzes crystals

    Science.gov (United States)

    Lee, Jiann-Shing; Liu, Hao-Chuan; Peng, Gao-De; Tseng, Yawteng

    2017-05-01

    A facile molten-salt route was used to synthesize hexagonal Cs0.33WO3, Rb0.33WO3 and K0.30WO3 crystals. The three isostructural compounds were successfully prepared from the reaction of MxWO3 powders (M = Cs, Rb, K) in the CsCl/NaCl, RbCl/NaCl and KCl/NaCl fluxes, respectively. The structure determination and refinement, based on single-crystal X-ray diffraction data, are in agreement with previous works, possessing space group P63/mcm. The a and c parameters vary non-linearly with increasing radii of the M+ cations (rM) that is coordinated to twelve oxygen atoms. Both the volumes of unit-cell and WO6 octahedra vary linearly with rM, which become smaller from Cs0.33WO3 to K0.30WO3. The distortion of WO6 octahedra as well as isotropic displacement parameters increases from Cs0.33WO3 to K0.30WO3. The geometry of the WO6 octahedron becomes more regular with increasing rM. These structural trends arise from the effective size of the M+ cation.

  2. Studies on growth, crystal structure and characterization of novel organic nicotinium trifluoroacetate single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Dhanaraj, P.V. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Rajesh, N.P., E-mail: rajeshnp@hotmail.com [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Sundar, J. Kalyana; Natarajan, S. [Department of Physics, Madurai Kamaraj University, Madurai 625 021 (India); Vinitha, G. [Department of Physics, Crescent Engineering College, Chennai 600 048 (India)

    2011-09-15

    Highlights: {yields} Good quality crystals of nicotinium trifluoroacetate in monoclinic system were grown for first time. {yields} Nicotinium trifluoroacetate crystal exhibits third order nonlinear optical properties. {yields} The optical spectrum of nicotinium trifluoroacetate crystal reveals the wide transmission in the entire range with cutoff wavelength at 286 nm. {yields} Nicotinium trifluoroacetate is a low dielectric constant material. - Abstract: An organic material, nicotinium trifluoroacetate (NTF) was synthesized and single crystals in monoclinic system were grown from aqueous solution for the first time. Its solubility and metastable zone width were estimated. The crystal structure of NTF was analyzed to reveal the molecular arrangements and the formation of hydrogen bonds in the crystal. High-resolution X-ray diffraction rocking curve measurements were performed to analyze the structural perfection of the grown crystals. Functional groups in NTF were identified by Fourier transform infrared spectral analysis. Thermal behaviour and stability of NTF were studied by thermogravimetric and differential thermal analysis and differential scanning calorimetry. Mechanical and dielectric properties of NTF crystals were analyzed. Optical studies reveal that NTF crystals are transparent in the wavelength range 286-1100 nm. The third order nonlinear optical parameters of NTF were derived by the Z-scan technique.

  3. Re-investigation of the crystal structure of enstatite under high-pressure conditions

    DEFF Research Database (Denmark)

    Periotto, Benedetta; Balic Zunic, Tonci; Nestola, Fabrizio

    2012-01-01

    A synthetic single crystal of pure orthoenstatite (MgSiO3, space group Pbca) has been investigated at high pressure for structural determinations by in situ single-crystal X‑ray diffraction using a diamond-anvil cell. Ten complete intensity data collections were performed up to 9.36 GPa. This study...... with different compositions. The structural evolution determined in this work confirms the high-pressure evolution found previously for other orthopyroxenes and removes some ambiguities originating from the less accurate published data on the MgSiO3 structure at high pressure. The structural compression...

  4. Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors

    Science.gov (United States)

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  5. Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors

    Directory of Open Access Journals (Sweden)

    Ke-Qin Zhang

    2013-03-01

    Full Text Available Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors.

  6. submitter Light Extraction From Scintillating Crystals Enhanced by Photonic Crystal Structures Patterned by Focused Ion Beam

    CERN Document Server

    Modrzynski, Pawel; Knapitsch, Arno; Kunicki, Piotr; Lecoq, Paul; Moczala, Magdalena; Papakonstantinou, Ioannis; Auffray, Etiennette

    2016-01-01

    “Photonic Crystals (PhC)” have been used in a variety of fields as a structure for improving the light extraction efficiency from materials with high index of refraction. In previous work we already showed the light extraction improvement of several PhC covered LYSO crystals in computer simulations and practical measurements. In this work, new samples are made using different materials and techniques which allows further efficiency improvements. For rapid prototyping of PhC patterns on scintillators we tested a new method using “Focused Ion Beam (FIB)” patterning. The FIB machine is a device similar to a “Scanning Electron Microscope (SEM)”, but it uses ions (mainly gallium) instead of electrons for the imaging of the samples' surface. The additional feature of FIB devices is the option of surface patterning in nano-scale which was exploited for our samples. Three samples using FIB patterning have been produced. One of them is a direct patterning of the extraction face of a 0.8×0.8×10 $mm^3$ LYS...

  7. Elastic properties of Ti-24Nb-4Zr-8Sn single crystals with bcc crystal structure

    International Nuclear Information System (INIS)

    Zhang, Y.W.; Li, S.J.; Obbard, E.G.; Wang, H.; Wang, S.C.; Hao, Y.L.; Yang, R.

    2011-01-01

    Research highlights: → The single crystals of Ti2448 alloy with the bcc crystal structure were prepared. → The elastic moduli and constants were measured by several resonant methods. → The crystal shows significant elastic asymmetry in tension and compression. → The crystal exhibits weak nonlinear elasticity with large elastic strain ∼2.5%. → The crystal has weak atomic interactions against crystal distortion to low symmetry. - Abstract: Single crystals of Ti2448 alloy (Ti-24Nb-4Zr-8Sn in wt.%) were grown successfully using an optical floating-zone furnace. Several kinds of resonant methods gave consistent Young's moduli of 27.1, 56.3 and 88.1 GPa and shear moduli of 34.8, 11.0 and 14.6 GPa for the , and oriented single crystals, and C 11 , C 12 and C 44 of 57.2, 36.1 and 35.9 GPa respectively. Uniaxial testing revealed asymmetrical elastic behaviors of the crystals: tension caused elastic softening with a large reversible strain of ∼4% and a stress plateau of ∼250 MPa, whereas compression resulted in gradual elastic stiffening with much smaller reversible strain. The crystals exhibited weak nonlinear elasticity with a large elastic strain of ∼2.5% and a high strength, approaching ∼20% and ∼30% of its ideal shear and ideal tensile strength respectively. The crystals showed linear elasticity with a small elastic strain of ∼1%. These elastic deformation characteristics have been interpreted in terms of weakened atomic interactions against crystal distortion to low crystal symmetry under external applied stresses. These results are consistent with the properties of polycrystalline Ti2448, including high strength, low elastic modulus, large recoverable strain and weak strengthening effect due to grain refinement.

  8. The crystal structure and twinning of neodymium gallium perovskite single crystals

    International Nuclear Information System (INIS)

    Ubizskii, S.B.; Vasylechko, L.O.; Savytskii, D.I.; Matkovskii, A.O.; Syvorotka, I.M.

    1994-01-01

    By means of X-ray structure analysis, the crystal structure of neodymium gallium perovskite (NGP) single crystals (NdGaO 3 ) being used as a substrate for HTSC film epitaxy has been refined and the position of atoms has been determined. The possibility of YBa 2 Cu 3 O 7-x film epitaxy on the plane (110) of NGP crystal as well as its advantages and pitfalls are analysed from structural data. The twinning types in the NGP crystal were established. The twinning structure of NGP substrates is found to be stable up to a temperature of 1173 K, as differentiated from the LaGaO 3 and LaAlO 3 substrates. It is intimated that the twinning in the NGP substrates oriented as (001) can result in creation of 90 degrees twin bonds in a film, and in the case of (110)-oriented plates it is possible to ignore the twinning presence in substrate completely. (author)

  9. Preparation and crystal structure of Ca4Sb2O

    International Nuclear Information System (INIS)

    Eisenmann, B.; Limartha, H.; Schaefer, H.

    1980-01-01

    The formerly described compound Ca 2 Sb is to be corrected to Ca 4 Sb 2 O as shown by X-ray diffractometer data of single crystals and neutron diffraction diagrams of powders. The compound crystallizes in the K 2 NiF 4 structure type. (orig.)

  10. Crystal structure of vanadite: Refinement of anisotropic displacement parameters

    Czech Academy of Sciences Publication Activity Database

    Laufek, F.; Skála, Roman; Haloda, J.; Císařová, I.

    2006-01-01

    Roč. 51, 3-4 (2006), s. 271-275 ISSN 1210-8197 Institutional research plan: CEZ:AV0Z30130516 Keywords : anisotropic displacement parameter * crystal structure * single-crystal X-ray refinement * vanadinite Subject RIV: DB - Geology ; Mineralogy

  11. Nucleation of colloidal crystals on configurable seed structures

    NARCIS (Netherlands)

    Hermes, M; Vermolen, E.C.M.; Leunissen, M.E.; Vossen, D.L.J.; van Oostrum, P.D.J.; Dijkstra, M.; van Blaaderen, A.

    2011-01-01

    Nucleation is an important stage in the growth of crystals. During this stage, the structure and orientation of a crystal are determined. However, short time- and length-scales make nucleation poorly understood. Micrometer-sized colloidal particles form an ideal model system to study nucleation due

  12. Crystal structure of arginine methyltransferase 6 from Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Chongyuan Wang

    Full Text Available Arginine methylation plays vital roles in the cellular functions of the protozoan Trypanosoma brucei. The T. brucei arginine methyltransferase 6 (TbPRMT6 is a type I arginine methyltransferase homologous to human PRMT6. In this study, we report the crystal structures of apo-TbPRMT6 and its complex with the reaction product S-adenosyl-homocysteine (SAH. The structure of apo-TbPRMT6 displays several features that are different from those of type I PRMTs that were structurally characterized previously, including four stretches of insertion, the absence of strand β15, and a distinct dimerization arm. The comparison of the apo-TbPRMT6 and SAH-TbPRMT6 structures revealed the fine rearrangements in the active site upon SAH binding. The isothermal titration calorimetry results demonstrated that SAH binding greatly increases the affinity of TbPRMT6 to a substrate peptide derived from bovine histone H4. The western blotting and mass spectrometry results revealed that TbPRMT6 methylates bovine histone H4 tail at arginine 3 but cannot methylate several T. brucei histone tails. In summary, our results highlight the structural differences between TbPRMT6 and other type I PRMTs and reveal that the active site rearrangement upon SAH binding is important for the substrate binding of TbPRMT6.

  13. Crystal structure of 5-hydroxy-5-propylbarbituric acid

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2015-11-01

    Full Text Available Molecules of the title compound, C7H10N2O4, systematic name 5-hydroxy-5-propylpyrimidine-2,4,6(1H,3H,5H-trione, form a hydrogen-bonded framework which is based on three independent hydrogen bonds, N—H...O(carbonyl, N—H...O(hydroxy and O—H...O(carbonyl. This framework has the topology of the 5-connected nov net. Each molecule is linked to five other molecules via six hydrogen bonds, and the descriptor of the hydrogen-bonded structure is F65[44.66-nov]. The crystal packing is isostructural with that of the previously reported 5-hydroxy-5-ethyl analogue.

  14. Technique for sparing previously irradiated critical normal structures in salvage proton craniospinal irradiation

    International Nuclear Information System (INIS)

    McDonald, Mark W; Wolanski, Mark R; Simmons, Joseph W; Buchsbaum, Jeffrey C

    2013-01-01

    Cranial reirradiation is clinically appropriate in some cases but cumulative radiation dose to critical normal structures remains a practical concern. The authors developed a simple technique in 3D conformal proton craniospinal irradiation (CSI) to block organs at risk (OAR) while minimizing underdosing of adjacent target brain tissue. Two clinical cases illustrate the use of proton therapy to provide salvage CSI when a previously irradiated OAR required sparing from additional radiation dose. The prior radiation plan was coregistered to the treatment planning CT to create a planning organ at risk volume (PRV) around the OAR. Right and left lateral cranial whole brain proton apertures were created with a small block over the PRV. Then right and left lateral “inverse apertures” were generated, creating an aperture opening in the shape of the area previously blocked and blocking the area previously open. The inverse aperture opening was made one millimeter smaller than the original block to minimize the risk of dose overlap. The inverse apertures were used to irradiate the target volume lateral to the PRV, selecting a proton beam range to abut the 50% isodose line against either lateral edge of the PRV. Together, the 4 cranial proton fields created a region of complete dose avoidance around the OAR. Comparative photon treatment plans were generated with opposed lateral X-ray fields with custom blocks and coplanar intensity modulated radiation therapy optimized to avoid the PRV. Cumulative dose volume histograms were evaluated. Treatment plans were developed and successfully implemented to provide sparing of previously irradiated critical normal structures while treating target brain lateral to these structures. The absence of dose overlapping during irradiation through the inverse apertures was confirmed by film. Compared to the lateral X-ray and IMRT treatment plans, the proton CSI technique improved coverage of target brain tissue while providing the least

  15. Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

    International Nuclear Information System (INIS)

    Gai, Zuoqi; Nakamura, Akiyoshi; Tanaka, Yoshikazu; Hirano, Nagisa; Tanaka, Isao; Yao, Min

    2013-01-01

    Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution. After crystallization of a certain protein–RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly

  16. Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

    Energy Technology Data Exchange (ETDEWEB)

    Gai, Zuoqi; Nakamura, Akiyoshi [Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Yoshikazu, E-mail: tanaka@sci.hokudai.ac.jp [Hokkaido University, Sapporo 060-0810 (Japan); Hokkaido University, Sapporo 060-0810 (Japan); Hirano, Nagisa [Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Isao; Yao, Min [Hokkaido University, Sapporo 060-0810 (Japan); Hokkaido University, Sapporo 060-0810 (Japan)

    2013-11-01

    Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution. After crystallization of a certain protein–RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly.

  17. Crystal structure and crystal growth of the polar ferrimagnet CaBaFe4O7

    Science.gov (United States)

    Perry, R. S.; Kurebayashi, H.; Gibbs, A.; Gutmann, M. J.

    2018-05-01

    Magnetic materials are a cornerstone for developing spintronic devices for the transport of information via magnetic excitations. To date, relatively few materials have been investigated for the purpose of spin transport, mostly due to the paucity of suitable candidates as these materials are often chemically complex and difficult to synthesize. We present the crystal growth and a structure solution on the high-temperature crystal structure of the layered, polar ferrimagnet CaBaFe4O7 , which is a possible new contender for spintronics research. The space group is identified as P 3 by refinement of single crystal and powder neutron diffraction data. At 400 K, the trigonal lattice parameters are a =11.0114 (11 )Å and c =10.330 (3 )Å . The structure is similar to the low-temperature phase with alternating layers of triangular and Kagome-arranged Fe-O tetrahedra. We also present details of the crystal growth by traveling solvent method.

  18. Synthesis, crystal structure and Thermogravimetry of ortho-phthalic ...

    Indian Academy of Sciences (India)

    satisfied by two chelated carboxylates while fifth and sixth co-ordination positions are satisfied by monodentate ... Keywords. o-Phthalic acid; coordination polymer; X-ray crystal structure; Copper(II); EPR; TGA. 1. .... Absorption coefficient.

  19. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  20. Phase relations, crystal structures and physical properties of nuclear fuels

    International Nuclear Information System (INIS)

    Tagawa, Hiroaki; Fujino, Takeo; Tateno, Jun

    1975-07-01

    Phase relations, crystal structures and physical properties of the compounds for nuclear fuels are presented, including melting point, thermal expansion, diffusion and magnetic and electric properties. Emphasis is on oxides, carbides and nitrides of thorium, uranium and plutonium. (auth.)

  1. Crystal structures of sol-gel deposited zirconia thin films

    International Nuclear Information System (INIS)

    Bell, J.M.; Cheary, R.W.; Rice, M.; Ben-Nissan, B.; Cocking, J.L.; Johnstone, G.R.

    1992-01-01

    The authors reports on the crystal structure of zirconia thin films by high temperature x-ray diffraction. The films were deposited by sol-gel processing onto polished stainless steel substrates, and dried at 200 deg C. X-ray diffraction at temperatures between 400 deg C and 800 deg C was carried out using an APEX diffractometer with a position sensitive detector. Previous results indicated that there was a transformation between the tetragonal phase and the monoclinic phase at approximately 770 deg C. Two experiments have been carried out: temperature runs, where the structure evolution is studied as a function of temperature; and time evolution of the structure at fixed temperatures. The results for both experiments, including structural analysis of the different phases found in the thin zirconia films and an analysis of the kinetics of the phase transformation(s) from the time evolution work are presented. This will include a comparison with theories of nucleation and crystallisation in single element films. Impurity phases introduced by interaction of the zirconia with the substrate have been observed, and the effect of increasing annealing time on the substrate-film interaction will also be discussed. 17 refs., 1 tab., 3 figs

  2. Crystal structure, thermal behavior, vibrational spectroscopy and ...

    Indian Academy of Sciences (India)

    64

    A single crystal was carefully selected under polarizing microscope and .... properties of our compound using infrared absorption and Raman scattering. ... pics in Raman at 1762 and 1782 cm-1 are assigned to the δ(HOH) mode of the water ...

  3. Formation of structured nanophases in halide crystals

    Czech Academy of Sciences Publication Activity Database

    Kulveit, Jan; Demo, Pavel; Polák, Karel; Sveshnikov, Alexey; Kožíšek, Zdeněk

    2013-01-01

    Roč. 5, č. 6 (2013), s. 561-564 ISSN 2164-6627 R&D Projects: GA ČR GAP108/12/0891 Institutional support: RVO:68378271 Keywords : halide crystals * nucleation Subject RIV: BM - Solid Matter Physics ; Magnetism http://www.aspbs.com/asem.html#v5n6

  4. Solvothermal syntheses, crystal structures, optical and thermal ...

    Indian Academy of Sciences (India)

    compounds 1–3 exhibit optical band gaps between 2.06 and 2.35 eV. Keywords. .... under a nitrogen stream of 100 mL min. −1 . 2.3 X-ray diffraction. Single-crystal ..... Liu G N, Guo G C, Wang M S, Cai L Z and Huang J S. 2010 Five dimeric ...

  5. The crystal structure of tRNA

    Indian Academy of Sciences (India)

    Madhu

    of yeast alanine tRNA by Robert Holley's group at Cornell. University ... decode nonsense codons) with John Smith and Brenner. However, my ... tRNA from 10 g of unfractionated tRNA. ... tRNA crystals were, in fact, protein (Hendrikson et al.

  6. Hydrothermal syntheses and single crystal structural ...

    Indian Academy of Sciences (India)

    Unknown

    Colourless. 84 lined stainless steel bomb. After heating in a pro- grammable oven at the respective temperatures and autogenous pressures for the notified time scale, cooling was carried out on a ramp of 10°C/h to room temperature. The crystals were collected by filtration, washed with, deionized water followed by diethyl-.

  7. Construction of crystal structure prototype database: methods and applications

    International Nuclear Information System (INIS)

    Su, Chuanxun; Lv, Jian; Wang, Hui; Wang, Yanchao; Ma, Yanming; Li, Quan; Zhang, Lijun

    2017-01-01

    Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery. (paper)

  8. Construction of crystal structure prototype database: methods and applications.

    Science.gov (United States)

    Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

    2017-04-26

    Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

  9. Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

    Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

  10. The crystal structure of the phosphatidylinositol 4-kinase IIalpha

    Czech Academy of Sciences Publication Activity Database

    Bäumlová, Adriana; Chalupská, Dominika; Rozycki, B.; Jovic, M.; Wisniewski, E.; Klíma, Martin; Dubánková, Anna; Kloer, D. P.; Nencka, Radim; Balla, T.; Bouřa, Evžen

    2015-01-01

    Roč. 22, č. 1 (2015), s. 5 ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : PI4K IIalpha * crystal structure Subject RIV: CE - Biochemistry

  11. Synthesis and thermal characterization of CdS nano crystals in previously formed template of maleic anhydride-octene 1-vinyl butyl terpolymer

    International Nuclear Information System (INIS)

    Akbarov, O.H; Mammadova, R.E; Malikov, E.Y.

    2008-01-01

    Full text: Nano crystals have dimensions in the range 10100 nm. Crystals in this size range possess unique properties, which enable scientists to manufacture materials and devices capable of performing unimaginable tasks. For that reason synthesis of this semiconductor nano crystals is expedient. Many useful methods have been used for preparing sulphide semiconductor nano crystals, such as colloidal chemistry method, sol-gel method, inverse micelle method, in situ synthesis and assemble on polymer template. The most significant method is in situ synthesis and assemble of sulphide semiconductor nano crystals on polymer. Compared with other methods, the stability of nanoparticles is improved by the protection and confinement of the copolymer. Because of confinement and protection effects of template environmental risk is prevented in this method. On the base of this principles in situ synthesis of CdS nano crystals in maleic anhydride-octene 1-vinyl butyl terpolymer was realized in this scientific work. First of all in specific condition maleic anhydride, octene 1, and vinyl butyl ether were polymerized to form a terpolymer as the result of radical ter polymerization. In second step CdS nano crystals were synthesized in N,N-dimethylformamide solution of maleic anhydride-octene 1-vinyl butyl terpolymer through the reaction of thiourea with cadmium chloride. In this process CdCI 2 x 2.5H 2 O was dissolved in N,N-dimethylformamide solution of previously formed terpolymer and was heated in 90 0 C temperature for 4 hours with vigorous stirring. Then desired amount of thiourea in N,N-dimethylformamide was quickly injected into the reaction flask using a syringe. The reaction continued for another 1 hour, and a yellow clear solution was obtained, which indicated the formation of CdS nano crystals

  12. Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

    Science.gov (United States)

    Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

    2017-05-05

    A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  13. Structure of initial crystals formed during human amelogenesis

    Science.gov (United States)

    Cuisinier, F. J. G.; Voegel, J. C.; Yacaman, J.; Frank, R. M.

    1992-02-01

    X-ray diffraction analysis revealed only the existence of carbonated hydroxyapatite (c.HA) during amelogenesis, whereas conventional transmission electron microscopy investigations showed that developing enamel crystals have a ribbon-like habit. The described compositional changes could be an indication for the presence of minerals different from c.HA. However, the absence of identification of such a mineral shows the need of studies by high resolution electron microscopy (HREM) of initial formed human enamel crystals. We demonstrate the existence of two crystal families involved in the early stages of biomineralization: (a) nanometer-size particles which appeared as a precursor phase; (b) ribbon-like crystals, with a structure closely related to c.HA, which by a progressive thickening process tend to attain the mature enamel crystal habit.

  14. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  15. Crystal structure and optical properties of silver nanorings

    Science.gov (United States)

    Zhou, Li; Fu, Xiao-Feng; Yu, Liao; Zhang, Xian; Yu, Xue-Feng; Hao, Zhong-Hua

    2009-04-01

    We report the polyol synthesis and crystal structure characterization of silver nanorings, which have perfect circular shape, smooth surface, and elliptical wire cross-section. The characterization results show that the silver nanorings have well-defined crystal of singly twinned along the whole ring. The spatial distribution of the scattering of a silver nanoring with slanted incidence reveals the unique focus effect of the nanoring, and the focus scattering varies with the incident wavelength. The silver nanorings with perfect geometry and well-defined crystal have potential applications in nanoscaled photonics, plasmonic devices, and optical manipulation.

  16. Crystal structures of two thiacalix[4]arene derivatives anchoring four ...

    Indian Academy of Sciences (India)

    Administrator

    Abstract. The crystal structures of two thiacalixarene derivatives anchoring thiadiazole functional groups at lower rim, C60H72O4S12N8 (1), C64H80O4S12N8 (2), have been determined by single crystal X-ray diffraction. The thiacalix[4]arene framework in both 1 and 2 adopts the 1,3-alternate conformation. Com- pound 1 ...

  17. Crystal structure of ethyl 2,4-dichloroquinoline-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Alberto Cabrera

    2015-12-01

    Full Text Available In the crystal structure of the title compound, C12H9Cl2NO2, the mean planes through the quinoline and carboxylate groups have r.m.s. deviations of 0.006 and 0.021 Å, respectively, and form a dihedral angle of 87.06 (19°. In the crystal, molecules are linked via very weak C—H...O hydrogen bonds, forming chains, which propagate along the c-axis direction.

  18. Band structures and localization properties of aperiodic layered phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yan Zhizhong, E-mail: zzyan@bit.edu.cn [Department of Applied Mathematics, Beijing Institute of Technology, Beijing 100081 (China); Zhang Chuanzeng [Department of Civil Engineering, University of Siegen, D-57078 Siegen (Germany)

    2012-03-15

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  19. Crystal structure and thermal property of polyethylene glycol octadecyl ether

    International Nuclear Information System (INIS)

    Meng, Jie-yun; Tang, Xiao-fen; Li, Wei; Shi, Hai-feng; Zhang, Xing-xiang

    2013-01-01

    Highlights: ► The crystal structure of C18En for n ≥ 20 is a monoclinic system. ► Polyethylene glycol octadecyl ether crystallizes perfectly. ► The number of repeat units has significant effect on the melting, crystallizing temperature and enthalpy. ► The thermal stable temperature increases rapidly with increasing the number of repeat unit. - Abstract: The crystal structure, phase change property and thermal stable temperature (T d ) of polyethylene glycol octadecyl ether [HO(CH 2 CH 2 O) n C 18 H 37 , C18En] with various numbers of repeat units (n = 2, 10, 20 and 100) as phase change materials (PCMs) were investigated using temperature variable Fourier transformed infrared spectroscopy (FTIR), wide-angle X-ray diffraction (XRD), differential scanning calorimetry (DSC), and thermogravimetric analysis (TG). C18En crystallizes perfectly at 0 °C; and the crystal structure for n ≥ 20 is a monoclinic system. The number of repeat units has great effect on the phase change properties of C18En. The thermal stable temperature increases rapidly with increasing the number of repeat units. They approach to that of PEG-2000 as the number of repeat units is more than 10. T d increases rapidly with increasing the number of repeat units. C18En are a series of promising polymeric PCMs

  20. Crystal structure of 4-methylsulfanyl-2-phenylquinazoline

    Directory of Open Access Journals (Sweden)

    Mohammed B. Alshammari

    2014-08-01

    Full Text Available In the title compound, C15H12N2S, the methylthioquinazoline group is planar with the methyl C displaced by only 0.116 (3 Å from the plane of the quinazoline moiety. The dihedral angle between the phenyl ring and the quinazoline ring system is 13.95 (5°. In the crystal, each molecule is linked by π–π stacking between to two adjacent inversion-related molecules. On one side, the inverted quinazoline groups interact with a centroid–centroid distance of 3.7105 (9 Å. On the other side, the quinazoline group interacts with the pyrimidine and phenyl rings of the second neighbour with centroid–centroid distances of 3.5287 (8 and 3.8601 (9 Å, respectively.

  1. Crystal structure of rubidium peroxide ammonia disolvate

    Directory of Open Access Journals (Sweden)

    Tobias Grassl

    2017-02-01

    Full Text Available The title compound, Rb2O2·2NH3, has been obtained as a reaction product of rubidium metal dissolved in liquid ammonia and glucuronic acid. As a result of the low-temperature crystallization, a disolvate was formed. To our knowledge, only one other solvate of an alkali metal peroxide is known: Na2O2·8H2O has been reported by Grehl et al. [Acta Cryst. (1995, C51, 1038–1040]. We determined the peroxide bond length to be 1.530 (11 Å, which is in accordance with the length reported by Bremm & Jansen [Z. Anorg. Allg. Chem. (1992, 610, 64–66]. One of the ammonia solvate molecules is disordered relative to a mirror plane, with 0.5 occupancy for the corresponding nitrogen atom.

  2. Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model

    Directory of Open Access Journals (Sweden)

    Alexander Gabriëlse

    2017-11-01

    Full Text Available In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO lattices not previously considered for the square shoulder model.

  3. The crystal structure of urea nitrate

    NARCIS (Netherlands)

    Harkema, Sybolt; Feil, D.

    1969-01-01

    The structure of urea nitrate has been solved, by the use of three-dimensional X-ray data. Data were collected using Cu Ke and Mo K0~ radiations. The structure consists of layers with urea and nitrate groups held together by hydrogen bonds. The positions of all hydrogen atoms were found. The final R

  4. A crystal structure prediction enigma solved

    DEFF Research Database (Denmark)

    Hoser, Anna Agnieszka; Sovago, Ioana; Lanzac, A.

    2017-01-01

    The seemingly unpredictable structure of gallic acid monohydrate form IV has been investigated using accurate X-ray diffraction measurements at temperatures of 10 and 123 K. The measurements demonstrate that the structure is commensurately modulated at 10 K and disordered at higher temperatures...

  5. Solving Crystal Structures from Powder Diffraction Data

    DEFF Research Database (Denmark)

    Christensen, A. Nørlund; Lehmann, M. S.; Nielsen, Mogens

    1985-01-01

    High resolution powder data from both neutron and X-ray (synchrotron) sources have been used to estimate the possibility of direct structure determination from powder data. Two known structures were resolved by direct methods with neutron and X-ray data. With synchrotron X-ray data, the measured ...

  6. Solid-melt interface structure and growth of Cu alloy single crystals

    International Nuclear Information System (INIS)

    Tomimitsu, Hiroshi; Kamada, Kohji.

    1983-01-01

    Crystal-melt interface behavior during the growth of Cu-base solid solutions by the Bridgman method is discussed on the basis of experimental evidence obtained by neutron diffraction topography. Advantages of neutron diffraction topography for the characterization of large single crystals, such as dealt with in this paper, are emphasized. Evidence was odserved of extremely regular crystal growth along directions, irrespective of the macroscopic growth direction. This contrasts with the previously believed (110) normal growth which is a conclusion of growth theory based on molecular kinetics at the solid-melt interface. In consequence, we believe that the kinetics at the interface is a minor factor in the meltgrowth of metal single crystals. Revised melt-growth theory should include both the growth and the formation of the regular structure as evidenced by neutron diffraction topography. (author)

  7. High-Q microwave resonators with a photonic crystal structure

    International Nuclear Information System (INIS)

    Schuster, M.

    2001-08-01

    The localisation of electromagnetic energy at a defect in a photonic crystal is similar to a well known effect employed to construct high-Q microwave resonators: In a whispering gallery (WHG-) mode resonator the high Q-factor is achieved by localisation of the electromagnetic field energy by total reflection inside a disk made of dielectric material. The topic of this work is to demonstrate, that WHG-like modes can exist in an air defect in a photonic crystal that extends over several lattice periods; and that a high-Q microwave resonator can be made, utilizing these resonant modes. In numerical simulations, the transmission properties of a photonic crystal structure with hexagonal lattice symmetry have been investigated with a transfer-matrix-method. The eigenmodes of a defect structure in a photonic crystal have been calculated with a quasi-3d finite element integration technique. Experimental results confirm the simulated transmission properties and show the existence of modes inside the band gap, when a defect is introduced in the crystal. Resonator measurements show that a microwave resonator can be operated with those defect modes. It was found out that the main losses of the resonator were caused by bad microwave properties of the used dielectric material and by metal losses on the top and bottom resonator walls. Furthermore, it turned out that the detection of the photonic crystal defect mode was difficult because of a lack of simulation possibilities and high housing mode density in the resonator. (orig.)

  8. Determining the crystal structure of fibrinogen.

    Science.gov (United States)

    Doolittle, R F

    2004-05-01

    Summary. I have enjoyed reading previous historical sketches that have appeared in Journal of Thrombosis and Haemostasis, and especially those by Ted Tuddenham on factor VIII and Bjorn Dahlback on activated protein C resistance. Like those authors, I have tried to capture some of the excitement-as well as the disappointments-that occurred along the way to a long-term goal.

  9. Crystal-Size-Dependent Structural Transitions in Nanoporous Crystals: Adsorption-Induced Transitions in ZIF-8

    KAUST Repository

    Zhang, Chen

    2014-09-04

    © 2014 American Chemical Society. Understanding the crystal-size dependence of both guest adsorption and structural transitions of nanoporous solids is crucial to the development of these materials. We find that nano-sized metal-organic framework (MOF) crystals have significantly different guest adsorption properties compared to the bulk material. A new methodology is developed to simulate the adsorption and transition behavior of entire MOF nanoparticles. Our simulations predict that the transition pressure significantly increases with decreasing particle size, in agreement with crystal-size-dependent experimental measurements of the N2-ZIF-8 system. We also propose a simple core-shell model to examine this effect on length scales that are inaccessible to simulations and again find good agreement with experiments. This study is the first to examine particle size effects on structural transitions in ZIFs and provides a thermodynamic framework for understanding the underlying mechanism.

  10. Crystal structure of aspartame anhydrate from powder diffraction data. Structural aspects of the dehydration process of aspartame

    NARCIS (Netherlands)

    Guguta, C.; Meekes, H.L.M.; Gelder, R. de

    2006-01-01

    Aspartame has three pseudo-polymorphic forms, two hydrates and a hemi-hydrate, for which crystal structures were determined from single-crystal diffraction data. This paper presents the crystal structure of the anhydrate, which was obtained by dehydrating the hemi-hydrate. The crystal structure of

  11. Synthesis, crystal structure and biological activity of novel diester cyclophanes

    International Nuclear Information System (INIS)

    Zhang, Pengfei; Yang, Bingqin; Fang, Xianwen; Cheng, Zhao; Yang, Meipan

    2012-01-01

    A series of novel diester cyclophanes was synthesized by esterification of 1,2-benzenedicarbonyl chloride with eight different diols under high dilution conditions. The structures of the compounds were verified by elemental analysis, 1 H nuclear magnetic resonance (NMR), IR spectroscopy and high resolution mass spectrometry (HRMS). The crystal structures of two compounds were characterized by single crystal X-ray diffractometry (XRD). All the new cyclophanes were evaluated for biological activities and the results showed that some of these compounds have low antibacterial or antifungal activities (author)

  12. Synthesis, crystal structure and biological activity of novel diester cyclophanes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Pengfei; Yang, Bingqin; Fang, Xianwen; Cheng, Zhao; Yang, Meipan, E-mail: yangbq@nwu.edu.cn [Department of Chemistry, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, Northwest University, Shaanxi (China)

    2012-10-15

    A series of novel diester cyclophanes was synthesized by esterification of 1,2-benzenedicarbonyl chloride with eight different diols under high dilution conditions. The structures of the compounds were verified by elemental analysis, {sup 1}H nuclear magnetic resonance (NMR), IR spectroscopy and high resolution mass spectrometry (HRMS). The crystal structures of two compounds were characterized by single crystal X-ray diffractometry (XRD). All the new cyclophanes were evaluated for biological activities and the results showed that some of these compounds have low antibacterial or antifungal activities (author)

  13. Photonic crystals, light manipulation, and imaging in complex nematic structures

    Science.gov (United States)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  14. On structure of some laminated crystals with organic molecules

    International Nuclear Information System (INIS)

    Volodina, G.F.; Ivanova, V.Ya.; Malinovskij, T.I.

    1982-01-01

    A survey is made of papers dealing with intercalation of organic molecules into crystals of dihalcogenides of some transition metals (TaS 2 , TiS 2 , NbS 2 , ZrS 2 , TaSe 2 ), variation of their structure and physical properties. Among the used intercalates ammonia, pyridine, aniline and other aromatic amines proved to be most satisfactory from the viewpoint of reaction rate and product stability. A possibility is discussed of intercalation into PbI 2 and CdI 2 crystals that are of the same structural type as dihalcogenides

  15. Systematic analysis of crystal and molecular structures

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Dohnálek, Jan

    2012-01-01

    Roč. 19, č. 2 (2012), s. 86-87 ISSN 1211-5894. [Struktura 2012. Kolokvium Krystalografické společnosti. 11.06.2012-14.06.2012, Klatovy] R&D Projects: GA ČR GA310/09/1407 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : structure databases * structure-function relations * organic and inorganic materials Subject RIV: EE - Microbiology, Virology

  16. Photonics of liquid-crystal structures: A review

    Energy Technology Data Exchange (ETDEWEB)

    Palto, S. P., E-mail: palto@online.ru; Blinov, L M; Barnik, M I; Lazarev, V V; Umanskii, B A; Shtykov, N M [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2011-07-15

    The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in detail. The formation of higher harmonics in the periodic distribution of the director field in a helical liquid crystal structure and, correspondingly, the new (anharmonic) mode of electro-optical effects are discussed. Another group of studies is devoted to bistable light switching by an electric field in chiral nematics. Polarization diffraction gratings controlled by an electric field are also considered. The results of studies devoted to microlasers on various photonic structures with cholesteric and nematic liquid crystals are considered in detail. Particular attention is given to the new regime: leaky-mode lasing. Designs of liquid crystal light amplifiers and their polarization, field, and spectral characteristics are considered in the last section.

  17. CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE

    Energy Technology Data Exchange (ETDEWEB)

    Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.

    2009-01-01

    Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein’s relationship to disease treatment such as that for pneumonia and other related pathologies.

  18. Crystal structure of clathrates of Hofmann dma-type

    International Nuclear Information System (INIS)

    NIshikiori, Sh.; Ivamoto, T.

