WorldWideScience

Sample records for crystal structures koordinatsionnye

  1. Inorganic Crystal Structure Database (ICSD)

    Science.gov (United States)

    SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

  2. Crystal structure of fipronil

    Directory of Open Access Journals (Sweden)

    Hyunjin Park

    2017-10-01

    Full Text Available The title compound, C12H4Cl2F6N4OS {systematic name: 5-amino-1-[2,6-dichloro-4-(trifluoromethylphenyl]-4-[(trifluoromethanesulfinyl]-1H-pyrazole-3-carbonitrile}, is a member of the phenylpyrazole group of acaricides, and one of the phenylpyrazole group of insecticides. The dihedral angle between the planes of the pyrazole and benzene rings is 89.03 (9°. The fluorine atoms of the trifluoromethyl substituent on the benzene ring are disordered over two sets of sites, with occupancy ratios 0.620 (15:0.380 (15. In the crystal, C—N...π interactions [N...ring centroid = 3.607 (4 Å] together with N—H...N and C—H...F hydrogen bonds form a looped chain structure along [10\\overline{1}]. Finally, N—H...O hydrogen bonds and C—Cl...π interactions [Cl...ring centroid = 3.5159 (16 Å] generate a three-dimensional structure. Additionally, there are a short intermolecular F... F contacts present.

  3. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    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 parac...

  4. Crystal structure of oxamyl

    Directory of Open Access Journals (Sweden)

    Eunjin Kwon

    2016-12-01

    Full Text Available The title compound, C7H13N3O3S [systematic name: (Z-methyl 2-dimethylamino-N-(methylcarbamoyloxy-2-oxoethanimidothioate], is an oxime carbamate acaride, insecticide and nematicide. The asymmetric unit comprises two independent molecules, A and B. The dihedral angles between the mean planes [r.m.s. deviations = 0.0017 (A and 0.0016 Å (B] of the acetamide and oxyimino groups are 88.80 (8° for A and 87.05 (8° for B. In the crystal, N/C—H...O hydrogen bonds link adjacent molecules, forming chains along the a axis. The chains are further linked by C—H...O hydrogen bonds, resulting in a three-dimensional network with alternating rows of A and B molecules in the bc plane stacked along the a-axis direction. The structure was refined as an inversion twin with a final BASF parameter of 0.16 (9.

  5. 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

  6. 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.

  7. Crystal structure of pyriproxyfen

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available In the title compound {systematic name: 4-phenoxyphenyl (RS-2-[(pyridin-2-yloxy]propyl ether}, C20H19NO3, which is a juvenile hormone mimic and insecticide, the dihedral angles between the plane of the central benene ring and those of the pendant pyridine ring and phenyl ring are 78.09 (6 and 82.14 (8°, respectively. The conformation of the O—C—C—O linkage is gauche [torsion angle = −75.0 (2°]. In the crystal, weak aromatic π–π stacking interactions [centroid–centroid separation = 3.8436 (13 Å] and C—H...π interactions link adjacent molecules, forming a three-dimensional network.

  8. 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.

  9. 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.

  10. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

    Preferred Customer

    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. INTRODUCTION. Coordination chemistry of molybdenum(VI) has attracted considerable attention ...

  11. Nuclear structures: Twinning and modulation in crystals

    Science.gov (United States)

    Petříček, Václav; Dušek, Michal

    2017-10-01

    Crystal structure analysis is a standard technique routinely applied to single crystals as well as powders. However the process is not so straightforward if the crystal sample is affected by twinning or if the structure is modulated. In such cases the standard procedures are not directly applicable. The main purpose of this contribution is to show how to solve and refine such difficult structures. While for twinned structures the basic property of crystal - translation symmetry in three dimensional space-remains valid, for modulated crystals a special superspace theory must be exploited in order to describe the atomic structure with crystallographic methods generalized for superspace.

  12. imide, crystal structure, thermal and dielectric studies

    Indian Academy of Sciences (India)

    IR and Raman spectroscopies and its crystal structure is confirmed by single crystal X-ray diffraction method. The X-ray studies on ... Di-cationic ionic liquids; crystal structure; dielectric; thermal properties. 1. Introduction. The chemistry of ionic ... exposed in various emerging areas as solvents of high tem- perature organic ...

  13. Crystal structure of 3-(diethylaminophenol

    Directory of Open Access Journals (Sweden)

    James A. Golen

    2015-12-01

    Full Text Available The title compound, C10H15NO, has two molecules in the asymmetric unit. Each molecule has a near-planar C8NO unit excluding H atoms and the terminal methyl groups on the diethylamino groups, with mean deviations from planarity of 0.036 and 0.063 Å. In the crystal, hydrogen bonding leads to four-membered O—H...O—H...O—H·· rings. No π–π interactions were observed in the structure.

  14. Synthesis, crystal structure, theoretical study and luminescence ...

    Indian Academy of Sciences (India)

    phenanthroline) has been synthesized and characterized by elemental analysis, infrared spectroscopy, ultraviolet-visible spectroscopy, X-ray single crystal analysis and fluorescent analysis. Its crystal structure is monoclinic with space group 2/ and ...

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

    Indian Academy of Sciences (India)

    In both the materials, the crystal structure has been determined by X-ray single crystal analysis at room temperature (293 K). The compound structures consist of K + (or NH 4 + ) cations and double chains of CdCl 6 octahedra sharing one edge extending along b -axis. The mixture of KA + /NH 4 + cations are located ...

  16. Crystal structure and hydrogen bonding interactions

    Indian Academy of Sciences (India)

    Giacovazzo C, Guagliardi A, Moliteni A G G, Polidori. G and Spagna R 1997 SIR97 (Release 1.02) - A program for automatic solution and refinement of crystal structure. 10. Sheldrick G M 1997 SHELXL-97, Programs for Crystal. Structure Analysis; University of Göttingen, Germany. 11. ORTEP3 for Windows and Farrugia L J ...

  17. Photonic crystal laser-driven accelerator structures

    CERN Document Server

    Cowan, Benjamin

    2005-01-01

    We discuss simulated photonic crystal structure designs, including two- and three-dimensional planar structures and fibers. The discussion of 2D structures demonstrates guiding of a speed-of-light accelerating mode by a defect in a photonic crystal lattice and reveals design considerations and trade-offs. With a three-dimensional lattice, we introduce a candidate geometry and discuss beam dynamics, coupling, and manufacturing techniques for that structure. In addition we discuss W-band scale tests of photonic crystal structures. The computational methods are also discussed.

  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. Crystal structure and morphology of syndiotactic polypropylene single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Bu, J.Z. [GE Plastics, Washington, WV (United States); Cheng, S.Z.D. [Univ. of Akron, OH (United States)

    1996-12-31

    In the past several years there have been an increased interest in the crystal structure and morphology of s-PP due to the new development of homogeneous metallocene catalysts which can produce s-PP having a high stereoregularity. In this research, the crystal structure and morphology of s-PP single crystals grown from the melt were investigated. A series of ten fractions of s-PP was studied with different molecular weights ranging from 10,300 to 234,000 (g/mol). These fractions all possess narrow molecular weight distributions (around 1.1-1.2) and high syndiotacticities ([r]{approximately}95%). The main techniques employed including transmission electron microscopy (TEM), atomic force microscopy (AFM), wide-angle X-ray diffraction (WAXD), and small-angle X-ray scattering (SAXS).

  1. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

    Møllerud, Stine; Frydenvang, Karla Andrea; Pickering, Darryl S

    2017-01-01

    -length structure has been determined of GluK2 by cryo electron microscopy to 7.6 Å resolution as well as 84 high-resolution crystal structures of N-terminal domains and ligand-binding domains, including agonist and antagonist bound structures, modulatory ions and mutations. However, there are still many unanswered...

  2. Crystal structure of cyclohexylammonium thiocyanate

    OpenAIRE

    Abdulaziz A. Bagabas; Sultan B. Alhoshan; Hazem A. Ghabbour; C. S. Chidan Kumar; Hoong-Kun Fun

    2015-01-01

    In the title salt, C6H11NH3 +?SCN?, the cyclo?hexyl?ammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial inter?actions. In the crystal, the components are linked by N?H?N and N?H?S hydrogen-bonding inter?actions, resulting in a three-dimensional network.

  3. Crystal structure of cyclohexylammonium thiocyanate

    Directory of Open Access Journals (Sweden)

    Abdulaziz A. Bagabas

    2015-01-01

    Full Text Available In the title salt, C6H11NH3+·SCN−, the cyclohexylammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial interactions. In the crystal, the components are linked by N—H...N and N—H...S hydrogen-bonding interactions, resulting in a three-dimensional network.

  4. 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...

  5. Tailoring quantum structures for active photonic crystals

    DEFF Research Database (Denmark)

    Kuznetsova, Nadezda

    This work is dedicated to the tailoring of quantum structures, with particular attention to the integration of selective area grown (SAG) active material into photonic crystal (PhC) slabs. The platform based on active PhC is vital to the realization of highly efficient elements with low energy......; in particular, the emission control of SAG QW matched the operating wavelength of photonic crystals. A strong photoluminescence signal in the slow light regime with the group index of 18 was demonstrated....

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Molecular and crystal structure of ivalin

    Energy Technology Data Exchange (ETDEWEB)

    Coetzer, J. (Council for Scientific and Industrial Research, Pretoria (South Africa). National Physical Research Lab.); Kruger, G.J.; Levendis, D.C. (Council for Scientific and Industrial Research, Pretoria (South Africa). National Chemical Research Lab.)

    1982-01-01

    The bromoacetate derivative of ivalin, which is a sesquiterpene lactone, crystallizes in the space group P2/sub 1/, with two molecules in the unit cell. Its structure was solved by standard X-ray methods. Full-matrix least-squares refinement converged at R=0,052. The proposed stereochemistry has been confirmed.

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

    Indian Academy of Sciences (India)

    Hydrothermal synthesis, crystal structure and luminescence property of a three dimensional Sm(III) coordination polymer with. 2,5-pyridinedicarboxylic acid. KRANTHI KUMAR GANGU, ANIMA S DADHICH and. SARATCHANDRA BABU MUKKAMALA. ∗. Department of Chemistry, GITAM University, Visakhapatnam 530 045, ...

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 12. Hydrothermal synthesis, crystal structure and luminescence property of a three dimensional Sm(III) coordination polymer with 2,5-pyridinedicarboxylic acid. Kranthi Kumar Gangu Anima S Dadhich Saratchandra Babu Mukkamala. Volume 127 Issue 12 ...

  13. Synthesis, crystal structure, theoretical study and luminescence ...

    Indian Academy of Sciences (India)

    Synthesis, crystal structure, theoretical study and luminescence property of a butterfly-like W/Cu/S cluster with 1,10-phenanthroline. AI-HUA CHENa,b, SU-CI MENGc,d, JIN-FANG ZHANGb,c and CHI ZHANGb,c,∗. aSchool of Chemical & Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051,.

  14. Theoretical investigation on crystal structure, detonation ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 125; Issue 4. Theoretical investigation on crystal structure, detonation ... The bond dissociation energies and bond orders for the weakest bonds were analysed to investigate the thermal stability of the title compound. The detonation and pressure were evaluated by ...

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

    Indian Academy of Sciences (India)

    Keywords. Selenidogermanates; nickel; solvothermal syntheses; crystal structures; optical properties ... The different coordination environments of Ni²⁺ ions indicate the influence of the denticity of ethylene polyamines on the formation of selenidogermanates in the presence of transition metal ions. Thecompounds 1–3 ...

  16. 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...... 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....

  17. Photonic Crystal Laser-Driven Accelerator Structures

    Energy Technology Data Exchange (ETDEWEB)

    Cowan, Benjamin M

    2007-08-22

    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.

  18. 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.

  19. 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.

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

    Indian Academy of Sciences (India)

    providing information about the complete crystal structure at room temperature of the new compounds. These materi- ... Data collection instrument. Kappa-APEX II. Kappa-APEX II. Radiation, graphite ..... graphic method of the mixed compounds K0.57(NH4)0.43CdCl3 and K0.25(NH4)0.75CdCl3. This study is restricted to ...

  1. 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...

  2. Flux growth and crystal structure of pyromorphite.

    Science.gov (United States)

    Akao, A; Aoki, H; Innami, Y; Minamikata, S; Yamada, T

    1989-01-01

    Single crystals of pyromorphite, Pb5(PO4)3Cl, were grown by standard flux growth technique with excess lead chloride used as the flux. Pyromorphite was first prepared by heating an intimate mixture of lead hydrogen phosphate and lead chloride in the molar ratio 6:4 at 100 degrees C for 1 h. A mixture of 60 wt% of pyromorphite and 40 wt% of lead chloride was heated at 850 degrees C for 15 h and then cooled at the rate of 3.4 degrees C/h. Hexagonal prismatic crystals of length 1 mm were obtained. The chemical composition has close to the theoretical value. The crystal is hexagonal, space group P6(3)/m with a = 9.9981(8), c = 7.344(1) A and Z = 2. The structure was refined to R = 0.058 and Rw = 0.053 with 502 independent reflections. The structure is in principal the same as that of barium chlorapatite; the chlorine ions occupy the (0, 0, 0) position.

  3. 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.

  4. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  5. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  6. 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.

  7. Diterbium heptanickel: a crystal structure redetermination

    Directory of Open Access Journals (Sweden)

    Volodymyr Levytskyy

    2014-08-01

    Full Text Available The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967. C. R. Acad. Sci. Ser. B, 265, 1280–1282; Lemaire & Paccard (1969. Bull. Soc. Fr. Mineral. Cristallogr. 92, 9–16; Buschow & van der Goot (1970. J. Less-Common Met. 22, 419–428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962 (4Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an intergrowth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m. and five Ni sites (.m., mm2, 3m., 3m., -3m.. The two different coordination polyhedra of Tb are a Frank–Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank–Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank–Kasper icosahedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-07

    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.

  9. Waveguide structures in anisotropic nonlinear crystals

    Science.gov (United States)

    Li, Da; Hong, Pengda; Meissner, Helmuth E.

    2017-02-01

    We report on the design and manufacturing parameters of waveguiding structures of anisotropic nonlinear crystals that are employed for harmonic conversions, using Adhesive-Free Bonding (AFB®). This technology enables a full range of predetermined refractive index differences that are essential for the design of single mode or low-mode propagation with high efficiency in anisotropic nonlinear crystals which in turn results in compact frequency conversion systems. Examples of nonlinear optical waveguides include periodically bonded walk-off corrected nonlinear optical waveguides and periodically poled waveguide components, such as lithium triborate (LBO), beta barium borate (β-BBO), lithium niobate (LN), potassium titanyl phosphate (KTP), zinc germanium phosphide (ZGP) and silver selenogallate (AGSE). Simulation of planar LN waveguide shows that when the electric field vector E lies in the k-c plane, the power flow is directed precisely along the propagation direction, demonstrating waveguiding effect in the planar waveguide. Employment of anisotropic nonlinear optical waveguides, for example in combination with AFB® crystalline fiber waveguides (CFW), provides access to the design of a number of novel high power and high efficiency light sources spanning the range of wavelengths from deep ultraviolet (as short as 200 nm) to mid-infrared (as long as about 18 μm). To our knowledge, the technique is the only generally applicable one because most often there are no compatible cladding crystals available to nonlinear optical cores, especially not with an engineer-able refractive index difference and large mode area.

  10. Topological complexity of crystal structures: quantitative approach.

    Science.gov (United States)

    Krivovichev, Sergey

    2012-05-01

    The topological complexity of a crystal structure can be quantitatively evaluated using complexity measures of its quotient graph, which is defined as a projection of a periodic network of atoms and bonds onto a finite graph. The Shannon information-based measures of complexity such as topological information content, I(G), and information content of the vertex-degree distribution of a quotient graph, I(vd), are shown to be efficient for comparison of the topological complexity of polymorphs and chemically related structures. The I(G) measure is sensitive to the symmetry of the structure, whereas the I(vd) measure better describes the complexity of the bonding network. © 2012 International Union of Crystallography

  11. Crystal structure of (ferrocenylmethyldimethylammonium hydrogen oxalate

    Directory of Open Access Journals (Sweden)

    Mamadou Ndiaye

    2015-08-01

    Full Text Available The crystal structure of the title salt, [Fe(C5H5(C8H13N](HC2O4, consists of discrete (ferrocenylmethyldimethylammonium cations and hydrogen oxalate anions. The anions are connected through a strong O—H...O hydrogen bond, forming linear chains running parallel to [100]. The cations are linked to the anions through bifurcated N—H...(O,O′ hydrogen bonds. Weak C—H...π interactions between neighbouring ferrocenyl moieties are also observed.

  12. Crystal structure of Staphylococcus aureus Cas9

    OpenAIRE

    Nishimasu, Hiroshi; Cong, Le; Yan, Winston X.; Ran, F. Ann; Zetsche, Bernd; Li, Yinqing; Kurabayashi, Arisa; Ishitani, Ryuichiro; Zhang, Feng; Nureki, Osamu

    2015-01-01

    The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. Recently, we harnessed Staphylococcus aureus Cas9 (SaCas9), which is significantly smaller than Streptococcus pyogenes Cas9 (SpCas9), to facilitate efficient in vivo genome editing. Here, we report the crystal structures of SaCas9 in complex with a single guide RNA (sgRNA) and its double-stranded DNA targets, containing the 5′-TTGAAT-3′ PAM and...

  13. Crystal structure of yeast Sco1

    Energy Technology Data Exchange (ETDEWEB)

    Abajian, Carnie; Rosenzweig, Amy C. (NWU)

    2010-03-05

    The Sco family of proteins are involved in the assembly of the dinuclear CuA site in cytochrome c oxidase (COX), the terminal enzyme in aerobic respiration. These proteins, which are found in both eukaryotes and prokaryotes, are characterized by a conserved CXXXC sequence motif that binds copper ions and that has also been proposed to perform a thiol:disulfide oxidoreductase function. The crystal structures of Saccharomyces cerevisiae apo Sco1 (apo-ySco1) and Sco1 in the presence of copper ions (Cu-ySco1) were determined to 1.8- and 2.3-{angstrom} resolutions, respectively. Yeast Sco1 exhibits a thioredoxin-like fold, similar to that observed for human Sco1 and a homolog from Bacillus subtilis. The Cu-ySco1 structure, obtained by soaking apo-ySco1 crystals in copper ions, reveals an unexpected copper-binding site involving Cys181 and Cys216, cysteine residues present in ySco1 but not in other homologs. The conserved CXXXC cysteines, Cys148 and Cys152, can undergo redox chemistry in the crystal. An essential histidine residue, His239, is located on a highly flexible loop, denoted the Sco loop, and can adopt positions proximal to both pairs of cysteines. Interactions between ySco1 and its partner proteins yeast Cox17 and yeast COX2 are likely to occur via complementary electrostatic surfaces. This high-resolution model of a eukaryotic Sco protein provides new insight into Sco copper binding and function.

  14. Simulating complex crystal structures using the phase-field crystal model

    Science.gov (United States)

    Alster, Eli; Montiel, David; Thornton, Katsuyo; Voorhees, Peter W.

    2017-11-01

    We introduce a phase-field crystal model that creates an array of complex three- and two-dimensional crystal structures via a numerically tractable three-point correlation function. The three-point correlation function is designed in order to energetically favor the principal interplanar angles of a target crystal structure. This is achieved via an analysis performed by examining the crystal's structure factor. This approach successfully yields energetically stable simple cubic, diamond cubic, simple hexagonal, graphene layers, and CaF2 crystals. To illustrate the ability of the method to yield a particularly complex and technologically important crystal structure, we show how this three-point correlation function method can be used to generate perovskite crystals.

  15. Crystal Structure of Human Nicotinamide Riboside Kinase

    Energy Technology Data Exchange (ETDEWEB)

    Khan,J.; Xiang, S.; Tong, L.

    2007-01-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD{sup +} as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 {angstrom} resolution and in a ternary complex with ADP and tiazofurin at 2.7 {angstrom} resolution. The active site is located in a groove between the central parallel {beta} sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  16. Crystal structure of human nicotinamide riboside kinase.

    Science.gov (United States)

    Khan, Javed A; Xiang, Song; Tong, Liang

    2007-08-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 A resolution and in a ternary complex with ADP and tiazofurin at 2.7 A resolution. The active site is located in a groove between the central parallel beta sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  17. 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.

  18. 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.

  19. Crystal structures of five 6-mercaptopurine derivatives

    Directory of Open Access Journals (Sweden)

    Lígia R. Gomes

    2016-03-01

    Full Text Available The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-ylsulfanyl]-1-(3-methoxyphenylethan-1-one (1, C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-ylsulfanyl]-1-(4-methoxyphenylethan-1-one (2, C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-ylsulfanyl]-1-(4-chlorophenylethan-1-one (3, C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-ylsulfanyl]-1-(4-bromophenylethan-1-one (4, C15H11BrN4O2S, and 1-(3-methoxyphenyl-2-[(9H-purin-6-ylsulfanyl]ethan-1-one (5, C14H12N4O2S. Compounds (2, (3 and (4 are isomorphous and accordingly their molecular and supramolecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the molecules of (1 and (5 are essentially planar but that in the case of the three isomorphous compounds (2, (3 and (4, these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1 all molecules are linked by weak C—H...O hydrogen bonds in their crystals. There is π–π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanylethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles.

  20. 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.

  1. Crystal structure of N-deacetyllappaconitine

    Directory of Open Access Journals (Sweden)

    Xin-Wei Shi

    2015-08-01

    Full Text Available The title compound, C30H42N2O7 [systematic name: (1S,4S,5S,7S,8S,9S,10S,11S,13R,14S,16S,17R-20-ethyl-4,8,9-trihydroxy-1,14,16-trimethoxyaconitan-4-yl 2-aminobenzoate], isolated from roots of Aconitum sinomontanum Nakai, is a typical aconitane-type C19-diterpenoid alkaloid, which crystallizes with two independent molecules in the asymmetric unit. The conformations of the two independent molecules are closely similar. Each molecule comprises four six-membered rings (A, B, D and E including one six-membered N-containing heterocyclic ring (E, and two five-membered rings (C and F. Rings A, B and E adopt chair conformations, while ring D displays a boat conformation. Five-membered rings C and F exhibit envelope conformations. IntramolecularN—H...O hydrogen bonds between the amino group and carbonyl O atom help to stabilize molecular structure. In the crystal, O—H...O hydrogen bonds link the molecules into zigzag chains propagating in [010].

  2. Crystal Structures of Respiratory Pathogen Neuraminidases

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao, Y.; Parker, D; Ratner, A; Prince, A; Tong, L

    2009-01-01

    Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7 {angstrom} resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.

  3. Crystal structure prediction supported with diffraction data

    Science.gov (United States)

    Tsujimoto, Naoto; Adachi, Daiki; Todo, Synge; Akashi, Ryosuke; Tsuneyuki, Shinji

    Atomistic computer simulation is of growing importance in the study of unidentified crystals, although prediction or determination of complicated structure is still a challenging problem due to its many degrees of freedom. Here we propose to utilize experimentally available data of powder diffraction to support and accelerate the structure simulation. In so-called direct-space methods for structure determination from powder diffraction, simplified interatomic potential energy or some other physical constraints are often used in combination with the cost function defined by diffraction data. On the other hand, we formulate a cost function called ``crystallinity'' to support simulation with accurate interatomic potential energy. Since the crystallinity here is defined as the sum of the diffraction intensities only at the peak positions detected in experiments, this method is applicable to low-quality diffraction data such as those obtained at high pressures. We apply this method to well-known polymorphs of SiO2 with up to 96 atoms in the simulation cell to find that it reproduces the correct structures efficiently with information of a very limited number of diffraction peaks.

  4. Crystal structure of a snake venom cardiotoxin

    Energy Technology Data Exchange (ETDEWEB)

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

    1987-05-01

    Cardiotoxin V/sup II/4 from Naja mossambica crystallizes in space group P6/sub 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 ..beta.. sheet, may be functionally relevant.

  5. Crystal structure of 4-(trimethylgermylbenzoic acid

    Directory of Open Access Journals (Sweden)

    Lena Knauer

    2015-06-01

    Full Text Available The title compound, [Ge(CH33(C7H5O2], was obtained as a by-product in the synthesis of the corresponding aldehyde. Two slightly different molecules are present in the asymmetric unit. In both molecules, the geometry of the aromatic ring plane is distorted by varying intensities. Additionally, the Ge atoms deviate from the mean aromatic ring planes. Whereas the distance of the Ge atom to the ring plane is only 0.101 (4 Å in the first molecule, this distance is increased to 0.210 (4 Å in the second. In the crystal structure, centrosymmetric O—H...O hydrogen-bonded dimers are formed. The title compound is isostructural with the Si analogue [Haberecht et al. (2004. Acta Cryst. E60, o329–0330].

  6. Crystal structure of Deep Vent DNA polymerase.

    Science.gov (United States)

    Hikida, Yasushi; Kimoto, Michiko; Hirao, Ichiro; Yokoyama, Shigeyuki

    2017-01-29

    DNA polymerases are useful tools in various biochemical experiments. We have focused on the DNA polymerases involved in DNA replication including the unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px). Many reports have described the different combinations between unnatural base pairs and DNA polymerases. As an example, for the replication of the Ds-Px pair, Deep Vent DNA polymerase exhibits high efficiency and fidelity, but Taq DNA polymerase shows much lower efficiency and fidelity. In the present study, we determined the crystal structure of Deep Vent DNA polymerase in the apo form at 2.5 Å resolution. Using this structure, we constructed structural models of Deep Vent DNA polymerase complexes with DNA containing an unnatural or natural base in the replication position. The models revealed that the unnatural Ds base in the template-strand DNA clashes with the side-chain oxygen of Thr664 in Taq DNA polymerase, but not in Deep Vent DNA polymerase. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  7. 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.

  8. 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.

  9. 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.

  10. Crystal structure and elastic constants of Dharwar cotton fibre using ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 30; Issue 5. Crystal structure and elastic constants of Dharwar cotton fibre using WAXS data. O M Samir R ... Using this data and employing linked atom least squares (LALS) method, we report here the molecular and crystal structure of these cotton fibres. Employing ...

  11. Crystal structure of human IRAK1.

    Science.gov (United States)

    Wang, Li; Qiao, Qi; Ferrao, Ryan; Shen, Chen; Hatcher, John M; Buhrlage, Sara J; Gray, Nathanael S; Wu, Hao

    2017-12-19

    Interleukin 1 (IL-1) receptor-associated kinases (IRAKs) are serine/threonine kinases that play critical roles in initiating innate immune responses against foreign pathogens and other types of dangers through their role in Toll-like receptor (TLR) and interleukin 1 receptor (IL-1R) mediated signaling pathways. Upon ligand binding, TLRs and IL-1Rs recruit adaptor proteins, such as myeloid differentiation primary response gene 88 (MyD88), to the membrane, which in turn recruit IRAKs via the death domains in these proteins to form the Myddosome complex, leading to IRAK kinase activation. Despite their biological and clinical significance, only the IRAK4 kinase domain structure has been determined among the four IRAK family members. Here, we report the crystal structure of the human IRAK1 kinase domain in complex with a small molecule inhibitor. The structure reveals both similarities and differences between IRAK1 and IRAK4 and is suggestive of approaches to develop IRAK1- or IRAK4-specific inhibitors for potential therapeutic applications. While the IRAK4 kinase domain is capable of homodimerization in the unphosphorylated state, we found that the IRAK1 kinase domain is constitutively monomeric regardless of its phosphorylation state. Additionally, the IRAK1 kinase domain forms heterodimers with the phosphorylated, but not unphosphorylated, IRAK4 kinase domain. Collectively, these data indicate a two-step kinase activation process in which the IRAK4 kinase domain first homodimerizes in the Myddosome, leading to its trans-autophosphorylation and activation. The phosphorylated IRAK4 kinase domain then forms heterodimers with the IRAK1 kinase domain within the Myddosome, leading to its subsequent phosphorylation and activation.