    1999-01-01

    Seven new clathrates Cd(DMA) 2 Ni(CN) 4 ·xG (x=1, G=aniline, 2,3-xylidine, 2,4-xylidine, 2,5-xylidine, 2,6-xylidine, 3,5-xylidine, and x=2, G=2,4,6-trimethylaniline) of Hofmann type are synthesized by amine substitution for dimethylamine (DMA). On the base of x-ray diffraction data it is shown that geometry of guest molecule in cage-like hollow determines the structure of the host and crystal structure of clathrates. Two-dimension metallocomplex of the host of studied clathrates is characterized by elastic folded structure appearing as a result of angular deformation of bond between Cd atoms and host cyanide bridge. Guest molecule orientation is fixed by hydrogen bond. Structural elasticity of the host complex directs to differences in crystal structure of clathrates formed and to considerable variety of incorporated guests [ru

  19. Simulation and design of the photonic crystal microwave accelerating structure

    International Nuclear Information System (INIS)

    Song Ruiying; Wu Congfeng; He Xiaodong; Dong Sai

    2007-01-01

    The authors have derived the global band gaps for general two-dimensional (2D) photonic crystal microwave accelerating structures formed by square or triangular arrays of metal posts. A coordinate-space, finite-difference code was used to calculate the complete dispersion curves for the lattices. The fundamental and higher frequency global photonic band gaps were determined numerically. The structure formed by triangular arrays of metal posts with a missing rod at the center has advantages of higher-order-modes (HOM) suppression and main mode restriction under the condition of a/b<0.2. The relationship between the RF properties and the geometrical parameters have been studied for the 9.37 GHz photonic crystal accelerating structure. The Rs, Q, Rs/Q of the new structure may be comparable to the disk-loaded accelerating structure. (authors)

  20. Synthesis and crystal structures of three new benzotriazolylpropanamides

    Directory of Open Access Journals (Sweden)

    Donna S. Amenta

    2017-06-01

    Full Text Available The base-catalyzed Michael addition of 2-methylacrylamide to benzotriazole afforded 3-(1H-benzotriazol-1-yl-2-methylpropanamide, C10H12N4O (1, in 32% yield in addition to small amounts of isomeric 3-(2H-benzotriazol-2-yl-2-methylpropanamide, C10H12N4O (2. In a similar manner, 3-(1H-benzotriazol-1-yl-N,N-dimethylpropanamide, C11H14N4O (3, was prepared from benzotriazole and N,N-dimethylacrylamide. All three products have been structurally characterized by single-crystal X-ray diffraction. The crystal structures of 1 and 2 comprise infinite arrays formed by N—H...O and N—H...N bridges, as well as π–π interactions, while the molecules of 3 are aggregated to simple π-dimers in the crystal.

  1. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research ... Purpose: To determine the exact structure and antimicrobial activity of 2-(3-(4 phenylpiperazin-1-yl) ... Besides HOMO– LUMO energy gap was performed at B3LYP/6-31G (d,p) level of theory.

  2. Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

    Science.gov (United States)

    Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

    2017-06-01

    We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

  3. Synthesis and crystal structure analysis of uranyl triple acetates

    Energy Technology Data Exchange (ETDEWEB)

    Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Serezhkina, Larisa B.; Serezhkin, Victor N. [Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Alekseev, Evgeny V., E-mail: e.alekseev@fz-juelich.de [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)

    2016-12-15

    Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.

  4. Studies of switching structures in ferroelectric liquid crystal devices

    International Nuclear Information System (INIS)

    Pabla, D.S.

    1998-01-01

    The fast, bistable electro-optic response of ferroelectric liquid crystal (FLC) devices has made them prime candidates for use in display applications. However, before these applications can become widely commercially viable a number of key issues relating to the switching within these devices need to be addressed. One of these is related to the fact that while there has been much work done on modelling the switching process in FLC devices, with some moderate success, in the main these models have not accurately accounted for the physical processes taking place. In order to rectify this situation we present a simple, multi-variable approach which includes important physical phenomenon such as stressed states, partial and domain switching. Through using this model we learn more about the dynamic molecular profiles which may exist in devices, and use this as a springboard to undertake a comprehensive theoretical and experimental study of the molecular profiles of chevron structures under different types of addressing pulses and voltages. This entails modelling the dynamic profiles using a simple non flow reorientation theory and comparing these simulations directly with experimental data obtained through the use of two different optical characterisation techniques. Our findings show quite conclusively that for monopolar addressing within low and high voltage regimes and for low voltage bipolar pulses during the early stages of switching, the dynamic reorientation near the surfaces and central regions of the device lags the reorientation within the bulk. The reverse however being true for the high voltage bipolar addressing case. These results for chevron structures differ from previous theoretical predictions made by others using equations derived from the flow coupled chiral smectic C continuum theory. These flow coupled simulations however, refer to reorientation in bookshelf structures rather than the chevron type structures thought to exist in FLC devices. As

  5. Studies of switching structures in ferroelectric liquid crystal devices

    Energy Technology Data Exchange (ETDEWEB)

    Pabla, D.S

    1998-07-01

    The fast, bistable electro-optic response of ferroelectric liquid crystal (FLC) devices has made them prime candidates for use in display applications. However, before these applications can become widely commercially viable a number of key issues relating to the switching within these devices need to be addressed. One of these is related to the fact that while there has been much work done on modelling the switching process in FLC devices, with some moderate success, in the main these models have not accurately accounted for the physical processes taking place. In order to rectify this situation we present a simple, multi-variable approach which includes important physical phenomenon such as stressed states, partial and domain switching. Through using this model we learn more about the dynamic molecular profiles which may exist in devices, and use this as a springboard to undertake a comprehensive theoretical and experimental study of the molecular profiles of chevron structures under different types of addressing pulses and voltages. This entails modelling the dynamic profiles using a simple non flow reorientation theory and comparing these simulations directly with experimental data obtained through the use of two different optical characterisation techniques. Our findings show quite conclusively that for monopolar addressing within low and high voltage regimes and for low voltage bipolar pulses during the early stages of switching, the dynamic reorientation near the surfaces and central regions of the device lags the reorientation within the bulk. The reverse however being true for the high voltage bipolar addressing case. These results for chevron structures differ from previous theoretical predictions made by others using equations derived from the flow coupled chiral smectic C continuum theory. These flow coupled simulations however, refer to reorientation in bookshelf structures rather than the chevron type structures thought to exist in FLC devices. As

  6. Magnetic assembly of nonmagnetic particles into photonic crystal structures.

    Science.gov (United States)

    He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

    2010-11-10

    We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

  7. Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

    Science.gov (United States)

    Marchewka, M. K.; Pietraszko, A.

    2008-02-01

    The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

  8. Structural science using single crystal and pulse neutron scattering

    International Nuclear Information System (INIS)

    Noda, Yukio; Kimura, Hiroyuki; Watanabe, Masashi; Ishikawa, Yoshihisa; Tamura, Itaru; Arai, Masatoshi; Takahashi, Miwako; Ohshima, Ken-ichi; Abe, Hiroshi; Kamiyama, Takashi

    2008-01-01

    The application to single crystal neutron structural analysis is overviewed. Special attention is paid to the pulse neutron method, which will be available soon under J-PARC project in Japan. New proposal and preliminary experiment using Sirius at KENS are described. (author)

  9. Crystal structure, characterization and magnetic properties of a 1D ...

    Indian Academy of Sciences (India)

    Crystal structure, characterization and magnetic properties of a 1D copper(II) polymer incorporating a Schiff base with carboxylate side arm. SHYAMAPADA SHIT MADHUSUDAN NANDY CORRADO RIZZOLI CÉDRIC DESPLANCHES SAMIRAN MITRA. Regular Article Volume 128 Issue 6 June 2016 pp 913-920 ...

  10. BiFeO3 Crystal Structure at Low Temperatures

    International Nuclear Information System (INIS)

    Palewicz, A.; Sosnowska, I.; Przenioslo, R.; Hewat, A.W.

    2010-01-01

    The crystal and magnetic structure of BiFeO 3 have been studied with the use of high resolution neutron diffraction between 5 K and 300 K. The atomic coordinates in BiFeO 3 are almost unchanged between 5 K and 300 K. (authors)

  11. Effect of domains configuration on crystal structure in ferroelectric ...

    Indian Academy of Sciences (India)

    2017-09-09

    Sep 9, 2017 ... It is well known that domains and crystal structure control the physical properties of ferroelectrics. ... The as-prepared ceramics were crushed to fine pow- ders. ..... [1] Gao J, Xue D, Wang Y, Wang D, Zhang L, Wu H et al 2011.

  12. Magnetic structure of URhSi single crystal

    Czech Academy of Sciences Publication Activity Database

    Prokeš, K.; Andreev, Alexander V.; Honda, F.; Sechovský, V.

    2003-01-01

    Roč. 261, - (2003), s. 131-138 ISSN 0304-8853 R&D Projects: GA ČR GA202/02/0739 Institutional research plan: CEZ:AV0Z1010914 Keywords : URhSi single crystal * magnetization * neutron diffraction * magnetic structure determination Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.910, year: 2003

  13. Fine structure of fields in 2D photonic crystal waveguides

    DEFF Research Database (Denmark)

    Lavrinenko, Andrei; Volkov, V. S.; Bozhevolnyi, S. I.

    2006-01-01

    We resolve fine structure of fields in a single-row missing photonic crystal waveguide by finite-difference time-domain modelling and SNOM measurements. Both linear dispersion and slow-light regimes in proximity of the cutoff are addressed in the analysis....

  14. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    Science.gov (United States)

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  15. Isomorph invariance of the structure and dynamics of classical crystals

    DEFF Research Database (Denmark)

    Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk

    2014-01-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework...

  16. short communication synthesis and crystal structure of a polymeric

    African Journals Online (AJOL)

    Preferred Customer

    A new polymeric zinc(II) complex, [ZnL2(PDA)]n, has been prepared by the reaction of zinc sulfate ... complex has been characterized by single-crystal X-ray diffraction. .... Molecular structure of the complex at 30% probability displacement.

  17. Characterization and crystal structures of new Schiff base macrocyclic compounds

    Czech Academy of Sciences Publication Activity Database

    Khalaji, A.D.; Ghoran, S.H.; Pojarová, Michaela; Dušek, Michal

    2015-01-01

    Roč. 56, č. 7 (2015), s. 1410-1414 ISSN 0022-4766 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : synthesis * macrocyclic Schiff base * single crystal structure analysis * spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.536, year: 2015

  18. Synthesis and structural characterization of CsNiP crystal

    Indian Academy of Sciences (India)

    Unknown

    The crystals obtained by this method were of good quality exhibiting ... type framework structure having Cs atoms inside it (figures. 3 and 4). This helps for .... Gopalakrishna G S, Prasad J S and Lokanath N K 2001 Proc. joint 4th and 6th ICSTR ...

  19. Variational cellular model of the molecular and crystal electronic structure

    International Nuclear Information System (INIS)

    Ferreira, L.G.; Leite, J.R.

    1977-12-01

    A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

  20. A unified picture of the crystal structures of metals

    Science.gov (United States)

    Söderlind, Per; Eriksson, Olle; Johansson, Börje; Wills, J. M.; Boring, A. M.

    1995-04-01

    THE crystal structures of the light actinides have intrigued physicists and chemists for several decades1. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic and hexagonal close packing. In contrast, the structures of the light actinides are very loosely packed and of low symmetry-tetragonal, orthorhombic and monoclinic. To understand these differences, we have performed total-energy calculations, as a function of volume, for both high-and low-symmetry structures of a simple metal (aluminium), a non-magnetic transition metal (niobium), a ferromagnetic transition metal (iron) and a light actinide (uranium). We find that the crystal structure of all of these metals is determined by the balance between electrostatic (Madelung) interactions, which favour high symmetry, and a Peierls distortion of the crystal lattice, which favours low symmetry. We show that simple metals and transition metals can adopt low-symmetry structures on expansion of the lattice; and we predict that, conversely, the light actinides will undergo transitions to structures of higher symmetry on compression.

  1. A unified picture of the crystal structures of metals

    International Nuclear Information System (INIS)

    Soederlind, P.; Eriksson, O.; Johansson, B.; Wills, J.M.; Boring, A.M.

    1995-01-01

    The crystal structures of the light actinides have intrigued physicists and chemists for several decades. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic hexagonal close packing. In contrast, the structures of the light actinides are very loosely packed and of low symmetry -tetragonal, orthorhombic and monoclinic. To understand these differences, we have have performed total-energy calculations, as a function of volume, for both high- and low-symmetry structures of a simple metal (aluminium), a non-magnetic transition metal (niobium), a ferromagnetic transition metal (iron) and a light actinide (uranium). We find that the crystal structure of all these metals is determined by the balance between electrostatic (Madelung) interactions, which favour high symmetry, and a Peierls distortion of the crystal lattice, which favours low symmetry. We show that simple metals and transition metals can adopt low-symmetry structures on expansion of the lattice; and we predict that, conversely, the light actinides will undergo transitions to structures of higher symmetry on compression. (author)

  2. `Pd20Sn13' revisited: crystal structure of Pd6.69Sn4.31

    Directory of Open Access Journals (Sweden)

    Wilhelm Klein

    2015-07-01

    Full Text Available The crystal structure of the title compound was previously reported with composition `Pd20Sn13' [Sarah et al. (1981. Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3:0.62 (3. One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b.

  3. Coefficient of crystal lattice matching as a parameter of substrate - crystal structure compatibility in silumins

    Directory of Open Access Journals (Sweden)

    J. Piątkowski

    2009-07-01

    Full Text Available Adding high-melting point elements (Mo, Nb, Ni, Ti, W to complex silumins results in hardening of the latter ones, owing to the formation of new intermetallic phases of the AlxMey type, with refinement of dendrites in α solution and crystals in β phase. The hardening is also due to the effect of various inoculants. An addition of the inoculant is expected to form substrates, the crystal lattice of which, or some (privileged lattice planes and interatomic spaces should bear a strong resemblance to the crystal nucleus. To verify this statement, using binary phase equilibria systems, the coefficient of crystal lattice matching, being one of the measures of the crystallographic similarity, was calculated. A compatibility of this parameter (up to 20% may decide about the structure compatibility between the substrate and crystal which, in turn, is responsible for the effectiveness of alloy modification. Investigations have proved that, given the temperature range of their formation, the density, the lattice type, and the lattice parameter, some intermetallic phases of the AlxMey type can act as substrates for the crystallisation of aluminium and silicon, and some of the silumin hardening phases.

  4. Band structures in Sierpinski triangle fractal porous phononic crystals

    International Nuclear Information System (INIS)

    Wang, Kai; Liu, Ying; Liang, Tianshu

    2016-01-01

    In this paper, the band structures in Sierpinski triangle fractal porous phononic crystals (FPPCs) are studied with the aim to clarify the effect of fractal hierarchy on the band structures. Firstly, one kind of FPPCs based on Sierpinski triangle routine is proposed. Then the influence of the porosity on the elastic wave dispersion in Sierpinski triangle FPPCs is investigated. The sensitivity of the band structures to the fractal hierarchy is discussed in detail. The results show that the increase of the hierarchy increases the sensitivity of ABG (Absolute band gap) central frequency to the porosity. But further increase of the fractal hierarchy weakens this sensitivity. On the same hierarchy, wider ABGs could be opened in Sierpinski equilateral triangle FPPC; whilst, a lower ABG could be opened at lower porosity in Sierpinski right-angled isosceles FPPCs. These results will provide a meaningful guidance in tuning band structures in porous phononic crystals by fractal design.

  5. Band structures in Sierpinski triangle fractal porous phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Kai; Liu, Ying, E-mail: yliu5@bjtu.edu.cn; Liang, Tianshu

    2016-10-01

    In this paper, the band structures in Sierpinski triangle fractal porous phononic crystals (FPPCs) are studied with the aim to clarify the effect of fractal hierarchy on the band structures. Firstly, one kind of FPPCs based on Sierpinski triangle routine is proposed. Then the influence of the porosity on the elastic wave dispersion in Sierpinski triangle FPPCs is investigated. The sensitivity of the band structures to the fractal hierarchy is discussed in detail. The results show that the increase of the hierarchy increases the sensitivity of ABG (Absolute band gap) central frequency to the porosity. But further increase of the fractal hierarchy weakens this sensitivity. On the same hierarchy, wider ABGs could be opened in Sierpinski equilateral triangle FPPC; whilst, a lower ABG could be opened at lower porosity in Sierpinski right-angled isosceles FPPCs. These results will provide a meaningful guidance in tuning band structures in porous phononic crystals by fractal design.

  6. Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface

    Directory of Open Access Journals (Sweden)

    Vasily F. Shabanov

    2013-08-01

    Full Text Available Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface.

  7. 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)

  8. Spatially periodic structures, under femtosecond pulsed excitation of crystals

    International Nuclear Information System (INIS)

    Martynovitch, Evgueni F.; Petite, Guillaume; Dresvianski, Vladimir P.; Starchenko, Anton A.

    2004-01-01

    Measuring the luminescence intensity of specially prepared irradiation defects induced in crystals, we observe that the longitudinal structure of quasi-interferences induced by two orthogonally polarized femtosecond pulses propagating together with different velocities is insensitive to the spatial broadening due to velocity dispersion in the crystals. On the contrary, it does depend on the pulse duration when it is changed by varying the spectral width of the radiation. It thus allows a direct measurement of the coherence time of such pulses. Stability of the axial selectivity is a good sign, taking away a number of serious limitations concerning possible applications

  9. Crystal structure representations for machine learning models of formation energies

    Energy Technology Data Exchange (ETDEWEB)

    Faber, Felix [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel Switzerland; Lindmaa, Alexander [Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping Sweden; von Lilienfeld, O. Anatole [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel Switzerland; Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Avenue Lemont Illinois 60439; Armiento, Rickard [Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping Sweden

    2015-04-20

    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a dataset of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37eV/atom for the respective representations.

  10. Crystal structure and magnetism of UOsAl

    Energy Technology Data Exchange (ETDEWEB)

    Andreev, A.V., E-mail: andreev@fzu.cz [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Daniš, S. [Department of Condensed Matter Physics, Charles University, Ke Karlovu 5, 121 16 Prague (Czech Republic); Šebek, J.; Henriques, M.S.; Vejpravová, J. [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Gorbunov, D.I. [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Dresden High Magnetic Field Laboratory (HLD-EMFL), Helmholtz-Zentrum, Dresden-Rossendorf, D-01314 Dresden (Germany); Havela, L. [Department of Condensed Matter Physics, Charles University, Ke Karlovu 5, 121 16 Prague (Czech Republic)

    2017-04-15

    Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn{sub 2} type, space group P6{sub 3}/mmc, with lattice parameters a=536.4 pm, c=845.3 pm. Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). The compound is a weakly temperature-dependent paramagnet with magnetic susceptibility of ≈1.5*10{sup −8} m{sup 3} mol{sup −1} (at T=2 K), which is slightly higher with magnetic field along the a-axis compared to the c-axis. The Sommerfeld coefficient of electronic specific heat has moderate value of γ=36 mJ mol{sup −1} K{sup −2}. - Highlights: • Crystal structure and magnetic properties were studied on single crystal of UOsAl with hexagonal structure of MgZn{sub 2} type. • Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). • UOsAl has paramagnetic ground state as the compounds with T=Fe and Ru, i.e. 3d and 4d analogues of Os.

  11. Icosahedral symmetry described by an incommensurately modulated crystal structure model

    DEFF Research Database (Denmark)

    Wolny, Janusz; Lebech, Bente

    1986-01-01

    A crystal structure model of an incommensurately modulated structure is presented. Although six different reciprocal vectors are used to describe the model, all calculations are done in three dimensions making calculation of the real-space structure trivial. Using this model, it is shown that both...... the positions of the bragg reflections and information about the relative intensities of these reflections are in full accordance with the diffraction patterns reported for microcrystals of the rapidly quenched Al86Mn14 alloy. It is also shown that at least the local structure possesses full icosahedral...

  12. Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

    KAUST Repository

    Dumbrack, Roland

    2016-01-26

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

  13. Twinning structures in near-stoichiometric lithium niobate single crystals

    International Nuclear Information System (INIS)

    Yao, Shuhua; Chen, Yanfeng

    2010-01-01

    A near-stoichiometric lithium niobate single crystal has been grown by the Czochralski method in a hanging double crucible with a continuous powder supply system. Twins were found at one of the three characteristic growth ridges of the as-grown crystal. The twin structure was observed and analyzed by transmission synchrotron topography. The image shifts ΔX and ΔY in the transmission synchrotron topograph were calculated for the 3 anti 2 anti 12 and 0 anti 222 reflections based on results from high-resolution X-ray diffractometry. It is confirmed that one of the {01 anti 1 anti 2} m planes is the composition face of the twin and matrix crystals. The formation mechanism of these twins is discussed. (orig.)

  14. Crystal structure of N-(quinolin-6-ylhydroxylamine

    Directory of Open Access Journals (Sweden)

    Anuruddha Rajapakse

    2014-11-01

    Full Text Available The title compound, C9H8N2O, crystallized with four independent molecules in the asymmetric unit. The four molecules are linked via one O—H...N and two N—H...N hydrogen bonds, forming a tetramer-like unit. In the crystal, molecules are further linked by O—H...N and N—H...O hydrogen bonds forming layers parallel to (001. These layers are linked via C—H...O hydrogen bonds and a number of weak C—H...π interactions, forming a three-dimensional structure. The crystal was refined as a non-merohedral twin with a minor twin component of 0.319.

  15. 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

  16. Band structure and optical properties of diglycine nitrate crystal

    International Nuclear Information System (INIS)

    Andriyevsky, Bohdan; Ciepluch-Trojanek, Wioleta; Romanyuk, Mykola; Patryn, Aleksy; Jaskolski, Marcin

    2005-01-01

    Experimental and theoretical investigations of the electron energy characteristics and optical spectra for diglycine nitrate crystal (DGN) (NH 2 CH 2 COOH) 2 .HNO 3 , in the paraelectric phase (T=295K) are presented. Spectral dispersion of light reflection R(E) have been measured in the range of 3-22eV and the optical functions n(E) and k(E) have been calculated using Kramers-Kronig relations. First principal calculations of the electron energy characteristic and optical spectra of DGN crystal have been performed in the frame of density functional theory using CASTEP code (CAmbridge Serial Total Energy Package). Optical transitions forming the low-energy edge of fundamental absorption are associated with the nitrate groups NO 3 . Peculiarities of the band structure and DOS projected onto glycine and NO 3 groups confirm the molecular character of DGN crystal

  17. First principles investigation of the structure of a bacteriochlorophyll crystal

    Energy Technology Data Exchange (ETDEWEB)

    Marchi, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)]|[Centre d`Etudes Saclay, Gif-sur-Yvette (France); Hutter, J.; Parrinello, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  18. High-brightness tapered laser diodes with photonic crystal structures

    Science.gov (United States)

    Li, Yi; Du, Weichuan; Kun, Zhou; Gao, Songxin; Ma, Yi; Tang, Chun

    2018-02-01

    Beam quality of tapered laser diodes is limited by higher order lateral mode. On purpose of optimizing the brightness of tapered laser diodes, we developed a novel design of tapered diodes. This devices based on InGaAs/AlGaAs asymmetry epitaxial structure, containing higher order lateral mode filtering schemes especially photonic crystal structures, which fabricated cost effectively by using standard photolithography and dry etch processes. Meanwhile, the effects of photonic crystal structures on mode control are also investigated theoretically by FDBPM (Finite-Difference Beam Propagation Method) calculation. We achieved a CW optical output power of 6.9W at 940nm for a single emitter with 4 mm cavity length. A nearly diffraction limited beam of M2 ≍1.9 @ 0.5W has been demonstrated, and a highest brightness of β =75MW/(cm2 ·sr) was reached.

  19. Crystal structure and thermal behavior of KB3O6

    International Nuclear Information System (INIS)

    Bubnova, R.S.; Fundamenskij, V.S.; Filatov, S.K.; Polyakova, I.G.

    2004-01-01

    The structure of potassium triborate prepared in metastable state by crystallization from melt at ∼ 800 deg C was studied by the method of X-ray diffraction analysis. It was ascertained that KB 3 O 6 belongs to monoclinic crystal system, space group P2 1 /c, a = 9.319(1), b = 6.648(1), c = 21.094(2) A, β = 94.38(1) deg, Z = 12. The compound is referred to a new structural type. Anion of the structure is a single boron-oxygen frame formed by three independent rigid triborate rings of [B 3 O 5 ] - , each of them consisting of two BO 3 triangles and BO 4 tetrahedron. Phase transformations during KB 3 O 6 heating up to 800 deg C, as well as thermal expansion in the range of 20-650 deg C, were studied [ru

  20. The crystal structure and the phase transitions of pyridinium trifluoromethanesulfonate

    International Nuclear Information System (INIS)

    Jesariew, Dominik; Ilczyszyn, Maria M; Pietraszko, Adam

    2014-01-01

    The calorimetric and optical studies and the structural properties of pyridinium trifluoromethanesulfonate (abbreviated as PyHOTf) are reported. A sequence of four fully reversible solid–solid phase transitions, at 223.0, 309.0, 359.9 and 394.3 K, has been discovered. The phase transition sequence was confirmed by x-ray diffraction data. The crystal structures of three phases (V, IV and III) have been determined from the single crystal x-ray diffraction data. Structural properties of the high temperature phases are characterized using powder x-ray diffraction data measured in the 290–425 K temperature range. The structural changes triggered by the temperature change are discussed in relation to the phase transitions. Two low temperature phases (V and IV) belong to the P4 3 2 1 2 space group of the tetragonal system. The intermediate phases (III and II) are monoclinic and the prototype high temperature phase (I) is a pseudo-cubic (tetragonal) one. The low temperature phases (V and IV) are well ordered. The crystal structure of intermediate (III and II) and prototype (I) phases are characterized by high disorder of the pyridinium cations and triflate anions. (papers)

  1. Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

    OpenAIRE

    Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

    1981-01-01

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

  2. One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

    Science.gov (United States)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

    2016-11-01

    Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

  3. Crystal structure of human protein kinase CK2

    DEFF Research Database (Denmark)

    Niefind, K; Guerra, B; Ermakowa, I

    2001-01-01

    The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalyt...... as a docking partner for various protein kinases. Furthermore it shows an inter-domain mobility in the catalytic subunit known to be functionally important in protein kinases and detected here for the first time directly within one crystal structure.......The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalytic...... subunits, which make no direct contact with one another. Each catalytic subunit interacts with both regulatory chains, predominantly via an extended C-terminal tail of the regulatory subunit. The CK2 structure is consistent with its constitutive activity and with a flexible role of the regulatory subunit...

  4. Crystal structure optimisation using an auxiliary equation of state

    Science.gov (United States)

    Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

    2015-11-01

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

  5. Crystal structure optimisation using an auxiliary equation of state

    International Nuclear Information System (INIS)

    Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; 3 Institute and Department of Materials Science and Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of))" data-affiliation=" (Centre for Sustainable Chemical Technologies and Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Global E3 Institute and Department of Materials Science and Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of))" >Walsh, Aron

    2015-01-01

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy–volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other “beyond” density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu 2 ZnSnS 4 and the magnetic metal-organic framework HKUST-1

  6. Crystal structure optimisation using an auxiliary equation of state

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T. [Centre for Sustainable Chemical Technologies and Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Walsh, Aron, E-mail: a.walsh@bath.ac.uk [Centre for Sustainable Chemical Technologies and Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Global E" 3 Institute and Department of Materials Science and Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy–volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other “beyond” density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu{sub 2}ZnSnS{sub 4} and the magnetic metal-organic framework HKUST-1.

  7. Purification, crystal structure determination and functional characterization of type III antifreeze proteins from the European eelpout Zoarces viviparus

    DEFF Research Database (Denmark)

    Wilkens, Casper; Poulsen, Jens-Christian Navarro; Ramløv, Hans

    2014-01-01

    Antifreeze proteins (AFPs) are essential components of many organisms adaptation to cold temperatures. Fish type III AFPs are divided into two groups, SP isoforms being much less active than QAE1 isoforms. Two type III AFPs from Zoarces viviparus, a QAE1 (ZvAFP13) and an SP (ZvAFP6) isoform......, are here characterized and their crystal structures determined. We conclude that the higher activity of the QAE1 isoforms cannot be attributed to single residues, but rather a combination of structural effects. Furthermore both ZvAFP6 and ZvAFP13 crystal structures have water molecules around T18...... equivalent to the tetrahedral-like waters previously identified in a neutron crystal structure. Interestingly, ZvAFP6 forms dimers in the crystal, with a significant dimer interface. The presence of ZvAFP6 dimers was confirmed in solution by native electrophoresis and gel filtration. To our knowledge...

  8. CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

    OpenAIRE

    Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

    2002-01-01

    The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

  9. Parallelization for X-ray crystal structural analysis program

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Hiroshi [Japan Atomic Energy Research Inst., Tokyo (Japan); Minami, Masayuki; Yamamoto, Akiji

    1997-10-01

    In this report we study vectorization and parallelization for X-ray crystal structural analysis program. The target machine is NEC SX-4 which is a distributed/shared memory type vector parallel supercomputer. X-ray crystal structural analysis is surveyed, and a new multi-dimensional discrete Fourier transform method is proposed. The new method is designed to have a very long vector length, so that it enables to obtain the 12.0 times higher performance result that the original code. Besides the above-mentioned vectorization, the parallelization by micro-task functions on SX-4 reaches 13.7 times acceleration in the part of multi-dimensional discrete Fourier transform with 14 CPUs, and 3.0 times acceleration in the whole program. Totally 35.9 times acceleration to the original 1CPU scalar version is achieved with vectorization and parallelization on SX-4. (author)

  10. Band structure and optical properties of opal photonic crystals

    Science.gov (United States)

    Pavarini, E.; Andreani, L. C.; Soci, C.; Galli, M.; Marabelli, F.; Comoretto, D.

    2005-07-01

    A theoretical approach for the interpretation of reflectance spectra of opal photonic crystals with fcc structure and (111) surface orientation is presented. It is based on the calculation of photonic bands and density of states corresponding to a specified angle of incidence in air. The results yield a clear distinction between diffraction in the direction of light propagation by (111) family planes (leading to the formation of a stop band) and diffraction in other directions by higher-order planes (corresponding to the excitation of photonic modes in the crystal). Reflectance measurements on artificial opals made of self-assembled polystyrene spheres are analyzed according to the theoretical scheme and give evidence of diffraction by higher-order crystalline planes in the photonic structure.

  11. An arc detector for neutron crystal structure investigations

    Energy Technology Data Exchange (ETDEWEB)

    Habib, N [Reactor and Neutron Physics Dept., Nuclear Research Center. AEA, Cairo (Egypt)

    1997-12-31

    An arc detector for neutron structure investigations of powder crystals using time-of-flight technique is described. In order to enable the measurement of integral intensity from about 1/4 of the Debye-Scherrer ring and for simplicity reasons, the scattering angle 20-90 degree was chosen and a special arc collimator was built. The arc collimator-detector had a divergency of about 20 minutes of arc, and the distance between detector-sample was 64 cm. Four {sup 3} He detectors were fixed on the arc of the collimator. Both efficiency and space sensitivity of the detector were determined using a point neutron source. Results of measurements show that parameters of the arc detector are acceptable for high resolution crystal structure investigations. 6 figs.

  12. Crystal structure of N′-hydroxypyrimidine-2-carboximidamide

    Directory of Open Access Journals (Sweden)

    Nithianantham Jeeva Jasmine

    2014-10-01

    Full Text Available The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The molecule adopts an E configuration about the C=N double bond. In the crystal, adjacent molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(10 ring motif. The dimers are further linked via N—H...N and O—H...N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N—H...O and weak C—H...O hydrogen bonds and offset π–π stacking interactions between adjacent pyrimidine rings [centroid–centroid distance = 3.622 (1 Å].

  13. CCDC 1515632: Experimental Crystal Structure Determination : hexakis(dimethyl sulfoxide)-manganese(ii) tetraiodide

    KAUST Repository

    Haque, M.A.; Davaasuren, Bambar; Rothenberger, Alexander; Wu, Tao

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  14. CCDC 1475929: Experimental Crystal Structure Determination : trimethylammonium tribromo-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  15. CCDC 1475930: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  16. CCDC 1475931: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  17. CCDC 1482638: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  18. Potassium and magnesium succinatouranilates – Synthesis and crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Novikov, S.A., E-mail: serg.alex.novikov@gmail.com [Samara National Research University, 443086 Samara (Russian Federation); Grigoriev, M.S. [Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 119071 Moscow (Russian Federation); Serezhkina, L.B.; Serezhkin, V.N. [Samara National Research University, 443086 Samara (Russian Federation)

    2017-04-15

    Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}] [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), where C{sub 4}H{sub 4}O{sub 4}{sup 2-} is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} with the same A{sub 2}Q{sup 02}{sub 3} crystallochemical formula (A=UO{sub 2}{sup 2+}, Q{sup 02}=C{sub 4}O{sub 4}H{sub 4}{sup 2-}), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ions is one of the factors, which affects the structure of [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A{sub 2}Q{sup 02}{sub 3} crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality. - Graphical abstract: Crystal structures of two new uranium(VI) coordination polymers with succinate linkers, namely K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), were determined by single-crystal XRD. Crystals of studied compounds are based on 2D or 1D structural units with the same composition and crystallochemical formula. Topological isomerism in A{sub 2}Q{sup 02}{sub 3} crystallochemical group and conformations of succinate anions in uranyl complexes are under discussion. - Highlights: • Two new uranium coordination polymers were synthesized. • Their structural units have the same composition and crystallochemical formula. • In spite the same composition and CCF dimensionality of units is different. • Structural features of uranyl CPs

  19. Solving RNA's structural secrets: interaction with antibodies and crystal structure of a nuclease resistant RNA

    International Nuclear Information System (INIS)

    Wallace, S.T.

    1998-10-01

    This Ph.D. thesis concerns the structural characterization of RNA. The work is split into two sections: 1) in vitro selection and characterization of RNAs which bind antibiotics and 2) crystal structure of a nuclease resistant RNA molecule used in antisense applications. Understanding antibiotic-RNA interactions is crucial in aiding rational drug design. We were interested in studying antibiotic interactions with RNAs small enough to characterize at the molecular and possibly at the atomic level. In order to do so, we previously performed in vitro selection to find small RNAs which bind to the peptide antibiotic viomycin and the aminoglycoside antibiotic streptomycin. The characterization of the viomycin-binding RNAs revealed the necessity of a pseudoknot-structure in order to interact with the antibiotic. The RNAs which were selected to interact with streptomycin require the presence of magnesium to bind the antibiotic. One of the RNAs, upon interacting with streptomycin undergoes a significant conformational change spanning the entire RNA sequence needed to bind the antibiotic. In a quest to design oligodeoxynucleotides (ODNs) which are able to specifically bid and inactivate the mRNA of a gene, it is necessary to fulfill two criteria: 1) increase binding affinity between the ODN and the target RNA and 2) increase the ODN's resistance to nuclease degradation. An ODN with an aminopropyl modification at the 2' position of its ribose has emerged as the most successful candidate at fulfilling both criteria. It is the most nuclease resistant modification known to date. We were interested in explaining how this modification is able to circumvent degradation by nucleases. A dodecamer containing a single 2'-O-aminopropyl modified nucleotide was crystallized and the structure was solved to a resolution of 1.6 A. In an attempt to explain the nuclease resistance, the crystal coordinates were modeled into the active exonuclease site of DNA polymerase I. We propose the

  20. Crystal Structure of the Human Laminin Receptor Precursor

    Energy Technology Data Exchange (ETDEWEB)

    Jamieson,K.; Wu, J.; Hubbard, S.; Meruelo, D.

    2008-01-01

    The human laminin receptor (LamR) interacts with many ligands, including laminin, prions, Sindbis virus, and the polyphenol (-)-epigallocatechin-3-gallate (EGCG), and has been implicated in a number of diseases. LamR is overexpressed on tumor cells, and targeting LamR elicits anti-cancer effects. Here, we report the crystal structure of human LamR, which provides insights into its function and should facilitate the design of novel therapeutics targeting LamR.

  1. Incommensurate composite crystal structure of scandium-II

    International Nuclear Information System (INIS)

    Fujihisa, Hiroshi; Gotoh, Yoshito; Yamawaki, Hiroshi; Sakashita, Mami; Takeya, Satoshi; Honda, Kazumasa; Akahama, Yuichi; Kawamura, Haruki

    2005-01-01

    The long-unknown crystal structure of the high pressure phase scandium-II was solved by powder x-ray diffraction and was found to have tetragonal host channels along the c axis and guest chains that are incommensurate with the host, as well as the high pressure phases of Ba, Sr, Bi, and Sb. The pressure dependences of the lattice constants, the incommensurability, the atomic distances, and the atomic volume were investigated

  2. Band structure and optical properties of opal photonic crystals

    OpenAIRE

    Pavarini, E.; Andreani, L. C.; Soci, C.; Galli, M.; Marabelli, F.; Comoretto, D.

    2005-01-01

    A theoretical approach for the interpretation of reflectance spectra of opal photonic crystals with fcc structure and (111) surface orientation is presented. It is based on the calculation of photonic bands and density of states corresponding to a specified angle of incidence in air. The results yield a clear distinction between diffraction in the direction of light propagation by (111) family planes (leading to the formation of a stop band) and diffraction in other directions by higher-order...

  3. Crystal structures of unsymmetrically mixed β-pyrrole substituted ...

    Indian Academy of Sciences (India)

    NiTPP(Ph)3(CN)5, 3 complex was synthesized and its solvated structure was examined by crystallography. ... sive interactions among the peripheral substituents.28,29 ... 1H NMR spectra of porphyrins were. 1047 ... Single crystals of MTPP(Ph)3Cl5 (M = 2H and Ni(II)) .... by ∼0.3–0.6ppm but β-pyrrole phenyls do not show.

  4. Crystal structure of the sodium-potassium pump

    DEFF Research Database (Denmark)

    Morth, J Preben; Pedersen, Bjørn Panyella; Toustrup-Jensen, Mads S

    2007-01-01

    The Na+,K+-ATPase generates electrochemical gradients for sodium and potassium that are vital to animal cells, exchanging three sodium ions for two potassium ions across the plasma membrane during each cycle of ATP hydrolysis. Here we present the X-ray crystal structure at 3.5 A resolution......-subunit is contained within a pocket between transmembrane helices and seems to be a novel regulatory element controlling sodium affinity, possibly influenced by the membrane potential. Udgivelsesdato: 2007-Dec-13...