  12. Structural derivation and crystal chemistry of apatites.

    Science.gov (United States)

    White, T J; ZhiLi, Dong

    2003-02-01

    The crystal structures of the [A(1)(2)][A(2)(3)](BO(4))(3)X apatites and the related compounds [A(1)(2)][A(2)(3)](BO(5))(3)X and [A(1)(2)][A(2)(3)](BO(3))(3)X are collated and reviewed. The structural aristotype for this family is Mn(5)Si(3) (D8(8) type, P6(3)/mcm symmetry), whose cation array approximates that of all derivatives and from which related structures arise through the systematic insertion of anions into tetrahedral, triangular or linear interstices. The construction of a hierarchy of space-groups leads to three apatite families whose high-symmetry members are P6(3)/m, Cmcm and P6(3)cm. Alternatively, systematic crystallographic changes in apatite solid-solution series may be practically described as deviations from regular anion nets, with particular focus on the O(1)-A(1)-O(2) twist angle phi projected on (001) of the A(1)O(6) metaprism. For apatites that contain the same A cation, it is shown that phi decreases linearly as a function of increasing average ionic radius of the formula unit. Large deviations from this simple relationship may indicate departures from P6(3)/m symmetry or cation ordering. The inclusion of A(1)O(6) metaprisms in structure drawings is useful for comparing apatites and condensed-apatites such as Sr(5)(BO(3))(3)Br. The most common symmetry for the 74 chemically distinct [A(1)(2)][A(2)(3)](BO(4))(3)X apatites that were surveyed was P6(3)/m (57%), with progressively more complex chemistries adopting P6(3) (21%), P3; (9%), P6 (4.3%), P2(1)/m (4.3%) and P2(1) (4.3%). In chemically complex apatites, charge balance is usually maintained through charge-coupled cation substitutions, or through appropriate mixing of monovalent and divalent X anions or X-site vacancies. More rarely, charge compensation is achieved through insertion/removal of oxygen to produce BO(5) square pyramidal units (as in ReO(5)) or BO(3) triangular coordination (as in AsO(3)). Polysomatism arises through the ordered filling of [001] BO(4) tetrahedral strings to

  13. 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.

  14. 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.

  15. Ordering of crystal structure by ionizing radiation

    Science.gov (United States)

    Chernov, I. P.; Momontov, A. P.; Cherdantsev, P. A.; Chakhlov, B. V.

    1994-12-01

    We have studied the action of ionizing radiation on defect-containing semiconductor crystals, metals, and alloys. Using modern methods for investigation of solids, Rutherford back scattering of channeled charged particles, x-ray diffraction, electron microscopy, and also calorimetric methods, we have established: a) irradiation (by x-ray beams, gamma rays, and electrons) of metals and alloys with an equivalent radiation dose less than 105 J/kg and of semiconductor crystals with a dose less than 103 J/kg does not lead to additional accumulation of defects but conversely leads to elimination of defects and transition of the crystal to a more equilibrium state; b) ionization processes play a determining role in rearrangment of defects in crystals exhibiting both semiconductor and metallic conductivity. We show that rearrangment of the crystal occurs as a result of stored energy in the crystal which is liberated due to chain reactions of annihilation of defects, initiated by ionization. Transition of the crystal to the equilibrium state is accompanied by improvement of its physical properties.

  16. Crystal structure and characterization of pyrroloquinoline quinone disodium trihydrate

    Directory of Open Access Journals (Sweden)

    Ikemoto Kazuto

    2012-06-01

    Full Text Available Abstract Background Pyrroloquinoline quinone (PQQ, a tricarboxylic acid, has attracted attention as a growth factor, and its application to supplements and cosmetics is underway. The product used for these purposes is a water-soluble salt of PQQ disodium. Although in the past, PQQ disodiumpentahydrates with a high water concentration were used, currently, low hydration crystals of PQQ disodiumpentahydrates are preferred. Results We prepared a crystal of PQQ disodium trihydrate in a solution of ethanol and water, studied its structure, and analyzed its properties. In the prepared crystal, the sodium atom interacted with the oxygen atom of two carboxylic acids as well as two quinones of the PQQ disodium trihydrate. In addition, the hydration water of the prepared crystal was less than that of the conventional PQQ disodium crystal. From the results of this study, it was found that the color and the near-infrared (NIR spectrum of the prepared crystal changed depending on the water content in the dried samples. Conclusions The water content in the dried samples was restored to that in the trihydrate crystal by placing the samples in a humid environment. In addition, the results of X-ray diffraction (XRD and X-ray diffraction-differential calorimetry (XRD-DSC analyses show that the phase of the trihydrate crystal changed when the crystallization water was eliminated. The dried crystal has two crystalline forms that are restored to the original trihydrate crystals in 20% relative humidity (RH. This crystalline (PQQ disodium trihydrate is stable under normal environment.

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

    African Journals Online (AJOL)

    isoindoline-1,3-dione, was characterized by proton nuclear magnetic resonance spectroscopy (NMR) and single crystal x-ray diffraction method. The target compound was tested for its antimicrobial activities and computational studies including density ...

  18. Structure and Properties of Liquid Crystals

    CERN Document Server

    Blinov, Lev M

    2011-01-01

    This book by Lev M. Blinov is ideal to guide researchers from their very first encounter with liquid crystals to the level where they can perform independent experiments on liquid crystals with a thorough understanding of their behaviour also in relation to the theoretical framework. Liquid crystals can be found everywhere around us. They are used in virtually every display device, whether it is for domestic appliances of for specialized technological instruments. Their finely tunable optical properties make them suitable also for thermo-sensing and laser technologies. There are many monographs written by prominent scholars on the subject of liquid crystals. The majority of them presents the subject in great depth, sometimes focusing on a particular research aspect, and in general they require a significant level of prior knowledge. In contrast, this books aims at an audience of advanced undergraduate and graduate students in physics, chemistry and materials science. The book consists of three parts: the firs...

  19. 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.

  20. PLANAR OPTICAL WAVEGUIDES WITH PHOTONIC CRYSTAL STRUCTURE

    DEFF Research Database (Denmark)

    2003-01-01

    Planar optical waveguide comprising a core region and a cladding region comprising a photonic crystal material, said photonic crystal material having a lattice of column elements, wherein at least a number of said column elements are elongated substantially in an axial direction for said core...... region. The invention also relates to optical devices comprising planar optical waveguides and methods of making waveguides and optical devices....

  1. The crystal structure of some rhenium and technetium dichalcogenides

    NARCIS (Netherlands)

    Lamfers, H.J; Meetsma, A.; Wiegers, G.A; deBoer, J.L.

    1996-01-01

    The crystal structures of ReSe2,ReS2, ReSSe and TcS2 are determined using single crystal X-ray diffraction. The compounds are triclinic with space group P (1) over bar. ReSe2, Res(2) and ReSSe have a distorted CdCl2-type structure; TcS2 has a distorted Cd(OH)(2)-type structure. In the case of Res,

  2. Structural distortion in thiourea-mixed ADP crystals

    Energy Technology Data Exchange (ETDEWEB)

    Jayarama, A. [Department of Physics, Mangalore University, Mangalagangotri 574199 (India)]. E-mail: jrmarasalike@yahoo.co.in; Dharmaprakash, S.M. [Department of Physics, Mangalore University, Mangalagangotri 574199 (India)

    2006-11-15

    Single crystals of ammonium dihydrogen phosphate (ADP) mixed with different mole concentrations of thiourea were grown using slow evaporation solution technique at 30deg. C. In order to study the effect of mixing thiourea on the structural characteristics of ADP, X-ray diffraction studies were carried out on the crystals using Shimadzu X-ray diffractometer with Cu K{alpha} radiation. X-ray study revealed that the structures of the thiourea-mixed ADP are slightly distorted compared to the pure ADP crystal structure. Inclusion of thiourea enhances the growth of (1-bar 00) plane of the ADP crystal. Thiourea-mixed ADP crystals were found to have maximum inclusion, as the thiourea concentration was 10mol%.

  3. 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.

  4. [Validation of the crystal structure of medicinal realgar in China].

    Science.gov (United States)

    Zhang, Zhi-Jie; Zhou, Qun; Wei, Jing-Zhi; Zhang, Yan-Ling; Sun, Su-Qin; Huang, Lu-Qi; Yuan, Si-Tong

    2011-02-01

    The crystal structure of medicated realgar in China was validated as alpha-As4 S4 by X-ray diffraction and Raman spectroscopy in the present paper. Ten batches of medicinal realgar were analyzed including realgar ore, medicinal realgar powder, and prepared Chinese medicine. Identification of two As4 S4 polymorphs confirmed that the crystal structure of medicated realgar in China is alpha-As4 S4. Studies on 18 batches of preparative realgar powder showed that processing of realgar can not change the crystal structure of realgar.

  5. X-Ray structural investigation of VAS-393 crystals

    CERN Document Server

    Martirosian, A H; Harurtjunian, V S

    2001-01-01

    X-ray structural study of VAS-393 crystals was performed. Investigations were carried out with the use of the Weissenberg rotating and powder (employing the Bjornstrem diagrams) methods. The lattice constants ''c'' and ''a''are calculated. The crystal is shown to belong to the trigonal syngony (medium category)

  6. Synthesis, characterization and crystal structure of new nickel ...

    Indian Academy of Sciences (India)

    Abstract. A novel nickel molybdenum complex with the 2,6-pyridine dicarboxylic acid ligand was successfully synthesized and characterized by thermogravimetric analysis and single crystal X-ray crystallography. The single-crystal X-ray data revealed that the structure is a hydrated 1-D polymer with two different Ni sites.

  7. Crystal Structure of Triosephosphate Isomerase from Trypanosoma cruzi in Hexane

    National Research Council Canada - National Science Library

    Xiu-Gong Gao; Ernesto Maldonado; Ruy Perez-Montfort; Georgina Garza-Ramos; Marietta Tuena de Gomez-Puyou; Armando Gomez-Puyou; Adela Rodriguez-Romero

    1999-01-01

    ... the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2- angstrom resolution...

  8. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly

    National Research Council Canada - National Science Library

    Marx, Ailie; Adir, Noam

    2013-01-01

    ... of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC...

  9. Improving nanocavity switching using Fano resonances in photonic crystal structures

    DEFF Research Database (Denmark)

    Heuck, Mikkel; Kristensen, Philip Trøst; Elesin, Yuriy

    2013-01-01

    We present a simple design for achieving Fano resonances in photonic crystal coupled waveguide-cavity structures. A coupled mode theory analysis shows an order of magnitude reduction in switching energy compared to conventional Lorentz resonances....

  10. 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.

  11. 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

    2017-04-01

    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.

  12. Membrane protein structures without crystals, by single particle electron cryomicroscopy.

    Science.gov (United States)

    Vinothkumar, Kutti R

    2015-08-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Quantitative crystal structure descriptors from multiplicative congruential generators.

    Science.gov (United States)

    Hornfeck, Wolfgang

    2012-03-01

    Special types of number-theoretic relations, termed multiplicative congruential generators (MCGs), exhibit an intrinsic sublattice structure. This has considerable implications within the crystallographic realm, namely for the coordinate description of crystal structures for which MCGs allow for a concise way of encoding the numerical structural information. Thus, a conceptual framework is established, with some focus on layered superstructures, which proposes the use of MCGs as a tool for the quantitative description of crystal structures. The multiplicative congruential method eventually affords an algorithmic generation of three-dimensional crystal structures with a near-uniform distribution of atoms, whereas a linearization procedure facilitates their combinatorial enumeration and classification. The outlook for homometric structures and dual-space crystallography is given. Some generalizations and extensions are formulated in addition, revealing the connections of MCGs with geometric algebra, discrete dynamical systems (iterative maps), as well as certain quasicrystal approximants.

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

    Indian Academy of Sciences (India)

    2017-09-09

    Sep 9, 2017 ... structure in ferroelectric ceramics. Keywords. Electronic ceramics; ferroelectricity; piezoelectricity. 1. Introduction. It is well known that ferroelectric domains and crystal structure control the physical properties of ferroelectrics. [1–5]. Therefore, intensive studies have focused on domain structures and the ...

  15. Protein dynamics derived from clusters of crystal structures

    NARCIS (Netherlands)

    van Aalten, D.M.F.; Conn, D.A.; de Groot, B.L.; Berendsen, H.J.C.; Findlay, J.B.C.; Amadei, A

    1997-01-01

    A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The ''essential dynamics'' procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes

  16. Three supramolecular compounds of 1,4-benzeneditetrazole (H2BDT): Syntheses, crystal structures, and crystal to crystal transformation

    Science.gov (United States)

    Deng, Ji-Hua; Wen, Ya-Qiong; Luo, Jie; Huang, Zhi-Qiang; Zhong, Di-Chang

    2017-08-01

    Three supramolecular compounds based on 1,4-benzeneditetrazole (H2BDT), (NH4)2(BDT) (1), [Mg(H2O)6](HBDT)2·2H2O (2), and [Mg(CH3OH)4(H2O)2](HBDT)2·2CH3OH (3) have been solvothermally synthesized and structurally characterized by single-crystal/powder X-ray diffraction. Structural analyses indicated that these compounds are 3D supramolecular structures stabilized by electrostatic interactions and intermolecular hydrogen bonds. The crystal to crystal transformation between 2 and 3 were investigated. The result showed that 2 is readily transform to 3 after immersed in methanol solution, while 3 can not be converted to 2 after immersed in distilled water solution.

  17. Improved Synthesis and Crystal Structure of Dalcetrapib

    Directory of Open Access Journals (Sweden)

    Frank Richter

    2012-10-01

    Full Text Available An improved synthesis of the Cholesteryl Ester Transfer Protein inhibitor dalcetrapib is reported. The precursor disulfide was reduced (a by Mg/MeOH or (b by EtSH/DBU/THF. The resulting thiol was acylated (a by a known procedure or (b in a one-pot process. Impurities were removed (a by dithiothreitol (DTT or (b by oxidation using H2O2. Dalcetrapib crystallized in space group P21/c.

  18. Datamining protein structure databanks for crystallization patterns of proteins.

    Science.gov (United States)

    Valafar, Homayoun; Prestegard, James H; Valafar, Faramarz

    2002-12-01

    A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%.

  19. Assessment of microarchitecture and crystal structure of hydroxyapatite in osteoporosis

    Directory of Open Access Journals (Sweden)

    Zairin Noor

    2016-02-01

    Full Text Available Osteoporosis is characterized by lower bone mineral density (BMD and microarchitectural degeneration, which tends to increase bone fragility and fracture risk. Bone microstructure depends on interactions between the mineral atoms, which may perform substitution or incorporation into bone crystals, and may dynamically take over the function of calcium or may become a complementary part. The mineral atoms may also become a composite in the hydroxyapatite crystals. The aim of this study was to find an association between the bone microstructure and hydoxyapatite crystal structure in osteoporosis, in comparison to normal bone. The subjects of this study were surgery patients at the Department of Orthopedics of Ulin General Hospital in Banjarmasin and other centers. Inclusion criteria consisted of the presence of fracture of trabecular bone, normal or osteoporotic BMD values, and no past history of chronic disease. Bone was obtained from fracture patients during surgery. The characteristics of the hydroxyapatite crystals were analyzed by X-ray diffraction (XRD and the microarchitecture by scanning electron microscopy (SEM. SEM showed degeneration of the microarchitecture of osteoporotic bone, in comparison with normal bone. On XRD there was a peak of hydoxyapatite crystals only and no other crystal phases. Diffraction patterns showed a larger crystal size in osteoporotic bone as compared to normal bone, indicating higher porosity. It may be concluded that there is a difference in crystal size and morphologic distribution of hydoxyapatite in osteoporotic bone, determining bone microarchitecture.

  20. Assessment of microarchitecture and crystal structure of hydroxyapatite in osteoporosis

    Directory of Open Access Journals (Sweden)

    Zairin Noor

    2011-04-01

    Full Text Available Osteoporosis is characterized by lower bone mineral density (BMD and microarchitectural degeneration, which tends to increase bone fragility and fracture risk. Bone microstructure depends on interactions between the mineral atoms, which may perform substitution or incorporation into bone crystals, and may dynamically take over the function of calcium or may become a complementary part. The mineral atoms may also become a composite in the hydroxyapatite crystals. The aim of this study was to find an association between the bone microstructure and hydoxyapatite crystal structure in osteoporosis, in comparison to normal bone. The subjects of this study were surgery patients at the Department of Orthopedics of Ulin General Hospital in Banjarmasin and other centers. Inclusion criteria consisted of the presence of fracture of trabecular bone, normal or osteoporotic BMD values, and no past history of chronic disease. Bone was obtained from fracture patients during surgery. The characteristics of the hydroxyapatite crystals were analyzed by X-ray diffraction (XRD and the microarchitecture by scanning electron microscopy (SEM. SEM showed degeneration of the microarchitecture of osteoporotic bone, in comparison with normal bone. On XRD there was a peak of hydoxyapatite crystals only and no other crystal phases. Diffraction patterns showed a larger crystal size in osteoporotic bone as compared to normal bone, indicating higher porosity. It may be concluded that there is a difference in crystal size and morphologic distribution of hydoxyapatite in osteoporotic bone, determining bone microarchitecture.

  1. short communication synthesis and crystal structure of a polymeric ...

    African Journals Online (AJOL)

    Preferred Customer

    of zinc sulfate, 4-nitrophenylacetic acid, and propane-1,3-diamine (PDA) in water. Structure of the complex has been characterized by single-crystal X-ray diffraction. The complex crystallizes as orthorhombic space group Pnma, with unit cell dimensions a = 15.732(1) Å, b = 23.912(1) Å, c = 5.5565(3) Å, V = 2090.2(2) Å3, ...

  2. The crystal and molecular structure of ammonium titanyl oxalate

    NARCIS (Netherlands)

    van de Velde, G.M.H.; Harkema, Sybolt; Gellings, P.J.

    1974-01-01

    Ammonium titanyl oxalate monohydrate, (NH4)2 TiO(C2O4)2·H2O, is monoclinic with cell parameters A = 13.473(2), B = 11.329(1), C = 17.646(2) Å, β = 126.66(1)°. The space group is P21/c with Z = 8, dc = 1.808 g cm−3 and dm = 1.80 g cm−3. The crystal structure was determined from single-crystal

  3. Hydrothermal syntheses and single crystal structural ...

    Indian Academy of Sciences (India)

    ), and Zn(II); OPTA = 1-oxopyridinium-2-thioacetato) was prepared from the appropriate metal acetates, 1-oxopyridinium-2-thioacetic acid (OPTAH), and potassium hydroxide in hydrothermal media and structurally characterized. The structure ...

  4. 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.

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

    Indian Academy of Sciences (India)

    Normal-coordinate structural decomposition (NSD) analysis of the heme in various heme proteins feature interesting trend in distortion of the macrocycle.30. Numerous crystal structure reports are available on variety of substituted porphyrins and metallopor- phyrins.31–38 Systematic analyses of the change in con-.

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

    Indian Academy of Sciences (India)

    Coordination polymer of Cu(II) bridged by o-phthalic acid alone is not known. The reaction of C u C l 2 .2 H 2 O with (2-butoxycarbonyl)benzoic acid yielded three dimensional coordination polymer bridged byo-phthalic acid. X-ray crystal structure shows structure with monoclinic P21/c space group. o-Phthalic acidmolecules ...

  7. Crystal structure and elastic constants of Dharwar cotton fibre using ...

    Indian Academy of Sciences (India)

    WINTEC

    Abstract. Wide-angle X-ray scattering (WAXS) recordings were carried out on raw Dharwar cotton fibres available in Karnataka. Using this data and employing linked atom least squares (LALS) method, we report here the molecular and crystal structure of these cotton fibres. Employing structural data, we have computed.

  8. Crystal structure of 1-bromo-2-(phenylselenylbenzene

    Directory of Open Access Journals (Sweden)

    Bronte J. Charette

    2015-03-01

    Full Text Available In the title compound, C12H9BrSe, the Se atom exhibits a bent geometry, with a C—Se—C bond angle of 99.19 (6°. The ortho Se and Br atoms are slightly displaced from opposite faces of the mean plane of the benzene ring [by 0.129 (2 and 0.052 (2 Å, respectively]. The planes of the benzene and phenyl rings form a dihedral angle of 72.69 (5°. In the crystal, π-stacking interactions between inversion-related phenyl rings are observed, with a centroid–centroid distance of 3.630 (1 Å.

  9. 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.

  10. Band structure peculiarities of magnetic photonic crystals

    Science.gov (United States)

    Gevorgyan, A. H.; Golik, S. S.

    2017-10-01

    In this work we studied light diffraction in magneto-photonic crystals (MPC) having large magneto-optical activity and modulation large depth. The case of arbitrary angles between the direction of the external static magnetic field and the normal to the border of the MPC layer is considered. The problem is solved by Ambartsumian's modified layer addition method. It is found that there is a new type of non-reciprocity, namely, the relation R (α) ≠ R (- α) takes place, where R is the reflection coefficient, and α is the incidence angle. It is shown the formation of new photonic band gap (PBG) at oblique incidence of light, which is not selective for the polarization of the incident light, in the case when the external magnetic field is directed along the medium axis. Such a system can be used as: a tunable polarization filter, polarization mirror, circular (elliptical) polarizer, tunable optical diode, etc.

  11. Crystal structure of 2-aminopyridinium 6-chloronicotinate

    Directory of Open Access Journals (Sweden)

    N. Jeeva Jasmine

    2015-09-01

    Full Text Available In the title salt, C5H7N+·C6H3ClNO−, the 2-aminopyridinium cation interacts with the carboxylate group of the 6-chloronicotinate anion through a pair of independent N—H...O hydrogen bonds, forming an R22(8 ring motif. In the crystal, these dimeric units are connected further via N—H...O hydrogen bonds, forming chains along [001]. In addition, weak C—H...N and C—H...O hydrogen bonds, together with weak π–π interactions, with centroid–centroid distances of 3.6560 (5 and 3.6295 (5 Å, connect the chains, forming a two-dimensional network parallel to (100.

  12. Structure and properties of MTiOXO sub 4 crystals

    CERN Document Server

    Latham, T J

    2000-01-01

    linked to chains of particular atoms along the three crystallographic axes. Dielectric measurements of a series of arsenate crystals and various doped phosphate crystals demonstrate that MTiOXO sub 4 isomorphs exhibit dielectric relaxation of a non-Debye type and appear to conform to the hopping charge-carrier and low frequency dispersion response models. A reduction in the ionic conductivity is observed in the arsenate crystals and phosphate crystals doped with trivalent ions. Arrhenius plots indicate that the activation energies of the mixed cation arsenate crystals are significantly higher than the other KTiOPO sub 4 isomorphs. This observation suggests that the modified oxygen framework in these mixed arsenate crystals contributes intrinsically to the large activation energies required for ionic conduction. This thesis is a study of the structural, optical and electrical properties of MTiOXO sub 4 crystals, where M is a monovalent cation such as K, Rb etc and X is P or As. Low and high-temperature single-...

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

    African Journals Online (AJOL)

    Conclusion: The test compound has a moderate antimicrobial activity and the optimized molecular structure of the studied compound using B3LYP/6-31G (d,p) method showed good agreement with the reported x-ray structure. Keywords: Isoindoline-1, 3-dione, X-ray analysis, Density function theory, Antimicrobial, Molecular ...

  14. 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. ...

  15. 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

  16. 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...... range of data was insufficient for a structure analysis, but the R-factor calculations showed the intensities extracted from the profile data to be of acceptable quality. The results were used to estimate the largest structure that might be solved using routine techniques. It was found that the limit...... would be near twenty atoms in the asymmetric part of a centro-symmetric structure....

  17. 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.

  18. 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

  19. 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)

  20. Crystal structure of 2-methoxy-1-nitronaphthalene

    Directory of Open Access Journals (Sweden)

    Hasna Yassine

    2015-10-01

    Full Text Available The asymmetric unit of the title compound, C11H9NO3, contains two molecules, A and B. In molecule A, the dihedral angle between the planes of the naphthalene ring system (r.m.s. deviation = 0.003 Å and the nitro group is 89.9 (2°, and the C atom of the methoxy group deviates from the naphthyl plane by 0.022 (2 Å. Equivalent data for molecule B are 0.008 Å, 65.9 (2° and −0.198 (2 Å, respectively. In the crystal, molecules are linked by weak C—H...O interactions, forming [100] chains of alternating A and B molecules. Weak aromatic π–π stacking contacts, with a range of centroid–centroid distances from 3.5863 (9 to 3.8048 (9 Å, are also observed.

  1. Utilization of Protein Crystal Structures in Industry

    Science.gov (United States)

    Ishikawa, Kohki

    In industry, protein crystallography is used in mainly two technologies. One is structure-based drug design, and the other is structure-based enzyme engineering. Some successful cases together with recent advances are presented in this article. The cases include the development of an anti-influenza drug, and the introduction of engineered acid phosphatase to the manufacturing process of nucleotides used as umami seasoning.

  2. 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.

  3. Crystallation, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes

    National Research Council Canada - National Science Library

    DeLucas, Lawrence

    1997-01-01

    .... This structure is currently being used for designing lead inhibitors. We have also purified PFPK-DHPS bifunctional enzyme for structure analysis and are presently screening for crystallization conditions...

  4. 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.

  5. 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.

  6. Diamond-Structured Photonic Crystals with Graded Air Spheres Radii

    Directory of Open Access Journals (Sweden)

    Dichen Li

    2012-05-01

    Full Text Available A diamond-structured photonic crystal (PC with graded air spheres radii was fabricated successfully by stereolithography (SL and gel-casting process. The graded radii in photonic crystal were formed by uniting different radii in photonic crystals with a uniform radius together along the Г‑Х direction. The stop band was observed between 26.1 GHz and 34.3 GHz by reflection and transmission measurements in the direction. The result agreed well with the simulation attained by the Finite Integration Technique (FIT. The stop band width was 8.2 GHz and the resulting gap/midgap ratio was 27.2%, which became respectively 141.4% and 161.9% of the perfect PC. The results indicate that the stop band width of the diamond-structured PC can be expanded by graded air spheres radii along the Г‑Х direction, which is beneficial to develop a multi bandpass filter.

  7. Crystal Structure Representation for Neural Networks using Topological Approach.

    Science.gov (United States)

    Fedorov, Aleksandr V; Shamanaev, Ivan V

    2017-08-01

    In the present work we describe a new approach, which uses topology of crystals for physicochemical properties prediction using artificial neural networks (ANN). The topologies of 268 crystal structures were determined using ToposPro software. Quotient graphs were used to identify topological centers and their neighbors. The topological approach was illustrated by training ANN to predict molar heat capacity, standard molar entropy and lattice energy of 268 crystals with different compositions and structures (metals, inorganic salts, oxides, etc.). ANN was trained using Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. Mean absolute percentage error of predicted properties was ≤8 %. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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.

  9. Crystal structure of thermally reversible maltodextrin gels

    Energy Technology Data Exchange (ETDEWEB)

    Reuther, F.; Schierbaum, F. (Akademie der Wissenschaften der DDR, Potsdam. Zentralinstitut fuer Ernaehrung); Gernat, C.; Damaschun, G. (Akademie der Wissenschaften der DDR, Berlin. Zentralinstitut fuer Molekularbiologie)

    1983-10-05

    Aqueous solutions of starch solidify at room temperature to form thermally irreversible gels. These gels exhibit the wide angle X-ray pattern of B-starch. In thermally reversible gels of a special digestion product of starch the B-pattern of starch is also observed. The property of thermal reversibility therefore is not due to amorphous or different crystalline structures, but is a consequence of smaller macromolecules.

  10. Synthesis, crystal structure and EPR spectra of tetraaquabis(methylisonicotinate) copper(II) disaccharinate single crystal

    Science.gov (United States)

    Çelik, Yunus; Bozkurt, Esat; Uçar, İbrahim; Karabulut, Bünyamin

    2011-10-01

    The crystal structure of the [Cu(mein)2(H2O)4]·(sac)2 complex (mein: methylisonicotinate, sac: saccharine) was investigated by single crystal X-ray diffraction technique. The vibrational spectrum was also discussed in relation with the other compounds containing methylisonicotinate and saccharinate complexes. The EPR spectra of [Cu(mein)2(H2O)4]·(sac)2 single crystal have been studied in the temperature range between 113 and 300 K in three mutually perpendicular planes and exhibit two sets of four hyperfine lines of Cu2+ ion. The ground state wave function of the Cu2+ ion is an admixture of dx2-y2 and dz2 states.

  11. Ultrafast investigations of slow light in photonic crystal structures

    NARCIS (Netherlands)

    Engelen, Rob Jacques Paul

    2008-01-01

    Optical structures with dimensions down to nanometer length scales have been a topic for investigation for an increasing number of researchers, due to their intriguing physical properties and their possible new optical applications. In this thesis, waveguides in two-dimensional photonic crystals are

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

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 40; Issue 6. Effect of domains configuration on crystal structure in ferroelectric ceramics as revealed by XRD and dielectric spectrum. JIWEN XU WEIDONG ZENG QINGNING LI LING YANG CHANGRONG ZHOU. Volume 40 Issue 6 October 2017 pp 1159-1163 ...

  13. synthesis and crystal structure of trinuclear potassium(i)

    African Journals Online (AJOL)

    water molecule. In the crystal structure, intra- and intermolecular hydrogen bonding interactions as well as weak ... high nitrogen content, high energy density, good thermal stability, and low melting point [1–6]. ... as, nitramine or tetrazole-functionalized based furazan had been investigated and were found to have shown.

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

    Indian Academy of Sciences (India)

    A new 1D polymeric copper(II) complex [{Cu(L)(CF3COO)}2]n has been synthesized using a potentially tetradentate Schiff base ... 1D copper(II) polymer; Schiff base; crystal structure; electrochemistry; EPR; magnetic properties. 1. Introduction ... number of copper(II) poly-clusters/assemblies may be mentioned in this regard ...

  15. synthesis, crystal structure and antimicrobial activity of a hetero ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    cyanide N atom. The effects of the complex on the antimicrobial activity against Staphylococcus aureus,. Escherichia coli, and Candida albicans were studied. KEY WORDS: Schiff base, Manganese(III) complex, Iron(II) complex, Heteronuclear, Crystal structure. INTRODUCTION. Schiff bases are a kind of important ligands ...

  16. Zinc (II) complexes of carboxamide derivatives: Crystal structures ...

    Indian Academy of Sciences (India)

    The two complexes were characterized by physicochemical and spectroscopic tools, and by X-ray crystal structures of both ligands and the complex 1. In complex 1, zinc(II) is chelated by three ligands with a distorted octahedral geometry. The DNA-binding properties of zinc complexes 1 and 2 have been investigated by ...

  17. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    DOI 10.1007/s12039-015-0978-8. Synthesis, characterization, X-ray crystal structure, electrochemical evaluation and anti-cancer studies of a mixed ligand Cu(II) complex of (E)-N -((2-hydroxynaphthalen-1-yl)methylene)acetohydrazide. IRAN SHEIKHSHOAIEa, S YOUSEF EBRAHIMIPOURa,∗, MAHDIEH SHEIKHSHOAIEa,.

  18. Theoretical study on the molecular and crystal structures of nitrogen ...

    Indian Academy of Sciences (India)

    mainly contributed by the p orbital of N atom and the valence band (HOCO) from the p orbital of F atom. Keywords. Molecular; crystal; structure; property; theoretical study. 1. Introduction ... the global search was confined to these groups only. By analyzing the simulation trajectory of molecular packing within seven space ...

  19. Structural stability and theoretical strength of Cu crystal under equal ...

    Indian Academy of Sciences (India)

    Thus, the Cu film becomes unstable and even changes its morphologies which affects the device manufacturing yield and ultimate reliability. The structural stability and theoretical strength of Cu crystal under equal biaxial loading have been investigated by combining the MAEAM with Milstein-modified Born stability criteria.

  20. Synthesis and Crystal Structures of New 5,5'-Azotetrazolates

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2012-03-01

    Full Text Available Five new 5,5'-azotetrazolate salts (amminsilver, trimethylsulfonium, tetramethyl-phosphonium, trimethylsulfoxonium, 2-(hydroxyethyltrimethylammonium were prepared and characterized. The crystal structures were determined by X-ray diffraction. Interactions between the ions are identified and discussed. The sensitivities of the highly energetic silver salt were measured by BAM (Bundesanstalt für Materialforschung und-prüfung methods.

  1. A new method to reconstruct the structure from crystal images

    NARCIS (Netherlands)

    Li, Y

    2017-01-01

    Biological molecules, especially the proteins, have a special and important function. We study their structure to understand their functions, and further make application, like the medical research. The routine method is diffraction, but not work for molecules which cannot grow into crystal and

  2. Crystal structures and atomic model of NADPH oxidase

    NARCIS (Netherlands)

    Magnani, Francesca; Nenci, Simone; Fananas, Elisa Millana; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W.; Mattevi, Andrea

    2017-01-01

    NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic

  3. 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 of the...

  4. Synthesis, crystal structure and catecholase activity of a Ni (II ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 6. Synthesis, crystal structure and ... The title complex 1 behaves as an effective catalyst towards oxidation of 3,5-ditertiarybutyl catechol (3,5-DTBC) in acetonitrile to its corresponding quinone derivative in air. The reaction follows first-order reaction kinetics ...

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 6. 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.

  6. Syntheses, characterization and crystal structures of potassium and ...

    Indian Academy of Sciences (India)

    Syntheses, characterization and crystal structures of potassium and barium complexes of a Schiff base ligand with different anions. Bhavesh Parmar Kamal Kumar Bisht Pratyush Maiti Parimal Paul Eringathodi Suresh. Special issue on Chemical Crystallography Volume 126 Issue 5 September 2014 pp 1373-1384 ...

  7. Synthesis and crystal structure of trinuclear potassium(I) complex ...

    African Journals Online (AJOL)

    A furazan-based trinuclear potassium(I) complex derived from the oxy-bridged bis(gem-dinitro)furazan (OBNF) and triaminoguanidinium (TGA) units was synthesized and characterized by elemental analyses, nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy. The single crystal X-ray structure of the ...

  8. Syntheses, characterization and crystal structures of potassium and ...

    Indian Academy of Sciences (India)

    Syntheses, characterization and crystal structures of potassium and barium complexes of a Schiff base ligand with different anions. BHAVESH PARMARa, KAMAL KUMAR BISHTa,b, PRATYUSH MAITIc, PARIMAL PAULa,b, and ERINGATHODI SURESHa,b,∗. aAnalytical Discipline and Centralized Instrument Facility, ...

  9. 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.

  10. 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.

  11. 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.

  12. Structural evolution in the crystallization of rapid cooling silver melt

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Z.A., E-mail: ze.tian@gmail.com [School of Physics and Electronics, Hunan University, Changsha 410082 (China); Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052 (Australia); Dong, K.J.; Yu, A.B. [Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052 (Australia)

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  13. Crystal structure of 1-methylimidazole 3-oxide monohydrate

    Directory of Open Access Journals (Sweden)

    Christopher S. Frampton

    2017-03-01

    Full Text Available 1-Methylimidazole 3-N-oxide (NMI-O crystallizes as a monohydrate, C4H6N2O·H2O, in the monoclinic space group P21 with Z′ = 2 (molecules A and B. The imidazole rings display a planar geometry (r.m.s. deviations = 0.0008 and 0.0002 Å and are linked in the crystal structure into infinite zigzag strands of ...NMI-O(A...OH2...NMI-O(B...OH2... units by O—H...O hydrogen bonds. These chains propagate along the b-axis direction of the unit cell.

  14. A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

    Science.gov (United States)

    Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

    2017-12-01

    Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

  15. Crystal Structure of Triosephosphate Isomerase from Trypanosoma cruzi in Hexane

    Science.gov (United States)

    Gao, Xiu-Gong; Maldonado, Ernesto; Perez-Montfort, Ruy; Garza-Ramos, Georgina; Tuena de Gomez-Puyou, Marietta; Gomez-Puyou, Armando; Rodriguez-Romero, Adela

    1999-08-01

    To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2- angstrom resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 angstrom from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.

  16. 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.

  17. 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...

  18. Intermetallic crystal structures as foams. Beyond Frank-Kasper.

    Science.gov (United States)

    Bonneau, Charlotte; O'Keeffe, Michael

    2015-02-02

    In many intermetallic structures, the atoms and bonds divide space into tilings by tetrahedra. The well-known Frank-Kasper phases are examples. The dual tilings divide space into a tiling by polyhedra that is topologically a foam. The number of faces of the dual polyhedron corresponds to the atom coordination number in the direct structure, and face sharing by adjacent polyhedra corresponds to bonds in the direct structure. A number of commonly occurring intermetallic crystal structures are shown as their duals. A major advantage of this alternative mode of depiction is that coordination of all of the atoms can be seen simultaneously.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Shuhua; Chen, Yanfeng [Nanjing Univ. (China). Dept. of Materials Science and Engineering; Hu, Xiaobo; Yan, Tan; Liu, Hong; Wang, Jiyang [Shandong Univ., Jinan (China). State Key Lab. of Crystal Materials; Qin, Xiaoyong [Deqing Huaying Electronics Co. (China)

    2010-04-15

    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 {delta}X and {delta}Y 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 {l_brace}01 anti 1 anti 2{r_brace}{sub m} planes is the composition face of the twin and matrix crystals. The formation mechanism of these twins is discussed. (orig.)

  20. Is the methanation reaction over Ru single crystals structure dependent?

    Science.gov (United States)

    Vendelbo, Søren B; Johansson, Martin; Nielsen, Jane H; Chorkendorff, Ib

    2011-03-14

    The influence of monoatomic steps and defects on the methanation reaction over ruthenium has been investigated. The experiments are performed on a Ru(0 1 54) ruthenium single crystal, which contains one monoatomic step atom for each 27 terrace atoms. The methanation activity is measured at one bar of hydrogen and CO in a high pressure cell, which enables simultaneous measurements of the local reactivity of the well defined single crystal surface and the global reactivity of the entire crystal and its auxiliary support. By adding sulfur we observe that the measured activity from the well defined stepped front-side of the crystal is poisoned faster than the entire crystal containing more defects. We also observe that additional sputtering of the well-defined front-side increases the reactivity measured on the surface. Based on this, we conclude that the methanation reaction takes place on undercoordinated sites, such as steps and kinks, and that the methanation reaction is extremely structure dependent. Simulations of the flow, temperature, and product distributions in the high pressure cell are furthermore presented as supplementary information.

  1. Two new bismuth thiourea bromides: crystal structure, growth, and characterization.

    Science.gov (United States)

    Li, Ming; Li, R K

    2014-02-14

    Crystals of two new bismuth thiourea bromides, bismuth trithiourea bromide (Bi[CS(NH2)2]3Br3, BTB) and bismuth protonated-hexathiourea bromide (Bi[CS(NH2)2H]6Br9, BHB), have been successfully grown from hydrobromic acid solution with different pH values by slow evaporation. Single crystal X-ray diffraction reveals that BTB is isostructural to its Cl-analog crystallizing in a monoclinic space group Cc with unit cell dimensions of a = 8.6238(7) Å, b = 12.2506(11) Å, c = 15.5040(13) Å, β = 90.7810(10)° and Z = 4. In contrast, BHB crystallizes in a trigonal space group R3[combining macron]c with unit cell dimensions of a = b = 12.748(17) Å, c = 40.45(11) Å, and Z = 6. The protonation of the thiourea in BHB is confirmed by the structure solution, IR and Raman spectroscopy. The UV diffuse reflection spectra clearly indicate that both of the two crystals have good optical transparency in the range below 2000 nm. Both compounds decompose above 190 °C, and BHB melts at around 140 °C while BTB possesses a phase transition at 145 °C as indicated by thermogravimetric (TG) and differential thermal analysis (DTA).

  2. Crystal structure and mechanistic investigation of the twister ribozyme.

    Science.gov (United States)

    Liu, Yijin; Wilson, Timothy J; McPhee, Scott A; Lilley, David M J

    2014-09-01

    We present a crystal structure at 2.3-Å resolution of the recently described nucleolytic ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a double-pseudoknot structure, with the active site at its center. Eight highly conserved nucleobases stabilize the core of the ribozyme through the formation of one Watson-Crick and three noncanonical base pairs, and the highly conserved adenine 3' of the scissile phosphate is bound in the major groove of an adjacent pseudoknot. A strongly conserved guanine nucleobase directs its Watson-Crick edge toward the scissile phosphate in the crystal structure, and mechanistic evidence supports a role for this guanine as either a general base or acid in a concerted, general acid-base-catalyzed cleavage reaction.

  3. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  4. Intermolecular force field development and crystal structure prediction

    Science.gov (United States)

    Gao, Daquan

    1998-11-01

    Chapter 1 is a general introduction for the following chapters that include three journal articles. Chapter 2 deals with force field development about a particular compound, Cl2. The crystal structure of Cl2 has been simulated by an isotropic force field that includes polar flattening of the Cl atom and a 5-center distributed monopole model. Polar flattening is achieved by moving the repulsion center toward the molecular center, which induces the short contact. The 5- center distributed monopole represents the molecular electrical potential that dictates the molecular orientation in the cell. This intermolecular force field can approximate the correct space group symmetry of solid state chlorine. Chapter 3 reports the implementation of a systematic way of developing intermolecular force field parameters. Intermolecular atom-atom force field parameters of the (exp-6-1) type for boron and hydrogen atoms in boron hydrides were determined. Using the resulting force field, minimum energy crystal structures were found with structural parameter values close to those of the observed structures. Chapter 4 discusses the new finding on space groups. Relationships between space groups, molecular symmetry and site symmetry, and molecular packing groups are treated. The number of molecules in the cell, Z, is the same as the order of the molecular packing group. The order of the space group is equal to or greater than Z depending upon the site symmetry of the molecular position. Several examples of application of this packing group treatment to ab initio crystal structure predictions are given.

  5. Rigidity analysis of protein biological assemblies and periodic crystal structures

    Science.gov (United States)

    2013-01-01

    Background We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu. Results We provide two types of results: on biological assemblies and on crystals. We found that when only isolated subchains are considered, structural and functional information may be missed. Indeed, the rigidity of biological assemblies is sometimes dependent on the count and placement of hydrogen bonds and other interactions among the individual subchains of the biological unit. Similarly, the rigidity of small crystals may be affected by the interactions between atoms belonging to different unit cells. We have analyzed a dataset of approximately 300 proteins, from which we generated 982 crystals (some of which are biological assemblies). We identified two types of behaviors. (a) Some crystals and/or biological assemblies will aggregate into rigid bodies that span multiple unit cells/asymmetric units. Some of them create substantially larger rigid cluster in the crystal/biological assembly form, while in other cases, the aggregation has a smaller effect just at the interface between the units. (b) In other cases, the rigidity properties of the asymmetric units are retained, because the rigid bodies did not combine. We also identified two interesting cases where rigidity analysis may be correlated with the functional behavior of the protein. This type of information, identified here for the first time, depends critically on the ability to create crystals and biological assemblies

  6. Crystal structure of 8-hydroxyquinoline: a new monoclinic polymorph

    Directory of Open Access Journals (Sweden)

    Raúl Castañeda

    2014-09-01

    Full Text Available In an attempt to grow 8-hydroxyquinoline–acetaminophen co-crystals from equimolar amounts of conformers in a chloroform–ethanol solvent mixture at room temperature, the title compound, C9H7NO, was obtained. The molecule is planar, with the hydroxy H atom forming an intramolecular O—H...N hydrogen bond. In the crystal, molecules form centrosymmetric dimers via two O—H...N hydrogen bonds. Thus, the hydroxy H atoms are involved in bifurcated O—H...N hydrogen bonds, leading to the formation of a central planar four-membered N2H2 ring. The dimers are bound by intermolecular π–π stacking [the shortest C...C distance is 3.2997 (17 Å] and C—H...π interactions into a three-dimensional framework. The crystal grown represents a new monoclinic polymorph in the space group P21/n. The molecular structure of the present monoclinic polymorph is very similar to that of the orthorhombic polymorph (space group Fdd2 studied previously [Roychowdhury et al. (1978. Acta Cryst. B34, 1047–1048; Banerjee & Saha (1986. Acta Cryst. C42, 1408–1411]. The structures of the two polymorphs are distinguished by the different geometries of the hydrogen-bonded dimers, which in the crystal of the orthorhombic polymorph possess twofold axis symmetry, with the central N2H2 ring adopting a butterfly conformation.

  7. Crystal growth, crystal structure, vibrational spectroscopy, linear and nonlinear optical properties of guanidinium phosphates

    Science.gov (United States)

    Němec, Ivan; Matulková, Irena; Held, Peter; Kroupa, Jan; Němec, Petr; Li, Dongxu; Bohatý, Ladislav; Becker, Petra

    2017-07-01

    Of the three guanidinium phosphates GuH2PO4 (space group P21/c), Gu2HPO4·H2O (space group P 4 bar 21 c) and Gu3PO4· 3/2 H2O (space group Cc) crystal structures and a vibrational spectroscopy study are presented. Large single crystals of GuH2PO4 and Gu2HPO4·H2O are grown. Refractive indices and their dispersion in the wavelength range 365 nm - 1083 nm are determined and used for the analysis of phase matching conditions for collinear SHG in the case of the non-centrosymmetric crystals of Gu2HPO4·H2O. The crystals are not phase-matchable within their transmission range. Both independent components of the SHG tensor of Gu2HPO4·H2O, determined by the Maker fringe method, are given, with d14 = 0.23 pm/V and d36 = 0.22 pm/V. In addition, the thermal stability and the anisotropy of thermal expansion of GuH2PO4 and Gu2HPO4·H2O is reported.

  8. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  9. 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.

  10. 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

    2015-11-14

    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 Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

  11. 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.

  12. Structural evolution in the crystallization of rapid cooling silver melt

    Science.gov (United States)

    Tian, Z. A.; Dong, K. J.; Yu, A. B.

    2015-03-01

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald's rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid-solid phase transition.

  13. 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].

  14. Structural investigation of cooperite (PtS) crystals

    Energy Technology Data Exchange (ETDEWEB)

    Rozhdestvina, V. I., E-mail: veronika@ascnet.ru [Russian Academy of Sciences, Institute of Geology and Nature Management, Far East Branch (Russian Federation); Udovenko, A. A. [Russian Academy of Sciences, Institute of Chemistry, Far East Branch (Russian Federation); Rubanov, S. V. [University of Melbourne, Bio21 Institute (Australia); Mudrovskaya, N. V. [Russian Academy of Sciences, Institute of Geology and Nature Management, Far East Branch (Russian Federation)

    2016-03-15

    The single-crystal structure of cooperite, a natural platinum sulfide PtS, is studied by X-ray diffraction supported by high-resolution scanning transmission electron microscopy and X-ray spectrum microanalysis. It is found that, in addition to the main reflections corresponding to the known tetragonal cell (a = 3.47 and c = 6.11 Å; space group P4{sub 2}/mmc), many weak reflections with intensities I ≤ 60σ(I) are clearly observed. These reflections fit the tetragonal cell (space group I4/mmm) with doubled parameters. In structures with small (P4{sub 2}/mmc) and large (I4/mmm) cells, the S atoms occupy statistically two special positions. It is shown that the chemical composition of the cooperite crystals deviates from the stoichiometric composition: sulfur-deficient specimens predominate.

  15. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatezinc

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-03-01

    Full Text Available The ZnII atom in the title complex, [ZnCl2(C4H6N2S22], is coordinated in a distorted tetrahedral manner by two Cl atoms and two terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. In the crystal, the complex molecules are connected through C—H...Cl hydrogen bonds and Cl...S contacts, leading to a two-dimensional structure extending parallel to the ab plane.

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

    Indian Academy of Sciences (India)

    acid bridged coordination polymer of Copper(II) ... Keywords. o-Phthalic acid; coordination polymer; X-ray crystal structure; Copper(II); EPR; TGA. 1. .... 3.2 EPR spectrum of. [{Cu(O2C-μ2-C6H5-μ1-CO2)2}.2H2O]n. The EPR spectrum of the complex was recorded as polycrystalline solid and has been shown in figure 1.

  17. 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.

  18. Synthesis and crystal structure of a trihydrate of dinuclear ...

    African Journals Online (AJOL)

    A new compound, [Cd2(C7H6N2)3(C6H4O2N)4]·3H2O (1), has been prepared under mild hydrothermal conditions and structurally characterized by single crystal X-ray diffraction. The two cadmium(II) ions are bridged by a carboxyl group from one 2-pyridinecarboxylate ligand. The thermal gravimetry (TG) data indicate ...

  19. 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...

  20. Crystal Structures of the β2-Adrenergic Receptor

    Science.gov (United States)

    Weis, William I.; Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Yao, Xiao-Jie; Day, Peter W.; Parnot, Charles; Fung, Juan J.; Ratnala, Venkata R. P.; Kobilka, Brian K.; Cherezov, Vadim; Hanson, Michael A.; Kuhn, Peter; Stevens, Raymond C.; Edwards, Patricia C.; Schertler, Gebhard F. X.; Burghammer, Manfred; Sanishvili, Ruslan; Fischetti, Robert F.; Masood, Asna; Rohrer, Daniel K.

    G protein coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome, and are responsible for the majority of signal transduction events involving hormones and neuro-transmitters across the cell membrane. GPCRs that bind to diffusible ligands have low natural abundance, are relatively unstable in detergents, and display basal G protein activation even in the absence of ligands. To overcome these problems two approaches were taken to obtain crystal structures of the β2-adrenergic receptor (β2AR), a well-characterized GPCR that binds cate-cholamine hormones. The receptor was bound to the partial inverse agonist carazolol and co-crystallized with a Fab made to a three-dimensional epitope formed by the third intracellular loop (ICL3), or by replacement of ICL3 with T4 lysozyme. Small crystals were obtained in lipid bicelles (β2AR-Fab) or lipidic cubic phase (β2AR-T4 lysozyme), and diffraction data were obtained using microfocus technology. The structures provide insights into the basal activity of the receptor, the structural features that enable binding of diffusible ligands, and the coupling between ligand binding and G-protein activation.

  1. Crystal structures of two (±-exo-N-isobornylacetamides

    Directory of Open Access Journals (Sweden)

    Dmitrijs Stepanovs

    2015-10-01

    Full Text Available The title compounds consist of a bornane skeleton with attached acetamide, C12H21NO (±-(1 {systematic name: (±-N-[(1RS,2RS,4RS-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl]acetamide}, and chloroacetamide, C12H20ClNO (±-(2 {systematic name: (±-2-chloro-N-[(1RS,2RS,4RS-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl]acetamide}, functionalities to the 2-exo-position. The crystal structure of the first monoclinic polymorph of (±-(1 has been reported previously [Ung et al. (2014. Monatsh. Chem. 145, 983–992]. Compound (±-(1 crystallizes in the space group P21/n with two independent molecules in the asymmetric unit, in contrast to the above-mentioned polymorph which crystallized in the space group C2/c with one molecule in the asymmetric unit. In the title compounds, the bicyclic bornane moieties have normal geometries. In the crystals of both compounds, molecules are linked by N—H...O hydrogen bonds, reinforced by C—H...O contacts, forming trans-amide chains propagating along the a-axis direction. In the case of compound (±-(1, neighbouring chains are linked by further C—H...O contacts, forming double-chain ribbons along [100].

  2. Crystal structures of two (±)-exo-N-isobornyl-acetamides.

    Science.gov (United States)

    Stepanovs, Dmitrijs; Posevins, Daniels; Turks, Maris

    2015-10-01

    The title compounds consist of a bornane skeleton with attached acetamide, C12H21NO (±)-(1) {systematic name: (±)-N-[(1RS,2RS,4RS)-1,7,7-tri-methylbi-cyclo-[2.2.1]heptan-2-yl]acetamide}, and chloro-acetamide, C12H20ClNO (±)-(2) {systematic name: (±)-2-chloro-N-[(1RS,2RS,4RS)-1,7,7-tri-methylbi-cyclo-[2.2.1]heptan-2-yl]-acetamide}, functionalities to the 2-exo-position. The crystal structure of the first monoclinic polymorph of (±)-(1) has been reported previously [Ung et al. (2014 ▸). Monatsh. Chem. 145, 983-992]. Compound (±)-(1) crystallizes in the space group P21/n with two independent mol-ecules in the asymmetric unit, in contrast to the above-mentioned polymorph which crystallized in the space group C2/c with one mol-ecule in the asymmetric unit. In the title compounds, the bicyclic bornane moieties have normal geometries. In the crystals of both compounds, mol-ecules are linked by N-H⋯O hydrogen bonds, reinforced by C-H⋯O contacts, forming trans-amide chains propagating along the a-axis direction. In the case of compound (±)-(1), neighbouring chains are linked by further C-H⋯O contacts, forming double-chain ribbons along [100].

  3. Crystal structure of human cytochrome P450 2D6.

    Science.gov (United States)

    Rowland, Paul; Blaney, Frank E; Smyth, Martin G; Jones, Jo J; Leydon, Vaughan R; Oxbrow, Amanda K; Lewis, Ceri J; Tennant, Mike G; Modi, Sandeep; Eggleston, Drake S; Chenery, Richard J; Bridges, Angela M

    2006-03-17

    Cytochrome P450 2D6 is a heme-containing enzyme that is responsible for the metabolism of at least 20% of known drugs. Substrates of 2D6 typically contain a basic nitrogen and a planar aromatic ring. The crystal structure of human 2D6 has been solved and refined to 3.0A resolution. The structure shows the characteristic P450 fold as seen in other members of the family, with the lengths and orientations of the individual secondary structural elements being very similar to those seen in 2C9. There are, however, several important differences, the most notable involving the F helix, the F-G loop, the B'helix, beta sheet 4, and part of beta sheet 1, all of which are situated on the distal face of the protein. The 2D6 structure has a well defined active site cavity above the heme group, containing many important residues that have been implicated in substrate recognition and binding, including Asp-301, Glu-216, Phe-483, and Phe-120. The crystal structure helps to explain how Asp-301, Glu-216, and Phe-483 can act as substrate binding residues and suggests that the role of Phe-120 is to control the orientation of the aromatic ring found in most substrates with respect to the heme. The structure has been compared with published homology models and has been used to explain much of the reported site-directed mutagenesis data and help understand the metabolism of several compounds.

  4. Crystal structure, thermal behavior and enzymatic degradation of poly(tetramethylene adipate) solution-grown chain-folded lamellar crystals.

    Science.gov (United States)

    Iwata, Tadahisa; Kobayashi, Shiomi; Tabata, Kenji; Yonezawa, Noriyuki; Doi, Yoshiharu

    2004-03-15

    Solution-grown chain-folded lamellar single crystals of poly(tetramethylene adipate) (PTMA) were prepared from a dilute solution of 2-methyl-1-propanol by isothermal crystallization. PTMA crystals were hexagonal-shaped and polyethylene decoration of the crystals resulted in a "six cross-sector" surface morphology and showed that the average direction of chain folding is parallel to the crystal growth planes of [110] and [010]. Chain-folded lamellar crystals gave well-resolved electron diffraction diagrams corresponding to all the equatorial reflections of the X-ray fiber diagram obtained from stretched PTMA melt-quenched film (beta structure). The unit cell parameters of the beta structure of PTMA were determined as a = 0.503 nm, b = 0.732 nm and c (fiber axis) = 1.442 nm with an orthorhombic crystal system. The fiber repeat distance is appropriate for an all-trans backbone conformation for the straight stems. The setting angle, with respect to the a axis, is +/-46 degrees for the corner and center chains. Thermal behavior of lamellar crystals has been investigated by means of transmission electron microscopy (TEM) and atomic force microscopy (AFM). The lamellar thickness at the edges of the crystal increased after thermal treatment with taking the molecular chains into recrystallization parts; the holes then opened up at the thickening front of the crystal. The morphological changes of lamellar crystals after enzymatic degradation by Lipase type XIII from Pseudomonas sp. and water-soluble products were characterized by TEM, AFM, gel permeation chromatography, high performance liquid chromatography and fast atom bombardment mass spectrometry. The degradation progressed mainly from the edges of the lamellar crystals without decreasing the molecular weights and the lamellar thicknesses. The central portion of single crystals was often degraded by enzymatic attacks. This result combined with thermal behavior indicates that the loosely chain-packing region exists

  5. 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).