  5. Crystal structure studies on plate/shelf like disodium ditungstate

    Indian Academy of Sciences (India)

    Inorganic materials; disodium ditungstate; crystal structure; scanning electron microscopy; X-ray ... generation, and horizontal electric furnace with quartz tube ... Unit cell dimensions: a = 7·22192(11) Е, b = 11·91559(17) Е, c = 14·74755(23) Е. Cell content: 8 Na2W2O7). Atom. Position. X(σ(X)). Y(σ(Y)). Z(σ(Z)). B(σ(B)). W (1).

  6. Crystal structure of the uranyl-oxide mineral rameauite

    Czech Academy of Sciences Publication Activity Database

    Plášil, Jakub; Škoda, R.; Čejka, J.; Bourgoin, V.; Boulliard, J.C.

    2016-01-01

    Roč. 28, č. 5 (2016), s. 959-967 ISSN 0935-1221 R&D Projects: GA MŠk LO1603 EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : rameauite * uranyl-oxide hydroxy-hydrate * crystal structure * Raman spectrum Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.362, year: 2016

  7. Growth and structural, optical, and electrical properties of zincite crystals

    Science.gov (United States)

    Kaurova, I. A.; Kuz'micheva, G. M.; Rybakov, V. B.

    2013-03-01

    An X-ray diffraction study of ZnO crystals grown by the hydrothermal method has revealed reflections that give grounds to assign them to the sp. gr. P3 rather than to P63 mc. The distribution of Zn1, Zn2, O1, and O2 over structural positions, along with vacancies and incorporated zinc atoms, explains the dissymmetrization observed in terms of the kinetic (growth) phase transition of the order-disorder type, which is caused by ordering Zn and O atoms over structural positions. The color of crystals of refined compositions (Zn0.975□0.025)Zn i(0.015)(O0.990□0.010) (green) and (Zn0.965□0.035)Zn i(0.035)O (bright green) is related to different oxygen contents, which is confirmed by the results of electron probe X-ray microanalysis and absorption spectroscopy. The degree of the structural quality of crystals, their resistivity, and activation energy are also related to oxygen vacancies.

  8. The Synthesis and Crystal Structure of Two New Hydrazone Compounds

    Directory of Open Access Journals (Sweden)

    Li-Hua Wang

    2016-05-01

    Full Text Available Two new hydrazone compounds, 4-formylimidazole-4-hydroxybenzhydrazone dihydrate (1 and 2-nitrobenzaldehyde-2-furan formylhydrazone (2, were synthesized via the classical synthesis method. Their structure was determined via elemental analysis and X-ray single crystal diffraction analysis. Compound 1 crystallizes in triclinic, space group P-1 with a = 7.0321(14 Å, b = 7.3723(15 Å, c = 13.008(3 Å, α = 98.66(3°, β = 101.69(3°, γ = 92.25(3°, V = 651.2(2 Å3, Z = 2, Dc = 1.358 g·cm−3, μ = 0.106 mm−1, F(000 = 280, and final R1 = 0.0564, wR2 = 0.1420. Compound 2 crystallizes in monoclinic, space group P21/c with a = 17.3618(9 Å, b = 9.1506(4 Å, c = 15.5801(7 Å, β = 104.532(5°, V = 2396.05(19 Å3, Z = 8, Dc = 1.437 g·cm−3, μ = 0.111 mm−1, F(000 = 1072, and final R1 = 0.0633, wR2 = 0.1649. Compound 1 forms a 2D-layered structure via the interactions of 1D chains and Compound 2 forms a 3D network structure via the interactions of 1D chains.

  9. 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...

  10. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  11. Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

    Science.gov (United States)

    Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

    1981-08-04

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

  12. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Shen, Yang [Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7 (Canada); Jiao, Ronghong [Department of Function Inspection, Hebei Provincial People' s Hospital, Shijiazhuang 050051 (China); Liu, Yanli; Deng, Lingfu [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Qi, Chao, E-mail: qichao@mail.ccnu.edu.cn [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer This is the first structural information of human Rab3B. Black-Right-Pointing-Pointer To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. Black-Right-Pointing-Pointer The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 A resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  13. Crystal structure of inactive form of Rab3B

    International Nuclear Information System (INIS)

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    2012-01-01

    Highlights: ► This is the first structural information of human Rab3B. ► To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. ► The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 Å resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  14. Facile synthesis of gold nanomaterials with unusual crystal structures.

    Science.gov (United States)

    Fan, Zhanxi; Huang, Xiao; Chen, Ye; Huang, Wei; Zhang, Hua

    2017-11-01

    Gold (Au) nanomaterials have attracted wide research attention, owing to their high chemical stability, promising catalytic properties, excellent biocompatibility, unique electronic structure and outstanding localized surface plasmon resonance (LSPR) absorption properties; all of which are closely related to their size and shape. Recently, crystal-phase-controlled synthesis of noble metal nanomaterials has emerged as a promising strategy to tune their physicochemical properties. This protocol describes the detailed experimental procedures for the crystal-phase-controlled syntheses of Au nanomaterials with unusual crystal structures under mild conditions. Briefly, pure hexagonal close-packed (hcp) Au square sheets (AuSSs) with a thickness of ∼2.4 nm are synthesized using a graphene-oxide-assisted method in which HAuCl 4 is reduced by oleylamine in a mixture of hexane and ethanol. By using pure hexane as the solvent, well-dispersed ultrathin hcp/face-centered cubic (fcc) Au nanowires with a diameter of ∼1.6 nm on graphene oxide can be obtained. Meanwhile, hcp/fcc Au square-like plates with a side length of 200-400 nm are prepared via the secondary growth of Au on the hcp AuSSs. Remarkably, hexagonal (4H) Au nanoribbons with a thickness of 2.0-6.0 nm can be synthesized with a one-pot colloidal method in which HAuCl 4 is reduced by oleylamine in a mixed solvent of hexane and 1,2-dichloropropane. It takes 17-37 h for the synthesis of these Au nanomaterials with unusual crystal structures. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) are used to characterize the resultant Au nanomaterials, which could have many promising applications, such as biosensing, near-IR photothermal therapy, catalysis and surface-enhanced Raman scattering (SERS).

  15. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Morshed, Nader [University of California, Berkeley, CA 94720 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Echols, Nathaniel, E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Adams, Paul D., E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California, Berkeley, CA 94720 (United States)

    2015-05-01

    A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  16. Crystal Structure of the Yeast Nicotinamidase Pnc1p

    OpenAIRE

    Hu, Gang; Taylor, Alexander B.; McAlister-Henn, Lee; Hart, P. John

    2007-01-01

    The yeast nicotinamidase Pnc1p acts in transcriptional silencing by reducing levels of nicotinamide, an inhibitor of the histone deacetylase Sir2p. The Pnc1p structure was determined at 2.9 Å resolution using MAD and MIRAS phasing methods after inadvertent crystallization during the pursuit of the structure of histidine-tagged yeast isocitrate dehydrogenase (IDH). Pnc1p displays a cluster of surface histidine residues likely responsible for its co-fractionation with IDH from Ni2+-coupled chro...

  17. Topological Characterization of Carbon Graphite and Crystal Cubic Carbon Structures.

    Science.gov (United States)

    Siddiqui, Wei Gao Muhammad Kamran; Naeem, Muhammad; Rehman, Najma Abdul

    2017-09-07

    Graph theory is used for modeling, designing, analysis and understanding chemical structures or chemical networks and their properties. The molecular graph is a graph consisting of atoms called vertices and the chemical bond between atoms called edges. In this article, we study the chemical graphs of carbon graphite and crystal structure of cubic carbon. Moreover, we compute and give closed formulas of degree based additive topological indices, namely hyper-Zagreb index, first multiple and second multiple Zagreb indices, and first and second Zagreb polynomials.

  18. Band structures in the nematic elastomers phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Shuai [Department of Mechanics, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044 (China); School of Civil Engineering and Architecture, Anyang Normal University, Anyang 455000 (China); Liu, Ying, E-mail: yliu5@bjtu.edu.cn [Department of Mechanics, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044 (China); Liang, Tianshu [Department of Mechanics, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044 (China)

    2017-02-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  19. Band structures in the nematic elastomers phononic crystals

    International Nuclear Information System (INIS)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    2017-01-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  20. Synthesis and Single Crystal X-Ray Structure Determination of 3,3',5 ...

    African Journals Online (AJOL)

    Single crystal structure determination at 100 K revealed needle-like crystals in an orthorhombic crystal system. The asymmetric unit of the cell consists of an isolated chloride ion, one half of a tetrahedral [MnCl4]2- anion, a [H2Me4bpz]2+ dication and one half of a molecule of water. Keywords: Crystal Engineering, Hydrogen ...

  1. Natural Cr3+-rich ettringite: occurrence, properties, and crystal structure

    Science.gov (United States)

    Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.; Murashko, Mikhail N.

    2017-08-01

    Cr3+-rich ettringite with Cr3+→Al substitution and Cr/(Cr + Al) ratios up to 0.40-0.50 was found in mineral assemblages of the Ma'aleh Adumim area of Mottled Zone (Judean Desert). The Cr3+-rich compositions were the latest in the thaumasite → ettringite-thaumasite solid solution → ettringite → ettringite-bentorite solid solution series. The mineral-forming solution was enriched in Cr3+ and had a pH buffered by afwillite at 11-12. Chromium was inherited from larnite rocks produced by high-temperature combustion metamorphic alteration of bioproductive calcareous sediments. The Cr/(Cr + Al) ratios are within 0.10-0.15 in most of the analysed crystals. This degree of substitution imparts pink colouration to the crystals, but does not affect their habit (a combination of monohedra and a prism). The habit changes to pyramid faces in coarse and later Cr3+-bearing crystals as Cr/(Cr + Al) ratios increase abruptly to 0.40-0.50. Single-crystal XRD analysis of one Cr-free and two Cr3+-rich samples and their structure determination and refinement indicate that the Cr-rich crystals (with Cr/(Cr + Al) to 0.3) preserve the symmetry and metrics of ettringite. The Ca-O bonding network undergoes differentiation with increase of Cr3+ concentration at octahedral M sites. The compression of Ca2 and expansion of Ca1 polyhedra sub-networks correlates with the degree of Cr3+→Al substitution.

  2. Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

    International Nuclear Information System (INIS)

    Caskey, Christopher M.; Holder, Aaron; Christensen, Steven T.; Biagioni, David; Ginley, David S.; Tumas, William; Perkins, John D.; Lany, Stephan; Zakutayev, Andriy; Shulda, Sarah; Diercks, David; Pylypenko, Svitlana; Richards, Ryan M.; Schwartz, Craig P.; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Sun, Wenhao; Orvananos, Bernardo

    2016-01-01

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn 3 N 4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

  3. Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Caskey, Christopher M. [National Renewable Energy Laboratory, Golden, Colorado 80401 (United States); Colorado School of Mines, Golden, Colorado 80401 (United States); Larix Chemical Science, Golden, Colorado 80401 (United States); Holder, Aaron; Christensen, Steven T.; Biagioni, David; Ginley, David S.; Tumas, William; Perkins, John D.; Lany, Stephan; Zakutayev, Andriy, E-mail: andriy.zakutayev@nrel.gov [National Renewable Energy Laboratory, Golden, Colorado 80401 (United States); Shulda, Sarah; Diercks, David; Pylypenko, Svitlana; Richards, Ryan M. [Colorado School of Mines, Golden, Colorado 80401 (United States); Schwartz, Craig P.; Nordlund, Dennis [SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Kukliansky, Alon; Natan, Amir [Tel Aviv University, Tel Aviv-Yafo (Israel); Prendergast, David; Sun, Wenhao [Lawrence Berkeley National Laboratory, Berkley, California 94720 (United States); Orvananos, Bernardo [Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); and others

    2016-04-14

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

  4. Crystal structures of two eukaryotic nucleases involved in RNA metabolism

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich

    RNA serves a number of functions in the cell: mRNAs are the carriers of information between gene and protein, tRNAs and rRNAs are involved in the synthesis of proteins, whereas a number of additional RNA species are responsible for other functions in the cell. The quality of the different RNAs...... RNAs. We have solved the structures of two nucleases involved in 3'-5' degradation of RNA; the S. pombe Pop2p and the S. cerevisiae Rrp6p. Pop2p is part of the main cytoplasmatic deadenylation complex in yeast, which also contains the nuclease Ccr4p. Deadenylation, where the poly(A)-tail is removed...... specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures...

  5. The crystal structure of human GDP-L-fucose synthase.

    Science.gov (United States)

    Zhou, Huan; Sun, Lihua; Li, Jian; Xu, Chunyan; Yu, Feng; Liu, Yahui; Ji, Chaoneng; He, Jianhua

    2013-09-01

    Human GDP-l-fucose synthase, also known as FX protein, synthesizes GDP-l-fucose from its substrate GDP-4-keto-6-deoxy-d-mannose. The reaction involves epimerization at both C-3 and C-5 followed by an NADPH-dependent reduction of the carbonyl at C-4. In this paper, the first crystal structure of human FX protein was determined at 2.37 Å resolution. The asymmetric unit of the crystal structure contains four molecules which form two homodimers. Each molecule consists of two domains, a Rossmann-fold NADPH-binding motif and a carboxyl terminal domain. Compared with the Escherichia coli GDP-l-fucose synthase, the overall structures of these two enzymes have four major differences. There are four loops in the structure of human FX protein corresponding to two α-helices and two β-sheets in that of the E. coli enzyme. Besides, there are seven different amino acid residues binding with NAPDH comparing human FX protein with that from E. coli. The structure of human FX reveals the key catalytic residues and could be useful for the design of drugs for the treatment of inflammation, auto-immune diseases, and possibly certain types of cancer.

  6. Magnetic activity at infrared frequencies in structured metallic photonic crystals

    International Nuclear Information System (INIS)

    O'Brien, S.; Pendry, J.P.

    2002-01-01

    We derive the effective permeability and permittivity of a nanostructured metallic photonic crystal by analysing the complex reflection and transmission coefficients for slabs of various thicknesses. These quantities were calculated using the transfer matrix method. Our results indicate that these structures could be used to realize a negative effective permeability, at least up to infrared frequencies. The origin of the negative permeability is a resonance due to the internal inductance and capacitance of the structure. We also present an analytic model for the effective permeability of the crystal. The model reveals the importance of the inertial inductance due to the finite mass of the electrons in the metal. We find that this contribution to the inductance has implications for the design of metallic magnetic structures in the optical region of the spectrum. We show that the magnetic activity in the structure is accompanied by the concentration of the incident field energy into very small volumes within the structure. This property will allow us to considerably enhance non-linear effects with minute quantities of material. (author)

  7. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    Science.gov (United States)

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  8. Crystal structure of bile salt hydrolase from Lactobacillus salivarius.

    Science.gov (United States)

    Xu, Fuzhou; Guo, Fangfang; Hu, Xiao Jian; Lin, Jun

    2016-05-01

    Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of BSH function, which has hampered the development of BSH-based strategies for improving human and animal health. As an initial step towards the structure-function analysis of BSH, C-terminally His-tagged BSH from Lactobacillus salivarius NRRL B-30514 was crystallized in this study. The 1.90 Å resolution crystal structure of L. salivarius BSH was determined by molecular replacement using the structure of Clostridium perfringens BSH as a starting model. It revealed this BSH to be a member of the N-terminal nucleophile hydrolase superfamily. Crystals of apo BSH belonged to space group P21212, with unit-cell parameters a = 90.79, b = 87.35, c = 86.76 Å (PDB entry 5hke). Two BSH molecules packed perfectly as a dimer in one asymmetric unit. Comparative structural analysis of L. salivarius BSH also identified potential residues that contribute to catalysis and substrate specificity.

  9. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE OF BIS-(2-HYDROXYBENZALDEHYDEDIAMINOGUANIZONE

    Directory of Open Access Journals (Sweden)

    Diana Dragancea, Vladimir B. Arion, Sergiu Shova

    2008-12-01

    Full Text Available The new ligand, bis(2-hydroxybenzaldehydediaminoguanizone (1 has been synthesized and characterized by elemental analysis, IR and 1H NMR spectroscopies. The crystal structure of the compound was determined by X-ray diffraction. The ligand C15H15N5O2·C2H5OH crystallizes in the monoclinic space group P21/c with unit cell parameters a = 8.9102(3, b = 10.0357(3, c = 19.7618(6 Å, β = 98.385(2°, Z = 4, V = 1748.21(9 Å3, R1 = 0.040. The amino form of the ligand adopts a planar conformation stabilized by two intramolecular hydrogen bonds of the type O–H···N, in which the H atoms of the central amino group are directed to the lone-pair regions of the azomethine nitrogen atoms.

  10. Crystal structures and conformers of CyMe4-BTBP

    Directory of Open Access Journals (Sweden)

    Lyczko Krzysztof

    2015-12-01

    Full Text Available The crystal structure of new conformation of the CyMe4-BTBP ligand (ttc has been presented. The ttt conformer of this compound in a form of THF solvate has been also crystallized. The geometries of six possible conformations (ttt, ttc, tct, tcc, ctc and ccc of the CyMe4-BTBP ligand have been modeled in the gas phase and in solutions (MeOH and H2O by DFT calculations using B3LYP/6-31G(d,p method. According to the calculations, in the three different media the conformers with trans orientation of the N atoms in the bipyridyl moiety are the most stable.

  11. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatecobalt(II

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-01-01

    Full Text Available The structure of the mononuclear title complex, [{(H3CS2C=NC[triple-bond] N}2CoCl2], consists of a CoII atom coordinated in a distorted tetrahedral manner by two Cl− ligands and the terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515 (su? Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.

  12. Crystal Structure of Na3MoCl6

    Directory of Open Access Journals (Sweden)

    Martin Beran

    2011-07-01

    Full Text Available The ternary chloride Na3MoCl6 is obtained as red crystals from a disproportionation reaction of molybdenum dichloride, {Mo6}Cl12, in an acidic NaCl/AlCl3 melt at 350 °C. The crystal structure (trigonal, P-31c, a = 687.1(1, c = 1225.3(2 pm, Z = 2, V = 501,0(1 106 pm3 is that of Na3CrCl6: within a hexagonal closest-packing of chloride ions two thirds of the octahedral voids are filled between the AB double layers with Na+/Mo3+, and between the BA layers with Na+.

  13. Crystal structure of homoserine O-acetyltransferase from Leptospira interrogans

    International Nuclear Information System (INIS)

    Wang Mingzhu; Liu Lin; Wang Yanli; Wei Zhiyi; Zhang Ping; Li Yikun; Jiang Xiaohua; Xu Hang; Gong Weimin

    2007-01-01

    Homoserine O-acetyltransferase (HTA, EC 2.3.1.31) initiates methionine biosynthesis pathway by catalyzing the transfer of acetyl group from acetyl-CoA to homoserine. This study reports the crystal structure of HTA from Leptospira interrogans determined at 2.2 A resolution using selenomethionyl single-wavelength anomalous diffraction method. HTA is modular and consists of two structurally distinct domains-a core α/β domain containing the catalytic site and a helical bundle called the lid domain. Overall, the structure fold belongs to α/β hydrolase superfamily with the characteristic 'catalytic triad' residues in the active site. Detailed structure analysis showed that the catalytic histidine and serine are both present in two conformations, which may be involved in the catalytic mechanism for acetyl transfer

  14. Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

    2006-05-19

    Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

  15. Crystal structure and thin film morphology of BBL ladder polymer

    Energy Technology Data Exchange (ETDEWEB)

    Song, H H [Department of Macromolecular Science, Han Nam University, Taejon (Korea, Republic of); Fratini, A V [Department of Chemistry, University of Dayton, Dayton, OH (United States); Chabinyc, M [Department of Chemistry, University of Dayton, Dayton, OH (United States); Price, G E [University of Dayton Research, Dayton, OH (United States); Agrawal, A K [Systran Corporation, Dayton, OH (United States); Wang, C S [University of Dayton Research, Dayton, OH (United States); Burkette, J [University of Dayton Research, Dayton, OH (United States); Dudis, D S [Materials Directorate, Wright Laboratory, Wright-Patterson Air Force Base, OH (United States); Arnold, F E [Materials Directorate, Wright Laboratory, Wright-Patterson Air Force Base, OH (United States)

    1995-03-01

    Crystal structure and morphology of poly[7-oxo-7H-benz(d,e)imidazo(4`,5`:5,6)-benzimidazo(2,1-a)isoquinoline-3,4:10,11-tetrayl-10-carbonyl] (BBL) ladder-like polymer were studied. The polymer forms a two-dimensional lattice of nematic liquid crystalline structure. An orthorhombic unit cell with cell parameters of a=7.87 b=3.37 c=11.97A was determined from the fiber diffraction pattern. In thin films, the rigid chains spontaneously form a layered structure across the film thickness, but in a very unusual manner, i.e. the very large molecular plane is standing perpendicularly to the film surface plane. The results are identical to our recent results of poly(p-phenylene benzobisthiazole) (PBT) film [7]. The polymer, however, lost its anisotropic order upon extrusion into a film and resulted in a fiber-like structure. (orig.)

  16. Structural and morphological characterization of fullerite crystals prepared from the vapor phase

    International Nuclear Information System (INIS)

    Haluska, M.; Fejdi, P.; Vybornov, M.; Kuzmany, H.

    1993-01-01

    Crystal structure, habits and surface structures of fullerite crystals prepared from vapor phase were characterized by X-ray analysis, interfacial angle measurements and optical and scanning electron microscopy (SEM). The study of selected C 60 crystals confirmed the fcc structure at room temperature. The crystal habit is determined by two types of morphological faces, namely {100} and {111}. SEM was used for the observation of thermal etched surfaces. (orig.)

  17. Microbial community structure of relict niter-beds previously used for saltpeter production.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA. The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA, respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

  18. Enzyme catalysis captured using multiple structures from one crystal at varying temperatures

    Directory of Open Access Journals (Sweden)

    Sam Horrell

    2018-05-01

    Full Text Available High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K to generate `structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a `top-hat' geometry, which was rapidly transformed to a `side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT, providing an unparallelled level of structural information during catalysis for redox enzymes.

  19. Crystal structure of the Japanese encephalitis virus envelope protein.

    Science.gov (United States)

    Luca, Vincent C; AbiMansour, Jad; Nelson, Christopher A; Fremont, Daved H

    2012-02-01

    Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-Å resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

  20. Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

    2006-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

  1. Synthesis and crystal structure of chromium-bearing anhydrous wadsleyite

    Science.gov (United States)

    Sirotkina, E. A.; Bindi, L.; Bobrov, A. V.; Aksenov, S. M.; Irifune, T.

    2018-04-01

    A chromium-bearing wadsleyite (Cr- Wad) was synthesized in the model system Mg2SiO4-MgCr2O4 at 14 GPa and 1600 °C and studied from the chemical and structural point of views. Microprobe data gave the formula Mg1.930Cr0.120Si0.945O4, on the basis of 4 oxygen atoms. The crystal structure has been studied by single-crystal X-ray diffraction. The orthorhombic unit-cell parameters are: a = 5.6909(5) Å, b = 11.4640(10) Å, c = 8.2406(9) Å, V = 537.62(9) Å3, Z = 8. The structure, space group Imma, was refined to R 1 = 5.99% in anisotropic approximation using 1135 reflections with F o > 4σ( F o) and 43 parameters. Chromium was found to substitute for both Mg at the octahedral sites and Si at the tetrahedral site, according to the reaction VIMg2+ + IVSi4+ = VICr3+ + IVCr3+. On the whole, the structural topology is nearly identical to that of pure wadsleyite. The successful synthesis of Cr- Wad may be important for the thermobarometry of mantle phase associations.

  2. Prediction of new ground-state crystal structure of T a2O5

    Science.gov (United States)

    Yang, Yong; Kawazoe, Yoshiyuki

    2018-03-01

    Tantalum pentoxide (T a2O5 ) is a wide-gap semiconductor which has important technological applications. Despite the enormous efforts from both experimental and theoretical studies, the ground-state crystal structure of T a2O5 is not yet uniquely determined. Based on first-principles calculations in combination with evolutionary algorithm, we identify a triclinic phase of T a2O5 , which is energetically much more stable than any phases or structural models reported previously. Characterization of the static and dynamical properties of the phase reveals the common features shared with previous metastable phases of T a2O5 . In particular, we show that the d spacing of ˜3.8 Å found in the x-ray diffraction patterns of many previous experimental works is actually the radius of the second Ta-Ta coordination shell as defined by radial distribution functions.

  3. Crystal structure of the human 4-1BB/4-1BBL complex.

    Science.gov (United States)

    Gilbreth, Ryan N; Oganesyan, Vaheh Y; Amdouni, Hamza; Novarra, Shabazz; Grinberg, Luba; Barnes, Arnita; Baca, Manuel

    2018-05-02

    4-1BBL is a member of the TNF superfamily and is the ligand for the TNFRsuperfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells and agonists of this receptor have garnered strong attention as potentialimmunotherapy agents. Broadly speaking, the structural features of TNF superfamilymembers, their receptors and ligand/receptor complexes are similar. However, apublished crystal structure of human 4-1BBL suggests that it may be unique in thisregard, exhibiting a three-bladed propeller-like trimer assembly that is distinctly different from that observed in other family members. This unusual structure also suggests that the human 4-1BB/4-1BBL complex may be structurally unique within the TNF/TNFR superfamily, but to date no structural data have been reported. Here we report the crystal structure of the human 4-1BB/4-1BBL complex at 2.4 Å resolution. In this structure, 4-1BBL does not adopt the unusual trimer assembly previously reported, but instead forms a canonical bell-shaped trimer typical of other TNF superfamily members. The structure of 4-1BB is also largely canonical as is the 4-1BB/4-1BBL complex. Mutational data support the 4-1BBL structure reported here as being biologically relevant, suggesting that the previously reported structure is not. Together, the data presented here offer insight into structure/function relationships in the 4-1BB/4-1BBL system and improve our structural understanding of the TNF/TNFR superfamily more broadly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Synthesis, crystal structure, physicochemical properties of hydrogen bonded supramolecular assembly of N,N-diethylanilinium-3, 5-dinitrosalicylate crystal

    Science.gov (United States)

    Rajkumar, M.; Chandramohan, A.

    2017-12-01

    An organic salt, N,N-diethylanilinium 3,5-dinitrosalicylate was synthesized and single crystals grown by employing the slow solvent evaporation solution growth technique in methanol-acetone (1:1) mixture. The electronic transitions of the salt crystal were studied by UV-Visible spectrum. The optical transmittance window and lower wavelength cut-off of grown crystal have been identified by UV-Vis-NIR studies. The FT-IR spectrum was recorded to confirm the presence of various functional groups in the grown crystal. 1H and 13C NMR spectrum were recorded to establish the molecular structure of the title crystal. Single crystal X-ray diffraction data indicated that the crystal belongs to monoclinic crystal system with P21/n space group. The thermal stability of the crystal was established by TG/DTA studies. The mechanical properties of the grown crystal were studied by Vickers' microhardness technique. The dielectric studies indicated that the dielectric constant and dielectric loss decrease exponentially with frequency at different temperatures.

  5. Synthesis and crystal structure of MgB12

    International Nuclear Information System (INIS)

    Adasch, Volker; Hess, Kai-Uwe; Ludwig, Thilo; Vojteer, Natascha; Hillebrecht, Harald

    2006-01-01

    Single crystals of MgB 12 were synthesized from the elements in a Mg/Cu melt at 1600deg. C. MgB 12 crystallizes orthorhombic in space group Pnma with a=16.632(3)A, b=17.803(4)A and c=10.396(2)A. The crystal structure (Z=30, 5796 reflections, 510 variables, R 1 (F)=0.049, wR 2 (I)=0.134) consists of a three dimensional net of B 12 icosahedra and B 21 units in a ratio 2:1. The B 21 units are observed for the first time in a solid compound. Mg is on positions with partial occupation. The summation reveals the composition MgB 12.35 or Mg 0.97 B 12 , respectively. This is in good agreement with the value of MgB 11.25 as expected by electronic reasons to stabilize the boron polyhedra B 12 2- and B 21 4-

  6. Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum.

    Science.gov (United States)

    Bhaumik, Prasenjit; Horimoto, Yasumi; Xiao, Huogen; Miura, Takuya; Hidaka, Koushi; Kiso, Yoshiaki; Wlodawer, Alexander; Yada, Rickey Y; Gustchina, Alla

    2011-07-01

    Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1Å, respectively. The apoenzyme crystallized in the orthorhombic space group P2(1)2(1)2(1) with two molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4(3) with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes. Published by Elsevier Inc.

  7. Structure and Chemical Durability of Lead Crystal Glass.

    Science.gov (United States)

    Angeli, Frédéric; Jollivet, Patrick; Charpentier, Thibault; Fournier, Maxime; Gin, Stéphane

    2016-11-01

    Silicate glasses containing lead, also called lead crystal glasses, are commonly used as food product containers, in particular for alcoholic beverages. Lead's health hazards require major attention, which can first be investigated through the understanding of Pb release mechanisms in solution. The behavior of a commercial crystal glass containing 10.6 mol % of PbO (28.3 wt %) was studied in a reference solution of 4% acetic acid at 22, 40, and 70 °C at early and advanced stages of reaction. High-resolution solid-state 17 O and 29 Si NMR was used to probe the local structure of the pristine and, for the first time, of the altered lead crystal glass. Inserted into the vitreous structure between the network formers as Si-O-Pb bonds, Pb does not form Pb-O-Pb clusters which are expected to be more easily leached. A part of K is located near Pb, forming mixed Si-O-(Pb,K) near the nonbridging oxygens. Pb is always released into the solution following a diffusion-controlled dissolution over various periods of time, at a rate between 1 and 2 orders of magnitude lower than the alkalis (K and Na). The preferential release of alkalis is followed by an in situ repolymerization of the silicate network. Pb is only depleted in the outermost part of the alteration layer. In the remaining part, it stays mainly surrounded by Si in a stable structural configuration similar to that of the pristine glass. A simple model is proposed to estimate the Pb concentration as a function of glass surface, solution volume, temperature, and contact time.

  8. 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.

  9. Crystal structure and solid-state properties of discrete hexa cationic ...

    Indian Academy of Sciences (India)

    Subsequently, weight loss of 33% in two stages from 242 to 691◦C can be assigned to the decomposition of triazole ligands. 3.3 Description of the crystal structure. The solid-state structure of ZnT was unambiguously determined by the single crystal X-ray diffraction tech- nique (figures 2 and 3). Compound ZnT crystallizes in.

  10. Crystal Structure of Mammalian Cysteine dioxygenase: A Novel Mononuclear Iron Center for Cysteine Thiol Oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons,C.; Liu, Q.; Huang, Q.; Hao, Q.; Begley, T.; Karplus, P.; Stipanuk, M.

    2006-01-01

    Cysteine dioxygenase is a mononuclear iron-dependent enzyme responsible for the oxidation of cysteine with molecular oxygen to form cysteinesulfinate. This reaction commits cysteine to either catabolism to sulfate and pyruvate or to the taurine biosynthetic pathway. Cysteine dioxygenase is a member of the cupin superfamily of proteins. The crystal structure of recombinant rat cysteine dioxygenase has been determined to 1.5 Angstroms resolution, and these results confirm the canonical cupin {beta}-sandwich fold and the rare cysteinyl-tyrosine intramolecular crosslink (between Cys93 and Tyr157) seen in the recently reported murine cysteine dioxygenase structure. In contrast to the catalytically inactive mononuclear Ni(II) metallocenter present in the murine structure, crystallization of a catalytically competent preparation of rat cysteine dioxygenase revealed a novel tetrahedrally coordinated mononuclear iron center involving three histidines (His86, His88, and His140) and a water molecule. Attempts to acquire a structure with bound ligand using either co-crystallization or soaks with cysteine revealed the formation of a mixed disulfide involving Cys164 near the active site, which may explain previously observed substrate inhibition. This work provides a framework for understanding the molecular mechanisms involved in thiol dioxygenation and sets the stage for exploring the chemistry of both the novel mononuclear iron center and the catalytic role of the cysteinyl-tyrosine linkage.

  11. Crystal structure of Homo sapiens protein LOC79017

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.; Phillips, Jr., George N. (UW)

    2010-02-08

    LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

  12. Crystal Structure of a Lipid G Protein-Coupled Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Michael A; Roth, Christopher B; Jo, Euijung; Griffith, Mark T; Scott, Fiona L; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M; Schuerer, Stephan C; Sanna, M Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C [Scripps; (Receptos)

    2012-03-01

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P1-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P1, resulting in the modulation of immune and stromal cell responses.

  13. Syntheses, Crystal Structures and Bioactivities of Two Novel Isatin Derivatives

    Institute of Scientific and Technical Information of China (English)

    SHANG Jian-li; LI Hui-dong; SHANG Jun; SONG Hai-bin; LI Zheng-ming; WANG Jian-guo

    2011-01-01

    Two novel compoundsl-(4-fluorobenzyl)-4-chloro-(Z)-3-benzoylhydrazono-2-indolinone(1) and 1-(4-methoxybenzyl)-(Z)-3-benzoylhydrazono-2-indolinone(2) were synthesized and their crystal structures were determined by single-crystal X-ray diffraction.Compound 1(C22H15ClFN3O2) crystallized in the triclinic system,space group P1- with a=0.94198(19) nm,b=1.4339(3) nm,c=1.5018(3) nm,a=101.58(3)°,β=102.96(3)°,γ=102.73°,V=1.8602(6) nm3,Mr=407.82,Dc=1.456 g/cm3,μ=0.240 mm-1,F(000)=840,Z=4,R1=0.0442 and wR2=0.1064.Compound 2(C23H19N3O3) crystallized in the triclinic system,space group P1- with a=1.0022(2) nm,b=1.0192(2) nm,c=1.0461(2) nm,a=99.86(3)°,β=117.30(3)°,γ=94.13(3)°,V=0.9215(3) nm3,Mr=385.41,Dc=1.389 g/cm3,μ=0.094mm-1,F(000)=404,Z=2,R1=0.0403 and wR2=0.1142.The preliminary herbicidal activities of the two compounds were also evaluated.

  14. Crystal structure of the yeast nicotinamidase Pnc1p.

    Science.gov (United States)

    Hu, Gang; Taylor, Alexander B; McAlister-Henn, Lee; Hart, P John

    2007-05-01

    The yeast nicotinamidase Pnc1p acts in transcriptional silencing by reducing levels of nicotinamide, an inhibitor of the histone deacetylase Sir2p. The Pnc1p structure was determined at 2.9A resolution using MAD and MIRAS phasing methods after inadvertent crystallization during the pursuit of the structure of histidine-tagged yeast isocitrate dehydrogenase (IDH). Pnc1p displays a cluster of surface histidine residues likely responsible for its co-fractionation with IDH from Ni(2+)-coupled chromatography resins. Researchers expressing histidine-tagged proteins in yeast should be aware of the propensity of Pnc1p to crystallize, even when overwhelmed in concentration by the protein of interest. The protein assembles into extended helical arrays interwoven to form an unusually robust, yet porous superstructure. Comparison of the Pnc1p structure with those of three homologous bacterial proteins reveals a common core fold punctuated by amino acid insertions unique to each protein. These insertions mediate the self-interactions that define the distinct higher order oligomeric states attained by these molecules. Pnc1p also acts on pyrazinamide, a substrate analog converted by the nicotinamidase from Mycobacterium tuberculosis into a product toxic to that organism. However, we find no evidence for detrimental effects of the drug on yeast cell growth.

  15. GPCR crystal structures: Medicinal chemistry in the pocket.

    Science.gov (United States)

    Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Löber, Stefan

    2015-07-15

    Recent breakthroughs in GPCR structural biology have significantly increased our understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystallized in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand binding pockets in GPCRs. In this review, we summarise the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity or efficacy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. New halides of neodymium and their crystal structures

    International Nuclear Information System (INIS)

    Loechner, U.

    1980-01-01

    The crystal structures of the peritectic phases NdClsub(2.27) (t-phase) and NdClsub(2.37) (rh-phase) were determined. The structure of the rh-phase was solved, from the t-phase only the elementary cell could be determined because no single crystals of sufficient quality were obtained. Jutting out feature of the rh-phase which has to be formulated as Nd 14 Cl 32 O is a polyeder cluster of 6 quadratic antiprisms the inner cubo octahedric cavity of which is occupied by an oxygen atom. The linkage of these polyeder cluster ensues only under each other along the triple axis of the rhomboedric system over 3 upper and 3 lower common borders each. Therewith for the first time a superlattice of the fluorite-type was found in which this unit exclusively occurs. The type of linkage of polyeder clusters causes the occurrence of an exceptional polyeder around the twovalent Nd ions which can be looked at as a zwitter polyeder of icosahedron and cube and therefore coordinates tenfold the twovalent neodymium. The strict order of chemically and crystallografically clearly differentiated cations is expressed by a hexagonal-rhomboedric superstructure of the fluorite-aristotyp with a doubled c-axis. The phase diagram of the system Nd-NdBr 3 was determined and a structure proposition was worked out for the first Vernier phase in there with n=4 of the series Lnsub(n)Xsub(2n+1). (SPI)

  17. Models of protein-ligand crystal structures: trust, but verify.

    Science.gov (United States)

    Deller, Marc C; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  18. Crystal structure of the Al2CuIr phase

    International Nuclear Information System (INIS)

    Meshi, L.; Ezersky, V.; Kapush, D.; Grushko, B.

    2010-01-01

    A new ternary Al 2 CuIr phase was revealed in the Al-Cu-Ir system. It is formed below 1063 o C from the β-phase (CsCl-type structure) extending at elevated temperatures from AlIr. The crystal structure of the Al 2 CuIr phase was determined using a combination of precession electron diffraction and X-ray powder diffraction techniques. The phase has an orthorhombic C-centered unit cell with lattice parameters a = 8.1196(7) A, b = 5.0646(2) A and c = 5.18513(3) A; its crystal symmetry can be described by the Cmme (no. 67) space group (Pearson symbol oC16). The unit cell of the new phase contains 8 Al, 4 Cu and 4 Ir atoms and exhibits a new structure type. The reliability factors characterizing the Rietveld refinement procedure are: R p = 4.45%, R wp = 6.45%, R B = 3.69% and R f = 2.41%.