  6. Iron-Ion Implantation into the Structure of Rock Crystal

    Directory of Open Access Journals (Sweden)

    A.V. Mukhametshin

    2017-03-01

    Full Text Available Iron ions with the energy of 40 keV have been implanted into colorless natural rock crystals to high fluencies of 1.0∙1017 and 1.5∙1017 ion/cm2. These crystals were selected from Svetlinsky deposits of the Southern Urals, which are well-known as minerals with high quality and low content of impurities. A radical change in the color of the crystals after iron-ion implantation and subsequent high-temperature annealing in air has been revealed. The origin of color changes has been studied by using optical methods, as well as Mössbauer and X-ray photoelectron spectroscopy. It has been established that the high-dose and high-energy flow of ions results in the formation of various kinds of structural defects on the surface layer of the matrix, such as electron-hole centers, as well as in the formation at a specific depth of the irradiated matrix of the ultrafine iron-containing phases with a structure, which is non-coherent to the structure of the original matrix. The subsequent high-temperature annealing of the implanted quartz has changed the color of the samples to orange-yellow. This color is similar to the color of natural citrine. The orange color richness of the heat-treated samples grew with increasing amounts of embedded iron impurity in the crystal. The nature of orange-yellow coloration of the implanted and annealed quartz plates can be explained by the formation of ultrafine hematite nanoparticles located in a layer at a depth of ~15 nm. The possibility of refining the color of minerals by ion-beam exposure has been discussed.

  7. crystal and magnetic structure of substituted lanthanum cobaltites

    NARCIS (Netherlands)

    Sonntag, R.; Neov, S.; Kozhukharov, V.; Neov, D.; ten Elshof, Johan E.

    1999-01-01

    The crystal and magnetic structures of the lanthanum cobaltites La0.6Sr0.4CoO3, La0.6Sr0.4Co0.9Fe0.1O3 and La0.6Ba0.4Co0.9Fe0.1O3 have been studied by neutron powder diffraction at temperatures of 2, 300 and 900 K. All compounds undergo a phase transition from cubic to rhombohedral structure. Below

  8. Fusion proteins as alternate crystallization paths to difficult structure problems

    Science.gov (United States)

    Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

    1994-01-01

    The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

  9. Advances in Nanophotonics: Active Photonic Crystal Structures and Devices

    DEFF Research Database (Denmark)

    Hvam, Jørn Märcher

    The nanostructuring of optical materials may significantly alter their optical and optoelectronic properties. Structuring on a length scale well below the wavelength of light may create new artificial atoms (quantum dots) or new effective media (metamaterials) that may be designed to have (optical......) properties that do not exist in nature. Periodic structuring on the length scale of the wavelength of light as in photonic crystals, on the other hand, dramatically influences the propagation of light as well as the fundamental interaction between light and matter. In this talk, I shall discuss some...... important consequences on spontaneous emission and lasing as well as some aspects of slow light and nonlinear interactions....

  10. Band structures in the nematic elastomers phononic crystals

    Science.gov (United States)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    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.

  11. Crystal chemistry and electrical properties of the delafossite structure

    Energy Technology Data Exchange (ETDEWEB)

    Marquardt, Meagen A. [Materials Science and Engineering Department, Iowa State University, 2220 Hoover Hall Ames, IA 50011 (United States); Ashmore, Nathan A. [Materials Science and Engineering Department, Iowa State University, 2220 Hoover Hall Ames, IA 50011 (United States); Cann, David P. [Materials Science and Engineering Department, Iowa State University, 2220 Hoover Hall Ames, IA 50011 (United States)]. E-mail: BaTiO3@iastate.edu

    2006-02-01

    Over the past few decades, the field of transparent conducting oxides has undergone tremendous advances. With the rapid growth of optoelectronic applications related to display technologies, traditional materials such as Sn-doped indium oxide (ITO) are now widely used as transparent electrodes. In addition, with the advent of p-type transparent conductors, through the transparent pn-junction building block, a wide range of functional transparent optoelectronic devices have been demonstrated including UV-emitting diodes, UV-detectors, and transparent thin film transistors. This paper will highlight the unique characteristics of oxide materials based on the delafossite structure with a focus on the interrelationship between the chemistry, crystal structure, process conditions, and electrical and optical properties. The delafossite structure (ABO{sub 2}) is characterized by a layer of linearly coordinated A cations stacked between edge-shared octahedral layers (BO{sub 6}). The A-site cation is comprised of Pt, Pd, Ag, or Cu ions nominally in a monovalent state. The B-site cation can consist of most trivalent transition metals, group III elements, rare earths, or charge compensated pairs (e.g. B{sup 2+}/B{sup 4+}). This layered structure leads to highly anisotropic physical properties. The crystal chemistry of the delafossite structure will be discussed in reference to phase stability, the stability of dopants, and the important physical properties such as the conductivity and optical transparency.

  12. Crystal structure of the Fe-member of usovite

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2015-06-01

    Full Text Available Crystals of the title compound, with the idealized composition Ba2CaFeAl2F14, dibarium calcium iron(II dialuminium tetradecafluoride, were obtained serendipitously by reacting a mixture of the binary fluorides BaF2, CaF2 and AlF3 in a leaky steel reactor. The compound crystallizes in the usovite structure type (Ba2CaMgAl2F14, with Fe2+ cations replacing the Mg2+ cations. The principal building units are distorted [CaF8] square-antiprisms (point group symmetry 2, [FeF6] octahedra (point group symmetry -1 and [AlF6] octahedra that are condensed into undulating 2∞[CaFeAl2F14]4− layers parallel (100. The Ba2+ cations separate the layers and exhibit a coordination number of 12. Two crystal structure models with a different treatment of the disordered Fe site [mixed Fe/Ca occupation, model (I, versus underoccupation of Fe, model (II], are discussed, leading to different refined formulae Ba2Ca1.310 (15Fe0.690 (15Al2F14 [model (I] and Ba2CaFe0.90 (1Al2F14 [model (II].

  13. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    Science.gov (United States)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain

  14. 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.

  15. Crystal structure and magnetism of UOsAl

    Science.gov (United States)

    Andreev, A. V.; Daniš, S.; Šebek, J.; Henriques, M. S.; Vejpravová, J.; Gorbunov, D. I.; Havela, L.

    2017-04-01

    Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn2 type, space group P63/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*10-8 m3 mol-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-1 K-2.

  16. Crystal structure of 2,5-dimethylanilinium hydrogen maleate

    Directory of Open Access Journals (Sweden)

    Maha Mathlouthi

    2014-11-01

    Full Text Available The crystal structure of the title salt, C8H12N+·C4H3O4−, consists of a 2,5-dimethylanilinium cation and an hydrogen maleate anion. In the anion, a strong intramolecular O—H...O hydrogen bond is observed, leading to an S(7 graph-set motif. In the crystal, the cations and anions pack in alternating layers parallel to (001. The ammonium group undergoes intermolecular N—H...O hydrogen-bonding interactions with the O atoms of three different hydrogen maleate anions. This results in the formation of ribbons extending parallel to [010] with hydrogen-bonding motifs of the types R44(12 and R44(18.

  17. 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.

  18. 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.

  19. Crystal Structure and Carbonate Species into Structure of Hydroxyapatite

    OpenAIRE

    元上, 康孝; 管野, 亨; 小林, 正義; 赤澤, 敏之; MOTOGAMI, Yasutaka; KANNO, Tohru; Kobayashi, Masayoshi; Akazawa, Toshiyuki

    1998-01-01

    The morphology of hydroxyapatite (HAp) had a significant effect on carbonates incorporated into HAp structures. A cattle bone-originated HAp (r-HAp) had two carbonates, OH-substituted and P04- substituted, and chemically synthesized HAp (s-HAp) had only the latter carbonate. This difference was ascribed to the increased calcium deficiency of r-HAp. Partial substitution of Sr for Ca caused expansion of the P-O bond and subjected the HAp structure to stress. This stress decreased the decomposit...

  20. Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii

    Energy Technology Data Exchange (ETDEWEB)

    Khiang, C.; Seetharaman, J; Kasprzak, J; Cherlyn, N; Patel, B; Love, C; Bujnicki, J; Sivaraman, J

    2010-01-01

    Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of D-fructose to D-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrix orenii (Hore{_}18220 in sequence databases). The structure of the Hore{_}18220 protein reveals a catalytic domain with a Rossmann-like fold and a b-sheet 'lid' for dimerization. Based on comparison of Hore{_}18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore{_}18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

  1. Crystal structure of mimivirus uracil-DNA glycosylase.

    Science.gov (United States)

    Kwon, Eunju; Pathak, Deepak; Chang, Hyeun Wook; Kim, Dong Young

    2017-01-01

    Cytosine deamination induced by stresses or enzymatic catalysis converts deoxycytidine into deoxyuridine, thereby introducing a G to A mutation after DNA replication. Base-excision repair to correct uracil to cytosine is initiated by uracil-DNA glycosylase (UDG), which recognizes and eliminates uracil from DNA. Mimivirus, one of the largest known viruses, also encodes a distinctive UDG gene containing a long N-terminal domain (N-domain; residues 1-130) and a motif-I (residues 327-343), in addition to the canonical catalytic domain of family I UDGs (also called UNGs). To understand the structural and functional features of the additional segments, we have determined the crystal structure of UNG from Acanthamoeba polyphaga mimivirus (mvUNG). In the crystal structure of mvUNG, residues 95-130 in the N-domain bind to a hydrophobic groove in the catalytic domain, and motif-I forms a short β-sheet with a positively charged surface near the active site. Circular dichroism spectra showed that residues 1-94 are in a random coil conformation. Deletion of the three additional fragments reduced the activity and thermal stability, compared to full-length mvUNG. The results suggested that the mvUNG N-domain and motif-I are required for its structural and functional integrity.

  2. 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.

  3. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    Energy Technology Data Exchange (ETDEWEB)

    Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.; Fremont, Daved H. (WU-MED)

    2012-03-13

    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-{angstrom} 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.

  4. Structural chemistry and number theory amalgamized: crystal structure of Na11Hg52.

    Science.gov (United States)

    Hornfeck, Wolfgang; Hoch, Constantin

    2015-12-01

    The recently elucidated crystal structure of the technologically important amalgam Na11Hg52 is described by means of a method employing some fundamental concept of number theory, namely modular arithmetical (congruence) relations observed between a slightly idealized set of atomic coordinates. In combination with well known ideas from group theory, regarding lattice-sublattice transformations, these allow for a deeper mutual understanding of both and provide the structural chemist with a slightly different kind of spectacles, thus enabling a distinct viw on complex crystal structures in general.

  5. Crystal structures of deprotonated nucleobases from an expanded DNA alphabet.

    Science.gov (United States)

    Matsuura, Mariko F; Kim, Hyo Joong; Takahashi, Daisuke; Abboud, Khalil A; Benner, Steven A

    2016-12-01

    Reported here is the crystal structure of a heterocycle that implements a donor-donor-acceptor hydrogen-bonding pattern, as found in the Z component [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine-pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ6-2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ido)sodium]-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1)], denoted Z-Sod, {[Na(C5H4N3O3)(H2O)]·C5H5N3O3·H2O}n, and ammonium 2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ide-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1), denoted Z-Am, NH4+·C5H4N3O3-·C5H5N3O3·H2O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.

  6. Crystal structures of ethylene glycol and ethylene glycol monohydrate.

    Science.gov (United States)

    Fortes, A Dominic; Suard, Emmanuelle

    2011-12-21

    We have carried out a neutron powder diffraction study of deuterated ethylene glycol (1,2-ethanediol), and deuterated ethylene glycol monohydrate with the D2B high-resolution diffractometer at the Institut Laue-Langevin. Using these data, we have refined the complete structure, including all hydrogen atoms, of the anhydrous phase at 220 K. In addition, we have determined the structure of ethylene glycol monohydrate at 210 K using direct space methods. Anhydrous ethylene glycol crystallizes in space-group P2(1)2(1)2(1) with four formula units in a unit-cell of dimensions a = 5.0553(1) Å, b = 6.9627(1) Å, c = 9.2709(2) Å, and V = 326.319(8) Å(3) [ρ(calc)(deuterated) = 1386.26(3) kg m(-3)] at 220 K. Ethylene glycol monohydrate crystallizes in space-group P2(1)/c with four formula units in a unit-cell of dimensions a = 7.6858(3) Å, b = 7.2201(3) Å, c = 7.7356(4) Å, β = 92.868(3)°, and V = 428.73(2) Å(3) [ρ(calc)(deuterated) = 1365.40(7) kg m(-3)] at 210 K. Both the structures are characterized by the gauche conformation of the ethylene glycol molecule; however, the anhydrous phase contains the tGg' rotamer (or its mirror, g'Gt), whereas the monohydrate contains the gGg' rotamer. In the monohydrate, each water molecule is tetrahedrally coordinated, donating two hydrogen bonds to, and accepting two hydrogen bonds from the hydroxyl groups of neighboring ethylene glycol molecules. There are substantial differences in the degree of weak C-D···O hydrogen bonding between the two crystals, which calls into question the role of these interactions in determining the conformation of the ethylene glycol molecule.

  7. 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).

  8. All-Optical Reconstruction of Crystal Band Structure.

    Science.gov (United States)

    Vampa, G; Hammond, T J; Thiré, N; Schmidt, B E; Légaré, F; McDonald, C R; Brabec, T; Klug, D D; Corkum, P B

    2015-11-06

    The band structure of matter determines its properties. In solids, it is typically mapped with angle-resolved photoemission spectroscopy, in which the momentum and the energy of incoherent electrons are independently measured. Sometimes, however, photoelectrons are difficult or impossible to detect. Here we demonstrate an all-optical technique to reconstruct momentum-dependent band gaps by exploiting the coherent motion of electron-hole pairs driven by intense midinfrared femtosecond laser pulses. Applying the method to experimental data for a semiconductor ZnO crystal, we identify the split-off valence band as making the greatest contribution to tunneling to the conduction band. Our new band structure measurement technique is intrinsically bulk sensitive, does not require a vacuum, and has high temporal resolution, making it suitable to study reactions at ambient conditions, matter under extreme pressures, and ultrafast transient modifications to band structures.

  9. 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...

  10. 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.

  11. Crystal structure of rofecoxib bound to human cyclooxygenase-2

    Energy Technology Data Exchange (ETDEWEB)

    Orlando, Benjamin J.; Malkowski, Michael G. (Buffalo)

    2016-10-26

    Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization conditions were identified that allowed the structural determination of human COX-2 in complex with Vioxx and the structure was subsequently determined to 2.7- Å resolution. The crystal structure provides the first atomic level details of the binding of Vioxx to COX-2. As anticipated, Vioxx binds with its methyl sulfone moiety located in the side pocket of the cyclooxygenase channel, providing support for the isoform selectivity of this drug.

  12. 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.

  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 structures of two (±)-exo-N-isobornylacetamides

    OpenAIRE

    Dmitrijs Stepanovs; Daniels Posevins; Maris Turks

    2015-01-01

    The title compounds consist of a bornane skeleton with attached acetamide, C12H21NO (?)-(1) {systematic name: (?)-N-[(1RS,2RS,4RS)-1,7,7-tri?methylbi?cyclo?[2.2.1]heptan-2-yl]acetamide}, and chloro?acetamide, C12H20ClNO (?)-(2) {systematic name: (?)-2-chloro-N-[(1RS,2RS,4RS)-1,7,7-tri?methylbi?cyclo?[2.2.1]heptan-2-yl]?acetamide}, functionalities to the 2-exo-position. The crystal structure of the first monoclinic polymorph of (?)-(1) has been reported previously [Ung et al. (2014 ?). Monatsh...

  15. Crystal structure of human tooth enamel studied by neutron diffraction

    Science.gov (United States)

    Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

    2015-02-01

    Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

  16. Crystal structure of tris(piperidinium hydrogen sulfate sulfate

    Directory of Open Access Journals (Sweden)

    Tamara J. Lukianova

    2015-12-01

    Full Text Available In the title molecular salt, 3C5H12N+·HSO4−·SO42−, each cation adopts a chair conformation. In the crystal, the hydrogen sulfate ion is connected to the sulfate ion by a strong O—H...O hydrogen bond. The packing also features a number of N—H...O hydrogen bonds, which lead to a three-dimensional network structure. The hydrogen sulfate anion accepts four hydrogen bonds from two cations, whereas the sulfate ion, as an acceptor, binds to five separate piperidinium cations, forming seven hydrogen bonds.

  17. Finite Element Modeling of Acoustic Shielding via Phononic Crystal structures

    OpenAIRE

    Lipp, Clémentine Sophie Sarah; Lozzi, Andrea

    2016-01-01

    Quality factor of Contour Mode Resonators (CMR) are mainly affected by energy losses due to acoustic waves leaving the resonator through the anchors. An engineering of the anchors in order to create a periodic variation in the acoustic impedance of the material, structures known as Phononic Crystals (PnCs), can help improve the Q factor by reflecting part of the acoustic waves. During this project, FEM models have been validated for both 1D and 2D PnCs. The behavior of the band diagram and qu...

  18. Observations on structural features and characteristics of biological apatite crystals. 8. Observation on fusion of human enamel crystals.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-12-01

    In a series of studies to investigate the basic structural features and characteristics of the biological apatite crystals, using a transmission electron microscope, we examined the ultrastructure of the human enamel, dentin, and bone crystals at near atomic resolution and showed the configuration of the hydroxyapatite structure through the cross and longitudinal sections of the crystals. Subsequently, based on the results of the observations by the authors of the ultrastructure of the tooth and bone, using the same approach, we have been able to directly examine the images of the lattice imperfections in the human tooth and bone crystals, such as the point defect structure, line defect, and face defect, in the crystals. In this report, we describe the images of the crystal fusion obtained by using the same approach from the sections of the human enamel crystals. The materials used for this study were the noncarious enamel from the freshly extracted human erupted lower first molars. The small cubes of the material were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with the HITACHI H-800 H and H-9000 type transmission electron microscopes operated at 200 kV and 300 kV. Each crystal was observed at an initial magnification of 300,000 times and at a final magnification of 10,000,000 times and over. We are, therefore, able to confirm that the fusion between the adjacent crystals can occur at some time during the life history of the human enamel. We sincerely believe that the electron micrographs shown in this report are the first to show the ultrastructures of the crystal fusion in the human enamel crystals at near atomic resolution.

  19. Crystal Initiation Structures in Developing Enamel: Possible Implications for Caries Dissolution of Enamel Crystals

    Directory of Open Access Journals (Sweden)

    Colin Robinson

    2017-06-01

    Full Text Available Investigations of developing enamel crystals using Atomic and Chemical Force Microscopy (AFM, CFM have revealed a subunit structure. Subunits were seen in height images as collinear swellings about 30 nM in diameter on crystal surfaces. In friction mode they were visible as positive regions. These were similar in size (30–50 nM to collinear spherical structures, presumably mineral matrix complexes, seen in developing enamel using a freeze fracturing/freeze etching procedure. More detailed AFM studies on mature enamel suggested that the 30–50 nM structures were composed of smaller units, ~10–15 nM in diameter. These were clustered in hexagonal or perhaps a spiral arrangement. It was suggested that these could be the imprints of initiation sites for mineral precipitation. The investigation aimed at examining original freeze etched images at high resolution to see if the smaller subunits observed using AFM in mature enamel were also present in developing enamel i.e., before loss of the organic matrix. The method used was freeze etching. Briefly samples of developing rat enamel were rapidly frozen, fractured under vacuum, and ice sublimed from the fractured surface. The fractured surface was shadowed with platinum or gold and the metal replica subjected to high resolution TEM. For AFM studies high-resolution tapping mode imaging of human mature enamel sections was performed in air under ambient conditions at a point midway between the cusp and the cervical margin. Both AFM and freeze etch studies showed structures 30–50 nM in diameter. AFM indicated that these may be clusters of somewhat smaller structures ~10–15 nM maybe hexagonally or spirally arranged. High resolution freeze etching images of very early enamel showed ~30–50 nM spherical structures in a disordered arrangement. No smaller units at 10–15 nM were clearly seen. However, when linear arrangements of 30–50 nM units were visible the picture was more complex but also

  20. Crystal structure of zwitterionic 4-(ammoniomethylbenzoate: a simple molecule giving rise to a complex supramolecular structure

    Directory of Open Access Journals (Sweden)

    Ana María Atria

    2014-11-01

    Full Text Available The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammoniomethylbenzoate zwitterion derived from 4-aminomethylbenzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15. In the crystal structure, N—H...O hydrogen bonds together with π–π stacking of the benzene rings [centroid–centroid distance = 3.8602 (18 Å] result in a strongly linked, compact three-dimensional structure.

  1. Crystal Structure and Dielectric Property of Bismuth Layer-Structured Dielectric Films with c-Axis Preferential Crystal Orientation

    Science.gov (United States)

    Mizutani, Yuki; Kiguchi, Takanori; Konno, Toyohiko J.; Funakubo, Hiroshi; Uchida, Hiroshi

    2010-09-01

    Thin films of bismuth layer-structured dielectrics (BLSDs), CaBi4Ti4O15, and SrBi4Ti4O15, were prepared by a chemical solution deposition (CSD) technique on various substrates, such as (111)Pt/TiO2/(100)Si, (100)LaNiO3/(111)Pt/TiO2/(100)Si, and (100)SrRuO3∥(100)SrTiO3 substrates. Conductive perovskite oxide LaNiO3 with (100) preferential crystal orientation was introduced into the interface between the BLSD film and the (111)Pt/TiO2/(100)Si substrate to control the crystal orientation of BLSD by lattice matching between pseudo-perovskite blocks in the BLSD crystal and the (100)LaNiO3 plane with the perovskite structure. The (00l) planes of BLSD crystals were preferentially oriented on the substrate surface of the (100)LaNiO3/(111)Pt/TiO2/(100)Si, whereas randomly-oriented BLSD crystals with lower crystallinity were only obtained on the surface of (111)Pt/TiO2/(100)Si substrate. The (001)-oriented BLSD films exhibited the leakage current densities below 10-7 A/cm2 at ±50 kV/cm, which is significantly lower than those for randomly-oriented films, above 10-6 A/cm2, The room-temperature dielectric constants (ɛr) of CaBi4Ti4O15 and SrBi4Ti4O15 thin films on the (100)LaNiO3/(111)Pt/TiO2/(100)Si substrate were both approximately 250, while those on the (100)SrRuO3∥(100)SrTiO3 substrate were approximately 220. The temperature dependence of the capacitances for the CaBi4Ti4O15 and SrBi4Ti4O15 films on the (100)LaNiO3/(111)Pt/TiO2/(100)Si substrate were approximately +17 and +10%, respectively, in the temperature range from 25 to 400 °C. These values were slightly larger than those of epitaxial BLSD films, but smaller than those of (Ba,Sr)TiO3 films.

  2. Oxoglaucine-lanthanide complexes: synthesis, crystal structure and cytotoxicity.

    Science.gov (United States)

    Liu, Yan-Cheng; Chen, Zhen-Feng; Shi, Yan-Fang; Huang, Ke-Bin; Geng, Bo; Liang, Hong

    2014-01-01

    To evaluate the in vitro cytotoxicity of oxoglaucine (OG) complexes: [Sm(OG)2(NO3)3]•H2O (1), [Eu(OG)2(NO3)3]•1.5CH3OH (2) and [Er(OG)2(NO3)3]•H2O (3) through comparison to oxoglaucine and lanthanide salts. The reactions of OG with corresponding lanthanide salts gave rise to complexes 1-3. The crystal structures of complexes 1-3 were determined by single-crystal X-ray diffraction analysis. The in vitro cytotoxicity of oxoglaucine and complexes 1-3 against five human cancer cell lines were evaluated by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl tetrazolium Bromide (MTT) method. Complexes 1-3 have similar mononuclear structures. The 50% inhibitory concentration (IC50) of complex 1 against SGC7901 cells was 32.1 μM; that of complex 2 against MCF-7 cells was 3.2 μM; those of complex 3 on HeLa and MCF-7 cells were 8.3 and 1.4 μM, respectively. The three OG-lanthanide complexes exhibited significantly enhanced cytotoxicity vs. OG and corresponding lanthanide salts.

  3. 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.

  4. Crystal structures of vortioxetine and its methanol monosolvate

    Directory of Open Access Journals (Sweden)

    Xin-Bo Zhou

    2015-08-01

    Full Text Available Vortioxetine, C18H22N2S, (1, systematic name 1-{2-[(2,4-dimethylphenylsulfanyl]phenyl}piperazine, a new drug used to treat patients with major depressive disorder, has been crystallized as the free base and its methanol monosolvate, C18H22N2S·CH3OH, (2. In both structures, the vortioxetine molecules have similar conformations: in (1, the dihedral angle between the aromatic rings is 80.04 (16° and in (2 it is 84.94 (13°. The C—S—C bond angle in (1 is 102.76 (14° and the corresponding angle in (2 is 103.41 (11°. The piperazine ring adopts a chair conformation with the exocyclic N—C bond in a pseudo-equatorial orientation in both structures. No directional interactions beyond normal van der Waals contacts could be identified in the crystal of (1, whereas in (2, the vortioxetine and methanol molecules are linked by N—H...O and O—H...N hydrogen bonds, generating [001] chains.

  5. 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...

  6. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  7. Crystal structure of Li3Ga(BO32

    Directory of Open Access Journals (Sweden)

    Robert W. Smith

    2017-03-01

    Full Text Available The crystal structure of trilithium gallium bis(orthoborate, Li3Ga(BO32, is isotypic with Li3Al(BO32 in a triclinic cell in space-group type P-1. The three Li and the unique Ga atom are coordinated by four O atoms each in tetrahedra, and the two B atoms are coordinated by three O atoms in orthoborate triangles. Chains with composition [Ga2(BO34]6− extend along the a axis. The Li atoms interleave these chains in tetrahedral interstices. A comparison is made between the structure model of the title compound and that of a previously reported model for a compound with the same composition [Abdullaev & Mamedov (1972. Zh. Strukt. Khim. 13, 943–946.

  8. Crystal structure of erioflorin isolated from Podanthus mitiqui (L.

    Directory of Open Access Journals (Sweden)

    Cristian Paz

    2017-03-01

    Full Text Available The title compound, erioflorin, C19H24O6 [systematic name: (1aR,3S,4Z,5aR,8aR,9R,10aR-1a,2,3,5a,7,8,8a,9,10,10a-decahydro-3-hydroxy-4,10a-dimethyl-8-methylidene-7-oxooxireno[5,6]cyclodeca[1,2-b]furan-9-yl methacrylate], is a tricyclic germacrane sesquiterpene lactone, which was isolated from Podanthus mitiqui (L.. The compound crystallizes in the space group P212121, and its molecular structure consists of a methacrylic ester of a ten-membered ring sesquiterpenoid annelated with an epoxide and a butyrolactone. The structure is stabilized by one intramolecular C—H...O hydrogen bond. An O—H...O hydrogen bond and further C—H...O interactions can be observed in the packing.

  9. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    Science.gov (United States)

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  10. The crystal structure of loparite: a new acentric variety

    Science.gov (United States)

    Popova, Elena A.; Lushnikov, Sergey G.; Yakovenchuk, Victor N.; Krivovichev, Sergey V.

    2017-12-01

    The crystal structure of a new structural variety of loparite (Na0.56Ce0.21La0.14Ca0.06Sr0.03Nd0.02Pr0.01)Σ=1.03(Ti0.83Nb0.15)Σ=0.98O3 from the Khibiny alkaline massif, Kola peninsula, Russia, was solved by direct methods and refined to R 1 = 0.029 for 492 unique observed reflections with I > 2σ( I). The mineral is orthorhombic, Ima2, a = 5.5129(2), b = 5.5129(2) and c = 7.7874(5) Å. Similarly to other perovskite-group minerals with the general formula ABO3, the crystal structure of loparite is based upon a three-dimensional framework of distorted corner-sharing BO6. The A cations are coordinated by 12 oxygen atoms and are situated in distorted cuboctahedral cavities. In contrast to the ideal perovskite-type structure ( Pm\\overset{-}{3} m ), the unit cell is doubled along the c axis and the a and b axes are rotated in the ab plane at 45o. The BO6 octahedron displays distortion characteristic for the d 0 transition metal cations with the out-of-center shift of the B site. The symmetry reduction is also attributable to the distortion of the BO6 octahedra which are tilted and rotated with respect to the c axis. The occurrence of a new acentric variety of loparite can be explained by the pecularities of its chemical composition characterized by the increased content of Ti compared to the previously studied samples.

  11. Optical switching of near infrared light transmission in metamaterial-liquid crystal cell structure.

    Science.gov (United States)

    Kang, Boyoung; Woo, J H; Choi, E; Lee, Hyun-Hee; Kim, E S; Kim, J; Hwang, Tae-Jong; Park, Young-Soon; Kim, D H; Wu, J W

    2010-08-02

    A metamaterial-liquid crystal cell structure is fabricated with the metamaterial as one of the liquid crystal alignment layers. Nano-sized double-split ring resonator in the metamaterial accommodates two distinct resonances in the near infrared regime. By adopting an azo-nematic liquid crystal in a twisted nematic liquid crystal cell structure, a photo-isomerization process is utilized to achieve an optical switching of light transmissions between two resonances. A single device of the metamaterial-liquid crystal cell structure has a potential application in the photonic switching in optical fiber telecommunications.

  12. Crystal structures of strontium and lead dithionate tetrahydrate

    Energy Technology Data Exchange (ETDEWEB)

    Matos Gomes, E. de (Oxford Univ. (UK). Clarendon Lab.)

    1991-02-01

    SrS{sub 2}O{sub 6}.4H{sub 2}O, M{sub r} = 319x8, hexagonal, P6{sub 4}22, a = 6x3529(9), c = 19x218 (3) A, V = 671x71 A{sup 3}, D{sub x} = 2x373 g cm{sup -3}, Z = 3, Mo K{alpha} radiation, {lambda} = 0x71069 A, {mu} = 59x93 cm{sup -1}, F(000) = 474, room temperature, R = 0x040 for 336 unique observed reflections. PbS{sub 2}O{sub 6}.4H{sub 2}O, M{sub r} = 439x4, hexagonal, P622, a = 6x3413 (9), c = 6x4622 A, V = 225x04 A{sup 3}, D{sub x} = 3x22 g cm{sup -3}, Z = 1, Mo K{alpha} radiation, {lambda} = 0x71069 A, {mu} = 193x56 cm{sup -1}, F(000) = 202, room temperature, R = 0x015 for 144 unique observed reflections. The crystal structure and absolute optical chirality of strontium dithionate tetrahydrate, SrS{sub 2}O{sub 6}.4H{sub 2}O, and lead dithionate tetrahydrate, PbS{sub 2}O{sub 6}.4H{sub 2}O, have been determined at room temperature by a combination of single-crystal X-ray diffraction, taking account of anomalous scattering, and optical measurements. The structure of SrS{sub 2}O{sub 6}.4H{sub 2}O is disordered about the twofold axis along (110). Disorder arises from the fact that the S{sub 2}O{sub 6}{sup 2-} ion occupies two sites on either side of this axis. The space group P6{sub 4}22 has been assigned to a dextrorotatory crystal. PbS{sub 2}O{sub 6}.4H{sub 2}O is a substructure of SrS{sub 2}O{sub 6}.4H{sub 2}O with a c axis three times smaller. The S{sub 2}O{sub 6}{sup 2-} ion is disordered at two sites on either side of (110) plus three sites around (001). The water O atoms occupy three sites around (001). The space group P622 has been assigned to a laevorotatory crystal. (orig.).

  13. Crystal structure of the human glucose transporter GLUT1

    Science.gov (United States)

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-01

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  14. Water polygons in high-resolution protein crystal structures

    Science.gov (United States)

    Lee, Jonas; Kim, Sung-Hou

    2009-01-01

    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 Å 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. PMID:19551896

  15. Crystal structure of dihydroorotate dehydrogenase from Leishmania major.

    Science.gov (United States)

    Cordeiro, Artur T; Feliciano, Patricia R; Pinheiro, Matheus P; Nonato, M Cristina

    2012-08-01

    Dihydroorotate dehydrogenase (DHODH) is the fourth enzyme in the de novo pyrimidine biosynthetic pathway and has been exploited as the target for therapy against proliferative and parasitic diseases. In this study, we report the crystal structures of DHODH from Leishmania major, the species of Leishmania associated with zoonotic cutaneous leishmaniasis, in its apo form and in complex with orotate and fumarate molecules. Both orotate and fumarate were found to bind to the same active site and exploit similar interactions, consistent with a ping-pong mechanism described for class 1A DHODHs. Analysis of LmDHODH structures reveals that rearrangements in the conformation of the catalytic loop have direct influence on the dimeric interface. This is the first structural evidence of a relationship between the dimeric form and the catalytic mechanism. According to our analysis, the high sequence and structural similarity observed among trypanosomatid DHODH suggest that a single strategy of structure-based inhibitor design can be used to validate DHODH as a druggable target against multiple neglected tropical diseases such as Leishmaniasis, Sleeping sickness and Chagas' diseases. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  16. 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.

  17. 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.

  18. Crystal Structure of the Human Cytomegalovirus Glycoprotein B.

    Directory of Open Access Journals (Sweden)

    Heidi G Burke

    2015-10-01

    Full Text Available Human cytomegalovirus (HCMV, a dsDNA, enveloped virus, is a ubiquitous pathogen that establishes lifelong latent infections and caused disease in persons with compromised immune systems, e.g., organ transplant recipients or AIDS patients. HCMV is also a leading cause of congenital viral infections in newborns. Entry of HCMV into cells requires the conserved glycoprotein B (gB, thought to function as a fusogen and reported to bind signaling receptors. gB also elicits a strong immune response in humans and induces the production of neutralizing antibodies although most anti-gB Abs are non-neutralizing. Here, we report the crystal structure of the HCMV gB ectodomain determined to 3.6-Å resolution, which is the first atomic-level structure of any betaherpesvirus glycoprotein. The structure of HCMV gB resembles the postfusion structures of HSV-1 and EBV homologs, establishing it as a new member of the class III viral fusogens. Despite structural similarities, each gB has a unique domain arrangement, demonstrating structural plasticity of gB that may accommodate virus-specific functional requirements. The structure illustrates how extensive glycosylation of the gB ectodomain influences antibody recognition. Antigenic sites that elicit neutralizing antibodies are more heavily glycosylated than those that elicit non-neutralizing antibodies, which suggest that HCMV gB uses glycans to shield neutralizing epitopes while exposing non-neutralizing epitopes. This glycosylation pattern may have evolved to direct the immune response towards generation of non-neutralizing antibodies thus helping HCMV to avoid clearance. HCMV gB structure provides a starting point for elucidation of its antigenic and immunogenic properties and aid in the design of recombinant vaccines and monoclonal antibody therapies.

  19. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Li, Fenglei [Iowa State Univ., Ames, IA (United States)

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  20. Crystal growth, electronic structure and luminescence properties of Nb/Yb co-doped RbTiOPO4 crystals

    Science.gov (United States)

    Liu, Jian; Li, Ziqing; Zhu, Pengfei; Duan, Xiulan

    2018-01-01

    Nb/Yb co-doped RbTiOPO4 (RTP) crystals were successfully grown by a top-seeded solution growth method from two different kinds of flux systems. 5%Nb/3%Yb: RTP crystal with more transparency was obtained from the mixed solvent containing MoO3. The chemical composition was analyzed by Electron Probe Microanalyzer (EPMA), and the result indicated that co-doping of Nb and Yb into RTP can greatly increase the concentration of Yb in RTP crystal. The addition of MoO3 into self-flux system can improve the quality of as-grown crystals, but it is not helpful to introduce Yb into crystal. The electronic structures of Nb/Yb: RTP crystals were analyzed using X-ray photoelectron spectra (XPS). The results show that the binding energy difference between O 1s and P 2p levels (ΔBE (O-P)) increases firstly with the increase of Yb content, and then decreases with Nb content increasing, which is associated with the covalency change of O-P bonds in crystals. However, the doping has little influence on the chemical bond properties of O-Ti. The FL spectra of Nb/Yb: RbTiOPO4 crystals were also analyzed, and five emission peaks characteristic of Yb3+ ions were observed.

  1. Synthesis, structure, crystal growth and characterization of a novel semiorganic nonlinear optical L-proline lithium bromide monohydrate single crystal

    Science.gov (United States)

    Sathiskumar, S.; Balakrishnan, T.; Ramamurthi, K.; Thamotharan, S.

    2015-03-01

    L-Proline lithium bromide monohydrate (LPLBM), a promising semiorganic nonlinear optical material, was synthesized and single crystals of LPLBM were grown from solution by slow evaporation technique. Single crystal X-ray structure solution reveals that the grown crystal belongs to monoclinic system with space group P21. Presence of various functional groups was identified by FT-IR and FT-Raman spectral analyses. UV-Vis-NIR spectroscopic study shows that the LPLBM crystal possesses 90% of transmittance in the range of 250-1100 nm. Vickers microhardness values, the dielectric constant and dielectric loss of the LPLBM crystal were reported. Elemental analysis by energy dispersive X-ray analysis shows the presence of carbon, nitrogen, oxygen and bromine. The surface morphology of the crystal was investigated using scanning electron microscopic study. The thermal stability of the LPLBM crystal was studied from TGA and DSC analysis. Second harmonic generation efficiency of the LPLBM crystal measured by Kurtz and Perry powder technique using Nd:YAG laser is about 0.3 times that of urea.

  2. Interface induced crystal structures of dioctyl-terthiophene thin films.

    Science.gov (United States)

    Werzer, Oliver; Boucher, Nicolas; de Silva, Johann P; Gbabode, Gabin; Geerts, Yves H; Konovalov, Oleg; Moser, Armin; Novak, Jiri; Resel, Roland; Sferrazza, Michele

    2012-06-05

    Temperature dependent structural and morphological investigations on semiconducting dioctyl-terthiophene (DOTT) thin films prepared on silica surfaces reveals the coexistence of surface induce order and distinct crystalline/liquid crystalline bulk polymorphs. X-ray diffraction and scanning force microscopy measurements indicate that at room temperature two polymorphs are present: the surface induced phase grows directly on the silica interface and the bulk phase on top. At elevated temperatures the long-range order gradually decreases, and the crystal G (340 K), smectic F (348 K), and smectic C (360 K) phases are observed. Indexation of diffraction peaks reveals that an up-right standing conformation of DOTT molecules is present within all phases. A temperature stable interfacial layer close to the silica-DOTT interface acts as template for the formation of the different phases. Rapid cooling of the DOTT sample from the smectic C phase to room temperature results in freezing into a metastable crystalline state with an intermediated unit cell between the room temperature crystalline phase and the smectic C phase. The understanding of such interfacial induced phases in thin semiconducting liquid crystal films allows tuning of crystallographic and therefore physical properties within organic thin films.

  3. 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.

  4. In situ X-ray crystallographic study of the structural evolution of colloidal crystals upon heating

    NARCIS (Netherlands)

    Zozulya, A.V.; Meijer, J.M.; Shabalin, A.; Ricci, A.; Westermeier, F.; Kurta, R.P.; Lorenz, U.; Singer, A.; Yefanow, O.; Petukhov, A.V.; Sprung, M.; Vartanyants, I. A.

    2013-01-01

    The structural evolution of colloidal crystals made of polystyrene hard spheres has been studied in situ upon incremental heating of a crystal in a temperature range below and above the glass transition temperature of polystyrene. Thin films of colloidal crystals having different particle sizes were

  5. Synthesis and single crystal structure analysis of 3,3',5,5'-tetramethyl ...

    African Journals Online (AJOL)

    The asymmetric units consist of tetrahedral [CoCl4]2- anions and tetramethyl bipyrazolium [H2Me4bpz]2+ dications and one water molecule which are connected through N—H····Cl and N—H····O hydrogen bond networks in the crystal lattice. Keywords: Crystal structure, Hydrogen bond and crystal engineering ...

  6. 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.

  7. Crystal Structure of the Human Cannabinoid Receptor CB1.

    Science.gov (United States)

    Hua, Tian; Vemuri, Kiran; Pu, Mengchen; Qu, Lu; Han, Gye Won; Wu, Yiran; Zhao, Suwen; Shui, Wenqing; Li, Shanshan; Korde, Anisha; Laprairie, Robert B; Stahl, Edward L; Ho, Jo-Hao; Zvonok, Nikolai; Zhou, Han; Kufareva, Irina; Wu, Beili; Zhao, Qiang; Hanson, Michael A; Bohn, Laura M; Makriyannis, Alexandros; Stevens, Raymond C; Liu, Zhi-Jie

    2016-10-20

    Cannabinoid receptor 1 (CB1) is the principal target of Δ9-tetrahydrocannabinol (THC), a psychoactive chemical from Cannabis sativa with a wide range of therapeutic applications and a long history of recreational use. CB1 is activated by endocannabinoids and is a promising therapeutic target for pain management, inflammation, obesity, and substance abuse disorders. Here, we present the 2.8 Å crystal structure of human CB1 in complex with AM6538, a stabilizing antagonist, synthesized and characterized for this structural study. The structure of the CB1-AM6538 complex reveals key features of the receptor and critical interactions for antagonist binding. In combination with functional studies and molecular modeling, the structure provides insight into the binding mode of naturally occurring CB1 ligands, such as THC, and synthetic cannabinoids. This enhances our understanding of the molecular basis for the physiological functions of CB1 and provides new opportunities for the design of next-generation CB1-targeting pharmaceuticals. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. 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

  9. 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. [...

  10. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis

    DEFF Research Database (Denmark)

    Sprogøe, Desiree; van den Broek, Lambertus A M; Mirza, Osman

    2004-01-01

    ', and C. Domain A comprises the (beta/alpha)(8)-barrel common to family 13. The catalytic active-site residues (Asp192 and Glu232) are located at the tips of beta-sheets 4 and 5 in the (beta/alpha)(8)-barrel, as required for family 13 members. The topology of the B' domain disfavors oligosaccharide......Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and alpha-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose...... binding and reduces the size of the substrate access channel compared to other family 13 members, underlining the role of this domain in modulating the function of these enzymes. It is remarkable that the fold of the C domain is not observed in any other known hydrolases of family 13. BiSP was found...

  11. 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)

  12. Crystal structure and electrical conductivity of imidazolium succinate

    Energy Technology Data Exchange (ETDEWEB)

    Pogorzelec-Glaser, K.; Pawlaczyk, C.; Markiewicz, E. [Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznan (Poland); Pietraszko, A. [Institute of Low Temperature and Structure Research, Okolna 2, 50-422 Wroclaw (Poland)

    2007-11-15

    Small single crystals of the imidazolium succinate were grown and their structure was re-examined using the X-ray diffraction method and a probable protonic conduction mechanism has been proposed. The electric conductivity of the powdered tablets was measured using the impedance spectroscopy method. The range of obtained values of conductivity as well as the activation energy (0.65 eV) of the imidazolium succinate is close to these of imidazolium malonate and imidazolium glutarate investigated previously [K. Pogorzelec-Glaser, J. Garbarczyk, Cz. Pawlaczyk, E. Markiewicz, Materials Science Poland 24 (2006) 245-253]. Metastable and virtual positions for proton transfer were indicated by means of calculations of the atomic displacement factors and the probability density function. (author)

  13. 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.

  14. 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.

  15. 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.

  16. Crystal structure of tris(ethylenediammonium hexasulfatopraseodymium(III hexahydrate

    Directory of Open Access Journals (Sweden)

    Peter Held

    2014-10-01

    Full Text Available In the title salt, (C2H10N23[Pr2(SO46]·6H2O, the PrIII cation is surrounded ninefold by five sulfate groups (two monodentate and three chelating and by one water molecule [range of Pr—O bond lengths 2.383 (3 to 2.582 (3 Å]. The [Pr(SO45(H2O] groups are arranged in sheets parallel to (010. Two crystal water molecules and two ethylenediammonium cations (one with point group symmetry -1 connect the sheets via O—H...O and N—H...O hydrogen bonds from weak up to medium strength into a three-dimensional framework structure.

  17. Systematic conformational bias in small-molecule crystal structures is rare and explicable

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.; Liebeschuetz, J.W.; Allen, F.H.

    2012-01-01

    Analysis of the Cambridge Structural Database, together with DFT and crystal structure prediction calculations, show that the observation of higher-energy planar conformers of biphenyl (BP) and cyclobutane (CB) is possible because of improved intermolecular interactions in their crystal structures.

  18. Structure determination from a single high-pressure-frozen virus crystal.

    Science.gov (United States)

    Burkhardt, Anja; Wagner, Armin; Warmer, Martin; Reimer, Rudolph; Hohenberg, Heinrich; Ren, Jingshan; Fry, Elizabeth E; Stuart, David I; Meents, Alke

    2013-02-01

    Successful cryogenic X-ray structure determination from a single high-pressure-frozen bovine enterovirus 2 crystal is reported. The presented high-pressure-freezing procedure is based on a commercially available device and allows the cryocooling of macromolecular crystals directly in their mother liquor without the time- and crystal-consuming search for optimal cryoconditions. The method is generally applicable and will allow cryogenic data collection from all types of macromolecular crystals.

  19. Crystal growth and structural analysis of zirconium sulphoselenide ...

    Indian Academy of Sciences (India)

    The grown crystals were examined under optical zoom microscope for their surface topography study. Hall effect measurements were carried out on grown crystals at room temperature. The negative value of Hall coefficient implies that these crystals are -type in nature. The conductivity is found to decrease with increase of ...

  20. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

    Science.gov (United States)

    Totir, Monica; Echols, Nathaniel; Nanao, Max; Gee, Christine L; Moskaleva, Alisa; Gradia, Scott; Iavarone, Anthony T; Berger, James M; May, Andrew P; Zubieta, Chloe; Alber, Tom

    2012-01-01

    Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.

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

    Science.gov (United States)

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

    2017-12-01

    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.

  2. Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1

    Directory of Open Access Journals (Sweden)

    Zhou Cong-Zhao

    2007-06-01

    Full Text Available Abstract Background As the third enzyme of the pentose phosphate pathway, 6-phosphogluconate dehydrogenase (6PGDH is the main generator of cellular NADPH. Both thioredoxin reductase and glutathione reductase require NADPH as the electron donor to reduce oxidized thioredoxin or glutathione (GSSG. Since thioredoxin and GSH are important antioxidants, it is not surprising that 6PGDH plays a critical role in protecting cells from oxidative stress. Furthermore the activity of 6PGDH is associated with several human disorders including cancer and Alzheimer's disease. The 3D structural investigation would be very valuable in designing small molecules that target this enzyme for potential therapeutic applications. Results The crystal structure of 6-phosphogluconate dehydrogenase (6PGDH/Gnd1 from Saccharomyces cerevisiae has been determined at 2.37 Å resolution by molecular replacement. The overall structure of Gnd1 is a homodimer with three domains for each monomer, a Rossmann fold NADP+ binding domain, an all-α helical domain contributing the majority to hydrophobic interaction between the two subunits and a small C-terminal domain penetrating the other subunit. In addition, two citrate molecules occupied the 6PG binding pocket of each monomer. The intact Gnd1 had a Km of 50 ± 9 μM for 6-phosphogluconate and of 35 ± 6 μM for NADP+ at pH 7.5. But the truncated mutants without the C-terminal 35, 39 or 53 residues of Gnd1 completely lost their 6PGDH activity, despite remaining the homodimer in solution. Conclusion The overall tertiary structure of Gnd1 is similar to those of 6PGDH from other species. The substrate and coenzyme binding sites are well conserved, either from the primary sequence alignment, or from the 3D structural superposition. Enzymatic activity assays suggest a sequential mechanism of catalysis, which is in agreement with previous studies. The C-terminal domain of Gnd1 functions as a hook to further tighten the dimer, but it is not

  3. Chemical composition, crystal structure, and their relationships with the intrinsic properties of spinel-type crystals based on bond valences.

    Science.gov (United States)

    Liu, Xiao; Wang, Hao; Lavina, Barbara; Tu, Bingtian; Wang, Weimin; Fu, Zhengyi

    2014-06-16

    Spinel-type crystals may possess complex and versatile chemical composition and crystal structure, which leads to difficulty in constructing relationships among the chemical composition, crystal structure, and intrinsic properties. In this work, we develop new empirical methods based on bond valences to estimate the intrinsic properties, namely, compressibility and thermal expansion of complex spinel-type crystals. The composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra is derived as a function of the composition-weighted average of bond valences, which can be calculated according to the experimental chemical composition and crystal structural parameters. We discuss the coupled effects of tetrahedral and octahedral frameworks on the aforementioned intrinsic properties. The bulk modulus could be quantitatively calculated from the composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra. In contrast, a quantitative estimation of the thermal expansion coefficient could be obtained from the composition-weighted average of bond force constants in octahedral coordination polyhedra. These empirical methods have been validated by the results obtained for a new complex quaternary spinel-type oxynitride Mg0.268Al2.577O3.733N0.267 as well as MgAl2O4 and Al2.85O3.45N0.55 from the literature. Further, these empirical methods have the potential to be extensively applied in other types of complex crystals.

  4. Crystal structure of the channelrhodopsin light-gated cation channel

    Science.gov (United States)

    Kato, Hideaki E.; Zhang, Feng; Yizhar, Ofer; Ramakrishnan, Charu; Nishizawa, Tomohiro; Hirata, Kunio; Ito, Jumpei; Aita, Yusuke; Tsukazaki, Tomoya; Hayashi, Shigehiko; Hegemann, Peter; Maturana, Andrés D.; Ishitani, Ryuichiro; Deisseroth, Karl; Nureki, Osamu

    2014-01-01

    Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 Å resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties. PMID:22266941

  5. Crystal structures of the TRIC trimeric intracellular cation channel orthologues.

    Science.gov (United States)

    Kasuya, Go; Hiraizumi, Masahiro; Maturana, Andrés D; Kumazaki, Kaoru; Fujiwara, Yuichiro; Liu, Keihong; Nakada-Nakura, Yoshiko; Iwata, So; Tsukada, Keisuke; Komori, Tomotaka; Uemura, Sotaro; Goto, Yuhei; Nakane, Takanori; Takemoto, Mizuki; Kato, Hideaki E; Yamashita, Keitaro; Wada, Miki; Ito, Koichi; Ishitani, Ryuichiro; Hattori, Motoyuki; Nureki, Osamu

    2016-12-01

    Ca 2+ release from the sarcoplasmic reticulum (SR) and endoplasmic reticulum (ER) is crucial for muscle contraction, cell growth, apoptosis, learning and memory. The trimeric intracellular cation (TRIC) channels were recently identified as cation channels balancing the SR and ER membrane potentials, and are implicated in Ca 2+ signaling and homeostasis. Here we present the crystal structures of prokaryotic TRIC channels in the closed state and structure-based functional analyses of prokaryotic and eukaryotic TRIC channels. Each trimer subunit consists of seven transmembrane (TM) helices with two inverted repeated regions. The electrophysiological, biochemical and biophysical analyses revealed that TRIC channels possess an ion-conducting pore within each subunit, and that the trimer formation contributes to the stability of the protein. The symmetrically related TM2 and TM5 helices are kinked at the conserved glycine clusters, and these kinks are important for the channel activity. Furthermore, the kinks of the TM2 and TM5 helices generate lateral fenestrations at each subunit interface. Unexpectedly, these lateral fenestrations are occupied with lipid molecules. This study provides the structural and functional framework for the molecular mechanism of this ion channel superfamily.

  6. 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.

  7. Crystal structure of a core spliceosomal protein interface

    Science.gov (United States)

    Schellenberg, Matthew J.; Edwards, Ross A.; Ritchie, Dustin B.; Kent, Oliver A.; Golas, Monika M.; Stark, Holger; Lührmann, Reinhard; Glover, J. N. Mark; MacMillan, Andrew M.

    2006-01-01

    The precise excision of introns from precursor mRNAs (pre-mRNAs) in eukaryotes is accomplished by the spliceosome, a complex assembly containing five small nuclear ribonucleoprotein (snRNP) particles. Human p14, a component of the spliceosomal U2 and U11/U12 snRNPs, has been shown to associate directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. Here we report the 2.5-Å crystal structure of a complex containing p14 and a peptide derived from the p14-associated U2 snRNP component SF3b155. p14 contains an RNA recognition motif (RRM), the surface of which is largely occluded by a C-terminal α-helix and a portion of the SF3b155 peptide. An analysis of RNA·protein crosslinking to wild-type and mutant p14 shows that the branch adenosine directly interacts with a conserved aromatic within a pocket on the surface of the complex. This result, combined with a comparison of the structure with known RRMs and pseudoRRMs as well as model-building by using the electron cryomicroscopy structure of a spliceosomal U11/U12 di-snRNP, suggests that p14·SF3b155 presents a noncanonical surface for RNA recognition at the heart of the mammalian spliceosome. PMID:16432215

  8. Crystal structure of the human σ1 receptor.

    Science.gov (United States)

    Schmidt, Hayden R; Zheng, Sanduo; Gurpinar, Esin; Koehl, Antoine; Manglik, Aashish; Kruse, Andrew C

    2016-04-28

    The human σ1 receptor is an enigmatic endoplasmic-reticulum-resident transmembrane protein implicated in a variety of disorders including depression, drug addiction, and neuropathic pain. Recently, an additional connection to amyotrophic lateral sclerosis has emerged from studies of human genetics and mouse models. Unlike many transmembrane receptors that belong to large, extensively studied families such as G-protein-coupled receptors or ligand-gated ion channels, the σ1 receptor is an evolutionary isolate with no discernible similarity to any other human protein. Despite its increasingly clear importance in human physiology and disease, the molecular architecture of the σ1 receptor and its regulation by drug-like compounds remain poorly defined. Here we report crystal structures of the human σ1 receptor in complex with two chemically divergent ligands, PD144418 and 4-IBP. The structures reveal a trimeric architecture with a single transmembrane domain in each protomer. The carboxy-terminal domain of the receptor shows an extensive flat, hydrophobic membrane-proximal surface, suggesting an intimate association with the cytosolic surface of the endoplasmic reticulum membrane in cells. This domain includes a cupin-like β-barrel with the ligand-binding site buried at its centre. This large, hydrophobic ligand-binding cavity shows remarkable plasticity in ligand recognition, binding the two ligands in similar positions despite dissimilar chemical structures. Taken together, these results reveal the overall architecture, oligomerization state, and molecular basis for ligand recognition by this important but poorly understood protein.

  9. Crystal structure of the RNA component of bacterial ribonuclease P

    Energy Technology Data Exchange (ETDEWEB)

    Torres-Larios, Alfredo; Swinger, Kerren K.; Krasilnikov, Andrey S.; Pan, Tao; Mondragon, Alfonso (NWU); (UC)

    2010-03-08

    Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 {angstrom} resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

  10. Crystal structure of inhibitor of ;#954;B kinase [beta

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Guozhou; Lo, Yu-Chih; Li, Qiubai; Napolitano, Gennaro; Wu, Xuefeng; Jiang, Xuliang; Dreano, Michel; Karin, Michael; Wu, Hao (Weill-Med); (Merck-Serono); (UCSD); (EMD Serono)

    2011-07-26

    Inhibitor of {kappa}B (I{kappa}B) kinase (IKK) phosphorylates I{kappa}B proteins, leading to their degradation and the liberation of nuclear factor {kappa}B for gene transcription. Here we report the crystal structure of IKK{beta} in complex with an inhibitor, at a resolution of 3.6 {angstrom}. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, {alpha}-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix-loop-helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with I{kappa}B{alpha} that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKK{beta} dimerization, but dimerization per se is not important for maintaining IKK{beta} activity and instead is required for IKK{beta} activation. Other IKK family members, IKK{alpha}, TBK1 and IKK-i, may have a similar trimodular architecture and function.

  11. Crystal structure of the Anopheles gambiae 3-hydroxykynurenine transaminase.

    Science.gov (United States)

    Rossi, Franca; Garavaglia, Silvia; Giovenzana, Giovanni Battista; Arcà, Bruno; Li, Jianyong; Rizzi, Menico

    2006-04-11

    In Anopheles gambiae, the vector for the most deadly malaria parasite Plasmodium falciparum, xanthurenic acid (XA) plays a key role in parasite gametogenesis and fertility. In mosquitoes, XA is produced by transamination of 3-hydroxykynurenine (3-HK), a reaction that represents the main route to prevent the accumulation of the potentially toxic 3-HK excess. Interfering with XA metabolism in A. gambiae therefore appears an attractive avenue for the development of malaria transmission-blocking drugs and insecticides. We have determined the crystal structure of A. gambiae 3-HK transaminase in its pyridoxal 5'-phosphate form and in complex with a newly synthesized competitive enzyme inhibitor. Structural inspection of the enzyme active site reveals the key molecular determinants for ligand recognition and catalysis. Major contributions toward inhibitor binding are provided by a salt bridge between the inhibitor carboxylate and Arg-356 and by a remarkable hydrogen bond network involving the anthranilic moiety of the inhibitor and backbone atoms of residues Gly-25 and Asn-44. This study may be useful for the structure-based design of specific enzyme inhibitors of potential interest as antimalarial agents.