  19. Crystal structure of 2-cyano-1-methylpyridinium perchlorate

    Directory of Open Access Journals (Sweden)

    Vu D. Nguyen

    2015-11-01

    Full Text Available The asymmetric unit of the title salt, C7H7N2+·ClO4−, comprises two independent formula units. The solid-state structure comprises corrugated layers of cations and of anions, approximately parallel to (010. The supramolecular layers are stabilized and connected by C—H...O hydrogen bonding to consolidate a three-dimensional architecture. A close pyridinium–perchlorate N...O contact [2.867 (5 Å] is noted. The crystal was refined as an inversion twin.

  20. Electrical and Structural Characterization of Web Dendrite Crystals

    Science.gov (United States)

    Schwuttke, G. H.; Koliwad, K.; Dumas, K. A.

    1985-01-01

    Minority carrier lifetime distributions in silicon web dendrites are measured. Emphasis is placed on measuring areal homogeneity of lifetime, show its dependency on structural defects, and its unique change during hot processing. The internal gettering action of defect layers present in web crystals and their relation to minority carrier lifetime distributions is discussed. Minority carrier lifetime maps of web dendrites obtained before and after high temperature heat treatment are compared to similar maps obtained from 100 mm diameter Czochralski silicon wafers. Such maps indicate similar or superior areal homogeneity of minority carrier lifetime in webs.

  1. Alkyltributylphosphonium chloride ionic liquids: synthesis, physicochemical properties and crystal structure.

    Science.gov (United States)

    Adamová, Gabriela; Gardas, Ramesh L; Nieuwenhuyzen, Mark; Puga, Alberto V; Rebelo, Luís Paulo N; Robertson, Allan J; Seddon, Kenneth R

    2012-07-21

    A series of alkyltributylphosphonium chloride ionic liquids, prepared from tributylphosphine and the respective 1-chloroalkane, C(n)H(2n+1)Cl (where n = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12 or 14), is reported. This work is a continuation of an extended series of tetraalkylphosphonium ionic liquids, where the focus is on the variability of n and its impact on the physical properties, such as melting points/glass transitions, thermal stability, density and viscosity. Experimental density and viscosity data were interpreted using QPSR and group contribution methods and the crystal structure of propyl(tributyl)phosphonium chloride is detailed.

  2. Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions

    International Nuclear Information System (INIS)

    Kiser, Philip D.; Lodowski, David T.; Palczewski, Krzysztof

    2007-01-01

    A 3.02 Å crystal structure of native GroEL from E. coli is presented. GroEL is a member of the ATP-dependent chaperonin family that promotes the proper folding of many cytosolic bacterial proteins. The structures of GroEL in a variety of different states have been determined using X-ray crystallography and cryo-electron microscopy. In this study, a 3.02 Å crystal structure of the native GroEL complex from Escherichia coli is presented. The complex was purified and crystallized in the absence of potassium ions, which allowed evaluation of the structural changes that may occur in response to cognate potassium-ion binding by comparison to the previously determined wild-type GroEL structure (PDB code http://www.rcsb.org/pdb/explore.do?structureId), in which potassium ions were observed in all 14 subunits. In general, the structure is similar to the previously determined wild-type GroEL crystal structure with some differences in regard to temperature-factor distribution

  3. The crystal structure and stability of molybdenum at ultrahigh pressures

    International Nuclear Information System (INIS)

    Jona, F; Marcus, P M

    2005-01-01

    Crystal structures and their stabilities for molybdenum under increasing hydrostatic pressures are investigated by first-principles calculations of the Gibbs free energy. Three structures are considered: body-centred cubic (bcc, the ground state at zero pressure), hexagonal close-packed (hcp) and face-centred cubic (fcc). For each structure and each pressure (up to 8 Mbar) the equilibrium states are found from minima of the Gibbs free energy at zero temperature. The stability is tested by calculating the elastic constants and checking whether they satisfy the appropriate stability conditions. The bcc structure is confirmed to be stable at zero pressure and at 6 Mbar. At and above 6.2 M-bar the ground-state structure changes to hcp, which is found to be stable at 7 M-bar. At 7.7 Mbar another transition occurs, and the ground-state structure changes from hcp to fcc. The fcc structure, which is unstable at zero pressure, becomes metastable over the range from 3 to 7.7 M-bar and becomes the ground state at higher pressures (at least up to 8 Mbar). Direct confirmation of these calculated transition pressures with experiment is not now possible, as the maximum static pressure currently reached experimentally is 5.6 Mbar, where Mo is found to be still in the bcc phase

  4. Magnetic and Crystal Structure of α-RuCl3

    Science.gov (United States)

    Sears, Jennifer

    The layered honeycomb material α-RuCl3 has been proposed as a candidate material to show significant bond-dependent Kitaev type interactions. This has prompted several recent studies of magnetism in this material that have found evidence for multiple magnetic transitions in the temperature range of 8-14 K. We will present elastic neutron scattering measurements collected using a co-aligned array of α-RuCl3 crystals, identifying zigzag magnetic order within the honeycomb planes with an ordering temperature of ~8 K. It has been reported that the ordering temperature depends on the c axis periodicity of the layered structure, with ordering temperatures of 8 and 14 K for three and two-layer periodicity respectively. While the in-plane magnetic order has been identified, it is clear that a complete understanding of magnetic ordering and interactions will depend on the three dimensional structure of the crystal. Evidence of a structural transition at ~150 K has been reported and questions remain about the structural details, in particular the stacking of the honeycomb layers. We will present x-ray diffraction measurements investigating the low and high temperature structures and stacking disorder in α-RuCl3. Finally, we will present inelastic neutron scattering measurements of magnetic excitations in this material. Work done in collaboration with K. W. Plumb (Johns Hopkins University), J. P. Clancy, Young-June Kim (University of Toronto), J. Britten (McMaster University), Yu-Sheng Chen (Argonne National Laboratory), Y. Qiu, Y. Zhao, D. Parshall, and J. W. Lynn (NCNR).

  5. AACSD: An atomistic analyzer for crystal structure and defects

    Science.gov (United States)

    Liu, Z. R.; Zhang, R. F.

    2018-01-01

    We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

  6. 1. The determination of crystal and magnetic structures

    International Nuclear Information System (INIS)

    Elemans, J.B.A.A.

    1975-01-01

    A theoretical foundation of the technique of thermal neutron scattering by powders is outlined. A description of the experimental set-up is given. A beam of themalized neutrons emerges from the reactor (HFR at Petten) through a slit system. It is diffracted by a manochromator crystal with a finite mosaic structure, a Cu (111) crystal being used. After passing through 10 cm pyrolytic graphite with a ''window'' from 0.23 to 0.29 nm as a lambda/2 filter, resulting in a wave length of 0.257 nm, the neutrons are taken off at a predetermined angle defined by a second slit system, resulting in a beam in which the sample is bathed. The neutrons scattered by the sample are detected by a counter moving in an arc with the position of the sample as center. The standard measurement time for a 10 cm 3 sample was two days. A discussion of the mathematical procedures for deriving the magnetic structure from the observed counts is given

  7. Crystal and molecular structure of neodymium (3) p-aminobenzoaate

    International Nuclear Information System (INIS)

    Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

    1981-01-01

    X-ray structural study (lambda MoKsub(α), automatic diffractometer, the method of heavy atom, anisotropic specification) of neodymium (3) n-aminobenzoate has been carried out. The crystals are monoclinic: a=9.882 (5), b=22.810 (12), c=9.851 (8)A, β=100.02 (5)deg, v=2186.59 A 3 , Z=4, sp. gr. P2 1 /n, R=0.046. The crystal structure of Nd(OOCC 6 H 4 NH 2 ) 3 xH 2 O consists of dimer-periodic layers alternating along the b axis. Surrounding of Nd atom in the chain is formed with four oxygen atoms of four carboxyl groups of bidentate-bridge and one carboxyl bidentate-cyclic ligands, one water molecule and N atom of ligand aminogroup from the neigbouring chain. The atom simultaneously bonds the neighbouring chains into continuous layer. The mean distances Nd-O, and Nd-N are equal to 2.45 and 2.74 A. An attempt to determine hydrogen atom coordinates has failed [ru

  8. Crystal structures of superconducting sodium intercalates of hafnium nitride chloride

    International Nuclear Information System (INIS)

    Oro-Sole, J.; Frontera, C.; Beltran-Porter, D.; Lebedev, O.I.; Van Tendeloo, G.; Fuertes, A.

    2006-01-01

    Sodium intercalation compounds of HfNCl have been prepared at room temperature in naphtyl sodium solutions in tetrahydrofuran and their crystal structure has been investigated by Rietveld refinement using X-ray powder diffraction data and high-resolution electron microscopy. The structure of two intercalates with space group R3-bar m and lattice parameters a=3.58131(6)A, c=57.752(6)A, and a=3.58791(8)A, c=29.6785(17)A is reported, corresponding to the stages 2 and 1, respectively, of Na x HfNCl. For the stage 2 phase an ordered model is presented, showing two crystallographically independent [HfNCl] units with an alternation of the Hf-Hf interlayer distance along the c-axis, according with the occupation by sodium atoms of one out of two van der Waals gaps. Both stages 1 and 2 phases are superconducting with critical temperatures between 20 and 24K, they coexist in different samples with proportions depending on the synthesis conditions, and show a variation in c spacing that can be correlated with the sodium stoichiometry. High-resolution electron microscopy images of the host and intercalated samples show bending of the HfNCl bilayers as well as stacking faults in some regions, which coexist in the same crystal with ordered domains

  9. Effects of thermo-order-mechanical coupling on band structures in liquid crystal nematic elastomer porous phononic crystals.

    Science.gov (United States)

    Yang, Shuai; Liu, Ying

    2018-08-01

    Liquid crystal nematic elastomers are one kind of smart anisotropic and viscoelastic solids simultaneously combing the properties of rubber and liquid crystals, which is thermal sensitivity. In this paper, the wave dispersion in a liquid crystal nematic elastomer porous phononic crystal subjected to an external thermal stimulus is theoretically investigated. Firstly, an energy function is proposed to determine thermo-induced deformation in NE periodic structures. Based on this function, thermo-induced band variation in liquid crystal nematic elastomer porous phononic crystals is investigated in detail. The results show that when liquid crystal elastomer changes from nematic state to isotropic state due to the variation of the temperature, the absolute band gaps at different bands are opened or closed. There exists a threshold temperature above which the absolute band gaps are opened or closed. Larger porosity benefits the opening of the absolute band gaps. The deviation of director from the structural symmetry axis is advantageous for the absolute band gap opening in nematic state whist constrains the absolute band gap opening in isotropic state. The combination effect of temperature and director orientation provides an added degree of freedom in the intelligent tuning of the absolute band gaps in phononic crystals. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Predicted crystal structures of molybdenum under high pressure

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bing; Zhang, Guang Biao [Institute for Computational Materials Science, School of Physics and Electronics, Henan University, Kaifeng 475004 (China); Wang, Yuan Xu, E-mail: wangyx@henu.edu.cn [Institute for Computational Materials Science, School of Physics and Electronics, Henan University, Kaifeng 475004 (China); Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Institute of Applied Physics, Guizhou Normal College, Guiyang 550018 (China)

    2013-04-15

    Highlights: ► A double-hexagonal close-packed (dhcp) structure of molybdenum is predicted. ► Calculated acoustic velocity confirms the bcc–dhcp phase transition at 660 GPa. ► The valence electrons of dhcp Mo are mostly localized in the interstitial sites. -- Abstract: The high-pressure structures of molybdenum (Mo) at zero temperature have been extensively explored through the newly developed particle swarm optimization (PSO) algorithm on crystal structural prediction. All the experimental and earlier theoretical structures were successfully reproduced in certain pressure ranges, validating our methodology in application to Mo. A double-hexagonal close-packed (dhcp) structure found by Mikhaylushkin et al. (2008) [12] is confirmed by the present PSO calculations. The lattice parameters and physical properties of the dhcp phase were investigated based on first principles calculations. The phase transition occurs only from bcc phase to dhcp phase at 660 GPa and at zero temperature. The calculated acoustic velocities also indicate a transition from the bcc to dhcp phases for Mo. More intriguingly, the calculated density of states (DOS) shows that the dhcp structure remains metallic. The calculated electron density difference (EDD) reveals that its valence electrons are localized in the interstitial regions.

  11. Structure of cleaved (001) USb2 single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shao-ping [Los Alamos National Laboratory; Hawley, Marilyn [Los Alamos National Laboratory; Bauer, Eric D [Los Alamos National Laboratory; Stockum, Phil B [STANFORD UNIV.; Manoharan, Hari C [STANFORD UNIV

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features observed in the STM will be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites) and the presence of contaminants

  12. Crystal structure of Fe2TiO5

    International Nuclear Information System (INIS)

    Shiojiri, M.; Sekimoto, S.; Maeda, T.; Ikeda, Y.; Iwauchi, K.

    1984-01-01

    The crystal structure of metal pseudobrookite, Fe 2 TiO 5 , is determined from high-resolution electron microscopy images observed and their computer simulated images, with the aid of electron diffraction and X-ray powder diffraction. The new structure has a monoclinic unit, containing eight molecules, with a = 2.223, b = 0.373, c = 0.980 nm, and β = 116.2 0 . The Fe, Ti, and O atoms occupy the positions (4c), +-(u, 0, w; 1/2 + u, 1/2, w), of C 2 3 (C2). The most probable parameters u and w, of Fe(1 to 4), Ti(1, 2), and O(1 to 10) are given. (author)

  13. Crystal chemistry of nephelines from ijolites and nepheline-rich pegmatites: influence of composition and genesis on the crystal structure investigated by X-ray diffraction

    DEFF Research Database (Denmark)

    Vulić, Predrag; Balić-Žunić, Tonči; Belmonte, Louise Josefine

    2011-01-01

    Ten nepheline single crystals from five different localities representing rocks from nepheline-syenite pegmatites to urtite, ijolite and cancrinite-ijolite were investigated chemically and structurally. The chemical compositions were determined by electron microprobe, whereas the crystal structur...

  14. Synthesis and crystal structure of the new vanadate AgCaVO{sub 4}. Comparison with the arcanite structure

    Energy Technology Data Exchange (ETDEWEB)

    Nenert, Gwilherm [PANalytical B.V., Almelo (Netherlands)

    2017-07-01

    We report the synthesis and the crystal structure of the new vanadate AgCaVO{sub 4} from laboratory powder X-ray data. Contrary to the previously reported AgBVO{sub 4} (B=Mg, Cd), AgCaVO{sub 4} exhibits the arcanite structure (β-K{sub 2}SO{sub 4}). Although it exhibits the same structure than arcanite, significant differences are observed. These differences are explained by deriving the atomic displacement field. The change of connectivity within the structure between β-K{sub 2}SO{sub 4} and AgCaVO{sub 4} results from a rotation of the VO{sub 4} tetrahedra giving rise to a change from a face sharing to an edge sharing octahedral chains. Additionally, the thermal expansion of AgCaVO{sub 4} has been investigated up to 800 C.

  15. Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila, reveals high thermostability and an unusual form of dimerization

    DEFF Research Database (Denmark)

    Hameed, Uzma; Price, Ian; Ikram-Ul-Haq

    2017-01-01

    and able to hydrolyze starch into dextrin between 90 and 100°C, with optimum activity at 98°C and pH8.5. The activity increased in the presence of Rb(1+), K(1+) and Ca(2+) ions, whereas other ions inhibited activity. The crystal structure of Tp-AmyS at 1.7Å resolution showed common features of the GH-13...... of salivary amylase from a previous crystal structure, and thus could be a functional feature of some amylases....

  16. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

    Science.gov (United States)

    Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

    2009-10-01

    This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

  17. 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.

  18. Colloidal Photonic Crystals Containing Silver Nanoparticles with Tunable Structural Colors

    Directory of Open Access Journals (Sweden)

    Chun-Feng Lai

    2016-05-01

    Full Text Available Polystyrene (PS colloidal photonic crystals (CPhCs containing silver nanoparticles (AgNPs present tunable structural colors. PS CPhC color films containing a high concentration of AgNPs were prepared using self-assembly process through gravitational sedimentation method. High-concentration AgNPs were deposited on the bottom of the substrate and acted as black materials to absorb background and scattering light. Brilliant structural colors were enhanced because of the absorption of incoherent scattering light, and color saturation was increased by the distribution AgNPs on the PS CPhC surfaces. The vivid iridescent structural colors of AgNPs/PS hybrid CPhC films were based on Bragg diffraction and backward scattering absorption using AgNPs. The photonic stop band of PS CPhCs and AgNPs/PS hybrid CPhCs were measured by UV–visible reflection spectrometry and calculated based on the Bragg–Snell law. In addition, the tunable structural colors of AgNPs/PS hybrid CPhC films were evaluated using color measurements according to the Commission International d’Eclairage standard colorimetric system. This paper presents a simple and inexpensive method to produce tunable structural colors for numerous applications, such as textile fabrics, bionic colors, catalysis, and paints.

  19. Water polygons in high-resolution protein crystal structures.

    Science.gov (United States)

    Lee, Jonas; Kim, Sung-Hou

    2009-07-01

    We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 A resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of "stable" water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state.

  20. Local structural ordering in surface-confined liquid crystals

    Science.gov (United States)

    Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

    2017-06-01

    The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

  1. Models of protein–ligand crystal structures: trust, but verify

    Science.gov (United States)

    Deller, Marc C.

    2015-01-01

    X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

  2. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    International Nuclear Information System (INIS)

    Forneris, Federico; Burnley, B. Tom; Gros, Piet

    2014-01-01

    Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na + and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na + ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail

  3. Structures of the OmpF porin crystallized in the presence of foscholine-12.

    Science.gov (United States)

    Kefala, Georgia; Ahn, Chihoon; Krupa, Martin; Esquivies, Luis; Maslennikov, Innokentiy; Kwiatkowski, Witek; Choe, Senyon

    2010-05-01

    The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 A, b = 210.5 A, c = 137 A, and beta = 100.5 degrees , and the resolution of 3.8 A. The second structure was solved at the resolution of 4.4 A and was refined in the P321 space group, with unit cell parameters a = 215.5 A, b = 215.5 A, c = 137.5 A, and gamma = 120 degrees . Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli.

  4. Crystal structure of a photobiologically active furanocoumarin from Artemisia reticulata

    Directory of Open Access Journals (Sweden)

    A. K. Bauri

    2016-04-01

    Full Text Available The title furanocoumarin, C14H12O4 [systematic name: 9-hydroxy-2-(prop-1-en-2-yl-2,3-dihydro-7H-furo[3,2-g]chromen-7-one], crystallizes with two independent molecules (A and B in the asymmetric unit. The two molecules differ essentially in the orientation of the propenyl group with respect to the mean plane of the furanocoumarin moiety; the O—C(H—C=C torsion angle is 122.2 (7° in molecule A and −10.8 (11° in molecule B. In the crystal, the A and B molecules are linked via O—H...O hydrogen bonds, forming zigzag –A–B–A–B– chains propagating along [001]. The chains are reinforced by bifurcated C—H...(O,O hydrogen bonds, forming ribbons which are linked via C—H...π and π–π interactions [intercentroid distance = 3.602 (2 Å], forming a three-dimensional structure.

  5. Understanding surface structure and chemistry of single crystal lanthanum aluminate

    KAUST Repository

    Pramana, Stevin S.

    2017-03-02

    The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10−10 Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions. Changing the oxygen pressure to 10−6 Torr enriched the Al site occupancy fraction at the outermost surface from 0.245(10) to 0.325(9). In contrast the LaO, which is located at the next sub-surface atomic layer, showed no chemical enrichment and the structural relaxation was lower than for the top AlO2 layer. Knowledge of the surface structure will aid the understanding of how and which type of interface will be formed when LaAlO3 is used as a substrate as a function of temperature and pressure, and so lead to improved design of device structures.

  6. The hydroxynitrile lyase from almond: crystal structure and mechanistical studies

    International Nuclear Information System (INIS)

    Dreveny, Ingrid

    2001-09-01

    Cyanogenesis is a defense process of several thousand plant species. Hydroxynitrile lyase (HNL), a key enzyme of this process, cleaves a cyanohydrin precursor into hydrocyanic acid and the corresponding aldehyde or ketone. The reverse reaction constitutes an important tool in industrial biocatalysis. Different classes of hydroxynitrile lyases have convergently evolved from FAD-dependent oxidoreductases, α/β hydrolases and alcohol dehydrogenases. The FAD-dependent hydroxynitrile lyases (FAD-HNLs) carry a flavin cofactor whose redox properties appear to be unimportant for catalysis. The high resolution crystal structure of the hydroxynitrile lyase from almond (Prunus amygdalus), PaHNL1, has been determined and constitutes the first 3D structure of an FAD-HNL. The overall fold and the architecture of the active site region showed that PaHNL1 belongs to the glucose-methanol-choline-oxidoreductase family, with closest structural similarity to glucose oxidase. There is strong evidence from the sequence and the reaction product that FAD-dependent hydroxynitrile lyases have evolved from an aryl alcohol oxidizing precursor. Structures of PaHNL1 in complex with its natural substrate mandelonitrile and the competitive inhibitor benzyl alcohol provided insight into the residues involved in catalysis and a mechanism without participation of the cofactor could be suggested. Although the catalytic residues differ between the α/β-hydrolase-type HNLs and PaHNL1, common general features relevant for hydroxynitrile lyase activity could be proposed. (author)

  7. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    Energy Technology Data Exchange (ETDEWEB)

    Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.; Li, Sheng; Tickle, Ian J.; Bricogne, Gérard; Saphire, Erica Ollmann (Scripps); (Globel Phasing); (UCSD)

    2016-11-09

    ABSTRACT

    Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV.

    IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the

  8. Welcome to Crystals: A New Open-Access, Multidisciplinary Forum for Growth, Structures and Properties of Crystals

    Directory of Open Access Journals (Sweden)

    Gerd Meyer

    2010-12-01

    Full Text Available The majority of the earth’s crust is made up of crystalline material. The research areas of mineralogy, petrology, chimie minerále (inorganic chemistry and, of course, crystallography outgrew from the fascination of mankind with the color and symmetry of crystals. Crystals have translational symmetry in two or three dimensions, quasicrystals have translational symmetry in higher spaces. Further symmetries may be observed by the eye, by microscopic techniques or by the diffraction of X-ray, electron, or neutron beams. Diffraction techniques are also used, due to Max von Laue’s eminent discovery a century ago, to determine crystal structures. [...

  9. Stress and stability of sputter deposited A-15 and bcc crystal structure tungsten thin films

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, M.J.; Stutz, C.E.

    1997-07-01

    Magnetron sputter deposition was used to fabricate body centered cubic (bcc) and A-15 crystal structure W thin films. Previous work demonstrated that the as-deposited crystal structure of the films was dependent on the deposition parameters and that the formation of a metastable A-15 structure was favored over the thermodynamically stable bcc phase when the films contained a few atomic percent oxygen. However, the A-15 phase was shown to irreversibly transform into the bcc phase between 500 C and 650 C and that a significant decrease in the resistivity of the metallic films was measured after the transformation. The current investigation of 150 nm thick, sputter deposited A-15 and bcc tungsten thin films on silicon wafers consisted of a series of experiments in which the stress, resistivity and crystal structure of the films was measured as a function of temperatures cycles in a Flexus 2900 thin film stress measurement system. The as-deposited film stress was found to be a function of the sputtering pressure and presputter time; under conditions in which the as-deposited stress of the film was {approximately}1.5 GPa compressive delamination of the W film from the substrate was observed. Data from the thermal studies indicated that bcc film stress was not affected by annealing but transformation of the A-15 structure resulted in a large tensile increase in the stress of the film, regardless of the as-deposited stress of the film. In several instances, complete transformation of the A-15 structure into the bcc phase resulted in {ge}1 GPa tensile increase in film stress.

  10. Stress and stability of sputter deposited A-15 and bcc crystal structure tungsten thin films

    International Nuclear Information System (INIS)

    O'Keefe, M.J.; Stutz, C.E.

    1997-01-01

    Magnetron sputter deposition was used to fabricate body centered cubic (bcc) and A-15 crystal structure W thin films. Previous work demonstrated that the as-deposited crystal structure of the films was dependent on the deposition parameters and that the formation of a metastable A-15 structure was favored over the thermodynamically stable bcc phase when the films contained a few atomic percent oxygen. However, the A-15 phase was shown to irreversibly transform into the bcc phase between 500 C and 650 C and that a significant decrease in the resistivity of the metallic films was measured after the transformation. The current investigation of 150 nm thick, sputter deposited A-15 and bcc tungsten thin films on silicon wafers consisted of a series of experiments in which the stress, resistivity and crystal structure of the films was measured as a function of temperatures cycles in a Flexus 2900 thin film stress measurement system. The as-deposited film stress was found to be a function of the sputtering pressure and presputter time; under conditions in which the as-deposited stress of the film was approximately1.5 GPa compressive delamination of the W film from the substrate was observed. Data from the thermal studies indicated that bcc film stress was not affected by annealing but transformation of the A-15 structure resulted in a large tensile increase in the stress of the film, regardless of the as-deposited stress of the film. In several instances, complete transformation of the A-15 structure into the bcc phase resulted in ge1 GPa tensile increase in film stress

  11. Crystal structure and thermal expansion of Mn(1-x)Fe(x)Ge.

    Science.gov (United States)

    Dyadkin, Vadim; Grigoriev, Sergey; Ovsyannikov, Sergey V; Bykova, Elena; Dubrovinsky, Leonid; Tsvyashchenko, Anatoly; Fomicheva, L N; Chernyshov, Dmitry

    2014-08-01

    A series of temperature-dependent single-crystal and powder diffraction experiments has been carried out using synchrotron radiation in order to characterize the monogermanides of Mn, Fe and their solid solutions. The MnGe single crystal is found to be enantiopure and we report the absolute structure determination. The thermal expansion, parametrized with the Debye model, is discussed from the temperature-dependent powder diffraction measurements for Mn(1-x)Fe(x)Ge (x = 0, 0.1, 0.2, 0.25, 0.3, 0.4, 0.5, 0.6, 0.7, 0.75, 0.8, 0.9). Whereas the unit-cell dimension and the Debye temperature follow a linear trend as a function of composition, the thermal expansion coefficient deviates from linear dependence with increasing Mn content. No structural phase transformations have been observed for any composition in the temperature range 80-500 K for both single-crystal and powder diffraction, indicating that the phase transition previously observed with neutron powder diffraction most probably has a magnetic origin.

  12. 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

  13. Crystal structure study of new lanthanide silicates with silico-carnotite structure

    International Nuclear Information System (INIS)

    Piccinelli, F.; Lausi, A.; Speghini, A.; Bettinelli, M.

    2012-01-01

    The crystal structures of new rare earth-based silicate compounds (Ca 3 Eu 2 Si 3 O 12 , Ca 3 Gd 2 Si 3 O 12 , Ca 3 Dy 2 Si 3 O 12 , Ca 3 Er 2 Si 3 O 12 and Ca 3 Lu 2 Si 3 O 12 ) have been determined using powder X-ray diffraction. From Rietveld refinement calculations on the collected powder patterns we observe a different distribution of the rare earth ions on the three available crystal sites characterized by different coordination numbers, depending on the ionic radius of the rare earth ion. The reasons of the instability of the silico-carnotite structure for lanthanide ions larger than Eu 3+ have been deduced. In addition, in order to detect crystal phase transitions, the powder patterns of Ca 3 Eu 2 Si 3 O 12 and Ca 3 Sm 2 Si 3 O 12 samples have been collected as a function of the temperature (RT-1000 °C range), but no phase transitions have been observed. - Graphical abstract: Synchrotron X-ray diffraction allows us the accurate determination of the RE 3+ ions distribution on the three available crystal sites of the silico-carnotite structure. Highlights: ► The structure of the Ca 3 M 2 Si 3 O 12 (M=Eu, Gd, Dy, Er and Lu) was determined. ► Different distribution of RE 3+ ions on the three available crystal sites was observed. ► The instability of the silico-carnotite structure for RE=La→Sm was discussed.

  14. Mechanosynthesis, crystal structure and magnetic characterization of neodymium orthoferrite

    Energy Technology Data Exchange (ETDEWEB)

    Serna, Pedro Vera; Campos, Cecilio Garcia [Division de Ingenierias, Universidad Politecnica de Tecamac (UPTECAMAC), Tecamac de Felipe Villanueva, Estado de Mexico (Mexico); De Jesus, Felix Sanchez; Miro, Ana Maria Bolarin [Area Academica de Ciencias de la Tierra y Materiales, Universidad Autonoma del Estado de Hidalgo (UAEH), Mineral de la Reforma, Hidalgo (Mexico); Loran, Jose Antonio Juanico [Division de Ingenieria Industrial Nanotecnologia, Universidad Politecnica del Valle de Mexico (UPVM), Tultitlan, Estado de Mexico (Mexico); Longwell, Jeffrey, E-mail: pedrovera.upt@gmail.com [Department of Languages and Linguistics, New Mexico State University (NMSU), Las Cruces, NM (United States)

    2016-03-15

    Neodymium orthoferrite NdFeO{sub 3} was obtained at room temperature by mechanosynthesis with a stoichiometric ratio of Nd2O{sub 3} and Fe{sub 2}O{sub 3} powders, whereas the traditional synthesis requires a temperature of approximately 1000 °C. The crystal structure was analyzed by X-ray diffraction analysis using Cu radiation and a LynxEye XE detector, whose strong fluorescence filtering enabled a high signal intensity. The analysis indicated that the obtained crystallites were nano-sized. The particle morphology was observed by scanning electron microscopy, and the magnetic saturation was tested by vibrating sample magnetometry. The synthesis of NdFeO{sub 3} was detected after a few hours of milling, indicating that the milling imparted mechanical energy to the system. (author)

  15. The crystal structure of γ-AlD3

    International Nuclear Information System (INIS)

    Brinks, H.W.; Brown, C.; Jensen, C.M.; Graetz, J.; Reilly, J.J.; Hauback, B.C.

    2007-01-01

    γ-AlD 3 was synthesized from LiAlD 4 and AlCl 3 via thermal decomposition of aluminum hydride etherate in presence of excess LiAlD 4 . γ-AlD 3 was determined by powder neutron diffraction and synchrotron X-ray diffraction to crystallize in the space group Pnnm. The orthorhombic structure has unit-cell dimensions a = 7.3360(3) A, b = 5.3672(2) A and c = 5.7562(1) A, and it consists of both corner- and edge-sharing AlD 6 octahedra where each hydrogen is shared between two octahedra. The average Al-D distances in octahedra with edge-sharing is 1.706 A and in the octahedra with only corner-sharing 1.719 A

  16. Optical nonreciprocal transmission in an asymmetric silicon photonic crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zheng; Chen, Juguang; Ji, Mengxi; Huang, Qingzhong; Xia, Jinsong; Wang, Yi, E-mail: yingwu2@126.com, E-mail: ywangwnlo@mail.hust.edu.cn [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Wu, Ying, E-mail: yingwu2@126.com, E-mail: ywangwnlo@mail.hust.edu.cn [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)

    2015-11-30

    An optical nonreciprocal transmission (ONT) is realized by employing the nonlinear effects in a compact asymmetric direct-coupled nanocavity-waveguide silicon photonic crystal structure with a high loaded quality factor (Q{sub L}) of 42 360 and large extinction ratio exceeding 30 dB. Applying a single step lithography and successive etching, the device can realize the ONT in an individual nanocavity, alleviating the requirement to accurately control the resonance of the cavities. A maximum nonreciprocal transmission ratio of 21.1 dB as well as a working bandwidth of 280 pm in the telecommunication band are obtained at a low input power of 76.7 μW. The calculated results by employing a nonlinear coupled-mode model are in good agreement with the experiment.

  17. Crystal structure of 4-methoxy-N-(piperidine-1-carbonothioylbenzamide

    Directory of Open Access Journals (Sweden)

    Khairi Suhud

    2017-10-01

    Full Text Available In the title compound, C14H18N2O2S, the piperidine ring has a chair conformation. Its mean plane is twisted with respect to the 4-methoxybenzoyl ring, with a dihedral angle of 63.0 (3°. The central N—C(=S—N(H—C(=O bridge is twisted with an N—C—N—C torsion angle of 74.8 (6°. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds, forming chains along the c-axis direction. Adjacent chains are linked by C—H...π interactions, forming layers parallel to the ac plane. The layers are linked by offset π–π interactions [intercentroid distance = 3.927 (3 Å], forming a supramolecular three-dimensional structure.

  18. Crystal structure and phase transitions of sodium potassium niobate perovskites

    Science.gov (United States)

    Tellier, J.; Malic, B.; Dkhil, B.; Jenko, D.; Cilensek, J.; Kosec, M.

    2009-02-01

    This paper presents the crystal structure and the phase transitions of K xNa 1- xNbO 3 (0.4 ≤ x ≤ 0.6). X-ray diffraction measurements were used to follow the change of the unit-cell parameters and the symmetry in the temperature range 100-800 K. At room temperature all the compositions exhibited a monoclinic metric of the unit cell with a small monoclinic distortion (90.32° ≤ β ≤ 90.34°). No major change of symmetry was evidenced in the investigated compositional range, which should be characteristic of the morphotropic phase-boundary region. With increasing temperature, the samples underwent first-order monoclinic-tetragonal and tetragonal-cubic transitions. Only the potassium-rich phases were rhombohedral at 100 K.

  19. Crystal and molecular structure of dysprosium (3) n-aminobenzoate

    International Nuclear Information System (INIS)

    Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

    1981-01-01

    The X ray diffraction investigation of the Dy(NH 2 C 6 H 4 COO) 3 x3H 2 O complex is carried out. Triclinic crystals have lattice parameters α=11.095(15), b=9.099(17), c=12.780 (15)A, α=108.051(12), β=89.072(10); γ=104.954(12) 0 , space group P anti 1, Z=2. The structure consists of dimer molecules. The third water molecule in the formula is an outer spherical one. The average lengths of Dy-O and Dy-OH 2 are 2.39 and 2.40 A respectively, the average value of Dy-O in bridge carboxylates (2.26A) is remarkably shorter. Hydrogen bonds between amine ligand ends, carboxylic groups oxygen and water molecules bind complex molecules into the three-dimensional frame [ru

  20. 1-Hydroxyethyl-2-Substituted Phenoxymethyl Benzimidazoles: Synthesis and Crystal Structures

    International Nuclear Information System (INIS)

    Wu, J.; Wang, Z.; Gu, H.; Chen, W.; Zhao, L.; Zhao, C.

    2016-01-01

    Five novel 1-hydroxyethyl-2-substituted phenoxymethyl benzimidazoles c1-c5 were successfully synthesized by a three-step route. Firstly, five substituted phenoxymethyl acids a1-a5 were prepared by the O-carboxymethylation reaction of the starting substituted phenols under microwave irradiation. Then, these compounds reacted with o-phenylendiamine to get the key intermediates 2-substituted phenoxymethyl benzimidazoles b1-b5. At last, the target compounds were synthesized by the N-hydroxyethylation reaction of b1-b5 with 2-chloroethyl alcohol through the solid-liquid phase transfer catalysis method, where tetrabutyl ammonium bromide (TBAB) was used as the catalyst. The structures of the target compounds were well characterized and verified by elemental analysis, MS, IR, 1H NMR, 13C NMR and single crystal X-ray diffraction analysis. (author)

  1. Crystal structure of 2,5-dimethylanilinium salicylate

    Directory of Open Access Journals (Sweden)

    A. Mani

    2015-09-01

    Full Text Available The title molecular salt, C8H12N+·C7H5O3− arose from the proton-transfer reaction between 2,5-xylidine and salicylic acid. In the anion, the dihedral angle between the planes of the aromatic ring and the –CO2− group is 11.08 (8°; this near planarity is consolidated by an intramolecular O—H...O hydrogen bond. In the crystal, the components are connected by N—H...O hydrogen bonds, with all three O atoms in the anion acting as acceptors; the result is a [100] chain. The structure also features weak C—H...O bonds and aromatic π–π stacking [centroid-to-centroid distance = 3.7416 (10 Å] interactions, which lead to a three-dimensional network.

  2. Co2+-doped diopside: crystal structure and optical properties

    Science.gov (United States)

    Gori, C.; Tribaudino, M.; Mezzadri, F.; Skogby, H.; Hålenius, U.

    2018-05-01

    Synthetic clinopyroxenes along the CaMgSi2O6-CaCoSi2O6 join were investigated by a combined chemical-structural-spectroscopic approach. Single crystals were synthesized by flux growth methods, both from Ca-saturated and Ca-deficient starting compositions. Single crystal structure refinements show that the incorporation of Co2+ at the octahedrally coordinated cation sites of diopside, increases the unit-cell as well as the M1 and the M2 polyhedral volumes. Spectroscopic investigations (UV-VIS-NIR) of the Ca-rich samples reveal three main optical absorption bands, i.e. 4 T 1g → 4 T 2g( F), 4 T 1g → 4 A 2g( F) and 4 T 1g → 4 T 1g( P) as expected for Co2+ at a six-coordinated site. The bands arising from the 4 T 1g → 4 T 2g( F) and the 4 T 1g → 4 T 1g( P) electronic transitions, are each split into two components, due to the distortions of the M1 polyhedron from ideal Oh-symmetry. In spectra of both types, a band in the NIR range at ca 5000 cm-1 is caused by the 4 A 2g → 4 T 1g( F) electronic transition in Co2+ in a cubic field in the M2 site. Furthermore, an additional component to a band system at 14,000 cm-1, due to electronic transitions in Co2+ at the M2 site, is recorded in absorption spectra of Ca-deficient samples. No variations in Dq and Racah B parameters for Co2+ at the M1 site in response to compositional changes, were demonstrated, suggesting complete relaxation of the M1 polyhedron within the CaMgSi2O6-CaCoSi2O6 solid solution.

  3. Two modifications of Y2Piv6(HPiv)6 crystals: synthesis and structures

    International Nuclear Information System (INIS)

    Kiseleva, E.A.; Troyanov, S.I.; Korenev, Yu.M.

    2006-01-01

    Crystal structure of solvate of yttrium pivalate YPiv 3 ·3HPiv is studied. Existing of two polymorphous modifications of the compound is detected. It is shown that α- and β-modifications of yttrium pivalate solvate have molecular crystal structures and are built of Y 2 Piv 6 (HPiv) 6 dimers. Difference of these two modifications is in package of dimer molecules and in center-symmetricity of dimers in α-modification structure. Molecular and crystal structure, crystal lattice parameters are determined [ru

  4. Structural and optical properties of WTe2 single crystals synthesized by DVT technique

    Science.gov (United States)

    Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

    2018-05-01

    Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

  5. Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons.

    Science.gov (United States)

    Habash, Jarjis; Boggon, Titus J; Raftery, James; Chayen, Naomi E; Zagalsky, Peter F; Helliwell, John R

    2003-07-01

    Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

  6. Crystal structure of the epithelial calcium channel TRPV6.

    Science.gov (United States)

    Saotome, Kei; Singh, Appu K; Yelshanskaya, Maria V; Sobolevsky, Alexander I

    2016-06-23

    Precise regulation of calcium homeostasis is essential for many physiological functions. The Ca(2+)-selective transient receptor potential (TRP) channels TRPV5 and TRPV6 play vital roles in calcium homeostasis as Ca(2+) uptake channels in epithelial tissues. Detailed structural bases for their assembly and Ca(2+) permeation remain obscure. Here we report the crystal structure of rat TRPV6 at 3.25 Å resolution. The overall architecture of TRPV6 reveals shared and unique features compared with other TRP channels. Intracellular domains engage in extensive interactions to form an intracellular 'skirt' involved in allosteric modulation. In the K(+) channel-like transmembrane domain, Ca(2+) selectivity is determined by direct coordination of Ca(2+) by a ring of aspartate side chains in the selectivity filter. On the basis of crystallographically identified cation-binding sites at the pore axis and extracellular vestibule, we propose a Ca(2+) permeation mechanism. Our results provide a structural foundation for understanding the regulation of epithelial Ca(2+) uptake and its role in pathophysiology.

  7. Crystal structure of bis(4-acetylanilinium tetrachloridocobaltate(II

    Directory of Open Access Journals (Sweden)

    Manickam Thairiyaraja

    2015-12-01

    Full Text Available The structure of the title salt, (C8H10NO2[CoCl4], is isotypic with the analogous cuprate(II structure. The asymmetric unit contains one 4-acetylanilinium cation and one half of a tetrachloridocobaltate(II anion for which the CoII atom and two Cl− ligands lie on a mirror plane. The Co—Cl distances in the distorted tetrahedral anion range from 2.2519 (6 to 2.2954 (9 Å and the Cl—Co—Cl angles range from 106.53 (2 to 110.81 (4°. In the crystal, cations are self-assembled by intermolecular N—H...O hydrogen-bonding interactions, leading to a C(8 chain motif with the chains running parallel to the b axis. π–π stacking interactions between benzene rings, with a centroid-to-centroid distance of 3.709 Å, are also observed along this direction. The CoCl42− anions are sandwiched between the cationic chains and interact with each other through intermolecular N—H...Cl hydrogen-bonding interactions, forming a three-dimensional network structure.

  8. Crystal structures and phase transformation of deuterated lithium imide, Li2ND

    International Nuclear Information System (INIS)

    Balogh, Michael P.; Jones, Camille Y.; Herbst, J.F.; Hector, Louis G.; Kundrat, Matthew

    2006-01-01

    We have investigated the crystal structure of deuterated lithium imide, Li 2 ND, by means of neutron and X-ray diffraction. An order-disorder transition occurs near 360K. Below that temperature Li 2 ND can be described to the same level of accuracy as a disordered cubic (Fd3-bar m) structure with partially occupied Li 32e sites or as a fully occupied orthorhombic (Ima2 or Imm2) structure. The high temperature phase is best characterized as disordered cubic (Fm3-bar m) with D atoms randomized over the 192l sites. Density functional theory calculations complement and support the diffraction analyses. We compare our findings in detail with previous studies

  9. Structural analysis of eight novel and 112 previously reported missense mutations in the interactive FXI mutation database reveals new insight on FXI deficiency.

    Science.gov (United States)

    Saunders, Rebecca E; Shiltagh, Nuha; Gomez, Keith; Mellars, Gillian; Cooper, Carolyn; Perry, David J; Tuddenham, Edward G; Perkins, Stephen J

    2009-08-01

    Factor XI (FXI) functions in blood coagulation. FXI is composed of four apple (Ap) domains and a serine protease (SP) domain. Deficiency of FXI leads to an injury-related bleeding disorder, which is remarkable for the lack of correlation between bleeding symptoms and FXI coagulant activity (FXI:C). The number of mutations previously reported in our interactive web database (http://www.FactorXI.org) is now significantly increased to 183 through our new patient studies and from literature surveys. Eight novel missense mutations give a total of 120 throughout the FXI gene (F11). The most abundant defects in FXI are revealed to be those from low-protein plasma levels (Type I: CRM-) that originate from protein misfolding, rather than from functional defects (Type II: CRM+). A total of 70 Ap missense mutations were analysed using a consensus Ap domain structure generated from the FXI dimer crystal structure. This showed that all parts of the Ap domain were affected. The 47 SP missense mutations were also distributed throughout the SP domain structure. The periphery of the Ap beta-sheet structure is sensitive to structural perturbation caused by residue changes throughout the Ap domain, yet this beta-sheet is crucial for FXI dimer formation. Residues located at the Ap4:Ap4 interface in the dimer are much less directly involved. We conclude that the abundance of Type I defects in FXI results from the sensitivity of the Ap domain folding to residue changes within this, and discuss how structural knowledge of the mutations improves our understanding of FXI deficiencies.

  10. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

    International Nuclear Information System (INIS)

    Streek, Jacco van de; Neumann, Marcus A.

    2010-01-01

    The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect

  11. Co-ordinated functions of Mms proteins define the surface structure of cubo-octahedral magnetite crystals in magnetotactic bacteria.

    Science.gov (United States)

    Arakaki, Atsushi; Yamagishi, Ayana; Fukuyo, Ayumi; Tanaka, Masayoshi; Matsunaga, Tadashi

    2014-08-01

    Magnetotactic bacteria synthesize magnetosomes comprised of membrane-enveloped single crystalline magnetite (Fe3 O4 ). The size and morphology of the nano-sized magnetite crystals (Mms (Mms5, Mms6, Mms7, and Mms13), was previously isolated from the surface of cubo-octahedral magnetite crystals in Magnetospirillum magneticum strain AMB-1. Analysis of an mms6 gene deletion mutant suggested that the Mms6 protein plays a major role in the regulation of magnetite crystal size and morphology. In this study, we constructed various mms gene deletion mutants and characterized the magnetite crystals formed by the mutant strains. Comparative analysis showed that all mms genes were involved in the promotion of crystal growth in different manners. The phenotypic characterization of magnetites also suggested that these proteins are involved in controlling the geometries of the crystal surface structures. Thus, the co-ordinated functions of Mms proteins regulate the morphology of the cubo-octahedral magnetite crystals in magnetotactic bacteria. © 2014 John Wiley & Sons Ltd.

  12. Crystal structure of ammonium and rubidium octacyanomolybdates (4)

    Energy Technology Data Exchange (ETDEWEB)

    Semenishin, D.I.; Glovyak, T.; Mys' kiv, M.G.

    1985-01-01

    By the method of monocrystal at the automatic diffractometer ''Syntex P2/sub 1/'' the crystal structure of ammonium and rubidium octacyanomolybdates (4)-(NH/sub 4/)/sub 4/(Mo(CN)/sub 8/)x0.5H/sub 2/O (1) (sp.gr. Pma5 2, a=15.50(3), b=14.118 (3), c=7.438 (1)A, Z=4, R=0.062 and Rb/sub 4/(Mo(CN)/sub 8/):3H/sub 2/O (2) (sp.gr. P4/sub 1/2/sub 1/2, a=9.300 (1), c=21.807 (3) A, Z=4, R=0.065) is determined. Mo atoms in the structure 1 occupy two 2(b) and 2(c) particular positions and are surrounded, each of them, by light CN-ligands. The mean values of Mo-C distances for Mo(1) are equal 2.216, for Mo(2)-2.235 A. Mo-N mean values, practically are identical in both molybdenum anions and are equal 3.353 A. MoCN angles are varied from 175.0 to 178.4. The dodecahedron with the only symmetry axis 2 corresponds to the Mo(1) coordination sphere whereas the Mo(2) atoms coordination polyhedron (CP) is the symmetry in antiprism. In the structure 2 Mo-C distances are in the limits of 2.130-2.160 and Mo-N 3.290-3.307 A. MoCN angles are varied from 176.0 to 179.3 deg, the (MoC/sub 8/) CP represents a symmetry 2 dodecahedron. The existence of two Mo coordination forms in the structure 1 is up to now the only example among structurally studied octacyanomolybdates (4).

  13. Bismuth zinc vanadate, BiZn2VO6: New crystal structure type and electronic structure

    International Nuclear Information System (INIS)

    Eliziario Nunes, Sayonara; Wang, Chun-Hai; So, Karwei; Evans, John S.O.; Evans, Ivana Radosavljević

    2015-01-01

    We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn 2 VO 6 , known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn 2 VO 6 adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO 4 tetrahedra, ZnO 6 octahedra and VO 4 tetrahedra, and Bi 2 O 12 dimers. It is the only known member of the BiM 2 AO 6 (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn 2 VO 6 , calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn 2 VO 6 , a new structure type in the BiM 2 AO 6 (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM 2 AO 6 (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation

  14. Steady distribution structure of point defects near crystal-melt interface under pulling stop of CZ Si crystal

    Science.gov (United States)

    Abe, T.; Takahashi, T.; Shirai, K.

    2017-02-01

    In order to reveal a steady distribution structure of point defects of no growing Si on the solid-liquid interface, the crystals were grown at a high pulling rate, which Vs becomes predominant, and the pulling was suddenly stopped. After restoring the variations of the crystal by the pulling-stop, the crystals were then left in prolonged contact with the melt. Finally, the crystals were detached and rapidly cooled to freeze point defects and then a distribution of the point defects of the as-grown crystals was observed. As a result, a dislocation loop (DL) region, which is formed by the aggregation of interstitials (Is), was formed over the solid-liquid interface and was surrounded with a Vs-and-Is-free recombination region (Rc-region), although the entire crystals had been Vs rich in the beginning. It was also revealed that the crystal on the solid-liquid interface after the prolonged contact with the melt can partially have a Rc-region to be directly in contact with the melt, unlike a defect distribution of a solid-liquid interface that has been growing. This experimental result contradicts a hypothesis of Voronkov's diffusion model, which always assumes the equilibrium concentrations of Vs and Is as the boundary condition for distribution of point defects on the growth interface. The results were disscussed from a qualitative point of view of temperature distribution and thermal stress by the pulling-stop.

  15. Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

    Science.gov (United States)

    Karthigha, S.; Krishnamoorthi, C.

    2018-03-01

    An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

  16. Protein crystal growth on board Shenzhou 3: a concerted effort improves crystal diffraction quality and facilitates structure determination

    International Nuclear Information System (INIS)

    Han, Y.; Cang, H.-X.; Zhou, J.-X.; Wang, Y.-P.; Bi, R.-C.; Colelesage, J.; Delbaere, L.T.J.; Nahoum, V.; Shi, R.; Zhou, M.; Zhu, D.-W.; Lin, S.-X.

    2004-01-01

    The crystallization of 16 proteins was carried out using 60 wells on board Shenzhou 3 in 2002. Although the mission was only 7 days, careful and concerted planning at all stages made it possible to obtain crystals of improved quality compared to their ground controls for some of the proteins. Significantly improved resolutions were obtained from diffracted crystals of 4 proteins. A complete data set from a space crystal of the PEP carboxykinase yielded significantly higher resolution (1.46 A vs. 1.87 A), I/sigma (22.4 vs. 15.5), and a lower average temperature factor (29.2 A 2 vs. 42.9 A 2 ) than the best ground-based control crystal. The 3-D structure of the enzyme is well improved with significant ligand density. It has been postulated that the reduced convection and absence of macromolecule sedimentation under microgravity have advantages/benefits for protein crystal growth. Improvements in experimental design for protein crystal growth in microgravity are ongoing

  17. Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hui; Mustafi, Sourajit M. [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); LeMaster, David M. [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); University at Albany – SUNY, Empire State Plaza, Albany, NY 12201 (United States); Li, Zhong [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); Héroux, Annie [Brookhaven National Laboratory, Upton, NY 11973 (United States); Li, Hongmin; Hernández, Griselda, E-mail: griselda@wadsworth.org [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); University at Albany – SUNY, Empire State Plaza, Albany, NY 12201 (United States)

    2014-03-01

    Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop. The primary known physiological function of FKBP12.6 involves its role in regulating the RyR2 isoform of ryanodine receptor Ca{sup 2+} channels in cardiac muscle, pancreatic β islets and the central nervous system. With only a single previously reported X-ray structure of FKBP12.6, bound to the immunosuppressant rapamycin, structural inferences for this protein have been drawn from the more extensive studies of the homologous FKBP12. X-ray structures at 1.70 and 1.90 Å resolution from P2{sub 1} and P3{sub 1}21 crystal forms are reported for an unligated cysteine-free variant of FKBP12.6 which exhibit a notable diversity of conformations. In one monomer from the P3{sub 1}21 crystal form, the aromatic ring of Phe59 at the base of the active site is rotated perpendicular to its typical orientation, generating a steric conflict for the immunosuppressant-binding mode. The peptide unit linking Gly89 and Val90 at the tip of the protein-recognition ‘80s loop’ is flipped in the P2{sub 1} crystal form. Unlike the >30 reported FKBP12 structures, the backbone conformation of this loop closely follows that of the first FKBP domain of FKBP51. The NMR resonances for 21 backbone amides of FKBP12.6 are doubled, corresponding to a slow conformational transition centered near the tip of the 80s loop, as recently reported for 31 amides of FKBP12. The comparative absence of doubling for residues along the opposite face of the active-site pocket in FKBP12.6 may in part reflect attenuated structural coupling owing to increased conformational plasticity around the Phe59 ring.

  18. 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.

  19. A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

    Science.gov (United States)

    Penttinen, Leena; Rutanen, Chiara; Saloheimo, Markku; Kruus, Kristiina; Rouvinen, Juha; Hakulinen, Nina

    2018-01-01

    Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

  20. A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

    Directory of Open Access Journals (Sweden)

    Leena Penttinen

    Full Text Available Coupled binuclear copper (CBC enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4 and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

  1. Crystal structure, growth and nonlinear optical studies of isonicotinamide p-nitrophenol: A new organic crystal for optical limiting applications

    Science.gov (United States)

    Vijayalakshmi, A.; Vidyavathy, B.; Vinitha, G.

    2016-08-01

    Isonicotinamide p-nitrophenol (ICPNP), a new organic material, was synthesized using methanol solvent. Single crystals of ICPNP were grown using a slow evaporation solution growth technique. Crystal structure of ICPNP is elucidated by single crystal X-ray diffraction analysis. It belongs to monoclinic crystal system with space group of P21/c. It forms two dimensional networks by O-H…O, N-H…O and C-H…O hydrogen bonds. The molecular structure of ICPNP was further confirmed by Fourier transform infrared (FTIR) spectral analysis. The optical transmittance range and the lower cut-off wavelength (421 nm) with the optical band gap (2.90 eV) of the ICPNP crystal were determined by UV-vis-NIR spectral study. Thermal behavior of ICPNP was studied by thermo gravimetric and differential thermal analyses (TG/DTA). The relative dielectric permittivity was calculated for various temperature ranges. Laser damage threshold of ICPNP crystal was found to be 1.9 GW/cm2 using an Nd:YAG laser. A Z-scan technique was employed to measure the nonlinear absorption coefficient, nonlinear refractive index and nonlinear optical susceptibility. Optical limiting behavior of ICPNP was observed at 35 mW input power.

  2. Active liquid-crystal deflector and lens with Fresnel structure

    Science.gov (United States)

    Shibuya, Giichi; Yamano, Shohei; Yoshida, Hiroyuki; Ozaki, Masanori

    2017-02-01

    A new type of tunable Fresnel deflector and lens composed of liquid crystal was developed. Combined structure of multiple interdigitated electrodes and the high-resistivity (HR) layer implements the saw-tooth distribution of electrical potential with only the planar surfaces of the transparent substrates. According to the numerical calculation and design, experimental devices were manufactured with the liquid crystal (LC) material sealed into the sandwiched flat glass plates of 0.7 mm thickness with rubbed alignment layers set to an anti-parallel configuration. Fabricated beam deflector with no moving parts shows the maximum tilt angle of +/-1.3 deg which can apply for optical image stabilizer (OIS) of micro camera. We also discussed and verified their lens characteristics to be extended more advanced applications. Transparent interdigitated electrodes were concentrically aligned on the lens aperture with the insulator gaps under their boundary area. The diameter of the lens aperture was 30 mm and the total number of Fresnel zone was 100. Phase retardation of the beam wavefront irradiated from the LC lens device can be evaluated by polarizing microscope images with a monochromatic filter. Radial positions of each observed fringe are plotted and fitted with 2nd degree polynomial approximation. The number of appeared fringes is over 600 in whole lens aperture area and the correlation coefficients of all approximations are over 0.993 that seems enough ideal optical wavefront. The obtained maximum lens powers from the approximations are about +/-4 m-1 which was satisfied both convex and concave lens characteristics; and their practical use for the tunable lens grade eyeglasses became more prospective.

  3. Crystal Structure of the FERM Domain of Focal Adhesion Kinase

    International Nuclear Information System (INIS)

    Ceccarelli, D.; Song, H.; Poy, F.; Schaller, M.; Eck, M.

    2006-01-01

    Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. Through phosphorylation of proteins assembled at the cytoplasmic tails of integrins, FAK promotes signaling events that modulate cellular growth, survival, and migration. The amino-terminal region of FAK contains a region of sequence homology with band 4.1 and ezrin/radixin/moesin (ERM) proteins termed a FERM domain. FERM domains are found in a variety of signaling and cytoskeletal proteins and are thought to mediate intermolecular interactions with partner proteins and phospholipids at the plasma membrane and intramolecular regulatory interactions. Here we report two crystal structures of an NH2-terminal fragment of avian FAK containing the FERM domain and a portion of the regulatory linker that connects the FERM and kinase domains. The tertiary folds of the three subdomains (F1, F2, and F3) are similar to those of known FERM structures despite low sequence conservation. Differences in the sequence and relative orientation of the F3 subdomain alters the nature of the interdomain interface, and the phosphoinositide binding site found in ERM family FERM domains is not present in FAK. A putative protein interaction site on the F3 lobe is masked by the proximal region of the linker. Additionally, in one structure the adjacent Src SH3 and SH2 binding sites in the linker associate with the surfaces of the F3 and F1 lobes, respectively. These structural features suggest the possibility that protein interactions of the FAK FERM domain can be regulated by binding of Src kinases to the linker segment

  4. Crystal Structure of an LSD-Bound Human Serotonin Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D.; Betz, Robin M.; Venkatakrishnan, A.J.; Levit, Anat; Lansu, Katherine; Schools, Zachary L.; Che, Tao; Nichols, David E.; Shoichet, Brian K.; Dror, Ron O.; Roth, Bryan L. (UNCSM); (UNC); (Stanford); (Stanford-MED); (UCSF)

    2017-01-01

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.

  5. Large scale structures in liquid crystal/clay colloids

    Science.gov (United States)

    van Duijneveldt, Jeroen S.; Klein, Susanne; Leach, Edward; Pizzey, Claire; Richardson, Robert M.

    2005-04-01

    Suspensions of three different clays in K15, a thermotropic liquid crystal, have been studied by optical microscopy and small angle x-ray scattering. The three clays were claytone AF, a surface treated natural montmorillonite, laponite RD, a synthetic hectorite, and mined sepiolite. The claytone and laponite were sterically stabilized whereas sepiolite formed a relatively stable suspension in K15 without any surface treatment. Micrographs of the different suspensions revealed that all three suspensions contained large scale structures. The nature of these aggregates was investigated using small angle x-ray scattering. For the clays with sheet-like particles, claytone and laponite, the flocs contain a mixture of stacked and single platelets. The basal spacing in the stacks was independent of particle concentration in the suspension and the phase of the solvent. The number of platelets in the stack and their percentage in the suspension varied with concentration and the aspect ratio of the platelets. The lath shaped sepiolite did not show any tendency to organize into ordered structures. Here the aggregates are networks of randomly oriented single rods.

  6. Large scale structures in liquid crystal/clay colloids

    International Nuclear Information System (INIS)

    Duijneveldt, Jeroen S van; Klein, Susanne; Leach, Edward; Pizzey, Claire; Richardson, Robert M

    2005-01-01

    Suspensions of three different clays in K15, a thermotropic liquid crystal, have been studied by optical microscopy and small angle x-ray scattering. The three clays were claytone AF, a surface treated natural montmorillonite, laponite RD, a synthetic hectorite, and mined sepiolite. The claytone and laponite were sterically stabilized whereas sepiolite formed a relatively stable suspension in K15 without any surface treatment. Micrographs of the different suspensions revealed that all three suspensions contained large scale structures. The nature of these aggregates was investigated using small angle x-ray scattering. For the clays with sheet-like particles, claytone and laponite, the flocs contain a mixture of stacked and single platelets. The basal spacing in the stacks was independent of particle concentration in the suspension and the phase of the solvent. The number of platelets in the stack and their percentage in the suspension varied with concentration and the aspect ratio of the platelets. The lath shaped sepiolite did not show any tendency to organize into ordered structures. Here the aggregates are networks of randomly oriented single rods

  7. Crystal Structure of an LSD-Bound Human Serotonin Receptor.

    Science.gov (United States)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D; Betz, Robin M; Venkatakrishnan, A J; Levit, Anat; Lansu, Katherine; Schools, Zachary L; Che, Tao; Nichols, David E; Shoichet, Brian K; Dror, Ron O; Roth, Bryan L

    2017-01-26

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT 2B . The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT 2B R and 5-HT 2A R-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Structural Transformations in Nematic Liquid Crystals with a Hybrid Orientation

    Science.gov (United States)

    Delev, V. A.; Krekhov, A. P.

    2017-12-01

    The structural transformations in a nematic liquid crystal (NLC) layer with a hybrid orientation (planar director orientation is created on one substrate and homeotropic director orientation is created on the other) are studied. In the case of a dc voltage applied to the NLC layer, the primary instability is flexoelectric. It causes the appearance of flexoelectric domains oriented along the director on the substrate with a planar orientation. When the voltage increases further, an electroconvective instability in the form of rolls moving almost normal to flexoelectric domains develops along with these domains. Thus, the following spatially periodic structures of different natures coexist in one system: equilibrium static flexoelectric deformation of a director and dissipative moving oblique electroconvection rolls. The primary instability in the case of an ac voltage is represented by electroconvection, which leads to moving oblique or normal rolls depending on the electric field frequency. Above the electroconvection threshold, a transition to moving "abnormal" rolls is detected. The wavevector of the rolls coincides with the initial director orientation on the substrate with a planar orientation, and the projection of the director at the midplane of the NLC layer on the layer plane makes a certain angle with the wavevector. The results of numerical calculations of the threshold characteristics of the primary instabilities agree well with the obtained experimental data.

  9. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  10. Crystal structure of bis(4-acetylanilinium tetrachloridomercurate(II

    Directory of Open Access Journals (Sweden)

    Manickam Thairiyaraja

    2015-12-01

    Full Text Available The structure of the title salt, (C8H10NO2[HgCl4], is isotypic with that of the cuprate(II and cobaltate(II analogues. The asymmetric unit contains one 4-acetylanilinium cation and one half of a tetrachloridomercurate(II anion (point group symmetry m. The Hg—Cl distances are in the range 2.4308 (7–2.5244 (11 Å and the Cl—Hg—Cl angles in the range of 104.66 (2–122.94 (4°, indicating a considerable distortion of the tetrahedral anion. In the crystal, cations are linked by an intermolecular N—H...O hydrogen-bonding interaction, leading to a C(8 chain motif with the chains extending parallel to the b axis. There is also a π–π stacking interaction with a centroid-to-centroid distance of 3.735 (2 Å between neighbouring benzene rings along this direction. The anions lie between the chains and interact with the cations through intermolecular N—H...Cl hydrogen bonds, leading to the formation of a three-dimensional network structure.

  11. Rapid X-ray crystal structure analysis in few second measurements using microstrip gas chamber

    CERN Document Server

    Ochi, A; Tanimori, T; Ohashi, Y; Toyokawa, H; Nishi, Y; Nishi, Y; Nagayoshi, T; Koishi, S

    2001-01-01

    X-ray crystal structure analysis using microstrip gas chamber was successfully carried out in a measurement time within a few seconds. The continuous rotation photograph method, in which most of the diffraction peaks can be obtained within one continuous rotation of the sample crystal (without stopping or oscillation), was applied for this measurement. As an example, the structure of a single crystal of ammonium bitartrate (r=1 mm, spherical) was measured. Diffraction spots from the sample, which were sufficient to obtain crystal structure, were successfully obtained by taking only 2 s measurements with a commercially available laboratory X-ray source.

  12. Temporal coupled mode analysis of one-dimensional magneto-photonic crystals with cavity structures

    Energy Technology Data Exchange (ETDEWEB)

    Saghirzadeh Darki, Behnam, E-mail: b.saghirzadeh@ec.iut.ac.ir; Zeidaabadi Nezhad, Abolghasem; Firouzeh, Zaker Hossein

    2016-12-01

    In this paper, we propose the time-dependent coupled mode analysis of one-dimensional magneto-photonic crystals including one, two or multiple defect layers. The performance of the structures, namely the total transmission, Faraday rotation and ellipticity, is obtained using the proposed method. The results of the developed analytic approach are verified by comparing them to the results of the exact numerical transfer matrix method. Unlike the widely used numerical method, our proposed analytic method seems promising for the synthesis as well as the analysis purposes. Moreover, the proposed method has not the restrictions of the previously examined analytic methods. - Highlights: • A time-dependent coupled mode analysis is proposed for the cavity-type 1D MPCs. • Analytical formalism is presented for the single, double and multiple-defect MPCs. • Transmission, Faraday rotation and ellipticity are gained using the proposed method. • The proposed analytic method has advantages over the previously examined methods.

  13. Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

    OpenAIRE

    Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

    2008-01-01

    The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the ...

  14. The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

    Science.gov (United States)

    Leontis, N B; Westhof, E

    1998-09-01

    A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings

  15. Crystal structure and vibrational spectra of melaminium arsenate

    Science.gov (United States)

    Anbalagan, G.; Marchewka, M. K.; Pawlus, K.; Kanagathara, N.

    2015-01-01

    The crystals of the new melaminium arsenate (MAS) [C3H7N6+ṡH2AsO4-] were obtained by the slow evaporation of an aqueous solution at room temperature. Single crystal X-ray diffraction analysis reveals that the crystal belongs to triclinic system with centro symmetric space group P-1. The crystals are built up from single protonated melaminium residues and single dissociated arsenate H2AsO4- anions. The protonated melaminium ring is almost planar. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the melaminium and arsenate residues forms a three-dimensional network. Vibrational spectroscopic analysis is reported on the basis of FT-IR and FT-Raman spectra recorded at room temperature. Hydrogen bonded network present in the crystal gives notable vibrational effect. DSC has also been performed for the crystal shows no phase transition in the studied temperature range (113-293 K).

  16. Crystallization: the hidden dimension of Hedge funds' fee structure

    OpenAIRE

    Elaut, Gert; Frömmel, Michael; Sjödin, John

    2014-01-01

    We investigate the implications of variations in the frequency with which hedge fund managers update their high-water mark on fees paid by investors. We first document the crystallization frequencies used by Commodity Trading Advisors (CTAs) and then perform simulations and a bootstrap analysis. We find a statistically and economically significant effect of the crystallization frequency on the total fee load. Hedge funds' total fee load increases significantly as the crystallization frequency...

  17. Analysis of phase transitions and crystal structures of novel benzothiophene derivatives

    Science.gov (United States)

    Zhang, Shuo

    Although single crystal X-ray diffraction remains the most important technique for analyzing periodically ordered structures at atomic resolution, single crystal X-ray diffraction of organic macromolecules is challenged by difficulty in growing single crystals of desired size and quality. Electron crystallography of organic macromolecules, on the other hand, is limited by image resolution due to radiation damage and highly dependent on high-resolution instrumentation. Novel alkylated benzothiophene derivatives synthesized previously can be readily fabricated into semiconductor devices for various applications (photodetectors, explosive sensors, field-effect transistors, light-emitting diodes, etc.) via solution process. The object of this research is to identify phase transitions of organic macromolecules of this kind via differential scanning calorimetry and temperature-resolved wide angle X-ray diffraction, and to determine their lattice parameters and space groups by reconstruction of their reciprocal space via transmission electron microscopy/selected area electron diffraction followed by refinement with X-ray diffraction, supplemented by polarized light microscopy. Computer simulation was performed to rationalize the molecular packing schemes, so as to understand the origin of their electronic performance from crystallographic perspective.

  18. Crystal structure of CdSO4(H2O: a redetermination

    Directory of Open Access Journals (Sweden)

    Chatphorn Theppitak

    2015-10-01

    Full Text Available The crystal structure of the title compound, cadmium sulfate monohydrate or poly[(μ2-aqua(μ4-sulfatocadmium], was redetermined based on modern CMOS (complementary metal oxide silicon data. In comparison with the previous study [Bregeault & Herpin (1970. Bull. Soc. Fr. Mineral. Cristallogr. 93, 37–42], all non-H atoms were refined with anisotropic displacement parameters and the hydrogen-bonding pattern unambiguously established due to location of the hydrogen atoms. In addition, a significant improvement in terms of precision and accuracy was achieved. In the crystal, the Cd2+ cation is coordinated by four O atoms of four sulfate anions and two O atoms of water molecules, forming a distorted octahedral trans-[CdO6] polyhedron. Each sulfate anion bridges four Cd2+ cations and each water molecule bridges two Cd2+ cations, leading to the formation of a three-dimensional framework, with Cd...Cd separations in the range 4.0757 (2–6.4462 (3 Å. O—H...O hydrogen-bonding interactions of medium strength between the coordinating water molecules and sulfate anions consolidate the crystal packing.

  19. Solar cell structure incorporating a novel single crystal silicon material

    Science.gov (United States)

    Pankove, Jacques I.; Wu, Chung P.

    1983-01-01

    A novel hydrogen rich single crystal silicon material having a band gap energy greater than 1.1 eV can be fabricated by forming an amorphous region of graded crystallinity in a body of single crystalline silicon and thereafter contacting the region with atomic hydrogen followed by pulsed laser annealing at a sufficient power and for a sufficient duration to recrystallize the region into single crystal silicon without out-gassing the hydrogen. The new material can be used to fabricate semiconductor devices such as single crystal silicon solar cells with surface window regions having a greater band gap energy than that of single crystal silicon without hydrogen.

  20. Raphide crystal structure in agave tequilana determined by x-ray originating from synchrotron radiation

    International Nuclear Information System (INIS)

    Tadokoro, Makoto; Ozawa, Yoshiki; Mitsumi, Minoru; Toriumi, Kohshiro; Ogura, Tetsuya

    2005-01-01

    The first single crystal structure of small natural raphides in an agave plant is completely determined using an intense X-ray originating from a synchrotron radiation. The SEM image shows that the tip of the crystal is approximately hundreds of nanometer in width sharply grow to stick to the tissue of herbivorous vermin. Furthermore, the crystal develops cracks that propagate at an inclination of approximately 45deg towards the direction of crystal growth such that the crystal easily splits into small pieces in the tissue. (author)

  1. CCDC 1059905: Experimental Crystal Structure Determination : 7,13-dimesitylindeno[1,2-b]thioxanthene

    KAUST Repository

    Shi, Xueliang; Kueh, Weixiang; Zheng, Bin; Huang, Kuo-Wei; Chi, Chunyan

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  2. CCDC 1048727: Experimental Crystal Structure Determination : bis(2-(hydroxyimino)propanoato)-tin(ii)

    KAUST Repository

    Khanderi, Jayaprakash; Davaasuren, Bambar; Alshankiti, Buthainah; Rothenberger, Alexander

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  3. CCDC 844303: Experimental Crystal Structure Determination : 1,1,3,3-Tetraphenyldiphosphoxane 1,3-disulfide

    KAUST Repository

    Al-Masri, H.T.; Emwas, Abdul-Hamid M.; Al-Talla, Zeyad; Al Kordi, Mohamed

    2012-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  4. CCDC 844302: Experimental Crystal Structure Determination : N-1-Naphthyl-P,P-diphenylphosphinoselenoic amide

    KAUST Repository

    Al-Masri, H.T.; Emwas, Abdul-Hamid M.; Al-Talla, Zeyad; Al Kordi, Mohamed

    2012-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  5. CCDC 1477679: Experimental Crystal Structure Determination : (1,3-dimesitylimidazolidin-2-ylidene)-trimethyl-indium

    KAUST Repository

    Wu, Melissa M.; Gill, Arran M.; Yunpeng, Lu; Yongxin, Li; Ganguly, Rakesh; Falivene, Laura; Garcí a, Felipe

    2017-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  6. CCDC 1477678: Experimental Crystal Structure Determination : (1,3-dimesitylimidazolidin-2-ylidene)-trimethyl-gallium

    KAUST Repository

    Wu, Melissa M.; Gill, Arran M.; Yunpeng, Lu; Yongxin, Li; Ganguly, Rakesh; Falivene, Laura; Garcí a, Felipe

    2017-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  7. CCDC 1024814: Experimental Crystal Structure Determination : 1,3-Dimesitylimidazolidine-2-selenone

    KAUST Repository

    Vummaleti, Sai V. C.; Nelson, David J.; Poater, Albert; Gó mez-Suá rez, Adriá n; Cordes, David B.; Slawin, Alexandra M. Z.; Nolan, Steven P.; Cavallo, Luigi

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  8. CCDC 930139: Experimental Crystal Structure Determination : Chloro-(1-cyclododecyl-3-mesitylimidazol-2-ylidene)-silver

    KAUST Repository

    Queval, Pierre

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  9. CCDC 1429311: Experimental Crystal Structure Determination : N-(5-Bromoquinolin-8-yl)benzamide

    KAUST Repository

    Xu, Jun; Shen, Chao; Zhu, Xiaolei; Zhang, Pengfei; Ajitha, Manjaly John; Huang, Kuo-Wei; An, Zhongfu; Liu, Xiaogang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  10. CCDC 933273: Experimental Crystal Structure Determination : Chloro-(1-cyclododecyl-3-mesitylimidazol-2-ylidene)-gold

    KAUST Repository

    Queval, Pierre; Jahier, Claire; Rouen, Mathieu; Artur, Isabelle; Legeay, Jean-Christophe; Falivene, Laura; Toupet, loic; Cré visy, Christophe; Cavallo, Luigi; Basle, Olivier; Mauduit, Marc

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  11. CCDC 963856: Experimental Crystal Structure Determination : catena-[bis(mu2-2-methylimidazole)-zinc

    KAUST Repository

    Shekhah, Osama; Swaidan, Raja; Belmabkhout, Youssef; du Plessis, Marike; Jacobs, Tia; Barbour, Leonard J.; Pinnau, Ingo; Eddaoudi, Mohamed

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  12. CCDC 951636: Experimental Crystal Structure Determination : bis(tetra-n-butylammonium) trichloro-(nitrosyl)-(oxalato)-ruthenium

    KAUST Repository

    Kuhn, Paul-Steffen; Cremer, Laura; Gavriluta, Anatolie; Jovanović, Katarina K.; Filipović, Lana; Hummer, Alfred A.; Bü chel, Gabriel E.; Dojčinović, Biljana P.; Meier, Samuel M.; Rompel, Annette; Radulović, Siniša; Tommasino, Jean Bernard; Luneau, Dominique; Arion, Vladimir B.

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  13. Synthesis, Crystal Structure and Anti-ischaemic Activity of (E)-1-{4 ...

    African Journals Online (AJOL)

    chloro- phenyl)prop-2-en-1-one (C28H29ClN2O3, Mr = 476.98) (5) was synthesized and studied by the single crystal X-ray diffraction method. Its structure was confirmed by 1HNMR, 13CNMR,HRMSand X-ray single crystal structure ...

  14. CCDC 870534: Experimental Crystal Structure Determination : Dichloro-trimethyl-tantalum(v)

    KAUST Repository

    Chen, Yin; Callens, E.; Abou-Hamad, E.; Merle, N.; White, A.J.P.; Taoufik, M.; Coperet, C.; Le Roux, E.; Basset, J.-M.

    2013-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  15. CCDC 1475931: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  16. CCDC 1475929: Experimental Crystal Structure Determination : trimethylammonium tribromo-tin(iv)

    KAUST Repository

    Dang, Yangyang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  17. CCDC 887968: Experimental Crystal Structure Determination : Dichloro-bis(tricyclohexylphosphine)-(3-phenylindenylidene)-ruthenium tetrahydrofuran solvate

    KAUST Repository

    Urbina-Blanco, C.A.

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  18. CCDC 713130: Experimental Crystal Structure Determination : bis(2,5-Dihydrobenzylammonium) hexachloro-osmium(iv)

    KAUST Repository

    Reiner, T.