  12. Crystal structure of an HIV assembly and maturation switch

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Jonathan M.; Zadrozny, Kaneil K.; Chrustowicz, Jakub; Purdy, Michael D.; Yeager, Mark; Ganser-Pornillos, Barbie K.; Pornillos, Owen

    2016-07-14

    Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysis during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate.

  13. Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe

    Energy Technology Data Exchange (ETDEWEB)

    Bulfer, Stacie L.; Hendershot, Jenna M.; Trievel, Raymond C. (Michigan); (UCSF)

    2013-09-18

    Lysine biosynthesis in fungi, euglena, and certain archaebacteria occurs through the {alpha}-aminoadipate pathway. Enzymes in the first steps of this pathway have been proposed as potential targets for the development of antifungal therapies, as they are absent in animals but are conserved in several pathogenic fungi species, including Candida, Cryptococcus, and Aspergillus. One potential antifungal target in the {alpha}-aminoadipate pathway is the third enzyme in the pathway, homoisocitrate dehydrogenase (HICDH), which catalyzes the divalent metal-dependent conversion of homoisocitrate to 2-oxoadipate (2-OA) using nicotinamide adenine dinucleotide (NAD{sup +}) as a cofactor. HICDH belogns to a family of {beta}-hydroxyacid oxidative decarboxylases that includes malate dehydrogenase, tartrate dehydrogenase, 6-phosphogluconate dehydrogenase, isocitrate dehydrogenase (ICDH), and 3-isopropylmalte dehydrogenase (IPMDH). ICDH and IPMDH are well-characterized enzymes that catalyze the decarboxylation of isocitrate to yield 2-oxoglutarate (2-OG) in the citric acid cycle and the conversion of 3-isopropylmalate to 2-oxoisovalerate in the leucine biosynthetic pathway, respectively. Recent structural and biochemical studies of HICDH reveal that this enzyme shares sequence, structural, and mechanistic homology with ICDH and IPMDH. To date, the only published structures of HICDH are from the archaebacteria Thermus thermophilus (TtHICDH). Fungal HICDHs diverge from TtHICDH in several aspects, including their thermal stability, oligomerization state, and substrate specificity, thus warranting further characterization. To gain insights into these differences, they determined crystal structures of a fungal Schizosaccharomyces pombe HICDH (SpHICDH) as an apoenzyme and as a binary complex with additive tripeptide glycyl-glycyl-glycine (GGG) to 1.55 {angstrom} and 1.85 {angstrom} resolution, respectively. Finally, a comparison of the SpHICDH and TtHICDH structures reveal differences in

  14. The crystal structure of a voltage-gated sodium channel.

    Science.gov (United States)

    Payandeh, Jian; Scheuer, Todd; Zheng, Ning; Catterall, William A

    2011-07-10

    Voltage-gated sodium (Na(V)) channels initiate electrical signalling in excitable cells and are the molecular targets for drugs and disease mutations, but the structural basis for their voltage-dependent activation, ion selectivity and drug block is unknown. Here we report the crystal structure of a voltage-gated Na(+) channel from Arcobacter butzleri (NavAb) captured in a closed-pore conformation with four activated voltage sensors at 2.7 Å resolution. The arginine gating charges make multiple hydrophilic interactions within the voltage sensor, including unanticipated hydrogen bonds to the protein backbone. Comparisons to previous open-pore potassium channel structures indicate that the voltage-sensor domains and the S4-S5 linkers dilate the central pore by pivoting together around a hinge at the base of the pore module. The NavAb selectivity filter is short, ∼4.6 Å wide, and water filled, with four acidic side chains surrounding the narrowest part of the ion conduction pathway. This unique structure presents a high-field-strength anionic coordination site, which confers Na(+) selectivity through partial dehydration via direct interaction with glutamate side chains. Fenestrations in the sides of the pore module are unexpectedly penetrated by fatty acyl chains that extend into the central cavity, and these portals are large enough for the entry of small, hydrophobic pore-blocking drugs. This structure provides the template for understanding electrical signalling in excitable cells and the actions of drugs used for pain, epilepsy and cardiac arrhythmia at the atomic level.

  15. Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum.

    Science.gov (United States)

    Lunev, Sergey; Bosch, Soraya S; Batista, Fernando de Assis; Wrenger, Carsten; Groves, Matthew R

    2016-07-01

    The de novo pyrimidine-biosynthesis pathway of Plasmodium falciparum is a promising target for antimalarial drug discovery. The parasite requires a supply of purines and pyrimidines for growth and proliferation and is unable to take up pyrimidines from the host. Direct (or indirect) inhibition of de novo pyrimidine biosynthesis via dihydroorotate dehydrogenase (PfDHODH), the fourth enzyme of the pathway, has already been shown to be lethal to the parasite. In the second step of the plasmodial pyrimidine-synthesis pathway, aspartate and carbamoyl phosphate are condensed to N-carbamoyl-L-aspartate and inorganic phosphate by aspartate transcarbamoylase (PfATC). In this paper, the 2.5 Å resolution crystal structure of PfATC is reported. The space group of the PfATC crystals was determined to be monoclinic P21, with unit-cell parameters a = 87.0, b = 103.8, c = 87.1 Å, α = 90.0, β = 117.7, γ = 90.0°. The presented PfATC model shares a high degree of homology with the catalytic domain of Escherichia coli ATC. There is as yet no evidence of the existence of a regulatory domain in PfATC. Similarly to E. coli ATC, PfATC was modelled as a homotrimer in which each of the three active sites is formed at the oligomeric interface. Each active site comprises residues from two adjacent subunits in the trimer with a high degree of evolutional conservation. Here, the activity loss owing to mutagenesis of the key active-site residues is also described.

  16. 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.

  17. 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.

  18. 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.

  19. Crystal Structure of a Full-Length β-Catenin

    Science.gov (United States)

    Xing, Yi; Takemaru, Ken-Ichi; Liu, Jing; Berndt, Jason D.; Zheng, Jie J.; Moon, Randall T.; Xu, Wenqing

    2014-01-01

    SUMMARY β-catenin plays essential roles in cell adhesion and Wnt signaling, while deregulation of β-catenin is associated with multiple diseases including cancers. Here, we report the crystal structures of full-length zebrafish β-catenin and a human β-catenin fragment that contains both the armadillo repeat and the C-terminal domains. Our structures reveal that the N-terminal region of the C-terminal domain, a key component of the C-terminal transactivation domain, forms a long α helix that packs on the C-terminal end of the armadillo repeat domain, and thus forms part of the β-catenin superhelical core. The existence of this helix redefines our view of interactions of β-catenin with some of its critical partners, including ICAT and Chibby, which may form extensive interactions with this C-terminal domain α helix. Our crystallographic and NMR studies also suggest that the unstructured N-terminal and C-terminal tails interact with the ordered armadillo repeat domain in a dynamic and variable manner. PMID:18334222

  20. Crystal structure of human quinone reductase type 2, a metalloflavoprotein.

    Science.gov (United States)

    Foster, C E; Bianchet, M A; Talalay, P; Zhao, Q; Amzel, L M

    1999-08-03

    In mammals, two separate but homologous cytosolic quinone reductases have been identified: NAD(P)H:quinone oxidoreductase type 1 (QR1) (EC 1.6.99.2) and quinone reductase type 2 (QR2). Although QR1 and QR2 are nearly 50% identical in protein sequence, they display markedly different catalytic properties and substrate specificities. We report here two crystal structures of QR2: in its native form and bound to menadione (vitamin K(3)), a physiological substrate. Phases were obtained by molecular replacement, using our previously determined rat QR1 structure as the search model. QR2 shares the overall fold of the major catalytic domain of QR1, but lacks the smaller C-terminal domain. The FAD binding sites of QR1 and QR2 are very similar, but their hydride donor binding sites are considerably different. Unexpectedly, we found that QR2 contains a specific metal binding site, which is not present in QR1. Two histidine nitrogens, one cysteine thiol, and a main chain carbonyl group are involved in metal coordination. The metal binding site is solvent-accessible, and is separated from the FAD cofactor by a distance of about 13 A.

  1. Synthesis and Crystal Structures of N-Substituted Pyrazolines

    Directory of Open Access Journals (Sweden)

    Balladka Kunhanna Sarojini

    2013-02-01

    Full Text Available Four pyrazole compounds, 3-(4-fluorophenyl-5-phenyl-4,5-dihydro-1H-pyrazole-1-carbaldehyde (1, 5-(4-bromophenyl-3-(4-fluorophenyl-4,5-dihydro-1H-pyrazole-1-carbaldehyde (2, 1-[5-(4-chlorophenyl-3-(4-fluorophenyl-4,5-dihydro-1H-pyrazol-1-yl]ethanone (3 and 1-[3-(4-fluorophenyl-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl]propan-1-one (4, have been prepared by condensing chalcones with hydrazine hydrate in the presence of aliphatic acids, namely formic acid, acetic acid and propionic acid. The structures were characterized by X-ray single crystal structure determination. The dihedral angles formed between the pyrazole and the fluoro-substituted rings are 4.64(7° in 1, 5.3(4° in 2 and 4.89(6° in 3. In 4, the corresponding angles for molecules A and molecules B are 10.53(10° and 9.78(10°, respectively.

  2. 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.

  3. Crystal structure of a chimaeric bacterial glutamate dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Tânia; Sharkey, Michael A.; Engel, Paul C.; Khan, Amir R.

    2016-05-23

    Glutamate dehydrogenases (EC 1.4.1.2–4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P)+as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD+versusNADP+, but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies, as shown by the apo structure of glutamate dehydrogenase fromClostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia colienzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP+cofactor from the parentE. colidomain II, although there are subtle differences in catalytic activity.

  4. 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-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. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Synthesis, single crystal structure and energy optimization of a multicomponent salt of imidazole and tetrabromoterepthalic acid

    Energy Technology Data Exchange (ETDEWEB)

    Singha, S.; Kumar, S., E-mail: skndey@gmail.com [Department of Physics, Jadavpur University, Kolkata-700032 (India); Dey, S. K., E-mail: skndey@gmail.com [Department of Physics, Jadavpur University, Kolkata-700032 (India); Department of Physics, NITMAS, 24 Paragana(S)-743368 (India)

    2015-06-24

    Single crystal of a multicomponent salt (IMTBTP) of imidazole with tetrabromoterepthalic acid has been synthesized by slow evaporation method at room temperature. The crystal structure of the salt has been determined by single crystal x-ray diffraction technique. The supramolecular structure analysis reveals that the multicomponent salt is formed by noncovalent hydrogen bonding interaction and Br···π interaction. The energy optimization and HOMO-LUMO energy gap calculation have been carried out by Density Functional Theory.

  6. Synthesis, single crystal structure and energy optimization of a multicomponent salt of imidazole and tetrabromoterepthalic acid

    Science.gov (United States)

    Singha, S.; Dey, S. K.; Kumar, S.

    2015-06-01

    Single crystal of a multicomponent salt (IMTBTP) of imidazole with tetrabromoterepthalic acid has been synthesized by slow evaporation method at room temperature. The crystal structure of the salt has been determined by single crystal x-ray diffraction technique. The supramolecular structure analysis reveals that the multicomponent salt is formed by noncovalent hydrogen bonding interaction and Br...π interaction. The energy optimization and HOMO-LUMO energy gap calculation have been carried out by Density Functional Theory.

  7. 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.

  8. 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.

  9. 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.

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

    KAUST Repository

    Reiner, Thomas

    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.

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

    KAUST Repository

    Al-Masri, H.T.

    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.

  12. 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.

  13. CCDC 713129: Experimental Crystal Structure Determination : (eta^6^-Benzylammonium)-dichloro-(dimethylsulfoxide-S)-ruthenium(ii) chloride

    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.

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

    KAUST Repository

    Wu, Melissa M.

    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.

  15. 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.

  16. 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.

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

    KAUST Repository

    Chen, Yin

    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.

  18. 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.

  19. 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.

  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. 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.

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

    KAUST Repository

    Reiner, Thomas

    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.

  3. 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.

  4. 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.

  5. 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.

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

    KAUST Repository

    Vummaleti, Sai V. C.

    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.

  7. Structural examination of lithium niobate ferroelectric crystals by combining scanning electron microscopy and atomic force microscopy

    Science.gov (United States)

    Efremova, P. V.; Ped'ko, B. B.; Kuznecova, Yu. V.

    2016-02-01

    The structure of lithium niobate single crystals is studied by a complex technique that combines scanning electron microscopy and atomic force microscopy. By implementing the piezoresponse force method on an atomic force microscope, the domain structure of lithium niobate crystals, which was not revealed without electron beam irradiation, is visualized

  8. CCDC 1011330: Experimental Crystal Structure Determination : 1,3,6,8-tetrakis(4-fluorophenyl)pyrene

    KAUST Repository

    El-Assaad, Tarek H.

    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.

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

    KAUST Repository

    Wu, Melissa M.

    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.

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

    KAUST Repository

    El-Assaad, Tarek H.

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

    KAUST Repository

    Roesle, Philipp

    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 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.

  13. 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.

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

    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.

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

    KAUST Repository

    Xu, Jun

    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 1419731: Experimental Crystal Structure Determination : dodecakis(mu-2-phenylethanethiolato)-hexa-nickel dichloromethane solvate

    KAUST Repository

    Joya, Khurram S.

    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. 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 ...

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

    KAUST Repository

    Al-Masri, H.T.

    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.

  19. 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.

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

    KAUST Repository

    Kuhn, Paul-Steffen

    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.

  1. 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.

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

    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.

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

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

    KAUST Repository

    Shekhah, Osama

    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.

  5. Synthesis, crystal structure and catecholase activity of a Ni(II ...

    Indian Academy of Sciences (India)

    Synthesis, crystal structure and catecholase activity of a Ni(II) complex derived from a tetradentate ... of the crystal are a = 30.6345(4)Å, b = 8.45340(10)Å, c = 7.75180(10)Å. Structural analysis reveals a tetradentate chelation behaviour of ..... Acc. Chem. Res. 35 183. 7. (a) Abuhijleh A L, Pollitte J and Woods C 1994 Inorg.

  6. 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.

  7. 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.

  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. 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.

  11. Crystal structure of a nematode-infecting virus.

    Science.gov (United States)

    Guo, Yusong R; Hryc, Corey F; Jakana, Joanita; Jiang, Hongbing; Wang, David; Chiu, Wah; Zhong, Weiwei; Tao, Yizhi J

    2014-09-02

    Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-δ fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, β-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection.

  12. 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.

  13. Observations on the structural features and characteristics of biological apatite crystals. 2. Observation on the ultrastructure of human enamel crystals.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1992-12-01

    In a series of studies to investigate the structural features of biological crystals, using an electron microscope, we examined the ultrastructure of human enamel crystals at near atomic resolution through the cross and longitudinal sections of the crystals. The materials used for this study were the middle layer of the noncarious enamel from freshly extracted human erupted permanent molars. The small cubes of the enamel were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with HITACHI H-500 and H-700 types of transmission electron microscopes operated at 125-200 kV. Each crystal was observed at the initial magnification of 300,000 times and at the final magnification of 10,000,000 times and over. Using this approach, the authors have been able to show the configuration of the hydroxyapatite in the cross and longitudinal sections of the enamel crystals and observe the basic hexagonal pattern of the unit cell viewed down the c-axis. The authors sincerely believe that the electron micrograph shown in this report is the first atomic image to be obtained from a hydroxyapatite crystal from the human enamel, using the sections.

  14. 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

    conjecture that crystalline solids with isomorphs include most or all formed by atoms or molecules interacting via metallic or van der Waals forces, whereas covalently bonded or hydrogen-bonded crystals are not expected to have isomorphs; crystals of ions or dipolar molecules constitute a limiting case...

  15. Identification of surface domain structure on enamel crystals using polyamidoamine dendrimer

    Science.gov (United States)

    Chen, Haifeng; Clarkson, Brian H.; Orr, Bradford; Majoros, Istvan; Banaszak Holl, Mark M.

    2002-03-01

    The control of hydroxyapatite crystal nucleation and crystal growth is central to the mineralization and remineralization of enamel and dentin of teeth. However, the precise biomolecular mechanisms involved remain obscure. The intimate association between the crystal's surface and extracellular protein components implies a modulating role for organic crystal interactions probably mediated via specific crystal surface domains. These include lattice defects and specific stereochemical arrays on associated organic molecules. The nature of protein-crystal interaction depends upon the physical forces of attraction / repulsion between specific biomolecular groups and crystal surface domains. The proposed study is to utilize specific polyamidoamine (PAMAM) dendrimers, also known as “artificial proteins”, acting as nanoprobe. These will be used to probe specific surface domain on the surface of the naturally derived crystals of hydroxyapatite and to determine how control of growth and dissolution may be affected at the biomolecular level. The hydroxyapatite crystals are extracted from the maturation stage enamel of rats. Three types of PAMAM dendrimers, respectively with amine-, carboxylic acid and methyl-capped surface, will be applied in the study. The dendrimer binding on the surface of the hydoxyapatite crystals will be characterized using atomic force microscopy (AFM). The different dendrimer binding on the crystals will disclose the specific surface domain structure on the crystals, which is assumed to be important in binding the extracellular protein.

  16. Surface Structure Study of Crystal Hydroxy-Apatite from Fluorosis Enamels

    OpenAIRE

    Abdillah Imron Nasution; Harun Asyiq Gunawan; Sri Angky Soekanto

    2013-01-01

    Fluorosis is a condition due to ingestion of excessive amounts of fluor which can cause the change in tooth structure and strength. However, there is still lack of explanation on the surface structure of crystal hydroxyapatite that influences the microscopic characteristic of fluorosis enamel. Objectives: To investigate the surface structure of crystal hydroxy-apatite in fluorosis enamel. Materials and Methods: Determination of fluor concentration and the surface structure of normal and fluor...

  17. Molecular and crystal structure of Cobalt(II) hydroselenite dihydrate

    Energy Technology Data Exchange (ETDEWEB)

    Gulya, A.P.; Shova, S.G.; Rudik, V.F. [Moldova State Univ. (Russian Federation)] [and others

    1994-05-01

    The results of the synthesis of [Co(HSeO{sub 3}){sub 2}(H{sub 2}O){sub 2}] and its examination both in solution and in solid state by the NMR method, IR spectroscopy, thermogravimetry, magnetochemistry, and x-ray diffraction analysis (R = 0.064) are given. The crystal has monoclinic symmetry. The unit cell parameters are a = 7.985(2) {angstrom}, b = 7.096(3) {angstrom}, c = 6.814(1) {angstrom}, {gamma} = 113.19(3){degree}, space group P2{sub 1}/n and Z = 2. The structure consists of [Co(HSeO{sub 3}){sub 2}(H{sub 2}O){sub 2}] centrosymmetric complexes. The coordination polyhedron of cobalt represents a distorted octahedron formed by the oxygen atoms of two water molecules and four selenite ions. The compound is of interest because it has the ability to introduce selenium into biomass and offers promise for the preparation of selenium-containing drugs.

  18. 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.

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

    DEFF Research Database (Denmark)

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

    as well as the controlled turnover of these in response to changing surrounding conditions is of vital importance to ensure optimal fitness of a cell. Central to both these processes is the degradation of RNA, either as a means of decreasing the level of particular RNAs or as a way to get rid of aberrant...... form the 3'-end of mRNA, is normally the first and also rate-limiting step in cellular mRNA degradation and therefore a key process in the control of eukaryotic mRNA turnover. Since Ccr4p is believed to be the main deadenylase the precise role of Pop2p in the complex is less clear. Nevertheless, Pop2p....... In the nucleus Rrp6p associates with the exosome and participates in the degradation of improperly processed precursor mRNAs and trimming of stable RNAs. The crystal structure of S. cerevisiae Rrp6p presented here displays a conserved DEDD nuclease core with a flanking HRDC domain believed to be involved in RNA...

  20. 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.

  1. 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.

  2. Crystal structure of advanced lithium titanate with lithium oxide additives

    Science.gov (United States)

    Hoshino, Tsuyoshi; Sasaki, Kazuya; Tsuchiya, Kunihiko; Hayashi, Kimio; Suzuki, Akihiro; Hashimoto, Takuya; Terai, Takayuki

    2009-04-01

    Li 2TiO 3 is one of the most promising candidates among solid breeder materials proposed for fusion reactors. However, the mass of Li 2TiO 3 was found to decrease with time in the sweep gas mixed with hydrogen. This mass change indicates that the oxygen content of the sample decreased, suggesting the change from Ti 4+ to Ti 3+. In the present paper, the crystal structure and the non-stoichiometry of Li 2TiO 3 added with Li 2O have been extensively investigated by means of X-ray diffraction (XRD) and thermogravimetry. In the case of the Li 2TiO 3 samples used in the present study, LiO-C 2H 5 or LiO-i-C 3H 7 and Ti(O-i-C 3H 7) 4 were mixed in the proportion corresponding to the molar ratio Li 2O/TiO 2 of either 2.00 or 1.00. In thermogravimetry, the mass of this sample decreased with time due to lithium deficiency, where no presence of oxygen deficiency was indicated.

  3. Crystal growth, structural, low temperature thermoluminescence and mechanical properties of cubic fluoroperovskite single crystal (LiBaF3)

    Science.gov (United States)

    Daniel, D. Joseph; Ramasamy, P.; Ramaseshan, R.; Kim, H. J.; Kim, Sunghwan; Bhagavannarayana, G.; Cheon, Jong-Kyu

    2017-10-01

    Polycrystalline compounds of LiBaF3 were synthesized using conventional solid state reaction route and the phase purity was confirmed using powder X-ray diffraction technique. Using vertical Bridgman technique single crystal was grown from melt. Rocking curve measurements have been carried out to study the structural perfection of the grown crystal. The single peak of diffraction curve clearly reveals that the grown crystal was free from the structural grain boundaries. The low temperature thermoluminescence of the X-ray irradiated sample has been analyzed and found four distinguishable peaks having maximum temperatures at 18, 115, 133 and 216 K. Activation energy (E) and frequency factor (s) for the individual peaks have been studied using Peak shape method and the computerized curve fitting method combining with the Tmax- TStop procedure. Nanoindentation technique was employed to study the mechanical behaviour of the crystal. The indentation modulus and Vickers hardness of the grown crystal have values of 135.15 GPa and 680.81 respectively, under the maximum indentation load of 10 mN.

  4. 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.

  5. Crystal structure of carbapenam synthetase (CarA).

    Science.gov (United States)

    Miller, Matthew T; Gerratana, Barbara; Stapon, Anthony; Townsend, Craig A; Rosenzweig, Amy C

    2003-10-17

    Carbapenam synthetase (CarA) is an ATP/Mg2+-dependent enzyme that catalyzes formation of the beta-lactam ring in (5R)-carbapenem-3-carboxylic acid biosynthesis. CarA is homologous to beta-lactam synthetase (beta-LS), which is involved in clavulanic acid biosynthesis. The catalytic cycles of CarA and beta-LS mediate substrate adenylation followed by beta-lactamization via a tetrahedral intermediate or transition state. Another member of this family of ATP/Mg2+-dependent enzymes, asparagine synthetase (AS-B), catalyzes intermolecular, rather than intramolecular, amide bond formation in asparagine biosynthesis. The crystal structures of apo-CarA and CarA complexed with the substrate (2S,5S)-5-carboxymethylproline (CMPr), ATP analog alpha,beta-methyleneadenosine 5'-triphosphate (AMP-CPP), and a single Mg2+ ion have been determined. CarA forms a tetramer. Each monomer resembles beta-LS and AS-B in overall fold, but key differences are observed. The N-terminal domain lacks the glutaminase active site found in AS-B, and an extended loop region not observed in beta-LS or AS-B is present. Comparison of the C-terminal synthetase active site to that in beta-LS reveals that the ATP binding site is highly conserved. By contrast, variations in the substrate binding pocket reflect the different substrates of the two enzymes. The Mg2+ coordination is also different. Several key residues in the active site are conserved between CarA and beta-LS, supporting proposed roles in beta-lactam formation. These data provide further insight into the structures of this class of enzymes and suggest that CarA might be a versatile target for protein engineering experiments aimed at developing improved production methods and new carbapenem antibiotics.

  6. Synthesis and Crystal Structures of Two New Oxaspirocyclic Compounds

    Directory of Open Access Journals (Sweden)

    Jinhe Jiang

    2016-10-01

    Full Text Available Two new oxaspirocyclic compounds, 8-(4-(dimethylaminobenzylidene-6,10-dioxaspiro[4.5]decane-7,9-dione (1 and 8-(4-hydroxybenzylidene-6,10-dioxaspiro[4.5]decane-7,9-dione (2 have been synthesized and their structures determined by single crystal X-ray crystallography. Compound 1, C17H19NO4, belongs to the monoclinic system, space group P21/c with a = 6.2554(13 Å, b = 14.605(3 Å, c = 16.265(3 Å, β = 95.97(3°, V = 1477.9(5 Å3, Z = 4, Dc = 1.354 g/cm3, F(000 = 640, μ(MoKa = 0.097 mm−1, the final R = 0.0570 and wR = 0.1667. Compound 2, C15H14O5, is also of the monoclinic system, space group P21/c with a = 10.739(2 Å, b = 18.348(4 Å, c = 6.7799(14 Å, β = 104.20(3°, V = 1295.1(5 Å3, Z = 4, Dc = 1.407 g/cm3, F(000 = 608, μ(MoKa = 0.106 mm−1, the final R = 0.0568 and wR = 0.1739. Some C–H···O intra- and intermolecular hydrogen bonds and π··· π stacking interactions are both observed in the two lattice structures. The difference between them is that one type of C–H···π supramolecular interaction (1 and one type of O–H···O intermolecular hydrogen bond (2 are observed.

  7. Structural, spectral and birefringence studies of semiorganic nonlinear optical single crystal: Calcium5-sulfosalicylate

    Science.gov (United States)

    Shalini, D.; Kalainathan, S.; Ambika, V. Revathi; Hema, N.; Jayalakshmi, D.

    2017-11-01

    Semi-organic nonlinear optical crystal Calcium5-Sulfosalicylate (CA5SS) was grown by slow evaporation solution growth technique. The cell parameters and molecular structure of the grown crystal were studied by single crystal x-ray diffraction analysis. The presence of various functional groups of the grown crystal was confirmed using Fourier transform infrared (FT-IR), Fourier transform Raman (FT-Raman) analysis. UV-Visible spectrum shows that CA5SS crystals have high transmittance in the range of 330-900 nm. The refractive index, birefringence and transient photoluminescence properties of the grown crystal were analyzed. The frequency doubling of the grown crystal (CA5SS) were studied and compared with that of KDP.

  8. Crystal structure prediction and its application in Earth and materials sciences.

    Science.gov (United States)

    Zhu, Qiang; Oganov, Artem R; Zhou, Xiang-Feng

    2014-01-01

    Evolutionary algorithms, based on physically motivated forms of variation operators and local optimization, proved to be a powerful approach in determining the crystal structure of materials. This review summarized the recent progress of the USPEX method as a tool for crystal structure prediction. In particular, we highlight the methodology in (1) prediction of molecular crystal structures and (2) variable-composition structure predictions, and their applications to a series of systems, including Mg(BH4)2, Xe-O, Mg-O compounds, etc. We demonstrate that this method has a wide field of applications in both computational materials design and studies of matter at extreme conditions.

  9. 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....... Though the orientated crystalline structures existed in the iP-1-B samples, no accelerating effect on crystal transition from II to I was found. Importantly, the final crystalline structures of iP-1-B in form I was found tunable under different melt pre-shear conditions, even though...... 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...