    2011-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  19. CCDC 721712: Experimental Crystal Structure Determination : (N-(2-Aminoethyl)-4-methylbenzenesulfonamidato)-(phenylalaninato)-ruthenium dimethylsulfoxide solvate

    KAUST Repository

    Reiner, Thomas; Jantke, Dominik; Miao, Xiao-He; Marziale, Alexander N.; Kiefer, Florian J.; Eppinger, Jö rg

    2013-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  20. CCDC 721713: Experimental Crystal Structure Determination : Dichloro-(ethyl phenylalaninate)-tris(pyridine)-ruthenium(ii)

    KAUST Repository

    Reiner, Thomas; Jantke, Dominik; Miao, Xiao-He; Marziale, Alexander N.; Kiefer, Florian J.; Eppinger, Jö rg

    2013-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  1. Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca.

    Science.gov (United States)

    Singh, D D; Saikrishnan, K; Kumar, Prashant; Dauter, Z; Sekar, K; Surolia, A; Vijayan, M

    2004-11-01

    The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit. The structure has been solved using molecular replacement to a resolution of 3 A. The structure of the subunit is similar to that of jacalin-like lectins.

  2. CCDC 1015953: Experimental Crystal Structure Determination : 1,3,6,8-tetrakis(4-phenoxyphenyl)pyrene

    KAUST Repository

    El-Assaad, Tarek H.; Auer, Manuel; Castañ eda, Raul; Hallal, Kassem M.; Jradi, Fadi M.; Mosca, Lorenzo; Khnayzer, Rony S.; Patra, Digambara; Timofeeva, Tatiana V.; Bredas, Jean-Luc; List-Kratochvil, Emil J. W.; Wex, Brigitte; Kaafarani, Bilal R.

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  3. CCDC 1010350: Experimental Crystal Structure Determination : dichloro-(methylenebis(di-t-butylphosphine))-palladium(ii)

    KAUST Repository

    Roesle, Philipp; Caporaso, Lucia; Schnitte, Manuel; Goldbach, Verena; Cavallo, Luigi; Mecking, Stefan

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  4. CCDC 1446070: Experimental Crystal Structure Determination : tris(Pentafluorophenyl)-(triethylsilyl formate)-boron

    KAUST Repository

    Chen, Jiawei

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  5. CCDC 1420581: Experimental Crystal Structure Determination : catena-[(mu-4,4'-sulfonyldibenzoato)-calcium ethylene

    KAUST Repository

    Plonka, Anna M.

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  6. CCDC 1420582: Experimental Crystal Structure Determination : catena-[(mu-4,4'-sulfonyldibenzoato)-calcium ethane

    KAUST Repository

    Plonka, Anna M.

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  7. CCDC 1420580: Experimental Crystal Structure Determination : catena-[(mu-4,4'-sulfonyldibenzoato)-calcium acetylene

    KAUST Repository

    Plonka, Anna M.

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  8. CCDC 1436717: Experimental Crystal Structure Determination : 2-bromo-4,5-diiodo-1,3-thiazole

    KAUST Repository

    Shi, Qinqin

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  9. CCDC 1436716: Experimental Crystal Structure Determination : 5-fluoro-4-iodo-2,1,3-benzothiadiazole

    KAUST Repository

    Shi, Qinqin

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  10. CCDC 1048728: Experimental Crystal Structure Determination : ammonium tris(2-(methoxyimino)propanoato)-tin(ii) dihydrate

    KAUST Repository

    Khanderi, Jayaprakash

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  11. CCDC 1048729: Experimental Crystal Structure Determination : bis(2-(hydroxyimino)-3-phenylpropanoato)-tin(ii)

    KAUST Repository

    Khanderi, Jayaprakash

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  12. CCDC 1515632: Experimental Crystal Structure Determination : hexakis(dimethyl sulfoxide)-manganese(ii) tetraiodide

    KAUST Repository

    Haque, M.A.

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  13. CCDC 713129: Experimental Crystal Structure Determination : (eta^6^-Benzylammonium)-dichloro-(dimethylsulfoxide-S)-ruthenium(ii) chloride

    KAUST Repository

    Reiner, T.; Waibel, M.; Marziale, Alexander N.; Jantke, Dominik; Kiefer, F.J.; Fassler, T.F.; Eppinger, Jö rg

    2011-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  14. CCDC 1011330: Experimental Crystal Structure Determination : 1,3,6,8-tetrakis(4-fluorophenyl)pyrene

    KAUST Repository

    El-Assaad, Tarek H.; Auer, Manuel; Castañ eda, Raul; Hallal, Kassem M.; Jradi, Fadi M.; Mosca, Lorenzo; Khnayzer, Rony S.; Patra, Digambara; Timofeeva, Tatiana V.; Bredas, Jean-Luc; List-Kratochvil, Emil J. W.; Wex, Brigitte; Kaafarani, Bilal R.

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  15. Structural templating in a nonplanar phthalocyanine using single crystal copper iodide

    OpenAIRE

    Rochford, L. A. (Luke A.); Ramadan, Alexandra J.; Keeble, Dean S.; Ryan, Mary P.; Heutz, Sandrine; Jones, T. S. (Tim S.)

    2015-01-01

    Solution-grown copper iodide crystals are used as substrates for the templated growth of the nonplanar vanadyl phthalocyanine using organic molecular beam deposition. Structural characterization reveals a single molecular orientation produced by the (111) Miller plane of the copper iodide crystals. These fundamental measurements show the importance of morphology and structure in templating interactions for organic electronics applications.

  16. CCDC 1446069: Experimental Crystal Structure Determination : tris(Pentafluorophenyl)-(triethylsilyl formate)-aluminium

    KAUST Repository

    Chen, Jiawei

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  17. CCDC 1427126: Experimental Crystal Structure Determination : bis(1,10-Phenanthroline)-copper pentafluoropropanoate

    KAUST Repository

    Huang, Yangjie

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  18. CCDC 1427127: Experimental Crystal Structure Determination : bis(1,10-Phenanthroline)-copper heptafluorobutanoate benzene solvate

    KAUST Repository

    Huang, Yangjie

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  19. CCDC 1482638: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  20. CCDC 1475930: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  1. U6+ minerals and inorganic compounds: insights into an expanded structural hierarchy of crystal structures

    International Nuclear Information System (INIS)

    Burns, P.C.

    2005-01-01

    The crystal structures of uranyl minerals and inorganic uranyl compounds are important for understanding the genesis of U deposits, the interaction of U mine and mill tailings with the environment, transport of actinides in soils and the vadose zone, the performance of geological repositories for nuclear waste, and for the development of advanced materials with novel applications. Over the past decade, the number of inorganic uranyl compounds (including minerals) with known structures has more than doubled, and reconsideration of the structural hierarchy of uranyl compounds is warranted. Here, 368 inorganic crystal structures that contain essential U 6+ are considered (of which 89 are minerals). They are arranged on the basis of the topological details of their structural units, which are formed by the polymerization of polyhedra containing higher-valence cations. Overarching structural categories correspond to those based upon isolated polyhedra (8), finite clusters (43), chains (57), sheets (204), and frameworks (56) of polyhedra. Within these categories, structures are organized and compared upon the basis of either their graphical representations, or in the case of sheets involving sharing of edges of polyhedra, upon the topological arrangement of anions within the sheets. (author)

  2. The crystal structure of Toxoplasma gondii pyruvate kinase 1.

    Directory of Open Access Journals (Sweden)

    Rebecca Bakszt

    2010-09-01

    Full Text Available Pyruvate kinase (PK, which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population.We have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers.We hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two α-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.

  3. The crystal structure of Toxoplasma gondii pyruvate kinase 1.

    Science.gov (United States)

    Bakszt, Rebecca; Wernimont, Amy; Allali-Hassani, Abdellah; Mok, Man Wai; Hills, Tanya; Hui, Raymond; Pizarro, Juan C

    2010-09-14

    Pyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population. We have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers. We hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two α-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.

  4. The Crystal Structure of Toxoplasma gondii Pyruvate Kinase 1

    Energy Technology Data Exchange (ETDEWEB)

    Bakszt, R.; Wernimont, A; Allali-Hassani, A; Mok, M; Hills, T; Hui, R; Pizarro, J

    2010-01-01

    Pyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population. We have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers. We hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two {alpha}-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.

  5. Crystal Structures, Thermal Analysis, and Dissolution Behavior of New Solid Forms of the Antiviral Drug Arbidol with Dicarboxylic Acids

    Directory of Open Access Journals (Sweden)

    Alex N. Manin

    2015-12-01

    Full Text Available Salts of the antiviral drug arbidol (umifenovir (Arb with maleate (Mlc and fumarate (Fum anions have been obtained, and their crystal structures have been described. The crystal structure of arbidol maleate has been redetermined by single crystal X-ray diffraction at 180K. A new arbidol cocrystal in zwitterion form with succinic acid (Suc has also been found and characterized. The arbidol zwitterion was not previously seen in any of the drug crystal forms, and the [Arb + Suc] cocrystal seems to be the first found instance. Analysis of the conformational preferences of the arbidol molecule in the crystal structures has shown that it adopts two types of conformations, namely “open” and “closed” ones. Thermal stability of the arbidol salts and cocrystal have been analyzed by means of differential scanning calorimetry, thermogravimetric, and mass-spectrometry analysis. The dissolution study of the arbidol salts and cocrystal performed in aqueous buffer solutions with pH 1.2 and 6.8 has shown that both the salts and the cocrystal dissolve incongruently to form an arbidol hydrochloride monohydrate at pH 1.2 and an arbidol base at pH 6.8, respectively. The cocrystal reaches the highest solubility level in both pH 1.2 and pH 6.8 solutions.

  6. crystal

    Science.gov (United States)

    Yu, Yi; Huang, Yisheng; Zhang, Lizhen; Lin, Zhoubin; Sun, Shijia; Wang, Guofu

    2014-07-01

    A Nd3+:Na2La4(WO4)7 crystal with dimensions of ϕ 17 × 30 mm3 was grown by the Czochralski method. The thermal expansion coefficients of Nd3+:Na2La4(WO4)7 crystal are 1.32 × 10-5 K-1 along c-axis and 1.23 × 10-5 K-1 along a-axis, respectively. The spectroscopic characteristics of Nd3+:Na2La4(WO4)7 crystal were investigated. The Judd-Ofelt theory was applied to calculate the spectral parameters. The absorption cross sections at 805 nm are 2.17 × 10-20 cm2 with a full width at half maximum (FWHM) of 15 nm for π-polarization, and 2.29 × 10-20 cm2 with a FWHM of 14 nm for σ-polarization. The emission cross sections are 3.19 × 10-20 cm2 for σ-polarization and 2.67 × 10-20 cm2 for π-polarization at 1,064 nm. The fluorescence quantum efficiency is 67 %. The quasi-cw laser of Nd3+:Na2La4(WO4)7 crystal was performed. The maximum output power is 80 mW. The slope efficiency is 7.12 %. The results suggest Nd3+:Na2La4(WO4)7 crystal as a promising laser crystal fit for laser diode pumping.

  7. Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

    Science.gov (United States)

    Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

    2014-02-01

    Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

  8. High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.

    Science.gov (United States)

    Clifton, Matthew C; Bruhn, Jessica F; Atkins, Kateri; Webb, Terry L; Baydo, Ruth O; Raymond, Amy; Lorimer, Donald D; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

    2015-10-01

    Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

    Science.gov (United States)

    van de Streek, Jacco; Neumann, Marcus A

    2010-10-01

    This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

  10. Comparison of multiple crystal structures with NMR data for engrailed homeodomain

    Energy Technology Data Exchange (ETDEWEB)

    Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

    2008-03-15

    Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

  11. Synthesis, crystal structure determination of two-dimensional ...

    Indian Academy of Sciences (India)

    Abstract. The 2-D polymeric complex (I) has the formula [Ag(phSE)(NO3)]n, which has been crystallized from methanol-acetonitrile mixture and characterized by elemental analysis and single-crystal X-ray diffraction analysis. In this polymer, each Ag(I) ion occupies distorted trigonal pyramidal geometry coordinating with two.

  12. Structural transitions in crystals of native aspartate carbamoyltransferase

    International Nuclear Information System (INIS)

    Gouaux, J.E.; Lipscomb, W.N.

    1989-01-01

    Screened precession x-ray photographs of crystals of native aspartate carbamoyltransferase ligated with L-aspartate and phosphate reveal the presence of a crystal unit-cell dimension that is intermediate between the T (tense) and R (relaxed) states. Characterizing the intermediate (I) crystal is a c-axis unit-cell dimension of 149 angstrom, halfway between the c-axis length of the T (c = 142 angstrom) and R (c = 156 angstrom) states, in the space group P321. Preservation of the P321 space group indicates that the intermediate crystal form retains a threefold axis of symmetry, and therefore the enzyme has at minimum a threefold axis; however, it is not known whether the molecular twofold axis is conserved. The I crystals are formed by soaking T-state crystals with L-aspartate and phosphate. By raising the concentration of L-aspartate the authors can further transform the I crystals, without fragmentation, to a form that has the same unit-cell dimensions as R-state crystals grown in the presence of N-(phosphonoacetyl)-L-aspartate

  13. Structural study of intermediate phase in layered perovskite SrBi sub 2 Ta sub 2 O sub 9 single crystal

    CERN Document Server

    Onodera, A; Yamashita, H

    2003-01-01

    The crystal structure of an intermediate phase of Bi-layered ferroelectric SrBi sub 2 Ta sub 2 O sub 9 single crystals was studied by means of X-ray diffraction. An analysis of the extinction rules and X-ray intensities demonstrated that the crystal structure is orthorhombic with space group A2 sub 1 am in the ferroelectric phase and Amam in the intermediate phase; this conclusion is in good agreement with the findings of previous powder neutron diffraction studies.

  14. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan [Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)

    2015-10-27

    The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

  15. Topotactic decomposition and crystal structure of white molybdenum trioxide--monohydrate: prediction of structure by topotaxy

    International Nuclear Information System (INIS)

    Oswald, H.R.; Guenter, J.R.; Dubler, E.

    1975-01-01

    Single crystals of the white MoO 3 . H 2 O modification (''α-molybdic acid'') were transformed by heating to 160 0 C into perfect pseudomorphs built up from oriented MoO 3 crystallites of known structure. From the mutual orientation relationship of the unit cells of both phases involved in this topotactic reaction, as determined by X-ray photographs, a model for the so far unknown crystal structure of white MoO 3 . H 2 O could be deduced. Independently, this structure was determined by X-ray diffractometer data then: space group P anti 1, a = 7.388, b = 3.700, c = 6.673 A, α = 107.8, β = 113.6, γ = 91.2 0 , Z = 2. The structure was solved from the Patterson function and refined until R = 0.088. It is built up from isolated double chains of strongly distorted [MoO 5 (H 2 O)]-octahedra sharing two common edges with each other. This result agrees well with the model derived from topotaxy, and it becomes evident how the MoO 3 lattice is formed through corner linking of the isolated double chains after the water molecules are removed. The study of topotactic phenomena seems rather generally applicable to deduce the main features of structures involved and for better understanding of structural relationships. (U.S.)

  16. Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8.

    Directory of Open Access Journals (Sweden)

    Sayaka Igari

    Full Text Available Methylenetetrahydrofolate reductase (MTHFR is one of the enzymes involved in homocysteine metabolism. Despite considerable genetic and clinical attention, the reaction mechanism and regulation of this enzyme are not fully understood because of difficult production and poor stability. While recombinant enzymes from thermophilic organisms are often stable and easy to prepare, properties of thermostable MTHFRs have not yet been reported.MTHFR from Thermus thermophilus HB8, a homologue of Escherichia coli MetF, has been expressed in E. coli and purified. The purified MTHFR was chiefly obtained as a heterodimer of apo- and holo-subunits, that is, one flavin adenine dinucleotide (FAD prosthetic group bound per dimer. The crystal structure of the holo-subunit was quite similar to the β(8α(8 barrel of E. coli MTHFR, while that of the apo-subunit was a previously unobserved closed form. In addition, the intersubunit interface of the dimer in the crystals was different from any of the subunit interfaces of the tetramer of E. coli MTHFR. Free FAD could be incorporated into the apo-subunit of the purified Thermus enzyme after purification, forming a homodimer of holo-subunits. Comparison of the crystal structures of the heterodimer and the homodimer revealed different intersubunit interfaces, indicating a large conformational change upon FAD binding. Most of the biochemical properties of the heterodimer and the homodimer were the same, except that the homodimer showed ≈50% activity per FAD-bound subunit in folate-dependent reactions.The different intersubunit interfaces and rearrangement of subunits of Thermus MTHFR may be related to human enzyme properties, such as the allosteric regulation by S-adenosylmethionine and the enhanced instability of the Ala222Val mutant upon loss of FAD. Whereas E. coli MTHFR was the only structural model for human MTHFR to date, our findings suggest that Thermus MTHFR will be another useful model for this important enzyme.

  17. Two Voriconazole salts: Syntheses, crystal structures, solubility and bioactivities

    Science.gov (United States)

    Tang, Gui-Mei; Wang, Yong-Tao

    2018-01-01

    Two Voriconazole salts, namely, (H2FZ)2+·2(Cl-) (1) and (HFZ)+·NO3- (2) (FZ = (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoro-4-pyrimidiny)-1-(1H-1,2,4-triazol-1-yl)-2-butanol) have been obtained through the reaction of Voriconazole, hydrochloric acid and nitrate acid, respectively. They were structurally characterized by FT-IR, elemental analyses (EA), single crystal X-ray diffraction, and thermogravimetric analysis (TGA). A variety of hydrogen bonds (Osbnd H⋯N, Nsbnd H⋯Cl/O, Csbnd H⋯N/OF/Cl) were observed in the compounds 1 and 2, through which a 3D supramolecular architecture is generated. Both two salts 1 and 2 show the promising bioactivities against Aspergillus species (Aspergillus niger, Aspergillus terreus, Aspergillus fumigatus and Aspergillus flavus) and Candida ones (Candida albicans, Candida krusei, Candida glabrata and Cryptococcus neoformans), which is obviously more excellent than that of FZ. Additionally, the solubility of two salts is considerably higher than that of the drug Voriconazole.

  18. Optics of anisotropic metamaterial based structurally chiral photonic crystals

    International Nuclear Information System (INIS)

    Gevorgyan, A H; Rafayelyan, M S

    2013-01-01

    Light transmission through and reflection from a medium layer with dielectric and magnetic helicities are discussed. The axes of the dielectric permittivity tensor, ε-hat , and the magnetic permeability tensor, μ-hat , as well as the medium helix axis are all parallel to each other and they are perpendicular to the boundary surfaces. The possibilities of formation of some new types of photonic bandgaps (PBGs) are presented for large anisotropies of the medium—namely, direct and indirect nonselective PBGs (with respect to the incident light polarization, in contrast to the usual direct PBGs, which are selective with respect to the polarization of the incident light). It is shown that a transmission region can arise among the three types of PBGs, in certain conditions, of course. In this paper we generalize the concept of nihility for structurally chiral media, such as cholesteric liquid crystals (CLCs) and we identify two types of CLC nihilities. It is shown that, for certain characteristic parameters of the medium, superluminal light propagation is possible in the transmission band. The influence of the anisotropy of the medium on the reflection spectra is considered and it is shown that one can tune the width, number and frequency range of PBGs of this layer, at essentially large limits, tuning the parameters of the layer. The case of oblique light incidence on the CLC layer is also discussed. (paper)

  19. Synthesis, crystal structure and applications of palladium thiosalicylate complexes

    Directory of Open Access Journals (Sweden)

    S.B. Moosun

    2017-05-01

    Full Text Available Three palladium thiosalicylate complexes [Pd(tb(bipy]·3H2O (1, [Pd2(tb2(bipy2]·(dtdb2 (2 and [Pd2(tb2(phen2]·dtdb·H2O (3 (bipy = bipyridine; phen = phenanthroline were prepared from the reaction of PdCl2(CH3CN2 with dithiosalicylic acid (dtdb which underwent cleavage to form thiobenzoate anion (tb in DMF/MeOH. Square planar geometries of the complexes with a N2SO coordination type were proposed on the basis of single crystal X-ray structural study. The presence of trapped and uncoordinated dtdb was observed in complexes 2 and 3. Complexes 1–3 were evaluated as catalysts for Heck coupling reactions of methyl acrylate with iodobenzene, and showed moderate activities at a very low catalyst loading. Complex 1 was found to inhibit the growth of bacteria and scavenge free radicals efficiently.

  20. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar

    2015-09-01

    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  1. Annealing effect of H+ -implanted single crystal silicon on strain and crystal structure

    International Nuclear Information System (INIS)

    Duo Xinzhong; Liu Weili; Zhang Miao; Gao Jianxia; Fu Xiaorong; Lin Chenglu

    2000-01-01

    The work focuses on the rocking curves of H + -implanted single silicon crystal detected by Four-Crystal X-ray diffractometer. The samples were annealed under different temperatures. Lattice defect in H + -implanted silicon crystals was detected by Rutherford Backscattering Spectrometry. It appeared that H-related complex did not crush until annealing temperature reached about 400 degree C. At that temperature H 2 was formed, deflated in silicon lattice and strained the lattice. But defects did not come into being in large quantity. The lattice was undamaged. When annealing temperature reached 500 degree C, strain induced by H 2 deflation crashed the silicon lattice. A large number of defects were formed. At the same time bubbles in the crystal and blister/flaking on the surface could be observed

  2. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Cornaby, Sterling [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Szebenyi, Doletha M. E. [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Smilgies, Detlef-M. [CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Schuller, David J.; Gillilan, Richard; Hao, Quan [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Bilderback, Donald H., E-mail: dhb2@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States)

    2010-01-01

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.

  3. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    International Nuclear Information System (INIS)

    Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

    2010-01-01

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used

  4. Influence of submelting on formation of single crystals of nickel alloy with cellular-dendritic structure

    International Nuclear Information System (INIS)

    Pankin, G.N.; Esin, V.O.; Ponomarev, V.V.

    1996-01-01

    A study was made into specific features of cellular - dendritic structure formation in single crystals of nickel base alloy ZhS26 which had been crystallized following the pattern of solid solution. The single crystals in growing were subjected to periodic partial remelting to suppress the transition of cellular structure into a cellular - dendritic one during directional solidification. The results obtained showed the possibility to stabilize cellular growth of solid solution by way of inversion of interphase surface motion in the process of directional crystallization. 4 refs.; 5 figs

  5. Synthesis, crystal structures and properties of lead phosphite compounds

    International Nuclear Information System (INIS)

    Song, Jun-Ling; Hu, Chun-Li; Xu, Xiang; Kong, Fang; Mao, Jiang-Gao

    2015-01-01

    Here, we report the preparation and characterization of two lead(II) phosphites, namely, Pb_2(HPO_3)_2 and Pb_2(HPO_3)(NO_3)_2 through hydrothermal reaction or simple solution synthesis, respectively. A new lead phosphite, namely, Pb_2(HPO_3)_2, crystallizes in the noncentrosymmetric space group Cmc2_1 (no. 36), which features 3D framework formed by the interconnection of 2D layer of lead(II) phosphites and 1D chain of [Pb(HPO_3)_5]_∞. The nonlinear optical properties of Pb_2(HPO_3)(NO_3)_2 have been studied for the first time. The synergistic effect of the stereo-active lone-pairs on Pb"2"+ cations and π-conjugated NO_3 units in Pb_2(HPO_3)(NO_3)_2 produces a moderate second harmonic generation (SHG) response of ∼1.8×KDP (KH_2PO_4), which is phase matchable (type I). IR, UV–vis spectra and thermogravimetric analysis (TGA) for the two compounds were also measured. - Graphical abstract: Two lead phosphites Pb_2(HPO_3)_2 and Pb_2(HPO_3)(NO_3)_2 are studied. A new lead phosphite Pb_2(HPO_3)_2 features a unique 3D framework structure and Pb_2(HPO_3)(NO_3)_2 shows a moderate SHG response of ∼1.8×KDP (KH_2PO_4). - Highlights: • A new lead phosphite, Pb_2(HPO_3)_2 is reported. • Pb_2(HPO_3)_2 features a unique 3D framework structure. • NLO property of Pb_2(HPO_3)(NO_3)_2 is investigated. • Pb_2(HPO_3)(NO_3)_2 produces a moderate SHG response of ∼1.8×KDP (KH_2PO_4).

  6. Crystal structure of a new natural (Ba, Nb) silicate

    International Nuclear Information System (INIS)

    Yamnova, N.A.; Pushcharovskii, D.Yu.; Voloshin, A.V.

    1990-01-01

    The structure of a new mineral Ba 3 (Ti 1.2 Nb 4.8 ) Si 4 O 25.4 is determined (166 reflections, method of least squares in anisotropic approximation, R = 0.040). The crystallographic parameters are: a = 9.03(1), c = 7.868(6) angstrom, Z = 1, space group P anti 62m. Like the previously investigated synthetic analogs Ba 3 Si 4 Nb 6 O 26 , Ba 3 Si 4 Ti 6 O 23 , and Ba 3 Si 4 Ta 6 O 26 , the structure contains a mixed framework of octahedral columns of triangular section, bound to the diortho groups [Si 2 O 7 ], of which the cavities contain the Ba atoms

  7. Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

    KAUST Repository

    Abe, Yuichiro

    2017-08-15

    Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

  8. Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

    KAUST Repository

    Abe, Yuichiro; Savikhin, Victoria; Yin, Jun; Grimsdale, Andrew C.; Soci, Cesare; Toney, Michael F.; Lam, Yeng Ming

    2017-01-01

    Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

  9. Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

    Science.gov (United States)

    Qiu, Wei; Dong, Aiping; Pizarro, Juan C; Botchkarsev, Alexei; Min, Jinrong; Wernimont, Amy K; Hills, Tanya; Hui, Raymond; Artz, Jennifer D

    2012-03-19

    Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control. To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed PvTrx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of PyTrx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of PyPrx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding. The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group

  10. CheShift-2 resolves a local inconsistency between two X-ray crystal structures

    International Nuclear Information System (INIS)

    Vila, Jorge A.; Sue, Shih-Che; Fraser, James S.; Scheraga, Harold A.; Dyson, H. Jane

    2012-01-01

    Since chemical shifts provide important and relatively accessible information about protein structure in solution, a Web server, CheShift-2, was developed for structure interrogation, based on a quantum mechanics database of 13 C α chemical shifts. We report the application of CheShift-2 to a local inconsistency between two X-ray crystal structures (PDB IDs 1IKN and 1NFI) of the complex between the p65/p50 heterodimer of NFκB and its inhibitor IκBα. The availability of NMR resonance assignments that included the region of the inconsistency provided an opportunity for independent validation of the CheShift-2 server. Application of the server showed that the 13 C α chemical shifts measured for the Gly270-Pro281 sequence close to the C-terminus of IκBα were unequivocally consistent with the backbone structure modeled in the 1IKN structure, and were inconsistent with the 1NFI structure. Previous NOE measurements had demonstrated that the position of a tryptophan ring in the region immediately N-terminal in this region was not consistent with either structure. Subsequent recalculation of the local structure in this region, based on the electron density of the deposited structure factors for 1IKN, confirmed that the local backbone structure was best modeled by 1IKN, but that the rotamer of Trp258 is consistent with the 1NFI structure, including the presence of a hydrogen bond between the ring NεH of Trp258 and the backbone carbonyl group of Gln278. The consensus between all of these measures suggests that the CheShift-2 server operates well under circumstances in which backbone chemical shifts are available but where local plasticity may render X-ray structural data ambiguous.

  11. Local layer structure of smectic liquid crystals by X-ray micro-diffraction

    CERN Document Server

    Takanishi, Y

    2003-01-01

    The local layer structure of smectic liquid crystal has been measured using time-resolved synchrotron X-ray micro-diffraction. Typical layer disorders observed in surface stabilized (anti-) ferroelectric liquid crystals, i.e. a stripe texture, a needed-like defect and a zigzag defect, are directly analyzed. The detailed analysis slows that the surface anchoring force due to the interaction between the liquid crystal molecule and the alignment thin film plays an important role to realize both the static and dynamic local layer structures. The layer structure of the circular domain observed in the liquid crystal of bent-shaped molecules found to depend on the applied electric field though the optical micrograph shows little difference. The frustrated, double and single layer structures of the bent-shaped molecule liquid crystal are determined depending on the terminal alkyl chain length. (author)

  12. Crystal structures of orthorhombic, hexagonal, and cubic compounds of the Sm(x)Yb(2−x)TiO5 series

    International Nuclear Information System (INIS)

    Aughterson, Robert D.; Lumpkin, Gregory R.; Reyes, Massey de los; Sharma, Neeraj; Ling, Christopher D.; Gault, Baptiste; Smith, Katherine L.; Avdeev, Maxim; Cairney, Julie M.

    2014-01-01

    A series of single phase compounds with nominal stoichiometry Sm (x) Yb (2−x) TiO 5 (x=2, 1.4, 1, 0.6, and 0) have been successfully fabricated to generate a range of crystal structures covering the most common polymorphs previously discovered in the Ln 2 TiO 5 series (Ln=lanthanides and yttrium). Four of the five samples have not been previously fabricated in bulk, single phase form so their crystal structures are refined and detailed using powder synchrotron and single crystal x-ray diffraction, neutron diffraction and transmission electron microscopy. Based on the phase information from diffraction data, there are four crystal structure types in this series; orthorhombic Pnma, hexagonal P6 3 /mmc, cubic (pyrochlore-like) Fd-3m and cubic (fluorite-like) Fm-3m. The cubic materials show modulated structures with variation between long and short range ordering and the variety of diffraction techniques were used to describe these complex crystal structure types. - Graphical abstract: A high resolution image of the compound Sm 0.6 Yb 1.4 TiO 5 showing contrast from lattice fringes and the corresponding fast Fourier transform (FFT) of the HREM image with pyrochlore related diffraction spots marked “P” and fluorite marked “F”. The crystal is oriented down the [1 1 0] zone axis based on the Fd-3m structure. The ideal crystal structure (no vacancies) of the cubic, pyrochlore-like (Sm 0.6 Yb 1.4 TiO 5 ). - Highlights: • First fabrication of bulk single-phase material with stoichiometry Sm 2 TiO 5 . • Systematic study of crystal structure types within Ln 2 TiO 5 series (Ln=lanthanides). • A novel technique using IFFT of HREM images to study cubic structures

  13. Electroerosion impulse effect on W single crystal structure

    International Nuclear Information System (INIS)

    Aleshina, S.A.; Khvostikova, V.D.; Zolotykh, B.N.; Marchuk, A.I.

    1977-01-01

    The mechanism has been studied of brittle failure of single crystal tungsten on planes of crystallographic orientations [100], [110]; [111] in the process of electro-erosion machining by pulses of energies ranging from 1200 to 5000 μJ and of duration of 1 μs. It is shown that the electro-erosion machining of single crystal tungsten is characterized by the formation of a defect layer with a grid of microcracks which lie at a depth of approximately 80 μm. The appearance and the distribution of cracks on the surface of single crystals depends on the crystallogrpahic orientation

  14. Calcium hydroxyapatite crystal deposition with intraosseous penetration involving the posterior aspect of the cervical spine: a previously unreported cause of neck pain.

    Science.gov (United States)

    Urrutia, Julio; Contreras, Oscar

    2017-05-01

    Calcific tendinitis is a frequent disorder caused by hydroxyapatite crystal deposition; however, bone erosions from calcific tendinitis are unusual. The spinal manifestation of this disease is calcific tendinitis of the longus colli muscle; this disease has never been described in the posterior aspect of the spine. We report a case of calcium hydroxyapatite crystal deposition involving the posterior cervical spine eroding the bone cortex. A 57-year-old woman presented with a 5-month history of left-sided neck pain. Radiographs showed C4-C5 interspinous calcification with lytic compromise of the posterior arch of C4. Magnetic resonance imaging confirmed a lytic lesion of the posterior arch of C4, with a soft tissue mass extending to the C4-C5 interspinous space; calcifications were observed as very low signal intensity areas on T1 and T2 sequences, surrounded by gadolinium-enhanced soft tissues. A computed tomography (CT) scan confirmed the bone erosions and the soft tissue calcifications. A CT-guided needle biopsy was performed; it showed vascularized connective tissue with inflammatory histiocytic infiltration and multinucleated giant cells; Alizarin Red stain confirmed the presence of hydroxyapatite crystals. The patient was treated with anti-inflammatories for 2 weeks. She has been asymptomatic in a 6-month follow-up; a CT scan at the last follow-up revealed reparative remodeling of bone erosions. This is the first report of calcium hydroxyapatite crystal deposition with intraosseous penetration involving the posterior aspect of the cervical spine. Considering that this unusual lesion can be misinterpreted as a tumor or infection, high suspicion is required to avoid unnecessary surgical procedures.

  15. Hydrogen-bonded co-crystal structure of benzoic acid and zwitterionic l-proline

    Directory of Open Access Journals (Sweden)

    Aaron M. Chesna

    2017-03-01

    Full Text Available The title compound [systematic name: benzoic acid–pyrrolidin-1-ium-2-carboxylate (1/1], C7H6O2·C5H9NO2, is an example of the application of non-centrosymmetric co-crystallization for the growth of a crystal containing a typically centrosymmetric component in a chiral space group. It co-crystallizes in the space group P212121 and contains benzoic acid and l-proline in equal proportions. The crystal structure exhibits chains of l-proline zwitterions capped by benzoic acid molecules which form a C(5[R33(11] hydrogen-bonded network along [100]. The crystal structure is examined and compared to that of a similar co-crystal containing l-proline zwitterions and 4-aminobenzoic acid.

  16. Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein

    International Nuclear Information System (INIS)

    Schiffer, M.; Ainsworth, C.; Xu, Z.B.; Carperos, W.; Olsen, K.; Solomon, A.; Stevens, F.J.; Chang, C.H.

    1989-01-01

    The authors have determined the structure of the immunoglobulin light-chain dimer Loc in a second crystal form that was grown from distilled water. The crystal structure was determined to 2.8-angstrom resolution; the R factor is 0.22. The two variable domains are related by local 2-fold axes and form an antigen binding pocket. The variable domain-variable domain interaction observed in this crystal form differs from the one exhibited by the protein when crystallized from ammonium sulfate in which the two variable domains formed a protrusion. The structure attained in the distilled water crystals is similar to, but not identical with, the one observed for the Mcg light-chain dimer in crystals grown from ammonium sulfate. Thus, two strikingly different structures were attained by this multisubunit protein in crystals grown under two different, commonly used, crystallization techniques. The quaternary interactions exhibited by the protein in the two crystal forms are sufficiently different to suggest fundamentally different interpretations of the structural basis for the function of this protein. This observation may have general implications regarding the use of single crystallographic determinations for detailed identification of structural and functional relationships. On the other hand, proteins whose structures can be altered by manipulation of crystallization conditions may provide useful systems for study of fundamental structural chemistry

  17. Thermal evolution of the crystal structure of the orthorhombic perovskite LaFeO3

    International Nuclear Information System (INIS)

    Dixon, Charlotte A.L.; Kavanagh, Christopher M.; Knight, Kevin S.; Kockelmann, Winfried; Morrison, Finlay D.; Lightfoot, Philip

    2015-01-01

    The thermal evolution of the crystal structure of the prototypical orthorhombic perovskite LaFeO 3 has been studied in detail by powder neutron diffraction in the temperature range 25previously shown by the derivative Bi 0.5 La 0.5 FeO 3 . However, an unexpected behavior is seen in the nature of the intra-octahedral distortion, which is used to rationalize the unique occurrence of a temperature dependent crossover of the a and c unit cell metrics in this compound. - Graphical abstract: The unusual thermal evolution of lattice metrics in the perovskite LaFeO 3 is rationalized from a detailed powder neutron diffraction study. - Highlights: • Crystal structure of the perovskite LaFeO 3 studied in detail by powder neutron diffraction. • Unusual thermal evolution of lattice metrics rationalized. • Contrasting behavior to Bi-doped LaFeO 3 . • Octahedral distortion/tilt parameters explain unusual a and c lattice parameter behavior

  18. Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.

    Science.gov (United States)

    Kim, Suhng Wook; Kim, Dong-Uk; Kim, Jin Kwang; Kang, Lin-Woo; Cho, Hyun-Soo

    2008-05-01

    We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.

  19. New crystal structures in hexagonal CuInS2 nanocrystals

    Science.gov (United States)

    Shen, Xiao; Hernández-Pagan, Emil A.; Zhou, Wu; Puzyrev, Yevgeniy S.; Idrobo, Juan C.; MacDonald, Janet E.; Pennycook, Stephen J.; Pantelides, Sokrates T.

    2013-03-01

    CuInS2 is one of the best candidate materials for solar energy harvesting. Its nanocrystals with a hexagonal lattice structure that is different from the bulk chalcopyrite phase have been synthesized by many groups. The structure of these CuInS2 nanocrystals has been previously identified as the wurtzite structure in which the copper and indium atoms randomly occupy the cation sites. Using first-principles total energy and electronic structure calculations based on density functional theory, UV-vis absorption spectroscopy, X-ray diffraction, and atomic resolution Z-contrast images obtained in an aberration-corrected scanning transmission electron microscope, we show that CuInS2 nanocrystals do not form random wurtzite structure. Instead, the CuInS2 nanocrystals consist of several wurtzite- related crystal structures with ordered cation sublattices, some of which are reported for the first time here. This work is supported by the NSF TN-SCORE (JEM), by NSF (WZ), by ORNL's Shared Research Equipment User Program (JCI) sponsored by DOE BES, by DOE BES Materials Sciences and Engineering Division (SJP, STP), and used resources of the National Energy Research Scientific Computing Center, supported by the DOE Office of Science under Contract No. DE-AC02-05CH11231.

  20. Ternary systems Sr-{Ni,Cu}-Si: Phase equilibria and crystal structure of ternary phases

    International Nuclear Information System (INIS)

    Nasir, Navida; Melnychenko-Koblyuk, Nataliya; Grytsiv, Andriy; Rogl, Peter; Giester, Gerald; Wosik, Jaroslaw; Nauer, Gerhard E.

    2010-01-01

    Phase relations were established in the Sr-poor part of the ternary systems Sr-Ni-Si (900 deg. C) and Sr-Cu-Si (800 deg. C) by light optical microscopy, electron probe microanalysis and X-ray diffraction on as cast and annealed alloys. Two new ternary compounds SrNiSi 3 (BaNiSn 3 -type) and SrNi 9-x Si 4+x (own-type) were found in the Sr-Ni-Si system along with previously reported Sr(Ni x Si 1-x ) 2 (AlB 2 -type). The crystal structure of SrNi 9-x Si 4+x (own-type, x=2.7, a=0.78998(3), c=1.1337(2) nm; space group P4/nbm) was determined from X-ray single crystal counter to be a low symmetry derivative of the cubic, parent NaZn 13 -type. At higher Si-content X-ray Rietveld refinements reveal the formation of a vacant site (□) corresponding to a formula SrNi 5.5 Si 6.5 □ 1.0 . Phase equilibria in the Sr-Cu-Si system are characterized by the compounds SrCu 2-x Si 2+x (ThCr 2 Si 2 -type), Sr(Cu x Si 1-x ) 2 (AlB 2 -type), SrCu 9-x Si 4+x (0≤x≤1.0; CeNi 8.5 Si 4.5 -type) and SrCu 13-x Si x (4≤x≤1.8; NaZn 13 -type). The latter two structure types appear within a continuous solid solution. Neither a type-I nor a type-IX clathrate compound was encountered in the Sr-{Cu,Ni}-Si systems. Structural details are furthermore given for about 14 new ternary compounds from related alloy systems with Ba. - Graphical abstract: The crystal structure of SrNi 9-x Si 4+x (own-type, x=2.7, a=0.78998(3), c=1.1337(2) nm; space group P4/nbm) was determined from X-ray single crystal counter to be a low symmetry derivative of the cubic, parent NaZn 13 -type and is related to CeNi 8.5 Si 4.5 -type.

  1. SYNTHESIS AND CRYSTAL STRUCTURE OF AN OXORHENIUM(V ...

    African Journals Online (AJOL)

    a

    2007 Chemical Society of Ethiopia. ______ ... 1Department of Chemistry, Nelson Mandela Metropolitan University, P.O. Box 77000, Port .... Details of the crystal data are given in Table 1, with selected bond lengths and angles in Table 2.

  2. Synthesis, crystal structures and properties of new quinolinium derivatives

    Science.gov (United States)

    Zhang, Xinyuan; Jiang, Xingxing; Li, Yin; Lin, Zheshuai; Zhang, Guochun; Wu, Yicheng

    2015-11-01

    Four phenyl-substituted quinolinium salts with different counter anions, C27H27NO4S, C26H25NO5S, C25H22NO5SCl, and C25H22NO5SBr, were synthesized and their single crystals were successfully grown from methanol solution by slow evaporation. Single crystal X-ray diffraction analyses showed that C27H27NO4S crystal belongs to the noncentrosymmetric orthorhombic space group Pna21, and the other three crystals belong to centrosymmetric monoclinic space group P21/n. Their first order hyperpolarization and macroscopic nonlinearity were analyzed and physical properties were characterized by UV-vis absorption spectroscopy, and differential scanning calorimetric and thermal gravimetric analysis.

  3. Free-standing nanomechanical and nanophotonic structures in single-crystal diamond

    Science.gov (United States)

    Burek, Michael John

    Realizing complex three-dimensional structures in a range of material systems is critical to a variety of emerging nanotechnologies. This is particularly true of nanomechanical and nanophotonic systems, both relying on free-standing small-scale components. In the case of nanomechanics, necessary mechanical degrees of freedom require physically isolated structures, such as suspended beams, cantilevers, and membranes. For nanophotonics, elements like waveguides and photonic crystal cavities rely on light confinement provided by total internal reflection or distributed Bragg reflection, both of which require refractive index contrast between the device and surrounding medium (often air). Such suspended nanostructures are typically fabricated in a heterolayer structure, comprising of device (top) and sacrificial (middle) layers supported by a substrate (bottom), using standard surface nanomachining techniques. A selective, isotropic etch is then used to remove the sacrificial layer, resulting in free-standing devices. While high-quality, crystalline, thin film heterolayer structures are readily available for silicon (as silicon-on-insulator (SOI)) or III-V semiconductors (i.e. GaAs/AlGaAs), there remains an extensive list of materials with attractive electro-optic, piezoelectric, quantum optical, and other properties for which high quality single-crystal thin film heterolayer structures are not available. These include complex metal oxides like lithium niobate (LiNbO3), silicon-based compounds such as silicon carbide (SiC), III-V nitrides including gallium nitride (GaN), and inert single-crystals such as diamond. Diamond is especially attractive for a variety of nanoscale technologies due to its exceptional physical and chemical properties, including high mechanical hardness, stiffness, and thermal conductivity. Optically, it is transparent over a wide wavelength range (from 220 nm to the far infrared), has a high refractive index (n ~ 2.4), and is host to a vast

  4. Anisotropic lattice softening near the structural phase transition in the thermosalient crystal 1,2,4,5-tetrabromobenzene.

    Science.gov (United States)

    Zakharov, Boris A; Michalchuk, Adam A L; Morrison, Carole A; Boldyreva, Elena V

    2018-03-28

    The thermosalient effect (crystal jumping on heating) attracts much attention as both an intriguing academic phenomenon and in relation to its potential for the development of molecular actuators but its mechanism remains unclear. 1,2,4,5-Tetrabromobenzene (TBB) is one of the most extensively studied thermosalient compounds that has been shown previously to undergo a phase transition on heating, accompanied by crystal jumping and cracking. The difference in the crystal structures and intermolecular interaction energies of the low- and high-temperature phases is, however, too small to account for the large stress that arises over the course of the transformation. The energy is released spontaneously, and crystals jump across distances that exceed the crystal size by orders of magnitude. In the present work, the anisotropy of lattice strain is followed across the phase transition by single-crystal X-ray diffraction, focusing on the structural evolution from 273 to 343 K. A pronounced lattice softening is observed close to the transition point, with the structure becoming more rigid immediately after the phase transition. The diffraction studies are further supported by theoretical analysis of pairwise intermolecular energies and zone-centre lattice vibrations. Only three modes are found to monotonically soften up to the phase transition, with complex behaviour exhibited by the remaining lattice modes. The thermosalient effect is delayed with respect to the structural transformation itself. This can originate from the martensitic mechanism of the transformation, and the accumulation of stress associated with vibrational switching across the phase transition. The finding of this study sheds more light on the nature of the thermosalient effect in 1,2,4,5-tetrabromobenzene and can be applicable also to other thermosalient compounds.

  5. Nanomechanical resonant structures in single-crystal diamond

    OpenAIRE

    Burek, Michael J.; Ramos, Daniel; Patel, Parth; Frank, Ian W.; Lončar, Marko

    2013-01-01

    With its host of outstanding material properties, single-crystal diamond is an attractive material for nanomechanical systems. Here, the mechanical resonance characteristics of freestanding, single-crystal diamond nanobeams fabricated by an angled-etching methodology are reported. Resonance frequencies displayed evidence of significant compressive stress in doubly clamped diamond nanobeams, while cantilever resonance modes followed the expected inverse-length-squared trend. Q-factors on the o...

  6. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

    Science.gov (United States)

    Xu, Qifang; Malecka, Kimberly L.; Fink, Lauren; Jordan, E. Joseph; Duffy, Erin; Kolander, Samuel; Peterson, Jeffrey; Dunbrack, Roland L.

    2016-01-01

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an “autophosphorylation complex.” We developed and applied a structural bioinformatics method to identify all such autophosphorylation kinase complexes in X-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which 5 complexes had not previously been described in the publications describing the crystal structures. These 5 consist of tyrosine residues in the N-terminal juxtamembrane regions of colony stimulating factor 1 receptor (CSF1R, Tyr561) and EPH receptor A2 (EPHA2, Tyr594), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr394) and insulin-like growth factor 1 receptor (IGF1R, Tyr1166), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser142). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro447 to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets. PMID:26628682

  7. Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses

    Directory of Open Access Journals (Sweden)

    Quevillon-Cheruel Sophie

    2007-01-01

    Full Text Available Abstract The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 Å resolution. The structure of AFV3-109 is a five stranded β-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.

  8. Functional validation of Ca2+-binding residues from the crystal structure of the BK ion channel.

    Science.gov (United States)

    Kshatri, Aravind S; Gonzalez-Hernandez, Alberto J; Giraldez, Teresa

    2018-04-01

    BK channels are dually regulated by voltage and Ca 2+ , providing a cellular mechanism to couple electrical and chemical signalling. Intracellular Ca 2+ concentration is sensed by a large cytoplasmic region in the channel known as "gating ring", which is formed by four tandems of regulator of conductance for K + (RCK1 and RCK2) domains. The recent crystal structure of the full-length BK channel from Aplysia californica has provided new information about the residues involved in Ca 2+ coordination at the high-affinity binding sites located in the RCK1 and RCK2 domains, as well as their cooperativity. Some of these residues have not been previously studied in the human BK channel. In this work we have investigated, through site directed mutagenesis and electrophysiology, the effects of these residues on channel activation by voltage and Ca 2+ . Our results demonstrate that the side chains of two non-conserved residues proposed to coordinate Ca 2+ in the A. californica structure (G523 and E591) have no apparent functional role in the human BK Ca 2+ sensing mechanism. Consistent with the crystal structure, our data indicate that in the human channel the conserved residue R514 participates in Ca 2+ coordination in the RCK1 binding site. Additionally, this study provides functional evidence indicating that R514 also interacts with residues E902 and Y904 connected to the Ca 2+ binding site in RCK2. Interestingly, it has been proposed that this interaction may constitute a structural correlate underlying the cooperative interactions between the two high-affinity Ca 2+ binding sites regulating the Ca 2+ dependent gating of the BK channel. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. CCDC 808551: Experimental Crystal Structure Determination : (4,7-Diphenyl-1,10-phenanthroline)-trifluoromethyl-silver tetrahydrofuran solvate

    KAUST Repository

    Weng, Zhiqiang; Lee, R.; Jia, Weiguo; Yuan, Yaofeng; Wang, Wenfeng; Feng, Xue; Huang, Kuo-Wei

    2011-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  10. CCDC 808552: Experimental Crystal Structure Determination : (4,7-Diphenyl-1,10-phenanthroline)(trifluoromethyl)-copper tetrahydrofuran solvate

    KAUST Repository

    Weng, Zhiqiang; Lee, R.; Jia, Weiguo; Yuan, Yaofeng; Wang, Wenfeng; Feng, Xue; Huang, Kuo-Wei

    2011-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  11. CCDC 949811: Experimental Crystal Structure Determination : bis(2,9-Dimethyl-1,10-phenanthroline)-copper hydrogen difluoride monohydrate

    KAUST Repository

    Liu, Yanpin; Chen, Chaohuang; Li, Huaifeng; Huang, Kuo-Wei; Tan, Jianwei; Weng, Zhiqiang

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  12. CCDC 1036004: Experimental Crystal Structure Determination : catena-[(mu5-5-(pyridin-3-ylamino)isophthalato)-copper unknown solvate

    KAUST Repository

    Chen, Zhijie; Adil, Karim; Weseliński, Łukasz J.; Belmabkhout, Youssef; Eddaoudi, Mohamed

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  13. Crystal structure of calcioburbankite and the characteristic features of the burbankite structure type

    International Nuclear Information System (INIS)

    Belovitskaya, Yu.V.; Pekov, I.V.; Gobechiya, E.R.; Kabalov, Yu.K.; Subbotin, V.V.

    2001-01-01

    The crystal structure of calcioburbankite (Na,Ca) 3 (Ca,RE,Sr,Ba) 3 (CO 3 ) 5 found in carbonatites from Vuoriyarvi (North Kareliya) was solved by the Rietveld method. The experimental data were collected on an ADP-2 diffractometer (λCuK α radiation; Ni filter; 16.00 deg. 1 + α 2 ) reflections was 455). All the calculations were performed within the sp. gr. P6 3 mc; a = 10.4974(1) A, c = 6.4309(1) A, V = 613.72(1) A 3 ; R wp = 2.49%. The structure was refined with the use of the anisotropic thermal parameters for the (Na,Ca) and (Sr,Ba,Ce) cations. The comparison of the crystal structures of all of the known hexagonal representatives of the burbankite family demonstrates that the burbankite structure type (sp. gr. P6 3 mc) is stable, irrespectively of the occupancy of the ten-vertex polyhedra predominantly with Ca, Sr, or Ba cations and the occupancies of the positions in the eight-vertex polyhedra

  14. Crystal structure mediates mode of cell death in TiO2 nanotoxicity

    International Nuclear Information System (INIS)

    Braydich-Stolle, Laura K.; Schaeublin, Nicole M.; Murdock, Richard C.; Jiang, Jingkun; Biswas, Pratim; Schlager, John J.; Hussain, Saber M.

    2009-01-01

    Certain properties that nanoparticles possess differentiate them from their bulk counterparts, and these characteristics must be evaluated prior to nanoparticle studies and include: size, shape, dispersion, physical and chemical properties, surface area, and surface chemistry. Early nanotoxicity studies evaluating TiO 2 have yielded conflicting data which identify either size or crystal structure as the mediating property for nano-TiO 2 toxicity. However, it is important to note that none of these studies examined size with the crystal structure composition controlled for or examined crystal structure while controlling the nanoparticle size. The goal of this study was to evaluate the role of size and crystal structure in TiO 2 nanotoxicity while controlling for as many other nanoproperties as possible using the HEL-30 mouse keratinocyte cell line as a model for dermal exposure. In the size-dependent studies, all the nanoparticles are 100% anatase, and aggregate sizes were determined in order to take into account the effect of agglomeration on size-dependent toxicity. In addition, varying crystal structures were assessed while the size of the nanoparticles was controlled. We were able to identify that both size and crystal structure contribute to cytotoxicity and that the mechanism of cell death varies based on crystal structure. The 100% anatase TiO 2 nanoparticles, regardless of size, induced cell necrosis, while the rutile TiO 2 nanoparticles initiated apoptosis through formation of reactive oxygen species (ROS).

  15. Crystal structure mediates mode of cell death in TiO{sub 2} nanotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Braydich-Stolle, Laura K.; Schaeublin, Nicole M.; Murdock, Richard C. [Wright-Patterson AFB, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force Research Laboratory (United States); Jiang, Jingkun; Biswas, Pratim [Washington University in St. Louis, Department of Energy, Environmental, and Chemical Engineering (United States); Schlager, John J.; Hussain, Saber M., E-mail: Saber.Hussain@wpafb.af.mi [Wright-Patterson AFB, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force Research Laboratory (United States)

    2009-08-15

    Certain properties that nanoparticles possess differentiate them from their bulk counterparts, and these characteristics must be evaluated prior to nanoparticle studies and include: size, shape, dispersion, physical and chemical properties, surface area, and surface chemistry. Early nanotoxicity studies evaluating TiO{sub 2} have yielded conflicting data which identify either size or crystal structure as the mediating property for nano-TiO{sub 2} toxicity. However, it is important to note that none of these studies examined size with the crystal structure composition controlled for or examined crystal structure while controlling the nanoparticle size. The goal of this study was to evaluate the role of size and crystal structure in TiO{sub 2} nanotoxicity while controlling for as many other nanoproperties as possible using the HEL-30 mouse keratinocyte cell line as a model for dermal exposure. In the size-dependent studies, all the nanoparticles are 100% anatase, and aggregate sizes were determined in order to take into account the effect of agglomeration on size-dependent toxicity. In addition, varying crystal structures were assessed while the size of the nanoparticles was controlled. We were able to identify that both size and crystal structure contribute to cytotoxicity and that the mechanism of cell death varies based on crystal structure. The 100% anatase TiO{sub 2} nanoparticles, regardless of size, induced cell necrosis, while the rutile TiO{sub 2} nanoparticles initiated apoptosis through formation of reactive oxygen species (ROS).

  16. Structuring β-Ga2O3 photonic crystal photocatalyst for efficient degradation of organic pollutants.

    Science.gov (United States)

    Li, Xiaofang; Zhen, Xiuzheng; Meng, Sugang; Xian, Jiangjun; Shao, Yu; Fu, Xianzhi; Li, Danzhen

    2013-09-03

    Coupling photocatalysts with photonic crystals structure is based on the unique property of photonic crystals in confining, controlling, and manipulating the incident photons. This combination enhances the light absorption in photocatalysts and thus greatly improves their photocatalytic performance. In this study, Ga2O3 photonic crystals with well-arranged skeleton structures were prepared via a dip-coating infiltration method. The positions of the electronic band absorption for Ga2O3 photonic crystals could be made to locate on the red edge, on the blue edge, and away from the edge of their photonic band gaps by changing the pore sizes of the samples, respectively. Particularly, the electronic band absorption of the Ga2O3 photonic crystal with a pore size of 135 nm was enhanced more than other samples by making it locate on the red edge of its photonic band gap, which was confirmed by the higher instantaneous photocurrent and photocatalytic activity for the degradation of various organic pollutants under ultraviolet light irradiation. Furthermore, the degradation mechanism over Ga2O3 photonic crystals was discussed. The design of Ga2O3 photonic crystals presents a prospective application of photonic crystals in photocatalysis to address light harvesting and quantum efficiency problems through manipulating photons or constructing photonic crystal structure as groundwork.

  17. Ultrasmall-angle X-ray scattering analysis of photonic crystal structure

    International Nuclear Information System (INIS)

    Abramova, V. V.; Sinitskii, A. S.; Grigor'eva, N. A.; Grigor'ev, S. V.; Belov, D. V.; Petukhov, A. V.; Mistonov, A. A.; Vasil'eva, A. V.; Tret'yakov, Yu. D.

    2009-01-01

    The results of an ultrasmall-angle X-ray scattering study of iron(III) oxide inverse opal thin films are presented. The photonic crystals examined are shown to have fcc structure with amount of stacking faults varying among the samples. The method used in this study makes it possible to easily distinguish between samples with predominantly twinned fcc structure and nearly perfect fcc stacking. The difference observed between samples fabricated under identical conditions is attributed to random layer stacking in the self-assembled colloidal crystals used as templates for fabricating the inverse opals. The present method provides a versatile tool for analyzing photonic crystal structure in studies of inverse opals made of various materials, colloidal crystals, and three-dimensional photonic crystals of other types.

  18. Synthesis and crystal structure of two lead (II) complexes with 1,10-phenanthroline ligand

    International Nuclear Information System (INIS)

    Olivera, Fiorella L.; Santillan, Guillermo A.

    2012-01-01

    Two coordination complexes have been synthesized by the reaction of lead nitrate (II) with 1,10-phenanthroline in methanol/water. The crystals of these complexes were obtained by using the diffusion method and structurally characterized by X-ray single crystal diffraction. Both complexes crystallized in the monoclinic space group P2 1 /c. The analysis by crystal X-ray diffraction reveals that in both complexes the coordination around the lead (II) ion is a distorted octahedral structure where the ion is bonded to the heterocyclic nitrogen atoms of chelating ligand 1,10-phenanthroline, three oxygen atoms of three nitrate groups and one oxygen from the water molecule. The difference between the complexes lies in the way of nitrate ion in presence of carboxylic acid aromatics. In addition, the crystal structure of complexes can be regarded as a 3D coordination polymer through Pb-O weak interactions, hydrogen bonds and π-π stacking interactions. (author).

  19. Crystal structure of the uranyl-oxide mineral rameauite

    Energy Technology Data Exchange (ETDEWEB)

    Plasil, Jakub [ASCR, Prague (Czech Republic). Inst. of Physics; Skoda, Radek [Masaryk Univ., Brno (Czech Republic). Dept. of Geological Sciences; Cejka, Jiri [National Museum, Prague (Czech Republic). Dept. of Mineralogy and Petrology; Bourgoin, Vincent; Boulliard, Jean-Claude [Pierre et Marie Curie Univ., Paris (France). Association Jean Wyart, Collection des Mineraux de Jussieu

    2016-12-15

    Rameauite is a rare supergene uranyl-oxide hydroxy-hydrate mineral that forms during hydration-oxidation weathering of uraninite. On the basis of single-crystal X-ray diffraction data collected on a microfocus source, rameauite is monoclinic, space group Cc, with a = 13.9458(19), b = 14.3105(19), c = 13.8959(18) Aa, β = 118.477(14) , V = 2437.7(6) Aa{sup 3} and Z = 4, with D{sub calc} = 5.467 g cm{sup -3}. The structure of rameauite (R = 0.060 for 1698 unique observed reflections) contains sheets of the β-U{sub 3}O{sub 8} topology, with both UO{sub 6} and UO{sub 7} bipyramids, which is similar to the sheets found in spriggite, ianthinite and wyartite. The sheets alternate with the interlayer, which contains K{sup +}, Ca{sup 2+} and H{sub 2}O molecules. Interstitial cations are linked into infinite chains that extend along [10-1]. Adjacent sheets are linked through K-O, Ca-O and H-bonds. The structural formula of rameauite is K{sub 2} Ca(H{sub 2}{sup [3]}O){sub 1}(H{sub 2}{sup [5]}O){sub 4}[(UO{sub 2}) {sub 6}O{sub 6}(OH){sub 4}](H{sub 2}{sup [4]}O){sub 1}. The empirical formula obtained from the average of eight electron-microprobe analyses is (on the basi s of 6 U p.f.u.) K{sub 1.87}(Ca{sub 1.10}Sr{sub 0.04}){sub Σ1.14}[(UO 2){sub 6}O{sub 6}(OH){sub 4.15}].6H{sub 2}O. The Raman spectrum is dominate d by U.O and O.H vibrations. A discussion of related uranyl-oxide minerals is given.

  20. Radial wave crystals: radially periodic structures from anisotropic metamaterials for engineering acoustic or electromagnetic waves.

    Science.gov (United States)

    Torrent, Daniel; Sánchez-Dehesa, José

    2009-08-07

    We demonstrate that metamaterials with anisotropic properties can be used to develop a new class of periodic structures that has been named radial wave crystals. They can be sonic or photonic, and wave propagation along the radial directions is obtained through Bloch states like in usual sonic or photonic crystals. The band structure of the proposed structures can be tailored in a large amount to get exciting novel wave phenomena. For example, it is shown that acoustical cavities based on radial sonic crystals can be employed as passive devices for beam forming or dynamically orientated antennas for sound localization.

  1. Preparation and crystal structure of Ca/sub 4/Sb/sub 2/O

    Energy Technology Data Exchange (ETDEWEB)

    Eisenmann, B; Limartha, H; Schaefer, H; Graf, H A

    1980-12-01

    The formerly described compound Ca/sub 2/Sb is to be corrected to Ca/sub 4/Sb/sub 2/O as shown by X-ray diffractometer data of single crystals and neutron diffraction diagrams of powders. The compound crystallizes in the K/sub 2/NiF/sub 4/ type structure.

  2. On the crystal structure of Z-phase Cr(V,Nb)N

    DEFF Research Database (Denmark)

    Danielsen, Hilmar Kjartansson; Hald, John; Grumsen, Flemming Bjerg

    2006-01-01

    The Z-phase Cr(YNb)N particles in various 9 to 12 pct Cr creep-resistant steels were investigated with electron diffraction, energy dispersive spectroscopy (EDS), and electron energy loss spectroscopy(EELS). In addition to the well-known tetragonal crystal structure for Z phase, a cubic crystal s...

  3. Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

    Science.gov (United States)

    Wang, Yuan; Liang, Zuozhong

    2017-12-01

    Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

  4. Crystal Structure of the Extracellular Cholinesterase-Like Domain from Neuroligin-2

    Energy Technology Data Exchange (ETDEWEB)

    Koehnke,J.; Jin, X.; Budreck, E.; Posy, S.; Scheiffele, P.; Hnoig, B.; Shapiro, L.

    2008-01-01

    Neuroligins (NLs) are catalytically inactive members of a family of cholinesterase-like transmembrane proteins that mediate cell adhesion at neuronal synapses. Postsynaptic neuroligins engage in Ca2+-dependent transsynaptic interactions via their extracellular cholinesterase domain with presynaptic neurexins (NRXs). These interactions may be regulated by two short splice insertions (termed A and B) in the NL cholinesterase domain. Here, we present the 3.3- Angstroms crystal structure of the ectodomain from NL2 containing splice insertion A (NL2A). The overall structure of NL2A resembles that of cholinesterases, but several structural features are unique to the NL proteins. First, structural elements surrounding the esterase active-site region differ significantly between active esterases and NL2A. On the opposite surface of the NL2A molecule, the positions of the A and B splice insertions identify a candidate NRX interaction site of the NL protein. Finally, sequence comparisons of NL isoforms allow for mapping the location of residues of previously identified mutations in NL3 and NL4 found in patients with autism spectrum disorders. Overall, the NL2 structure promises to provide a valuable model for dissecting NL isoform- and synapse-specific functions.

  5. Crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana provides insights into its product specificity.

    Science.gov (United States)

    Zhang, Weiwei; Wang, Wenhe; Liu, Zihe; Xie, Yongchao; Wang, Hao; Mu, Yajuan; Huang, Yao; Feng, Yue

    2016-09-16

    Specifier proteins are important components of the glucosinolate-myrosinase system, which mediate plant defense against herbivory and pathogen attacks. Upon tissue disruption, glucosinolates are hydrolyzed to instable aglucones by myrosinases, and then aglucones will rearrange to form defensive isothiocyanates. Specifier proteins can redirect this reaction to form other products, such as simple nitriles, epithionitriles and organic thiocyanates instead of isothiocyanates based on the side chain structure of glucosinolate and the type of the specifier proteins. Nevertheless, the molecular mechanism underlying the different product spectrums of various specifier proteins was not fully understood. Here in this study, we solved the crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana (AtESP) at 2.3 Å resolution. Structural comparisons with the previously solved structure of thiocyanate forming protein, TFP from Thlaspi arvense (TaTFP) reveal that AtESP shows a dimerization pattern different from TaTFP. Moreover, AtESP harbors a slightly larger active site pocket than TaTFP and several residues around the active site are different between the two proteins, which might account for the different product spectrums of the two proteins. Together, our structural study provides important insights into the molecular mechanisms of specifier proteins and shed light on the basis of their different product spectrums. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. XTALOPT version r11: An open-source evolutionary algorithm for crystal structure prediction

    Science.gov (United States)

    Avery, Patrick; Falls, Zackary; Zurek, Eva

    2018-01-01

    Version 11 of XTALOPT, an evolutionary algorithm for crystal structure prediction, has now been made available for download from the CPC library or the XTALOPT website, http://xtalopt.github.io. Whereas the previous versions of XTALOPT were published under the Gnu Public License (GPL), the current version is made available under the 3-Clause BSD License, which is an open source license that is recognized by the Open Source Initiative. Importantly, the new version can be executed via a command line interface (i.e., it does not require the use of a Graphical User Interface). Moreover, the new version is written as a stand-alone program, rather than an extension to AVOGADRO.

  7. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    DEFF Research Database (Denmark)

    Neumann, M A; van de Streek, J; Fabbiani, F P A

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination...

  8. Investigation of melt structure and crystallization processes by high-temperature Raman spectroscopy method

    International Nuclear Information System (INIS)

    Voron'ko, Yu.K.; Kudryavtsev, A.B.; Osiko, V.V.; Sobol', A.A.

    1988-01-01

    A review of studies dealing with the melts of alkali, rare earth and other element phosphates, gallates, germanates, niobates and tungstates, which are carried out by the method of high-temperature Raman spectroscopy, is given. The effect of the melt structure on the mechanism of the substance cystallization is considered. It is shown that vitrification and supercooling of the melt, as well as its crystallization in the from of metastable structures, are related to the effect of nonconformity between the melt and crystal strucure. The effect of nonconformity between anion motives in the melt and crystal creates obstacles for equilibrium structure nucleation, which results in the formation mainly of metastable forms with lattice structure for from the structure of the melt, though cases of equilibrium phase crystallization are also possible. 37 refs.; 13 figs.; 2 tabs

  9. First principles study of structural, electronic and optical properties of KCl crystal

    International Nuclear Information System (INIS)

    Chen, Z.J.; Xiao, H.Y.; Zu, X.T.

    2006-01-01

    The structural, electronic and optical properties of KCl crystal in B1, B2, B3 and T1 structures have been systematically studied using first-principle pseudopotential calculations. In addition, pressure-induced phase transition has also been investigated. It was found that when the pressure is below 2.8 GPa, the B1 structure is the most stable. Above 2.8 GPa KCl crystal will undergo a structural phase transition from the relatively open NaCl structure into the more dense CsCl atomic arrangement. Our results also suggested that at about 1.2 GPa structural phase transition from B3 to T1 will occur. When the pressure arrives at 39.9 GPa, the phase transition will occur from B2 to T1. In addition, we found KCl Crystal has indirect band gap in B2 structure and direct band gap in B1, B3 and T1 structures. The band gap value is the smallest in the T1 structure and is the largest in the B1 and B3 structures. Our calculations are found to be in good agreement with available experimental and theoretical results. The dielectric function and energy loss function of KCl crystal in four structures (B1, B2, B3 and T1) have been calculated as well as the anisotropy of the optical properties of KCl crystal in T1 structure

  10. Effects of tellurium concentration on the structure of melt-grown ZnSe crystals

    International Nuclear Information System (INIS)

    Atroshchenko, Lyubov V.; Galkin, Sergey N.; Rybalka, Irina A.; Voronkin, Evgeniy F.; Lalayants, Alexandr I.; Ryzhikov, Vladimir D.; Fedorov, Alexandr G.

    2005-01-01

    It has been shown that isovalent doping by tellurium positively affects the structural perfection of ZnSe crystals related to the completeness of the wurtzite-sphalerite phase transition. The optimum concentration range of tellurium in ZnSe crystals is 0.3-0.6 mass %. X-ray diffraction studies have shown that in ZnSe 1-x Te x crystals at tellurium concentrations below 0.3 mass % twinning and packing defects occur, while tellurium concentrations above 0.6 mass % lead to formation of tetragonal crystal lattice

  11. Copper coordination polymers constructed from thiazole-5-carboxylic acid: Synthesis, crystal structures, and structural transformation

    Energy Technology Data Exchange (ETDEWEB)

    Meundaeng, Natthaya; Rujiwatra, Apinpus [Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Prior, Timothy J., E-mail: t.prior@hull.ac.uk [Chemistry, University of Hull, Kingston upon Hull HU6 7RX (United Kingdom)

    2017-01-15

    We have successfully prepared crystals of thiazole-5-carboxylic acid (5-Htza) (L) and three new thiazole-5-carboxylate-based Cu{sup 2+} coordination polymers with different dimensionality, namely, 1D [Cu{sub 2}(5-tza){sub 2}(1,10-phenanthroline){sub 2}(NO{sub 3}){sub 2}] (1), 2D [Cu(5-tza){sub 2}(MeOH){sub 2}] (2), and 3D [Cu(5-tza){sub 2}]·H{sub 2}O (3). These have been characterized by single crystal X-ray diffraction and thermogravimetry. Interestingly, the 2D network structure of 2 can directly transform into the 3D framework of 3 upon removal of methanol molecules at room temperature. 2 can also undergo structural transformation to produce the same 2D network present in the known [Cu(5-tza){sub 2}]·1.5H{sub 2}O upon heat treatment for 2 h. This 2D network can adsorb water and convert to 3 upon exposure to air. - Highlights: • Rare examples of coordination polymers of thiazole-5-carboxylic acid were prepared. • Non-covalent interactions play a key role on the assembly of the complexes in solid state. • Structural transformation of a 2D framework to a 3D upon removal of methanol is observed.

  12. The crystal structures of three pyrazine-2,5-dicarboxamides: three-dimensional supramolecular structures

    Directory of Open Access Journals (Sweden)

    Dilovan S. Cati

    2017-05-01

    Full Text Available The complete molecules of the title compounds, N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (I, 3,6-dimethyl-N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C20H20N6O2 (II, and N2,N5-bis(pyridin-4-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (III, are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each molecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7° in (I, 75.83 (8° in (II and by 82.71 (6° in (III. In the crystal of (I, molecules are linked by N—H...N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (II, molecules are also linked by N—H...N hydrogen bonds, forming layers lying parallel to the (10-1 plane. As in (I, the layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (III, molecules are again linked by N—H...N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π–π interactions [intercentroid distance = 3.739 (1 Å]. The sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. Compound (I crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008, 11, 1–4]. The molecular structures of the two polymorphs are compared.

  13. Lanthanum tris[di(chloromethyl)phosphinate] dihydrate: crystal structure

    International Nuclear Information System (INIS)

    Aleksandrov, G.G.; Sergienko, V.S.; Afonin, E.G.

    2001-01-01

    X-ray diffraction analysis of the LaL 3 · 2H 2 O crystals, HL - di(chloromethyl)phosphinic acid, is conducted. Every of two crystallografically non-equivalent atoms La(1), La(2) is bound with six O(P) atoms of six L - anions performing function of bidentate μ 2 -bridge ligand in the top of pentagonal bipyramid and with O(w) atom of water molecule. La(H 2 O)L 3 particles of the both types are associated in polymer chains along the x axis of the crystal. Chains are conducted through hydrogen bonds O-H···O between coordinated and crystallization molecules of water as well as through short contacts Cl···Cl. Monophase state of polycrystal sample of complex was shown by method of X-ray diffraction of powder [ru

  14. Shear effects on crystallization behaviors and structure transitions of isotactic poly-1-butene

    DEFF Research Database (Denmark)

    Li, Jingqing; Guan, Peipei; Zhang, Yao

    2014-01-01

    Different melt pre-shear conditions were applied to isotactic poly-1-butene (iP-1-B) and the effect on the crystallization behaviors and the crystalline structure transitions of iP-1-B were investigated. The polarized optical microscope observations during isothermal crystallization process...... revealed that the applied melt pre-shear within the experimental range could enhance the nucleation of crystal II and accelerate the diameter growth of the formed spherulites. If the applied melt pre-shear rate was large enough, Shish-Kebabs structure could be formed. After the isothermal crystallization...... was formed in the melt pre-sheared iP-1-B samples. Further investigations were applied with synchrotron radiation instruments. Wide angle X-ray scattering (WAXS) and small angle X-ray scattering (SAXS) after the crystal transition showed that the applied melt pre-shear could result in orientated fine...

  15. Polarization singularities of optical fields caused by structural dislocations in crystals

    International Nuclear Information System (INIS)

    Savaryn, V; Vasylkiv, Yu; Krupych, O; Skab, I; Vlokh, R

    2013-01-01

    We analyze polarization singularities of optical beams that propagate through crystals possessing structural dislocations. We show that screw dislocations of crystalline structure can lead to the appearance of purely screw-type dislocations of light wavefronts. This can happen only in crystals that belong to trigonal and cubic systems. These polarization singularities will give rise to optical vortices with the topological charge equal to ±1, whenever a crystal sample is placed between crossed circular polarizers. We have also found that edge dislocations present in the cubic and trigonal crystals, with the Burgers vector perpendicular to the three-fold symmetry axes, can impose mixed screw-edge dislocations in the wavefronts of optical beams and generate singly charged optical vortices. The results of our analysis can be applied for detecting and identifying dislocations of different types available in crystals. (paper)

  16. Crystallization and structure of chromium cast iron with addition of Mo and Ni

    International Nuclear Information System (INIS)

    Pietrowski, S.

    1998-01-01

    The aim of the presented paper is to show the results of examination of the crystallization process using the method of thermal-derivative analysis (ATD) and the structure examination of chromium cast iron, chromium molybdenum c. i. and chromium molybdenum nickel c.i. It was found that molybdenum in amount over 2 wt % causes the crystallization of eutectic carbides M 23 C 6 and M 6 C. The M 23 C 6 carbide crystallizes upon the crystallization of eutectic carbides M 3 C and M 7 C 3 . It is shown that ATD method facilitates both interpretation and control of the crystallization as well as formation of the cast iron structure at the solid state. (author)

  17. Crystal and electronic structure study of Mn doped wurtzite ZnO nanoparticles

    Directory of Open Access Journals (Sweden)

    O.M. Ozkendir

    2016-08-01

    Full Text Available The change in the crystal and electronic structure properties of wurtzite ZnO nanoparticles was studied according to Mn doping in the powder samples. The investigations were conducted by X-ray Absorption Fine Structure Spectroscopy (XAFS technique for the samples prepared with different heating and doping processes. Electronic analysis was carried out by the collected data from the X-ray Absorption Near-Edge Structure Spectroscopy (XANES measurements. Additional crystal structure properties were studied by Extended-XAFS (EXAFS analysis. Longer heating periods for the undoped wurtzite ZnO samples were determined to own stable crystal geometries. However, for some doped samples, the distortions in the crystal were observed as a result of the low doping amounts of Mn which was treated as an impurity. Besides, the changes in oxygen locations were determined to create defects and distortions in the samples.

  18. Single-Crystal X-ray Structure of Anti-Candida Agent, (E)-3- (1H ...

    African Journals Online (AJOL)

    The molecules are packed in crystal structure by weak non-classical intermolecular ... precipitate the Mannich base hydrochloride 1. Imidazole (2.4 g .... conducted by full- matrix least-squares .... This research project was supported by a grant.

  19. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

  20. Crystal Structure of Escherichia coli L-Arabinose Isomerase (ECAI), The Putative Target of Biological Tagatose Production

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty,B.; Chance, M.

    2006-01-01

    Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 Angstroms resolution. The subunit structure of ECAI is organized into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.