  10. Crystal Structure of a Model Spider Silk Peptide

    Science.gov (United States)

    Chen, Shujun; Gido, Samuel; Valluzzi, Regina; Kaplan, David

    2001-03-01

    Crystallization study on a novel model silk peptide has been carried out using optical microscopy, AFM, TEM and electron diffraction. The sequence of the peptide, (E)5(GDVGGAGATGGS)2(E)5, is based on the GXYGGZ motif in the less repetitive amorphous blocks of Nephila clavipes spider dragline silk. When the peptide was crystallized out of aqueous solution, spherulites as well as dendritic crystals on the order of several to tens of microns in diameter were observed under polarizing optical microscope, depending on drying speed, volume of the droplet and concentration. The same crystals were collected and sonicated in methanol, a non-solvent, to yield individual crystals that were later examined in the electron microscope. Regular-shaped lamellar crystals of micron size were observed in the TEM. The lamellar thickness as determined by Pt/Pd shadowing and AFM is 50 Å. Selected area electron diffraction showed single crystal diffraction patterns indicating a possible orthorhombic unit cell of 9.91 x 5.57 x 20.40 Å.

  11. 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.

  12. Atomic resolution of structural changes in elastic crystals of copper(II) acetylacetonate

    Science.gov (United States)

    Worthy, Anna; Grosjean, Arnaud; Pfrunder, Michael C.; Xu, Yanan; Yan, Cheng; Edwards, Grant; Clegg, Jack K.; McMurtrie, John C.

    2018-01-01

    Single crystals are typically brittle, inelastic materials. Such mechanical responses limit their use in practical applications, particularly in flexible electronics and optical devices. Here we describe single crystals of a well-known coordination compound—copper(II) acetylacetonate—that are flexible enough to be reversibly tied into a knot. Mechanical measurements indicate that the crystals exhibit an elasticity similar to that of soft materials such as nylon, and thus display properties normally associated with both hard and soft matter. Using microfocused synchrotron radiation, we mapped the changes in crystal structure that occur on bending, and determined the mechanism that allows this flexibility with atomic precision. We show that, under strain, the molecules in the crystal reversibly rotate, and thus reorganize to allow the mechanical compression and expansion required for elasticity and still maintain the integrity of the crystal structure.

  13. Effect of zinc acetate addition on crystal growth, structural, optical, thermal properties of glycine single crystals

    Directory of Open Access Journals (Sweden)

    S. Anbu Chudar Azhagan

    2017-05-01

    Full Text Available In the present study, γ-glycine has been crystallized by using zinc acetate dihydrate as an additive for the first time by slow solvent evaporation method. The second harmonic conversion efficiency of γ-glycine crystal was determined using Kurtz and Perry powder technique and was found to be 3.66 times greater than that of standard inorganic material potassium dihydrogen phosphate (KDP. The analytical grade chemicals of glycine and zinc acetate dihydrate were taken in six different molar ratios: 1:0.2, 1:0.4, 1:0.6, 1:0.7, 1:0.8, and 1:0.9 respectively to find out the γ-polymorph of glycine. The lower molar concentration of zinc acetate yield only α-polymorph where as the higher molar concentration of zinc acetate inhibits the γ-polymorph of glycine which was confirmed by single crystal XRD and powder XRD studies. Inductively coupled plasma optical emission spectrometry (ICP-OES was carried out to quantify the concentration of zinc element in the grown glycine single crystals. The concentration of zinc element in the presence of grown γ-glycine single crystal is found to be 0.73 ppm. UV–Visible–NIR transmittance spectra were recorded for the samples to analyse the transparency in visible and near infrared region (NIR. The optical band gap Eg was estimated for γ-glycine single crystal using UV–Visible–NIR study. Functional groups present in the samples were identified by FTIR spectroscopic analysis. Differential scanning calorimetry technique was employed to determine the phase transition, thermal stability and melting point of the grown crystal.

  14. Field induced heliconical structure of cholesteric liquid crystal

    Science.gov (United States)

    Lavrentovich, Oleg D.; Shiyanovsii, Sergij V.; Xiang, Jie; Kim, Young-Ki

    2017-06-27

    A diffraction grating comprises a liquid crystal (LC) cell configured to apply an electric field through a cholesteric LC material that induces the cholesteric LC material into a heliconical state with an oblique helicoid director. The applied electric field produces diffracted light from the cholesteric LC material within the visible, infrared or ultraviolet. The axis of the heliconical state is in the plane of the liquid crystal cell or perpendicular to the plane, depending on the application. A color tuning device operates with a similar heliconical state liquid crystal material but with the heliconical director axis oriented perpendicular to the plane of the cell. A power generator varies the strength of the applied electric field to adjust the wavelength of light reflected from the cholesteric liquid crystal material within the visible, infrared or ultraviolet.

  15. Preparation, crystal structure, and characterization of an inorganic ...

    Indian Academy of Sciences (India)

    Author Affiliations. Jing-Ping Wang1 Hong-Yu Niu1 Jing-Yang Niu1. Institute of Molecular and Crystal Engineering, School of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475001, PR China ...

  16. Assessment of microarchitecture and crystal structure of hydroxyapatite in osteoporosis

    OpenAIRE

    Zairin Noor; Sumitro, Sutiman B.; Mohammad Hidayat; Agus Hadian Rahim; Ahmad Taufiq

    2011-01-01

    Osteoporosis is characterized by lower bone mineral density (BMD) and microarchitectural degeneration, which tends to increase bone fragility and fracture risk. Bone microstructure depends on interactions between the mineral atoms, which may perform substitution or incorporation into bone crystals, and may dynamically take over the function of calcium or may become a complementary part. The mineral atoms may also become a composite in the hydroxyapatite crystals. The aim of this study was to ...

  17. Tuning contorted hexabenzocoronene crystal structure and texture for organic field-effect transistors

    Science.gov (United States)

    Hiszpanski, Anna; Woll, Arthur; Loo, Yueh-Lin

    2012-02-01

    Crystallography conducted on single crystals reveals contorted hexabenzocoronene (HBC) can adopt either herringbone (Pbcn) or slip-stack (P21/c) packing motifs. By adjusting the molecule-solvent interactions during solvent-vapor annealing (SVA), we can controllably crystallize thin films of HBC and access both packing motifs. In HBC films annealed with dichloromethane (DCM) vapor, molecule-solvent interactions are strong and yield highly oriented Pbcn crystals. However, in films annealed with hexanes vapor, molecule-solvent interactions are weaker and randomly oriented P21/c crystals form. In addition to tuning the molecule-solvent interactions via solvent choice, the interactions may also be modulated by selectively fluorinating the peripheral aromatic rings of HBC. With increased fluorination, we decrease molecule-solvent interactions during SVA. As such, we can coax these HBC derivatives to adopt the P21/c crystal structure even with DCM SVA. Further, more fluorinated HBCs form more oriented crystals when exposed to DCM vapors. Transistors fabricated with crystalline HBC active layers suggest that the mobilities of these devices are, to first order, determined by the extent of crystal orientation and less so by the crystal structure. The ability to independently access both crystal structures with varying degrees of orientation has allowed us to decouple their relative contributions to device performance.

  18. Direct observation of defect structure in protein crystals by atomic force and transmission electron microscopy.

    OpenAIRE

    Devaud, G; Furcinitti, P S; Fleming, J.C.; Lyon, M K; Douglas, K

    1992-01-01

    We have examined the structure of S-layers isolated from Sulfolobus acidocaldarius using atomic force microscopy (AFM) and transmission electron microscopy (TEM). From the AFM images, we were able to directly observe individual dimers of the crystal, defects in the crystal structure, and twin boundaries. We have identified two types of boundaries, one defined by a mirror plane and the other by a glide plane. This work shows that twin boundaries are highly structured regions that are directly ...

  19. Crystal Structure Prediction could have helped the Experimentalists with Polymorphism in Benzamide!

    OpenAIRE

    2008-01-01

    Abstract Benzamide was the first molecular material for which polymorphism was reported as long as 176 years ago. Unfortunately, due to very similar cell metrics leading to massive peak overlap, the metastable form reported by Liebig escaped structural characterization by XRD until recently. With the help of crystal structure prediction this old riddle of ?Liebig's? polymorph of benzamide could have been solved many years earlier. Performing state of the art crystal structure predi...

  20. Incorporation of iodine into apatite structure: a crystal chemistry approach using Artificial Neural Network

    OpenAIRE

    Jianwei eWang

    2015-01-01

    Materials with apatite crystal structure have a great potential for incorporating the long-lived radioactive iodine isotope (129I) in the form of iodide (I−) from nuclear waste streams. Because of its durability and potentially high iodine content, the apatite waste form can reduce iodine release rate and minimize the waste volume. Crystal structure and composition of apatite (A5(XO4)3Z) was investigated for iodide incorporation into the channel of the structure using Artificial Neural Networ...

  1. Structural, optical and dielectric studies of lithium sulphate monohydrate single crystals

    Directory of Open Access Journals (Sweden)

    Najar F.A.

    2017-02-01

    Full Text Available Optical, dielectric, and thermal properties of lithium sulphate monohydrate crystals grown by slow evaporation method have been studied. The crystal structure was resolved by direct methods using single crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R-value of 0.0174. Plasma energy, Penn gap, Fermi energy and electronic polarizability of the grown crystal were calculated from single crystal XRD data. The electronic polarizability of lithium sulfate monohydrate was also calculated and compared with the theoretical data using Clausius-Mossotti equation. Optical band gap calculated from optical data for the grown crystal is 4.49 eV. Fourier Transform Infrared Spectroscopy study confirmed the presence of water in the crystal structure. The AC conductivity, dielectric constant and dielectric loss of the grown crystal were systemically investigated, showing a peak at about 130 °C which could be attributed to the water molecules in the crystal structure. The anomalous dielectric properties shown by the crystal have been correlated with its thermal behavior. The title crystal obeys Jonscher’s power law relation; σ(ω = σo+ Aωs, with temperature dependent exponent s < 1. The activation energy calculated for the material is 0.24 eV and suggests protonic conduction by hopping mechanism in addition to cationic conduction by lithium ions. The micro-indentation study was also carried out which revealed that the crystal belongs to a category of soft materials.

  2. 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.

  3. 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.

  4. The fabrication and characterization of quantum dots-conjugated opal photonic crystals structure.

    Science.gov (United States)

    Isnaeni; Cho, Yong-Hoon

    2010-06-04

    We have fabricated opal photonic crystal structure, which is assembled from quantum dots-conjugated polystyrene spheres. We found that the quantum dots (QD) emission from QD-conjugated photonic crystal (PC) structure experienced not only shifting to shorter wavelength, but also an asymmetrical broadening. This photonic crystal structure uses less quantum dots and may lead to great application such as single photon source and QD laser, since we may sharpen and broaden the QD emission by selecting the proper position of stop band.

  5. Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form

    NARCIS (Netherlands)

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

    2006-01-01

    Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 angstrom resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on `as-isolated' E. coli bacterioferritin.

  6. Synthesis and crystal structure of a polymeric zinc(II) complex ...

    African Journals Online (AJOL)

    A new polymeric zinc(II) complex, [ZnL2(PDA)]n, has been prepared by the reaction of zinc sulfate, 4-nitrophenylacetic acid, and propane-1,3-diamine (PDA) in water. Structure of the complex has been characterized by single-crystal X-ray diffraction. The complex crystallizes as orthorhombic space group Pnma, with unit cell ...

  7. 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 stu...

  8. Analysis of morphology of crystals based on identification of interfacial structure

    NARCIS (Netherlands)

    Liu, X.Y.; Briels, Willem J.; Boek, E.S.; Boek, E.S.; Bennema, P.

    1995-01-01

    A new theoretical approach for the prediction of the growth habit of crystals is presented. This approach is based on a newly derived relation between the growth rate of crystal surfaces and habit-controlling factors, and includes a key step: a so-called interface structure (IS) analysis. This

  9. 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...

  10. The crystal structure of paramagnetic copper(ii) oxalate (CuC2O4):

    DEFF Research Database (Denmark)

    Christensen, Axel Nørlund; Lebech, Bente; Andersen, Niels Hessel

    2014-01-01

    -gas reveals that the material contains no crystal water and reduces to pure Cu at 295 °C. Magnetic susceptibility measurements in the temperature range from 2 K to 300 K show intriguing paramagnetic behaviour with no sign of magnetic order down to 2 K. A crystal structure investigation is made based on powder...

  11. Hot embossing of photonic crystal polymer structures with a high aspect ratio

    DEFF Research Database (Denmark)

    Schelb, Mauno; Vannahme, Christoph; Kolew, Alexander

    2011-01-01

    Hot embossing is a promising approach for mass production of photonic crystal structures. This paper describes the fabrication of a replication tool for two-dimensional photonic crystal patterns and its replication in substrates of poly(methylmethacrylate) (PMMA) and cyclic olefin copolymer (COC...

  12. Crystal orientation effects on the piezoelectric field of strained zinc-blende quantum-well structures

    DEFF Research Database (Denmark)

    Duggen, Lars; Willatzen, Morten; Lassen, Benny

    2008-01-01

    A three-layered zinc-blende quantum-well structure is analyzed subject to both static and dynamic conditions for different crystal growth directions taking into account piezoelectric effects and lattice mismatch. It is found that the strain component Szz in the quantum-well region strongly depends...... on the crystal growth direction and that a piezoelectric strain contribution exists in zinc blende as in wurtzite, albeit smaller. It is also found in the absence of loss effects that resonance frequencies, giving large strains in the structure, depend strongly on the crystal growth direction. Due to the higher...... symmetry of the zinc-blende structure, we find in a one-dimensional model that piezoelectric effects do not affect strain values for zinc-blende structures grown along the [001] direction in contrast to the corresponding wurtzite result. However, zinc-blende structures grown along a general crystal...

  13. Single crystals of DPPH grown from diethyl ether and carbon disulfide solutions - crystal structures, IR, EPR and magnetization studies.

    Science.gov (United States)

    Zilić, Dijana; Pajić, Damir; Jurić, Marijana; Molčanov, Krešimir; Rakvin, Boris; Planinić, Pavica; Zadro, Krešo

    2010-11-01

    Single crystals of the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) obtained from diethyl ether (ether) and carbon disulfide (CS₂) were characterized by the X-ray diffraction, IR, EPR and SQUID magnetization techniques. The X-ray structural analysis and IR spectra showed that the DPPH form crystallized from ether (DPPH1) is solvent free, whereas that one obtained from CS₂ (DPPH2) is a solvate of the composition 4DPPH·CS₂. Principal values of the g-tensor were estimated by the X-band EPR spectroscopy at room and low (10 K) temperatures. Magnetization studies revealed the presence of antiferromagnetically coupled dimers in both types of crystals. However, the way of dimerization as well as the strength of exchange couplings are different in the two DPPH samples, which is in accord with their crystal structures. The obtained results improved parameters accuracy and enabled better understanding of properties of DPPH as a standard sample in the EPR spectrometry. Copyright © 2010 Elsevier Inc. All rights reserved.

  14. Structural Variation in Polyoxomolybdate Hybrid Crystals Comprising Ionic-Liquid Surfactants

    Directory of Open Access Journals (Sweden)

    Takeru Ito

    2014-03-01

    Full Text Available Polyoxomolybdate inorganic-organic hybrid crystals were synthesized with 1-decyl-3-methylimidazolium and 1-dodecyl-3-methylimidazolium as ionic-liquid surfactants. Both hybrid crystals possessed alternate stacking of surfactant layers and octamolybdate (Mo8 monolayers, while the molecular structures of Mo8 were different depending on the surfactants and solvents employed for crystallization. Each Mo8 anion was connected by two sodium cations to form infinite one-dimensional chain. The surfactant chains in these crystals were arranged in a complicatedly bent manner, which will be induced by the weak C–H···O hydrogen bonds between the Mo8 anions and ionic-liquid surfactants.

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

    African Journals Online (AJOL)

    NICO

    acid chloride with 1-[bis(4-methoxyphenyl)- methyl] piperazine at room temperature with a total yield of 74 %. The structure of the product was characterized with 1H NMR, 13C NMR and. HRMS. The structure of compound 5 was finally confirmed utilizing single-crystal X-ray structure determination. The molecular structure of ...

  16. Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Olfa Mtioui-Sghaier

    2015-07-01

    Full Text Available The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005. Eur. J. Inorg. Chem. pp. 3080–3087; Cavalcante et al. (2013. Polyhedron, 54, 13–25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octahedra, both with point group symmetry 2. The distortion of the octahedra is reflected by variation of bond lengths and angles from 2.002 (3–2.274 (4 Å, 80.63 (11–108.8 (2° for equatorial and 158.4 (2– 162.81 (14° for axial angles (ZnO6, and of 1.769 (3–2.171 (3 Å, 73.39 (16–104.7 (2, 150.8 (2–164.89 (15° (MoO6, respectively. In the crystal structure, the same type of MO6 octahedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexagonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octahedral voids.

  17. 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.

  18. In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID.

    Science.gov (United States)

    Michalska, Karolina; Tan, Kemin; Chang, Changsoo; Li, Hui; Hatzos-Skintges, Catherine; Molitsky, Michael; Alkire, Randy; Joachimiak, Andrzej

    2015-11-01

    A prototype of a 96-well plate scanner for in situ data collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection at T = 100 K, crystals in a crystallization buffer show remarkably low mosaicity (Data presented here show that cryo-cooling can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software, in situ data collection will become available for the SBC user program including remote access.

  19. Crystal structure of (S-2-amino-2-methylsuccinic acid

    Directory of Open Access Journals (Sweden)

    Isao Fujii

    2015-10-01

    Full Text Available The title compound, C5H9NO4, crystallized as a zwitterion. There is an intramolecular N—H...O hydrogen bond involving the trans-succinic acid and the ammonium group, forming an S(6 ring motif. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming C(7 chains along the c-axis direction. The chains are linked by N—H...O and C—H...O hydrogen bonds, forming sheets parallel to the bc plane. Further N—H...O hydrogen bonds link the sheets to form a three-dimensional framework.

  20. Self-assembled ordered structures in thin films of HAT5 discotic liquid crystal

    Directory of Open Access Journals (Sweden)

    Piero Morales

    2010-05-01

    Full Text Available Thin films of the discotic liquid crystal hexapentyloxytriphenylene (HAT5, prepared from solution via casting or spin-coating, were investigated by atomic force microscopy and polarizing optical microscopy, revealing large-scale ordered structures substantially different from those typically observed in standard samples of the same material. Thin and very long fibrils of planar-aligned liquid crystal were found, possibly formed as a result of an intermediate lyotropic nematic state arising during the solvent evaporation process. Moreover, in sufficiently thin films the crystallization seems to be suppressed, extending the uniform order of the liquid crystal phase down to room temperature. This should be compared to the bulk situation, where the same material crystallizes into a polymorphic structure at 68 °C.

  1. 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.

  2. Determination of the Crystal Structure of Lead Tungstate by Neutron Diffraction

    CERN Document Server

    Cousson, A; Paulus, W

    1999-01-01

    The crystal structure of lead tungstate, PbWO4, is tetragonal, scheelite type, space group I4/a. This compound, due to the difference in the vapour pressure of the two raw oxides, WO3 and PbO, used in the crystal growth, is frequently subjected to lead deficiency. It has been reported by one group that lead vacancies can order in a crystal structure derived from the scheelite type, but of lower symmetry and described by the space group P4/nnc or P-4. We report here on neutron diffraction measurements performed on three different single crystals, two of them being presented to us as possibly presenting the lead deficient phase. Our measurements do not show any indication of structural distortion, even at 70 K for one of the samples. The existence of a lead deficient structure remains unconfirmed.

  3. Space-Filling Curves as a Novel Crystal Structure Representation for Machine Learning Models

    CERN Document Server

    Jasrasaria, Dipti; Rappoport, Dmitrij; Aspuru-Guzik, Alan

    2016-01-01

    A fundamental problem in applying machine learning techniques for chemical problems is to find suitable representations for molecular and crystal structures. While the structure representations based on atom connectivities are prevalent for molecules, two-dimensional descriptors are not suitable for describing molecular crystals. In this work, we introduce the SFC-M family of feature representations, which are based on Morton space-filling curves, as an alternative means of representing crystal structures. Latent Semantic Indexing (LSI) was employed in a novel setting to reduce sparsity of feature representations. The quality of the SFC-M representations were assessed by using them in combination with artificial neural networks to predict Density Functional Theory (DFT) single point, Ewald summed, lattice, and many-body dispersion energies of 839 organic molecular crystal unit cells from the Cambridge Structural Database that consist of the elements C, H, N, and O. Promising initial results suggest that the S...

  4. Crystal structure of raw pure Mysore silk fibre based on (Ala-Gly)2 ...

    Indian Academy of Sciences (India)

    Unknown

    2005-03-23

    in). We have carried out crystal structure analysis of raw pure Mysore silk fibers belonging to Bombyx mori on the basis of model parameters of Marsh et al using Linked-Atom-Least-Squares technique. The intensity of all the.

  5. Synthesis and Crystal Structure of Ethyl 2-(benzo[d]oxazol-2-yl)-5 ...

    African Journals Online (AJOL)

    NICO

    2012-10-10

    benzoxazol-2-yl)-3-(o-tolylamino)-5-oxo-. 2,5-dihydroisoxazole-4-carboxylate (5). The X-ray single crystal diffraction analysis showed that the molecular structure of 5 possesses of an intramolecular hydrogen bond from reso-.

  6. Single crystal particles of a mesoporous mixed transition metal oxide with a wormhole structure.

    Science.gov (United States)

    Lee, B; Lu, D; Kondo, J N; Domen, K

    2001-10-21

    A new type of mesoporous mixed transition metal oxide of Nb and Ta (NbTa-TIT-1) has been prepared through a two-step calcination, which consists of single crystal particles with wormhole mesoporous structure.

  7. Nonreciprocal transmission in a nonlinear photonic-crystal Fano structure with broken symmetry

    DEFF Research Database (Denmark)

    Yu, Yi; Chen, Yaohui; Hu, Hao

    2015-01-01

    Nanostructures that feature nonreciprocal light trans- mission are highly desirable building blocks for realizing photonic integrated circuits. Here, a simple and ultracompact photonic-crystal structure, where a waveguide is coupled to a single nanocavity, is proposed and experimentally demon...

  8. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

    Directory of Open Access Journals (Sweden)

    Monica Totir

    Full Text Available Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.

  9. Programmatic conversion of crystal structures into 3D printable files using Jmol.

    Science.gov (United States)

    Scalfani, Vincent F; Williams, Antony J; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M; Liddie, Jahred M; Bara, Jason E

    2016-01-01

    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. A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD. Over 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (>350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website created in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically

  10. 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...... in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib....

  11. Crystal structure of the TbZnSn{sub 2} and TbZnSn ternary compounds

    Energy Technology Data Exchange (ETDEWEB)

    Pavlyuk, V. [Ivan Franko National University of Lviv, Department of Inorganic Chemistry, Kyryla and Mefodia Street 6, 79005 Lviv (Ukraine); Czestochowa Jan Dlugosz University, Institute of Chemistry and Environmental Protection, al. Armii Krajowej 13/15, 42200 Czestochowa (Poland)], E-mail: pavlyuk@franko.lviv.ua; Oshchapovsky, I. [Ivan Franko National University of Lviv, Department of Inorganic Chemistry, Kyryla and Mefodia Street 6, 79005 Lviv (Ukraine); Marciniak, B. [Czestochowa Jan Dlugosz University, Institute of Chemistry and Environmental Protection, al. Armii Krajowej 13/15, 42200 Czestochowa (Poland)

    2009-05-27

    The crystal structures of the TbZnSn{sub 2} and TbZnSn compounds were determined by X-ray single crystal diffraction. The TbZnSn{sub 2} compound crystallizes with the HfCuSi{sub 2} structure type (space group P4/nmm) and TbZnSn crystallizes with the YPtAs structure type (space group P6{sub 3}/mmc)

  12. 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.

  13. Crystal growth and structural analysis of zirconium sulphoselenide ...

    Indian Academy of Sciences (India)

    Wintec

    tion on the lattice parameter, unit cell volume and X-ray density in the series of ZrSxSe3–x single crystals have been studied and found to decrease in all these parameters with rise in sulphur proportion. The grown cry- stals were examined under optical zoom microscope for their surface topography study. Hall effect ...

  14. Synthesis and Spectroscopic, Thermal and Crystal Structure Studies ...

    African Journals Online (AJOL)

    NICO

    salt containing discrete hydrazinium cations and hydrogen succinate anions. The crystal packing consists of infinite chains of anions and cations that are alternatively linked through O–H···N and bifurcated N–H···O bonds and this chain is connected to ad- jacent antiparallel chains by N–H···O hydrogen bonding.

  15. Is the methanation reaction over Ru single crystals structure dependent?

    DEFF Research Database (Denmark)

    Vendelbo, Søren Bastholm; Johansson, Martin; Nielsen, Jane Hvolbæk

    2011-01-01

    The influence of monoatomic steps and defects on the methanation reaction over ruthenium has been investigated. The experiments are performed on a Ru(0 1 54) ruthenium single crystal, which contains one monoatomic step atom for each 27 terrace atoms. The methanation activity is measured at one bar...

  16. Synthesis, Crystal Structure and Antifungal/Antibacterial Activity of Some Novel Highly Functionalized Benzoylaminocarbothioyl Pyrrolidines

    OpenAIRE

    DÖNDAŞ, H. Ali; NURAL, Yahya; DURAN, Nizami

    2006-01-01

    A series of novel highly functionalized benzoylaminocarbothioyl pyrrolidines were prepared from benzoylisothiocyanate and substituted pyrrolidines in excellent yield. The crystal structure of the novel 1-benzoylaminocarbothioyl-5-(naphthyl)- pyrrolidine-2,3,4-tricarboxylicacid trimethyl ester (3a) was determined by X-ray crystal structure analysis. The synthesized compounds were characterized and screened for their in vitro antibacterial and antifungal activities and toxicity. The p...

  17. Change in the crystal structure of germanium-containing lithiophosphate upon heating

    Energy Technology Data Exchange (ETDEWEB)

    Ksenofontov, D. A., E-mail: ksenofant@rambler.ru; Kabalov, Yu. K. [Moscow State University (Russian Federation); Dem' yanets, L. N. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-03-15

    The crystal structure of lithiophosphate with phosphorus atoms partially replaced by germanium, Li{sub 3.17}(P{sub 0.69}Ge{sub 0.24}Mo{sub 0.07})O{sub 4}, at temperatures of 25, 150, 300, 450, and 600 deg. C has been refined by the Rietveld method using powder data. New additional Bragg reflections are observed at T = 600 deg. C, which indicate a change in the crystal structure of this compound.

  18. Change in the crystal structure of germanium-containing lithiophosphate upon heating

    Science.gov (United States)

    Ksenofontov, D. A.; Kabalov, Yu. K.; Dem'yanets, L. N.

    2010-03-01

    The crystal structure of lithiophosphate with phosphorus atoms partially replaced by germanium, Li3.17(P0.69Ge0.24Mo0.07)O4, at temperatures of 25, 150, 300, 450, and 600°C has been refined by the Rietveld method using powder data. New additional Bragg reflections are observed at T = 600°C, which indicate a change in the crystal structure of this compound.

  19. Metamict Minerals: an Insight into a Relic Crystal Structure Using XRD, Raman Spectroscopy, SAED and HRTEM

    OpenAIRE

    Tomašić, Nenad; Bermanec, Vladimir; Gajović, Andreja; Rajić Linarić, Maša

    2008-01-01

    Metamict minerals are characterized by an amorphization of their crystal structure due to radiation damage, and they present an interesting challenge to the mineral and material scientist. The mechanisms of the crystal structure's metamictization and thermally induced recrystallization have been found not only to be of interest for solving mineralogical and geological problems, but also for helping with practical problems, like nuclear-waste storage. This paper gives an overview of the common...

  20. Structural and optical properties of europium doped zirconia single crystals fibers grown by laser floating zone

    OpenAIRE

    Soares, M.R.N.; Nico, C.; Peres, M.; Ferreira, N.; Fernandes, A.J.S.; Monteiro, T.; COSTA, F.M.