  1. Crystal Structure and Regulation of the Citrus Pol III Repressor MAF1 by Auxin and Phosphorylation.

    Science.gov (United States)

    Soprano, Adriana Santos; Giuseppe, Priscila Oliveira de; Shimo, Hugo Massayoshi; Lima, Tatiani Brenelli; Batista, Fernanda Aparecida Heleno; Righetto, Germanna Lima; Pereira, José Geraldo de Carvalho; Granato, Daniela Campos; Nascimento, Andrey Fabricio Ziem; Gozzo, Fabio Cesar; de Oliveira, Paulo Sérgio Lopes; Figueira, Ana Carolina Migliorini; Smetana, Juliana Helena Costa; Paes Leme, Adriana Franco; Murakami, Mario Tyago; Benedetti, Celso Eduardo

    2017-09-05

    MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate. Additionally, mTOR phosphorylated recombinant CsMAF1 and the mTOR inhibitor AZD8055 blocked canker formation in normal but not CsMAF1-silenced plants. These results indicate that the role of TOR on cell growth induced by Xanthomonas citri depends on CsMAF1 and that auxin controls CsMAF1 interaction with Pol III in citrus. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. The crystal structure of a multifunctional protein: phosphoglucose isomerase/autocrine motility factor/neuroleukin.

    Science.gov (United States)

    Sun, Y J; Chou, C C; Chen, W S; Wu, R T; Meng, M; Hsiao, C D

    1999-05-11

    Phosphoglucose isomerase (PGI) plays a central role in both the glycolysis and the gluconeogenesis pathways. We present here the complete crystal structure of PGI from Bacillus stearothermophilus at 2.3-A resolution. We show that PGI has cell-motility-stimulating activity on mouse colon cancer cells similar to that of endogenous autocrine motility factor (AMF). PGI can also enhance neurite outgrowth on neuronal progenitor cells similar to that observed for neuroleukin. The results confirm that PGI is neuroleukin and AMF. PGI has an open twisted alpha/beta structural motif consisting of two globular domains and two protruding parts. Based on this substrate-free structure, together with the previously published biological, biochemical, and modeling results, we postulate a possible substrate-binding site that is located within the domains' interface for PGI and AMF. In addition, the structure provides evidence suggesting that the top part of the large domain together with one of the protruding loops might participate in inducing the neurotrophic activity.

  3. Crystal structure of (E-pent-2-enoic acid

    Directory of Open Access Journals (Sweden)

    Tim Peppel

    2015-05-01

    Full Text Available The molecule of the title compound, C5H8O2, a low-melting α,β-unsaturated carboxylic acid, is essentially planar [maximum displacement = 0.0239 (13 Å]. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...O hydrogen bonds.

  4. Zinc(II) complexes of carboxamide derivatives: Crystal structures ...

    Indian Academy of Sciences (India)

    can form complexes with a variety of metal ions. Recently, bi- ... tural analyses of both ligands and complex 1 by single crystal X-ray ..... software over a Red Hat Linux IBM cluster using den- .... Change in the relative viscosity (η/ηo)1/3 of CT-.

  5. Modeling local structure using crystal field and spin Hamiltonian parameters: the tetragonal FeK3+-OI2- defect center in KTaO3 crystal

    International Nuclear Information System (INIS)

    Gnutek, P; Rudowicz, C; Yang, Z Y

    2009-01-01

    The local structure and the spin Hamiltonian (SH) parameters, including the zero-field-splitting (ZFS) parameters D and (a+2F/3), and the Zeeman g factors g || and g perpendicular , are theoretically investigated for the Fe K 3+ -O I 2- center in KTaO 3 crystal. The microscopic SH (MSH) parameters are modeled within the framework of the crystal field (CF) theory employing the CF analysis (CFA) package, which also incorporates the MSH modules. Our approach takes into account the spin-orbit interaction as well as the spin-spin and spin-other-orbit interactions omitted in previous studies. The superposition model (SPM) calculations are carried out to provide input CF parameters for the CFA/MSH package. The combined SPM-CFA/MSH approach is used to consider various structural models for the Fe K 3+ -O I 2- defect center in KTaO 3 . This modeling reveals that the off-center displacement of the Fe 3+ ions, Δ 1 (Fe 3+ ), combined with an inward relaxation of the nearest oxygen ligands, Δ 2 (O 2- ), and the existence of the interstitial oxygen O I 2- give rise to a strong tetragonal crystal field. This finding may explain the large ZFS experimentally observed for the Fe K 3+ -O I 2- center in KTaO 3 . Matching the theoretical MSH predictions with the available structural data as well as electron magnetic resonance (EMR) and optical spectroscopy data enables predicting reasonable ranges of values of Δ 1 (Fe 3+ ) and Δ 2 (O 2- ) as well as the possible location of O I 2- ligands around Fe 3+ ions in KTaO 3 . The defect structure model obtained using the SPM-CFA/MSH approach reproduces very well the ranges of the experimental SH parameters D, g || and g perpendicular and importantly yields not only the correct magnitude of D but also the sign, unlike previous studies. More reliable predictions may be achieved when experimental data on (a+2F/3) and/or crystal field energy levels become available. Comparison of our results with those arising from alternative models existing

  6. How to distinguish perfect quasi-crystals from twins and other structures using diffraction experiments?

    International Nuclear Information System (INIS)

    Wolny, J.

    1992-01-01

    Performing diffraction experiments for various lengths of coherent scattering and using the scaling of peak intensities on a number of atoms one can experimentally distinguish quasi-crystals from the other structures (e.g. twins or random). For perfect quasi-crystals peak intensities scale as N 2 , for other structures this scaling depends on concentration of atoms, behaving critical for Penrose concentration. 3 figs., 8 refs. (author)

  7. Temperature driven structural-memory-effects in carbon nanotubes filled with Fe3C nano crystals

    Science.gov (United States)

    Boi, Filippo S.; Zhang, Xiaotian; Corrias, Anna

    2018-02-01

    We report the observation of novel temperature-driven structural-memory-effects in carbon nanotubes (CNTs) filled with Fe3C nano-crystals. These structural-transitions were measured by means of temperature (T) dependent x-ray diffraction (XRD) in the T-range from 298 K to 12 K. A clear reversible 2θ-shift in the 002-peak of the graphitic-CNTs-walls is found with the decrease of the temperature. As determined by Rietveld refinement, such 2θ-shift translates in a not previously reported decrease in the value of the CNT graphitic c-axis with the decrease of the temperature (from 298 K to 12 K). Also, a clear reversible 2θ-shift in the 031 and 131 diffraction-peaks of Fe3C is observed within the same T-range. Rietveld refinements confirm the existence of such memory-effect and also reveal a gradual decrease of the 010-axis of Fe3C with the decrease of the temperature. These observations imply that the observed structural-memory-effect is a characteristic of CNTs when Fe3C is the encapsulated ferromagnet. The generality of such memory-effects was further confirmed by additional measurements performed on other types of CNTs characterized by continuous Fe3C-filling. XRD measurements in the T-range from 298 K to 673 K revealed also an unusual reversible decrease of the Fe3C-peak intensities with the increase of the temperature. These observations can have important implications on the magnetic data recording applications of these nanostructures by helping in better understanding the unusual temperature-dependent magnetic instabilities of iron-based nano-crystals which have been recently reported in literature.

  8. Growth, crystal structure, spectral properties and laser performance of Yb3+:NaLu(MoO4)2 crystal

    International Nuclear Information System (INIS)

    Yu, Yi; Zhang, Lizhen; Huang, Yisheng; Lin, Zhoubin; Wang, Guofu

    2013-01-01

    A double molybdate Yb 3+ :NaLu(MoO 4 ) 2 crystal was successfully grown from a flux of Na 2 Mo 2 O 7 by the top-seeded solution growth method, for the first time to our knowledge. The crystal belongs to the tetragonal system with space group I4 1 /a, and the unit-cell parameters are a = b = 5.159 Å, c = 11.246 Å. Na and Lu atoms co-occupy the same lattice site, which leads to the disordered structure of NaLu(MoO 4 ) 2 crystal. The thermal expansion coefficients of the crystal are 1.35 × 10 −5 K −1 along the c-axis, and 1.01 × 10 −5 K −1 along the a-axis. The full-width at half-maximum of the emission bands are 67 nm for the σ-polarization and 50 nm for the π-polarization at about 1020 nm. The maximum emission cross-sections for the σ- and π-polarizations are 2.79 × 10 −20 cm 2 and 2.94 × 10 −20 cm 2 , respectively. 0.3 W output power at 1025 nm was obtained at an absorbed pump power of 1.7 W, with a slope efficiency of 24%. (paper)

  9. Growth, crystal structure, spectral properties and laser performance of Yb3+:NaLu(MoO4)2 crystal

    Science.gov (United States)

    Yu, Yi; Zhang, Lizhen; Huang, Yisheng; Lin, Zhoubin; Wang, Guofu

    2013-10-01

    A double molybdate Yb3+:NaLu(MoO4)2 crystal was successfully grown from a flux of Na2Mo2O7 by the top-seeded solution growth method, for the first time to our knowledge. The crystal belongs to the tetragonal system with space group I41/a, and the unit-cell parameters are a = b = 5.159 Å, c = 11.246 Å. Na and Lu atoms co-occupy the same lattice site, which leads to the disordered structure of NaLu(MoO4)2 crystal. The thermal expansion coefficients of the crystal are 1.35 × 10-5 K-1 along the c-axis, and 1.01 × 10-5 K-1 along the a-axis. The full-width at half-maximum of the emission bands are 67 nm for the σ-polarization and 50 nm for the π-polarization at about 1020 nm. The maximum emission cross-sections for the σ- and π-polarizations are 2.79 × 10-20 cm2 and 2.94 × 10-20 cm2, respectively. 0.3 W output power at 1025 nm was obtained at an absorbed pump power of 1.7 W, with a slope efficiency of 24%.

  10. Solid dispersions of Myricetin with enhanced solubility: Formulation, characterization and crystal structure of stability-impeding Myricetin monohydrate crystals

    Science.gov (United States)

    Mureşan-Pop, M.; Pop, M. M.; Borodi, G.; Todea, M.; Nagy-Simon, T.; Simon, S.

    2017-08-01

    Three solid dispersion forms of Myricetin combined with the Polyvinylpyrrolidone were successfully prepared by spray drying method, and characterized by X-ray powder diffraction, thermal analysis, infrared spectroscopy and optical microscopy. Zeta potential measurements provided indications on solid dispersions stability in aqueous suspension related to their storage at elevated temperature and relative humidity, which depends on the Myricetin load. By increase of Myricetin load, the stability of the solid dispersion is impeded due to growth of Myricetin monohydrate crystals. The amorphous dispersions with 10% and 50% Myricetin load are stable and, compared to pure Myricetin, their aqueous solubility is enhanced by a factor of 47 and 13, respectively. The dispersion with 80% Myricetin load is unstable on storage, and this behavior acts in conjunction with the development of Myricetin monohydrate crystals. Single-crystal X-ray diffraction results obtained for Myricetin monohydrate reveal a structure of an infinite 2D network of hydrogen-bonded molecules involving all six hydroxyl groups of Myricetin. The water molecules are positioned in between the infinite chains, and contribute via H-bonds to robust crystal packing. The calculated needle-like morphology of monohydrate form is in agreement with the optical microscopy results. The study shows that the solid amorphous dispersions with up to 50% Myricetin load are a viable option for achieving substantial solubility improvement of Myricetin, and supports their potential use in pharmaceutical applications.

  11. Ba3NbAs3O: synthesis, crystal structure, Raman spectroscopy and bonding analysis

    International Nuclear Information System (INIS)

    Monconduit, L.; Tillard, M.; Favier, F.; Belin, C.

    1999-01-01

    The crystal structure of Ba 3 NbAs 3 O has been solved by crystal X-ray analysis (CAD-4 automatic diffractometer, Mo Kα radiation). The compound crystallizes in space group Pnma, a=6.724(2), b=11.100(2), c=13.462(3) A, V=1004.7(4) A 3 , Z=4. The structure has been refined to R1=0.0343 for 964 independent reflections, it can be described as packing of nearly tetrahedral NbAs 3 O 6- anions, their coordination by Ba 2+ cations forming interconnected trigonal prisms. The chemical bonding has been analyzed by MO calculations and Raman spectroscopy. (orig.)

  12. Molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine

    International Nuclear Information System (INIS)

    Kuleshova, L.N.; Khrustalev, V.N.; Struchkov, Yu.T.; Soldatenkov, A.T.; Bekro, I.A.; Mamyrbekova, Zh.A.; Soldatova, S.A.

    1996-01-01

    The molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine was determined. The crystal is orthorhombic: sp. gr. Pca21; a=15.764, b=5.635, and c=25.536 A; and Z=8. The structure was solved by direct methods; R1=0.051, for 2643 unique refections. Symmetry-independent molecules are related by a pseudocenter of symmetry. The piperidine cycle has an asymmetric half-chair conformation. The orientation of substituents is determined. In the crystal, intermolecular OH...O hydrogen bonds link the molecules into chains parallel to the Y-axis

  13. Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures.

    Science.gov (United States)

    Tasolamprou, Anna C; Zhang, Lei; Kafesaki, Maria; Koschny, Thomas; Soukoulis, Costas M

    2015-06-01

    We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. The angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

  14. The crystal structures of some alkyldiaminium perchlorates, permanganates and hexachlouranates (IV)

    International Nuclear Information System (INIS)

    Marais, M.A.

    1984-12-01

    The diquaternary nitrogen cations N,N,N,N 1 ,N 1 ,N 1 -hexaalkyl-1,2-ethane-diaminium and N,N,N,N 1 ,N 1 ,N 1 -hexaalkyl-1,6-hexanediaminium (alkyl = n-octyl for example) are important potential solvent extractants for the extraction of transition metals (Co, Cu) and uranium from HCl medium. Since the alkyldiaminium skeleton constitutes the active centre in solution, the conformations of the cations in association with typical metallate counter-ions were of interest. The crystal structures of the hexachloro-uranate (IV) and permanganate salts of the hexamethyl ethanediaminium ion, as well as the hexachlorouranate (IV) and perchlorate salts of the hexamethyl hexanediaminium ion were therefore determined by X-ray crystallography. No evidence of any deformation of the cation skeleton from their previously well-established conformations were, however, found. The structures can all be understood as typical ionic salts in which the packing and structural features are dominated by the relatively large cations. In the permanganate salt of the N,N,N,N 1 ,N 1 ,N 1 -1,2-ethanediaminium cation the bridging methylene groups display an unusual type of positional disorder, for which there is only one precedent (also discovered in this laboratory). The values of the Mn-O and U-Cl bond lengths in the permanganate and hexachlorouranate ions were determined with a precision comparable to that of the most accurate values obtained so far in other salts. These distances are also in excellent agreement with previous values, and provide further confirmation for two bond lengths for which very few estimates were previously available

  15. Theoretical Exploration of Various Lithium Peroxide Crystal Structures in a Li-Air Battery

    Directory of Open Access Journals (Sweden)

    Kah Chun Lau

    2015-01-01

    Full Text Available We describe a series of metastable Li2O2 crystal structures involving different orientations and displacements of the O22− peroxy ions based on the known Li2O2 crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li2O2 crystal structure (i.e., Föppl structure, all of these newly found metastable Li2O2 crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O22− O-O vibration mode (ω ~ 799–865 cm−1, which is in the range of that commonly observed in Li-air battery experiments, regardless of the random O22− orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li2O2 powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li2O2 compounds that are grown electrochemically under the environment of Li-O2 cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li2O2 crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O22− vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li2O2 crystal structures, as all of them similarly share the similar O22− vibration mode. However considering that the discharge voltage in most Li-O2 cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li2O2 crystal structures appears to be thermodynamically feasible.

  16. Effect of antimony incorporation on structural properties of CuInS{sub 2} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Ben Rabeh, M., E-mail: mohamedbenrabeh@yahoo.f [Laboratoire de Photovoltaique et Materiaux Semi-Conducteurs - ENIT BP 37, Le belvedere, 1002 Tunis (Tunisia); Chaglabou, N., E-mail: nadia_chaglabou@yahoo.f [Laboratoire de Photovoltaique et Materiaux Semi-Conducteurs - ENIT BP 37, Le belvedere, 1002 Tunis (Tunisia); Kanzari, M., E-mail: Mounir.Kanzari@ipeit.rnu.t [Laboratoire de Photovoltaique et Materiaux Semi-Conducteurs - ENIT BP 37, Le belvedere, 1002 Tunis (Tunisia)

    2010-02-15

    CuInS{sub 2} (CIS) single crystals doped with 1, 2, 3 and 4 atomic percent (at.%) of antimony (Sb) were grown by the horizontal Bridgman method. The effect of Sb doping on the structural properties of CIS crystal was studied by means of X-ray diffraction (XRD), energy dispersive X-ray analysis (EDAX), scanning electron microscopy (SEM) and PL measurements. X-ray diffraction data suggests that the doping of Sb in the CIS single crystals does not affect the tetragonal (chalcopyrite) crystal structure and exhibited a (1 1 2) preferred orientation. In addition, with increasing Sb concentration, the X-ray diffraction analysis show that Sb doped CIS crystals are more crystallized and the diffraction peaks of the CuInS{sub 2} phase were more pronounced in particular the (1 1 2) plane. EDAX study revealed that Sb atoms can occupy the indium site and/or occupying the sulfur site to make an acceptor. PL spectra of undoped and Sb doped CIS crystals show two emission peaks at 1.52 and 1.62 eV, respectively which decreased with increasing atomic percent antimony. Sb doped CIS crystals show p-type conductivity.

  17. Effect of antimony incorporation on structural properties of CuInS2 crystals

    International Nuclear Information System (INIS)

    Ben Rabeh, M.; Chaglabou, N.; Kanzari, M.

    2010-01-01

    CuInS 2 (CIS) single crystals doped with 1, 2, 3 and 4 atomic percent (at.%) of antimony (Sb) were grown by the horizontal Bridgman method. The effect of Sb doping on the structural properties of CIS crystal was studied by means of X-ray diffraction (XRD), energy dispersive X-ray analysis (EDAX), scanning electron microscopy (SEM) and PL measurements. X-ray diffraction data suggests that the doping of Sb in the CIS single crystals does not affect the tetragonal (chalcopyrite) crystal structure and exhibited a (1 1 2) preferred orientation. In addition, with increasing Sb concentration, the X-ray diffraction analysis show that Sb doped CIS crystals are more crystallized and the diffraction peaks of the CuInS 2 phase were more pronounced in particular the (1 1 2) plane. EDAX study revealed that Sb atoms can occupy the indium site and/or occupying the sulfur site to make an acceptor. PL spectra of undoped and Sb doped CIS crystals show two emission peaks at 1.52 and 1.62 eV, respectively which decreased with increasing atomic percent antimony. Sb doped CIS crystals show p-type conductivity.

  18. Crystal structure of raw pure Mysore silk fibre based on (Ala-Gly)2 ...

    Indian Academy of Sciences (India)

    Unknown

    2005-03-23

    Mar 23, 2005 ... at sites 1′ and 2′ by the 2-fold screw symmetry, respec- tively. ..... Demura M, Minami M, Asakura T and Cross T A 1998 Structure of Bombyx more ... A34 3–11. Spek A L 2003 Single-Crystal structure validation with the pro- ... Takahashi Y, Gehoh M and Yuzuriha K 1999 Structure refinement and diffuse ...

  19. Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

    International Nuclear Information System (INIS)

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

    2010-01-01

    Tools for systematic comparisons of NMR and crystal structures developed by the JCSG were applied to two proteins with known functions: the T. maritima anti-σ factor antagonist TM1081 and the mouse γ-glutamylamine cyclotransferase A2LD1 (gi:13879369). In an attempt to exploit the complementarity of crystal and NMR data, the combined use of the two structure-determination techniques was explored for the initial steps in the challenge of searching proteins of unknown functions for putative active sites. The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the

  20. Opal-based photonic crystal with double photonic bandgap structure

    Science.gov (United States)

    Romanov, S. G.; Yates, H. M.; Pemble, M. E.; DeLa Rue, R. M.

    2000-09-01

    The interior surfaces of one part of a piece of artificial opal have been coated with GaP so that the remaining part of the opal crystal remains empty, thus forming a photonic heterostructure. Two Bragg resonances have been observed in the optical transmission and reflectance spectra. These two resonances were found to behave differently with changes in the polarization of the incident light and the angle of propagation of the light with respect to the (111) planes of opal. Depolarization of the light was observed to occur most effectively at frequencies within the stop-bands, apparently due to the re-coupling of the propagating electromagnetic wave to a different system of eigenmodes when it crosses the interface separating two parts of the double photonic crystal.

  1. Energetic band structure of Zn3P2 crystals

    Science.gov (United States)

    Stamov, I. G.; Syrbu, N. N.; Dorogan, A. V.

    2013-01-01

    Optical functions n, k, ε1, ε2 and d2ε2/dE2 have been determined from experimental reflection spectra in the region of 1-10 eV. The revealed electronic transitions are localized in the Brillouin zone. The magnitude of valence band splitting caused by the spin-orbital interaction ΔSO is lower than the splitting caused by the crystal field ΔCR in the center of Brillouin zone and L and X points. The switching effects are investigated in Zn3P2 crystals. The characteristics of experimental samples with electric switching, adjustable resistors, and time relays based on Zn3P2 are presented.

  2. Crystal structure of β-d,l-fructose

    Directory of Open Access Journals (Sweden)

    Tomohiko Ishii

    2015-10-01

    Full Text Available The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of d- and l-fructose (1,3,4,5,6-pentahydroxyhexan-2-one, arabino-hexulose or levulose, and it was confirmed that d-fructose (or l-fructose formed β-pyranose with a 2C5 (or 5C2 conformation. In the crystal, two O—H...O hydrogen bonds between the hydroxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral molecules into a column along the a axis. The columns are linked by other O—H...O hydrogen bonds between d- and l-fructose molecules, forming a three-dimensional network.

  3. PDF analysis on re-crystallized structure from amorphous BiT

    Energy Technology Data Exchange (ETDEWEB)

    Yoneda, Yasuhiro [Japan Atomic Energy Research Institute, Synchrotron Radiation Research Center, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)]. E-mail: yoneda@spring8.or.jp; Kohara, Shinji [Synchrotron Radiation Research Laboratory, Japan Synchrotron Radiation, Research Institute, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); Hamazaki, Shin' ichi [Department of Electronics, Iwaki Meisei University, Iino 5-5-1, Chuohdai, Fukushima 970-8551 (Japan); Takashige, Masaaki [Department of Electronics, Iwaki Meisei University, Iino 5-5-1, Chuohdai, Fukushima 970-8551 (Japan); Mizuki, Jun' ichiro [Japan Atomic Energy Research Institute, Synchrotron Radiation Research Center, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)

    2005-08-15

    A glass sample of composition Bi{sub 4}Ti{sub 3}O{sub 12} was prepared by rapid quenching. The as-quenched sample was confirmed to be amorphous by synchrotron X-ray measurements. The crystallization process of the amorphous sample was also investigated by high-energy X-ray diffraction and by atomic pair distribution function analysis. The perovskite layer in the crystal Bi{sub 4}Ti{sub 3}O{sub 12} is transformed to a pyrochlore structure in the amorphous sample. The amorphous sample first crystallized to a metastable phase by acquiring long-range ordering of the pyrochlore structure at T {sub cryst1}, and then secondary crystallized into a reverted Bi{sub 4}Ti{sub 3}O{sub 12} structure at T {sub cryst2}.

  4. A comparative study on the crystal structure of bicycle analogues to the natural phytotoxin helminthosporins

    Science.gov (United States)

    Barbosa, Luiz Cláudio de Almeida; Teixeira, Robson Ricardo; Nogueira, Leonardo Brandão; Maltha, Celia Regina Alvares; Doriguetto, Antônio Carlos; Martins, Felipe Terra

    2016-02-01

    Herein we described structural insights of a series of analogues to helminthosporin phytotoxins. The key reaction used to prepare the compounds corresponded to the [3 + 4] cycloaddition between the oxyallyl cation generated from 2,4-dibromopentan-3-one and different furans. Their structures were confirmed upon IR, NMR and X-ray diffraction analyses. While bicycles 7, 8 and 9 crystallize in the centrosymmetric monoclinic space group P21/c, compound 10 was solved in the noncentrosymmetric orthorhombic space group P212121. The solid materials obtained were shown to be racemic crystals (7, 8, 9) or racemic conglomerate (10). In all compounds, there is formation of a bicycle featured by fused tetrahydropyranone and 2,5-dihydrofuran rings. They adopt chair and envelope conformations, respectively. Crystal packing of all compounds is stabilized through C-H•••O contacts. Conformational aspects as well as similarities and differences among the crystal structures of the synthesized analogues are discussed.

  5. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    DEFF Research Database (Denmark)

    Yennawar, Hemant; Møller, Magda; Gillilan, Richard

    2011-01-01

    The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer...

  6. Crystal structure of 2-diazoimidazole-4,5-dicarbonitrile

    Directory of Open Access Journals (Sweden)

    Damon A. Parrish

    2015-07-01

    Full Text Available In the title compound, C5N6, all the atoms are approximately coplanar. In the crystal, molecules are packed with short contact distances of 2.885 (2 (between the diazo N atom connected to the ring and a cyano N atom on a neighboring molecule and 3.012 (2 Å (between the terminal diazo N atom and an N atom of a neighboring imidazole ring.

  7. Crystal structure of bromidobis(naphthalen-1-ylantimony(III

    Directory of Open Access Journals (Sweden)

    Omar bin Shawkataly

    2014-10-01

    Full Text Available In the title compound, [SbBr(C10H72], the SbIII atom has a distorted trigonal–pyramidal coordination geometry and the planes of the two naphthalene ring systems make a dihedral angle of 80.26 (18°. An intramolecular C—H...Br hydrogen bond forms an S(5 ring motif. In the crystal, weak C—H...Br interactions link the molecules into helical chains along the b-axis direction.

  8. Crystal structure of 2-cyano-N-(furan-2-ylmethylacetamide

    Directory of Open Access Journals (Sweden)

    Shivanna Subhadramma

    2015-07-01

    Full Text Available In the title compound, C8H8N2O2, the acetamide unit is inclined to the furan ring by 76.7 (1°. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds, generating C(4 chains along [100]. The carbonyl O atom is a bifurcated acceptor and an R12(6 ring is formed.

  9. Classification of crystal structure using a convolutional neural network.

    Science.gov (United States)

    Park, Woon Bae; Chung, Jiyong; Jung, Jaeyoung; Sohn, Keemin; Singh, Satendra Pal; Pyo, Myoungho; Shin, Namsoo; Sohn, Kee-Sun

    2017-07-01

    A deep machine-learning technique based on a convolutional neural network (CNN) is introduced. It has been used for the classification of powder X-ray diffraction (XRD) patterns in terms of crystal system, extinction group and space group. About 150 000 powder XRD patterns were collected and used as input for the CNN with no handcrafted engineering involved, and thereby an appropriate CNN architecture was obtained that allowed determination of the crystal system, extinction group and space group. In sharp contrast with the traditional use of powder XRD pattern analysis, the CNN never treats powder XRD patterns as a deconvoluted and discrete peak position or as intensity data, but instead the XRD patterns are regarded as nothing but a pattern similar to a picture. The CNN interprets features that humans cannot recognize in a powder XRD pattern. As a result, accuracy levels of 81.14, 83.83 and 94.99% were achieved for the space-group, extinction-group and crystal-system classifications, respectively. The well trained CNN was then used for symmetry identification of unknown novel inorganic compounds.

  10. Cyclic saturation dislocation structures of multiple-slip-oriented copper single crystals

    International Nuclear Information System (INIS)

    Li, X.W.; Chinese Academy of Sciences, Shenyang; Umakoshi, Y.; Li, S.X.; Wang, Z.G.

    2001-01-01

    The dislocation structures of [011] and [ anti 111] multiple-slip-oriented Cu single crystals cyclically saturated at constant plastic strain amplitudes were investigated through transmission electron microscopy. The results obtained on [001] multiple-slip-oriented Cu single crystals were also included for summarization. Unlike the case for single-slip-oriented Cu single crystals, the crystallographic orientation has a strong effect on the saturation dislocation structure in these three multiple-slip-oriented crystals. For the [011] crystal, different dislocation patterns such as veins, PSB walls, labyrinths and PSB ladders were observed. The formation of PSB ladders is believed to be a major reason for the existence of a plateau region in the cyclic stress-strain (CSS) curve for the [011] crystal. The cyclic saturation dislocation structure of a [ anti 111] crystal cycled at a low applied strain amplitude γ pl of 2.0 x 10 -4 was found to consist of irregular cells, which would develop into a more regular arrangement (e. g. PSB ladder-like) and the scale of which tends to decrease with increasing γ pl . Finally, three kinds of representative micro-deformation mode were summarized and termed as labyrinth-mode (or [001]-mode), cell-mode (or [ anti 111]-mode) and PSB ladder-mode (or [011]-mode). (orig.)

  11. Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.

    Science.gov (United States)

    Nishimasu, Rieko; Komori, Hirofumi; Higuchi, Yoshiki; Nishimasu, Hiroshi; Hiroaki, Hidekazu

    2010-10-21

    Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.

  12. Praseodymium valency from crystal structure in Pr-Ba-Cu-O and (Y-Pr)-Ba-Cu-O single crystals

    International Nuclear Information System (INIS)

    Collin, G.; Albouy, P.A.; Monod, P.; Ribault, M.

    1990-01-01

    The substitution of Pr to Y leads to materials with a general formula (Y 1-v Pr v ) (Ba 2-x Pr x ) (Cu 3-y vac y ) O 6+x/2-y+z and with a structural transition around v + x' ∼ 0.5. For v + x 0.5 the crystals are tetragonal, La 1.5 Ba 1.5 Cu 3 O 7±z type, with the characteristic tri-twinning of this phase. The Pr valency, in the range 3-3.2 + depending on preparation conditions, is determined from interatomic distances. Orthorhombic crystals of Pr Ba Cu O prepared at high temperatures exhibit a high amount of defects, y ∼ 0.25 on the Cu(1) site and are semiconductors with a T -1/4 activation law attributed to the praseodymium valence fluctuation

  13. Comparison of NMR and crystal structures for the proteins TM1112 and TM1367

    International Nuclear Information System (INIS)

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

    2010-01-01

    NMR structures of the proteins TM1112 and TM1367 solved by the JCSG in solution at 298 K could be superimposed with the corresponding crystal structures at 100 K with r.m.s.d. values of <1.0 Å for the backbone heavy atoms. For both proteins the structural differences between multiple molecules in the asymmetric unit of the crystals correlated with structural variations within the bundles of conformers used to represent the NMR solution structures. A recently introduced JCSG NMR structure-determination protocol, which makes use of the software package UNIO for extensive automation, was further evaluated by comparison of the TM1112 structure obtained using these automated methods with another NMR structure that was independently solved in another PSI center, where a largely interactive approach was applied. The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper-limit distance constraints derived from the molecular models that represent the results of structure

  14. Rapid fabrication of 2D and 3D photonic crystals and their inversed structures

    International Nuclear Information System (INIS)

    Huang, C-K; Chan, C-H; Chen, C-Y; Tsai, Y-L; Chen, C-C; Han, J-L; Hsieh, K-H

    2007-01-01

    In this paper a new technique is proposed for the fabrication of two-dimensional (2D) and three-dimensional (3D) photonic crystals using monodisperse polystyrene microspheres as the templates. In addition, the approaches toward the creation of their corresponding inversed structures are described. The inversed structures were prepared by subjecting an introduced silica source to a sol-gel process; programmed heating was then performed to remove the template without spoiling the inversed structures. Utilizing these approaches, 2D and 3D photonic crystals and their highly ordered inversed hexagonal multilayer or monolayer structures were obtained on the substrate

  15. Origin of the complex crystal structures of elements at intermediate pressure

    International Nuclear Information System (INIS)

    Ackland, G J; Macleod, I R

    2004-01-01

    We present a unifying theory for the observed complex structures of sp-bonded elements under pressure on the basis of nearly free electron picture. In the intermediate pressure regime, the dominant contribution to crystal structure arises from Fermi-surface Brillouin zone interactions-structures which allow this are favoured. This simple theory explains the observed crystal structures, transport properties and the evolution of internal and unit cell parameters with pressure and appears to hold for elements in groups I-VI. We illustrate it with experimental data for these elements and ab initio calculations for Li

  16. Regio-Regular Oligo and Poly(3-hexyl thiophene): Precise Structural Markers from the Vibrational Spectra of Oligomer Single Crystals.

    KAUST Repository

    Brambilla, Luigi; Tommasini, Matteo; Botiz, Ioan; Rahimi, Khosrow; Agumba, John O.; Stingelin, Natalie; Zerbi, Giuseppe

    2014-01-01

    , namely, amorphous, semicrystalline, polycrystalline and single crystal. We have based our analysis on the spectra of the (3HT)8 single crystal (whose structure has been determined by selected area electron diffraction) taken as reference

  17. Reversible Single-Crystal-to-Single-Crystal Structural Transformation in a Mixed-Ligand 2D Layered Metal-Organic Framework: Structural Characterization and Sorption Study

    Directory of Open Access Journals (Sweden)

    Chih-Chieh Wang

    2017-12-01

    Full Text Available A 3D supramolecular network, [Cd(bipy(C4O4(H2O2]·3H2O (1 (bipy = 4,4′-bipyridine and C4O42− = dianion of H2C4O4, constructed by mixed-ligand two-dimensional (2D metal-organic frameworks (MOFs has been reported and structurally determined by the single-crystal X-ray diffraction method and characterized by other physicochemical methods. In 1, the C4O42− and bipy both act as bridging ligands connecting the Cd(II ions to form a 2D layered MOF, which are then extended to a 3D supramolecular network via the mutually parallel and interpenetrating arrangements among the 2D-layered MOFs. Compound 1 shows a two-step dehydration process with weight losses of 11.0% and 7.3%, corresponding to the weight-loss of three guest and two coordinated water molecules, respectively, and exhibits an interesting reversible single-crystal-to-single-crystal (SCSC structural transformation upon de-hydration and re-hydration for guest water molecules. The SCSC structural transformation have been demonstrated and monitored by single-crystal and X-ray powder diffraction, and thermogravimetic analysis studies.

  18. Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1

    Energy Technology Data Exchange (ETDEWEB)

    Koenigsberg, Andrea L.; Heldwein, Ekaterina E.; Sandri-Goldin, Rozanne M.

    2017-08-02

    Inner tegument protein UL37 is conserved among all three subfamilies of herpesviruses. Studies of UL37 homologs from two alphaherpesviruses, herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), have suggested that UL37 plays an essential albeit poorly defined role in intracellular capsid trafficking. At the same time, HSV and PRV homologs cannot be swapped, which suggests that in addition to a conserved function, UL37 homologs also have divergent virus-specific functions. Accurate dissection of UL37 functions requires detailed maps in the form of atomic-resolution structures. Previously, we reported the crystal structure of the N-terminal half of UL37 (UL37N) from PRV. Here, we report the crystal structure of HSV-1 UL37N. Comparison of the two structures reveals that UL37 homologs differ in their overall shapes, distributions of surface charges, and locations of projecting loops. In contrast, the previously identified R2 surface region is structurally conserved. We propose that within the N-terminal half of UL37, functional conservation is centered within the R2 surface region, whereas divergent structural elements pinpoint regions mediating virus-specific functions and may engage different binding partners. Together, the two structures can now serve as templates for a structure-guided exploration of both conserved and virus-specific functions of UL37.

    IMPORTANCEThe ability to move efficiently within host cell cytoplasm is essential for replication in all viruses. It is especially important in the neuroinvasive alphaherpesviruses, such as human herpes simplex virus 1 (HSV-1), HSV-2, and veterinarian pseudorabies virus (PRV), that infect the peripheral nervous system and have to travel long distances along axons. Capsid movement in these viruses is controlled by capsid-associated tegument proteins, yet their specific roles have not yet been defined. Systematic exploration of the roles of tegument proteins in capsid trafficking requires

  19. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

    Science.gov (United States)

    2014-01-01

    We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5–22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10–25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function. PMID:24392845

  20. Study of structural and optical properties of YAG and Nd:YAG single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kostić, S. [Institute of Physics, University of Belgrade, P.O. Box 68, Pregrevica 118, Zemun, Belgrade (Serbia); Lazarević, Z.Ž., E-mail: lzorica@yahoo.com [Institute of Physics, University of Belgrade, P.O. Box 68, Pregrevica 118, Zemun, Belgrade (Serbia); Radojević, V. [Faculty of Technology and Metallurgy, University of Belgrade, Belgrade (Serbia); Milutinović, A.; Romčević, M.; Romčević, N.Ž. [Institute of Physics, University of Belgrade, P.O. Box 68, Pregrevica 118, Zemun, Belgrade (Serbia); Valčić, A. [Faculty of Technology and Metallurgy, University of Belgrade, Belgrade (Serbia)

    2015-03-15

    Highlights: • Transparent YAG and pale pink Nd:YAG single crystals were produced by the Czochralski technique. • Growth mechanisms and shape of the liquid/solid interface and incorporation of Nd{sup 3+} were studied. • The structure of the crystals was investigated by X-ray diffraction, Raman and IR spectroscopy. • The 15 Raman and 17 IR modes were observed. • The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. - Abstract: Yttrium aluminum garnet (YAG, Y{sub 3}Al{sub 5}O{sub 12}) and yttrium aluminum garnet doped with neodymium (Nd:YAG) single crystals were grown by the Czochralski technique. The critical diameter and the critical rate of rotation were calculated. Suitable polishing and etching solutions were determined. As a result of our experiments, the transparent YAG and pale pink Nd:YAG single crystals were produced. The obtained crystals were studied by X-ray diffraction, Raman and IR spectroscopy. The crystal structure was confirmed by XRD. The 15 Raman and 17 IR modes were observed. The Raman and IR spectroscopy results are in accordance with X-ray diffraction analysis. The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. The absence of a core was confirmed by viewing polished crystal slices. Also, it is important to emphasize that the obtained Nd:YAG single crystal has a concentration of 0.8 wt.% Nd{sup 3+} that is characteristic for laser materials.