    2011-01-01

    Yttria stabilized zirconia single crystal fibers doped with europium ions were developed envisaging optical applications. The laser floating zone technique was used in order to grow millimetric high quality single crystal fibers. The as-grown fibers are completely transparent and inclusion free, exhibiting a cubic structure. Under ultraviolet (UV) excitation, a broad emission band appears at 551 nm. The europium doped fibers are translucent with a tetragonal structure and exhibit an intense r...

  1. 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.

  2. 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.

  3. Effect of Partial Crystallization on the Structural and Luminescence Properties of Er(3+)-Doped Phosphate Glasses.

    Science.gov (United States)

    Lopez-Iscoa, Pablo; Salminen, Turkka; Hakkarainen, Teemu; Petit, Laeticia; Janner, Davide; Boetti, Nadia G; Lastusaari, Mika; Pugliese, Diego; Paturi, Petriina; Milanese, Daniel

    2017-04-28

    Er-doped phosphate glass ceramics were fabricated by melt-quenching technique followed by a heat treatment. The effect of the crystallization on the structural and luminescence properties of phosphate glasses containing Al₂O₃, TiO₂, and ZnO was investigated. The morphological and structural properties of the glass ceramics were characterized by Field Emission-Scanning Electron Microscopy (FE-SEM), X-ray Diffraction (XRD), and micro-Raman spectroscopy. Additionally, the luminescence spectra and the lifetime values were measured in order to study the influence of the crystallization on the spectroscopic properties of the glasses. The volume ratio between the crystal and the glassy phases increased along with the duration of the heat treatment. The crystallization of the glass ceramics was confirmed by the presence of sharp peaks in the XRD patterns and different crystal phases were identified depending on the glass composition. Sr(PO₃)₂ crystals were found to precipitate in all the investigated glasses. As evidenced by the spectroscopic properties, the site of the Er(3+) ions was not strongly affected by the heat treatment except for the fully crystallized glass ceramic which does not contain Al₂O₃, TiO₂, and ZnO. An increase of the lifetime was also observed after the heat treatment of this glass. Therefore, we suspect that the Er(3+) ions are incorporated in the precipitated crystals only in this glass ceramic.

  4. Supervised self-organizing maps in crystal property and structure prediction

    NARCIS (Netherlands)

    Willighagen, E.L.; Wehrens, R.; Melssen, W.J.; Gelder, R. de; Buydens, L.M.C.

    2007-01-01

    This article shows, the use of supervised self-organizing maps (SOMs) to explore large numbers of experimental or simulated crystal structures and to visualize structure-property relationships. The examples show how powder diffraction patterns together with one or more structural properties, such as

  5. Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor

    DEFF Research Database (Denmark)

    Svensson, L Anders; Bondensgaard, Kent; Nørskov-Lauritsen, Leif

    2008-01-01

    The crystal structure of the complex between an N-terminally truncated G129R human prolactin (PRL) variant and the extracellular domain of the human prolactin receptor (PRLR) was determined at 2.5A resolution by x-ray crystallography. This structure represents the first experimental structure...

  6. Electric field generation of Skyrmion-like structures in a nematic liquid crystal.

    Science.gov (United States)

    Cattaneo, Laura; Kos, Žiga; Savoini, Matteo; Kouwer, Paul; Rowan, Alan; Ravnik, Miha; Muševič, Igor; Rasing, Theo

    2016-01-21

    Skyrmions are particle-like topological objects that are increasingly drawing attention in condensed matter physics, where they are connected to inversion symmetry breaking and chirality. Here we report the generation of stable Skyrmion-like structures in a thin nematic liquid crystal film on chemically patterned patchy surfaces. Using the interplay of material elasticity and surface boundary conditions, we use a strong electric field to quench the nematic liquid crystal from a fully aligned phase to vortex-like nematic liquid crystal structures, centered on patterned patches, which carry two different sorts of topological defects. Numerical calculations reveal that these are Skyrmion-like structures, seeded from the surface boojum topological defects and swirling towards the second confining surface. These observations, supported by numerical methods, demonstrate the possibility to generate, manipulate and study Skyrmion-like objects in nematic liquid crystals on patterned surfaces.

  7. Crystal structure and phase transitions in perovskite-like C(NH2)(3)SnCl3

    DEFF Research Database (Denmark)

    Szafranski, M.; Ståhl, Kenny

    2007-01-01

    X-ray single-crystal diffraction, high-temperature powder diffraction and differential thermal analysis at ambient and high pressure have been employed to study the crystal structure and phase transitions of guanidinium trichlorostannate, C(NH2)(3)SnCl3. At 295 K the crystal structure is orthorho...

  8. Crystal structure of Cs2[Th(NO36

    Directory of Open Access Journals (Sweden)

    Patrick Woidy

    2014-08-01

    Full Text Available Dicaesium hexanitratothorate(IV, Cs2[Th(NO36], was synthesized in the form of colourless crystals by reaction of thorium nitrate and caesium nitrate in aqueous solution. The Th atom is located on an inversion centre and is coordinated by six chelating nitrate anions. The resulting ThO12 coordination polyhedron is best described as a slightly distorted icosahedron. The Cs atom also has a coordination number of 12, but its coordination polyhedron is considerably more distorted. The crystal packing can be derived from an hexagonal dense packing (hcp of idealized spherical CsO12 and ThO12 units. The CsO12 units form a distorted hcp arrangement and half of the octahedral sites are occupied by the ThO12 units.

  9. Structural phase transitions and topological defects in ion Coulomb crystals

    Energy Technology Data Exchange (ETDEWEB)

    Partner, Heather L. [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Nigmatullin, Ramil [Institute of Quantum Physics, Ulm Univ., Ulm (Germany); Burgermeister, Tobias [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Keller, Jonas [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Pyka, Karsten [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Plenio, Martin B. [Center for Integrated Quantum Science and Technology, Ulm Univ., Ulm, (Germany):Institute for Theoretical Physics, Ulm Univ.,Ulm, (Germany); Retzker, Alex [Racah Institute of Physics, The Hebrew University of Jerusalem, Givat Ram (Israel); Zurek, Wojciech Hubert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); del Campo, Adolfo [Univ. of Massachusetts, Amherst, MA (United States). Dept. of Physics; Mehlstaubler, Tanja E. [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany)

    2014-11-19

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed non-adiabatically. For a second order phase transition, the Kibble-Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation.

  10. Significant Reduction of Graphene Thermal Conductivity by Phononic Crystal Structure

    OpenAIRE

    Yang, Lina; CHEN, JIE; Yang, Nuo; Li, Baowen

    2014-01-01

    We studied the thermal conductivity of graphene phononic crystal (GPnC), also named as graphene nanomesh, by molecular dynamics simulations. The dependences of thermal conductivity of GPnCs on both length and temperature are investigated. It is found that the thermal conductivity of GPnCs is significantly lower than that of graphene and can be efficiently tuned by changing the porosity and period length. For example, the ratio of thermal conductivity of GPnC to thermal conductivity of graphen...

  11. Crystal structure of 3-[(2-acetylphenoxycarbonyl]benzoic acid

    Directory of Open Access Journals (Sweden)

    Mohammad Shoaib

    2014-11-01

    Full Text Available In the title compound, C16H12O5, synthesized from isopthaloyl chloride and 2′-hydroxyacetophenone, the dihedral angle between the planes of the aromatic rings is 71.37 (9°. In the crystal, carboxylic acid inversion dimers generate R22(8 loops. The dimers are linked by C—H...O interactions, generating (101 sheets.

  12. Crystal structure of 4-amino-2,6-dichlorophenol

    Directory of Open Access Journals (Sweden)

    Kyle J. McDonald

    2015-06-01

    Full Text Available The title compound, C6H5Cl2NO, has a single planar molecule in the asymmetric unit with the non-H atoms possessing a mean deviation from planarity of 0.020 Å. In the crystal, O—H...N hydrogen bonds lead to the formation of infinite chains along [101] which are further linked by N—H...O hydrogen bonds, forming (010 sheets.

  13. Supercoiled DNA; plectonemic structure and liquid crystal formation

    CERN Document Server

    Maarel, J R C; Jesse, W; Backendorf, C; Egelhaaf, S U; Lapp, A

    2003-01-01

    We have investigated the phase behaviour of pUC18 plasmid solutions with phase separation experiments and polarized light microscopy. Furthermore, the configuration of the superhelix is monitored with small-angle neutron scattering. The phase diagram is interpreted with liquid crystal theory including the effects of charge, orientation entropy, excluded volume, as well as the elastic, entropic and electrostatic contributions to the molecular free energy.

  14. Synthesis and crystal structures of three isophthalato-bridged ...

    Indian Academy of Sciences (India)

    a pitch of 15.04Е. Unfortunately a one-dimensional right-handed helical chain was not found in com- plex 2. Both compounds 2 and 3 crystallize in the same chiral space groups, P212121. The absolute struc- ture parameters of –0.04(2) and 0.032(16), respec- tively, confirm the homochiral nature of complexes 2 and 3.

  15. Crystal structure of cyclo-hexyl-ammonium thio-cyanate.

    Science.gov (United States)

    Bagabas, Abdulaziz A; Alhoshan, Sultan B; Ghabbour, Hazem A; Chidan Kumar, C S; Fun, Hoong-Kun

    2015-01-01

    In the title salt, C6H11NH3 (+)·SCN(-), the cyclo-hexyl-ammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial inter-actions. In the crystal, the components are linked by N-H⋯N and N-H⋯S hydrogen-bonding inter-actions, resulting in a three-dimensional network.

  16. Crystal structure of akuammicine, an indole alkaloid from Catharanthus roseus

    Directory of Open Access Journals (Sweden)

    Mahdi Yahyazadeh

    2017-11-01

    Full Text Available The title compound, C20H22N2O2, an alkaloid isolated from the Madagascar periwinkle, crystallizes in P1 with two independent but closely similar molecules in the unit cell. The molecules are linked into pairs by two N—H...O=C hydrogen bonds. The absolute configuration was confirmed by anomalous dispersion effects as S at the 3 and 15 positions, and R at the 7 position.

  17. 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.

  18. Scintillating crystals for hadron structure studies and instrumentation

    Science.gov (United States)

    Ngwenya, Blessed; Horn, Tanja; Pegg, Ian

    2017-09-01

    Deep exclusive and semi-inclusive processes like deeply virtual photon or neutral pion production play a critical role in 3D hadron imaging at the 12 GeV Jefferson Lab and the future Electron-Ion Collider. Measurements require detectors capable of identifying the final state photon or meson. Electromagnetic CALorimeters (ECAL) are well suited for this providing both particle identification and reconstruction. A typical ECAL is a light-transparent, homogeneous, crystal calorimeter with dimensions large enough to contain the complete shower of secondary particles. Important characteristics include high resolution, timing, and radiation hardness. The material of choice is PbWO4, which features a small Moliere radius, very good energy and position resolution, fast response, and radiation resistance. One company in the world is manufacturing PbWO4 but the quality is not satisfactory, in particular regarding light-yield and radiation hardness, which depend on the manufacturing process. It is important to understand the production and how impurities and the crystallization process affect the crystal's properties. This presentation will review the physics and detection requirements of neutral final states and present the development of a setup to grow PbWO4 using a Czochralsky method. Supported in part by: NSF PHY1306227 and PHY1714133, South Africa Washington International Program.

  19. 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.

  20. Structure of KTiOPO{sub 4} single crystals grown by the top-seeded solution and spontaneous flux crystallization methods

    Energy Technology Data Exchange (ETDEWEB)

    Novikova, N. E., E-mail: natnov@ns.crys.ras.ru; Verin, I. A.; Sorokina, N. I.; Alekseeva, O. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Voronkova, V. I. [Moscow State University (Russian Federation); Tseitlin, M. [Ariel University Center of Samaria (Israel); Roth, M. [Hebrew University of Jerusalem, Faculty of Science (Israel)

    2008-11-15

    This paper reports on the results of precision X-ray structural investigations of KTiOPO{sub 4} single crystals grown by one method (crystallization from a solution in the melt) in two variants (the spontaneous formation of crystallization centers or top-seeded solution growth during slow cooling of saturated solution melts). It is shown that spontaneous flux crystallization leads to the formation of a larger number of defects. Potassium atoms are found to be disordered. The splitting of the K1 and K2 potassium positions is equal to 0.347(4) and 0.279(3) A, respectively, for the crystals grown by the top-seeded solution method and 0.308(5) and 0.321(4) A, respectively, for the crystals grown through the spontaneous flux crystallization.

  1. Synthesis, growth, structure determination and optical properties of chalcone derivative single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Karthi, S., E-mail: girijaeaswaradas@gmail.com; Girija, E. K., E-mail: girijaeaswaradas@gmail.com [Department of Physics, Periyar University, Salem - 636011 (India)

    2014-04-24

    Acquiring large nonlinear optical (NLO) efficient organic material is essential for the development of optoelectronics and photonic devices. Chalcone is the donor - Π - acceptor - Π - donor (D-Π-A-Π-D) type conjugated molecule with appreciable hyperpolarizability of potential interest in NLO applications. The addition of vinyl and electron donor groups in the chalcone molecule may enhance the second harmonic generation (SHG) efficiency. Here we report the synthesis, crystal growth and characterization of a chalcone derivative 1-(4-methylphenyl)-5-(4-methoxyphenyl)-penta-2,4-dien-1-one (MPMPP). The MPMPP crystal was grown by slow evaporation solution growth technique from acetone. The grown crystal structure was studied by single crystal X-ray diffraction. The SHG efficiency of the grown crystal was determined by Kurtz and Perry method.

  2. Crystal structure control in Au-free self-seeded InSb wire growth

    Energy Technology Data Exchange (ETDEWEB)

    Mandl, Bernhard; Dick, Kimberly A; Deppert, Knut [Department of Solid State Physics, Lund University, S-22 100 Lund (Sweden); Kriegner, Dominik; Keplinger, Mario; Bauer, Guenther; Stangl, Julian, E-mail: Bernhard.Mandl@jku.at [Institute of Solid State- and Semiconductor Physics, Johannes Kepler University Linz, A-4040 Linz (Austria)

    2011-04-08

    In this work we demonstrate experimentally the dependence of InSb crystal structure on the ratio of Sb to In atoms at the growth front. Epitaxial InSb wires are grown by a self-seeded particle assisted growth technique on several different III-V substrates. Detailed investigations of growth parameters and post-growth energy dispersive x-ray spectroscopy indicate that the seed particles initially consist of In and incorporate up to 20 at.% Sb during growth. By applying this technique we demonstrate the formation of zinc-blende, 4H and wurtzite structure in the InSb wires (identified by transmission electron microscopy and synchrotron x-ray diffraction), and correlate this sequential change in crystal structure to the increasing Sb/In ratio at the particle-wire interface. The low ionicity of InSb and the large diameter of the wire structures studied in this work are entirely outside the parameters for which polytype formation is predicted by current models of particle seeded wire growth, suggesting that the V/III ratio at the interface determines crystal structure in a manner well beyond current understanding. These results therefore provide important insight into the relationship between the particle composition and the crystal structure, and demonstrate the potential to selectively tune the crystal structure in other III-V compound materials as well.

  3. 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.

  4. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.

    Science.gov (United States)

    Biedermannová, Lada; Schneider, Bohdan

    2015-11-01

    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.

  5. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

    Science.gov (United States)

    Biedermannová, Lada; Schneider, Bohdan

    2015-01-01

    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. PMID:26527137

  6. 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.

  7. Crystal structure and high-pressure studies of WAl 2, an aluminide crystallizing with the CrSi 2 structure type

    Science.gov (United States)

    Gu, Q. F.; Jung, D. Y.; Krauss, G.; Steurer, W.

    2008-10-01

    The novel intermetallic compound WAl 2 crystallizes with space group P6 422 and lattice parameters a=4.7422(1) Å, c=6.6057(2) Å. The crystal structure was solved from single-crystal X-ray diffraction data. WAl 2 was found to be the first aluminide that is isotypic with CrSi 2. A high-pressure powder X-ray diffraction study showed its stability up to at least 31.5(1) GPa. The bulk modulus was calculated by fitting a third-order Birch-Murnaghan equation of state to the pressure-volume data as K0=168(11) GPa and its pressure derivative K'=7.7(1.0). Partially covalent bonding between W and Al atoms was indicated by means of the electron localization function (ELF) and explains the anisotropic compression behavior. Quantum chemical calculations identify WAl 2 as a potential high-temperature phase.

  8. Title Crystal structure of bis(pyrazinamide dibenzoat cobalt(II diaqua

    Directory of Open Access Journals (Sweden)

    Necmi DEGE

    2017-06-01

    Full Text Available The crystal structure of the complex, (C24H24CoN6O8, was determined at 296 K. Structure of single crystal compound were investigated using single crystal X-ray diffraction. The unit cell parameters of the crystal structure are a=7.1823 Å, b=18.2190 Å, c=10.4149 Å, α=90°, β=109.879°, γ=90° ve Z=2. The complex crystallizes in the centrosymmetric monoclinic space group P21/c. In the crystal structure, the anions and cations are linked with three dimensions via O—H···O and N—H···O interactions. Pyrazinamide (PZA is used as a first step drug in the treatment of tuberculosis for over 50 years [1]. It shortens the total healing time as being bactericide for some specific bacteria. PZA and its derivatives are widely used due to their antimicrobial properties [1]. It is also used to reduce the duration of chemotherapy [2].

  9. Crystal structure of diethylammonium aniline-4-sulfonate anilinium-4-sulfonate

    Directory of Open Access Journals (Sweden)

    Assane Toure

    2016-12-01

    Full Text Available The title compound, C4H12N+·C6H6NO3S−·C6H7NO3S, consists of an ion pair and a zwitterionic neutral molecule. The cation adopts an extended conformation [C—C—N—C torsion angles = 177.1 (3 and −178.4 (3°]. In the crystal, the components are linked by N—H...O and N—H...N hydrogen bonds, generating a three-dimensional network, which is consolidated by weak C—H...O interactions.

  10. Crystal structure of 2-bromo-4,6-dinitroaniline

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-11-01

    Full Text Available In the title compound, C6H4BrN3O4, the dihedral angles between the nitro groups and the aniline ring are 2.04 (3 and 1.18 (4°, respectively. In the crystal, N—H...O and C—H...O hydrogen bonds and weak side-on C—Br...π interactions [3.5024 (12 Å] link adjacent molecules, forming a three-dimensional network. A close O...Br contact [3.259 (2 Å] may also add additional stability.

  11. Crystal structure of 2,6-dimethyl-4-pyridone hemihydrate

    Directory of Open Access Journals (Sweden)

    Dalena M. Nguyen

    2015-08-01

    Full Text Available The title compound (systematic name: 2,6-dimethyl-1H-pyridin-4-one hemihydrate, C7H9NO·0.5H2O, has a single planar molecule in the asymmetric unit with the non-H atoms possessing a mean deviation from planarity of 0.021 Å. There is also half of a water molecule present in the asymmetric unit. In the crystal, infinite (001 sheets are formed by N—H...O and O—H...O hydrogen bonds.

  12. Crystal structure of 5-[(4-carboxybenzyloxy]isophthalic acid

    Directory of Open Access Journals (Sweden)

    Md. Serajul Haque Faizi

    2016-08-01

    Full Text Available The molecular shape of the title compound, C16H12O7, is bent around the central CH2—O bond. The two benzene rings are almost perpendicular to one another, making a dihedral angle of 87.78 (7°. In the crystal, each molecule is linked to three others by three pairs of O—H...O hydrogen bonds, forming undulating sheets parallel to the bc plane and enclosing R22(8 ring motifs. The sheets are linked by C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional network.

  13. Crystal structure of ethyl 2-chloro-6-methylquinoline-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Hasna Hayour

    2014-09-01

    Full Text Available In the title compound, C13H12ClNO2, the dihedral angle between the planes of the quinoline ring system (r.m.s. deviation = 0.029 Å and the ester group is 54.97 (6°. The C—O—C—Cm (m = methyl torsion angle is −140.62 (16°. In the crystal, molecules interact via aromatic π–π stacking [shortest centroid–centroid separation = 3.6774 (9 Å] generating (010 sheets.

  14. Gallium arsenide single crystal solar cell structure and method of making

    Science.gov (United States)

    Stirn, Richard J. (Inventor)

    1983-01-01

    A production method and structure for a thin-film GaAs crystal for a solar cell on a single-crystal silicon substrate (10) comprising the steps of growing a single-crystal interlayer (12) of material having a closer match in lattice and thermal expansion with single-crystal GaAs than the single-crystal silicon of the substrate, and epitaxially growing a single-crystal film (14) on the interlayer. The material of the interlayer may be germanium or graded germanium-silicon alloy, with low germanium content at the silicon substrate interface, and high germanium content at the upper surface. The surface of the interface layer (12) is annealed for recrystallization by a pulsed beam of energy (laser or electron) prior to growing the interlayer. The solar cell structure may be grown as a single-crystal n.sup.+ /p shallow homojunction film or as a p/n or n/p junction film. A Ga(Al)AS heteroface film may be grown over the GaAs film.

  15. Crystallization Behaviors and Structure Transitions of Biocompatible and Biodegradable Diblock Copolymers

    Directory of Open Access Journals (Sweden)

    Feifei Xue

    2014-08-01

    Full Text Available Biocompatible and biodegradable block copolymers (BBCPs containing crystalline blocks become increasingly important in polymer science, and have great potential applications in polymer materials. Crystallization in polymers is accompanied by the adoption of an extended conformation, or often by chain folding. It is important to distinguish between crystallization in homopolymers and in block copolymers. In homopolymers, chain folding leads to metastable structures introduced by the crystallization kinetics. In contrast, equilibrium chain folding in diblocks can be achieved as the equilibrium number of the folds is controlled by the size of the second block. The structures of BBCPs, which are determined by the competition between crystallization, microphase separation, kinetics and processing, have a tremendous influence on the final properties and applications. In this review, we present the recent advances on crystalline–crystalline diblock copolymer in our group.

  16. Crystal structures of model lithium halides in bulk phase and in clusters

    Science.gov (United States)

    Lanaro, G.; Patey, G. N.

    2017-04-01

    We employ lattice energy calculations and molecular dynamics simulations to compare the stability of wurtzite and rock salt crystal structures of four lithium halides (LiF, LiCl, LiBr, and LiI) modeled using the Tosi-Fumi and Joung-Cheatham potentials, which are models frequently used in simulation studies. Both infinite crystals and finite clusters are considered. For the Tosi-Fumi model, we find that all four salts prefer the wurtzite structure both at 0 K and at finite temperatures, in disagreement with experiments, where rock salt is the stable structure and wurtzite exists as a metastable state. For Joung-Cheatham potentials, rock salt is more stable for LiF and LiCl, but the wurtzite structure is preferred by LiBr and LiI. It is clear that the available lithium halide force fields need improvement to bring them into better accord with the experiment. Finite-size clusters that are more stable as rock salt in the bulk phase tend to solidify as small rock salt crystals. However, small clusters of salts that prefer the wurtzite structure as bulk crystals tend to form structures that have hexagonal motifs, but are not finite-size wurtzite crystals. We show that small wurtzite structures are unstable due to the presence of a dipole and rearrange into more stable, size-dependent structures. We also show that entropic contributions can act in favor of the wurtzite structure at higher temperatures. The possible relevance of our results for simulation studies of crystal nucleation from melts and/or aqueous solutions is discussed.

  17. HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure.

    Science.gov (United States)

    Cooper, Richard I; Flack, Howard D; Watkin, David J

    2017-11-01

    The resonant-scattering contributions to single-crystal X-ray diffraction data enable the absolute structure of crystalline materials to be determined. Crystal structures can be determined even if they contain considerably disordered regions because a correction is available via a discrete Fourier transform of the residual electron density to approximate the X-ray scattering from the disordered region. However, the corrected model cannot normally account for resonant scattering from atoms in the disordered region. Straightforward determination of absolute structure from crystals where the strongly resonantly scattering atoms are not resolved has therefore not been possible. Using an approximate resonant-scattering correction to the X-ray scattering from the disordered regions, we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refinement or other post-refinement determination methods. Results show that in favourable cases the HUG method works well and the absolute structure can be correctly determined. It offers no useful improvement in cases where the original correction for the disordered region scattering density is problematic, for example, when a large fraction of the scattering density in the crystal is disordered, or when voids are not occupied equally by the disordered species. Crucially, however, if the approach does not work for a given structure, the statistics for the absolute structure measures are not improved, meaning it is unlikely to lead to misassignment of absolute structure.

  18. Mesoporous Single-crystal CoSn(OH)6 Hollow Structures with Multilevel Interiors

    OpenAIRE

    Wang, Zhiyu; Wang, Zichen; Wu, Haobin; Lou, Xiong Wen (David)

    2013-01-01

    Hollow nanostructures represent a unique class of functional nanomaterials with many applications. In this work, a one-pot and unusual ?pumpkin-carving? protocol is demonstrated for engineering mesoporous single-crystal hollow structures with multilevel interiors. Single-crystal CoSn(OH)6 nanoboxes with uniform size and porous shell are synthesized by fast growth of CoSn(OH)6 nanocubes and kinetically-controlled etching in alkaline medium. Detailed investigation on reaction course suggests th...

  19. Clarifying process versus structure in human intelligence: Stop talking about fluid and crystallized.

    OpenAIRE

    Johnson, W.; Gottesman, I I

    2006-01-01

    Blair presumes the validity of the fluid-crystallized model throughout his article. Two comparative evaluations recently demonstrated that this presumption can be challenged. The fluid-crystallized model offers little to the understanding of the structural manifestation of general intelligence and other more specific abilities. It obscures important issues involving the distinction of pervasive learning disabilities (low general intelligence) from specific, content-related disabilities that i...

  20. Synthesis and crystal structure of 1-[2-(3-ethyl-2,2 ...

    African Journals Online (AJOL)

    The title compound 1-[2-(3-ethyl-2,2-dimethylcyclobutyl)acetyl]-3-phenylthiourea has been synthesized and its crystal structure was studied. The crystal belongs to triclinic system, space group P-1, a = 10.200(2) Ǻ, b = 12.395(3) Å, c = 15.679(3) Å, α = 92.99(2)o, β = 106.00(3)o, γ = 111.95(3)o, V = 1740.4(6) Å3, Z = 2, ...

  1. Crystal structures of the solvates of diethylaminogossypol with ethyl acetate and pyridine

    Science.gov (United States)

    The crystal structures of diethylaminogossypol with ethyl acetate (DEAG-EA) and pyridine (DEAG-P) were studied by room-temperature X-ray diffraction. The host-to-guest molecule ratio in these complexes is 2:1 for DEAG-EA and 2:5 for DEAG-P. The crystal and cell parameters for DEAG-EA are C34H40N2O6...

  2. Crystal structure of 3-diethylaminomethyl-2,2'-biphenol

    Science.gov (United States)

    Ng, Seik Weng; Wojciechowski, Grzegorz; Brzezinski, Bogumil

    2002-10-01

    Crystals of 3-diethylaminomethyl-2,2'-biphenol were examined using X-ray diffraction and FT-IR spectroscopy. Their space group is P2 1/ c with a=7.305(1), b=13.816(2), c=29.232(4) Å, β=92.411(3)° and Z=8. The unit cell contains two symmetry-independent zwitterions. The hydrogen atom of the protonated diethylaminomethyl group is linked to the negatively charged phenolate oxygen atom, which in turn is linked to the hydroxyl group by a short hydrogen bond (molecule a: N⋯O=2.604(3), O⋯ O=2.512(3) Å; molecule b: N⋯O=2.593(4), O⋯ O=2.489(4) Å). The OH⋯O -⋯H +N bifurcated intramolecular hydrogen bonds are crystallographically asymmetric. The IR spectrum of the crystals confirms very well the results obtained by the X-ray study. Instead of continuous absorption, only broad bands are found indicating relatively low proton polarisability in the two types of intramolecular hydrogen bonds.

  3. Crystal structure, electrical properties and electronic band structure of tantalum ditelluride

    CERN Document Server

    Vernes, A; Bensch, W; Heid, W; Naether, C

    1998-01-01

    Motivated by the unexpectedly strong influence of the Te atoms on the structural and bonding properties of the transition metal tellurides, we have performed a detailed study of TaTe sub 2. Experimentally, this comprises a crystal structure determination as well as electrical resistivity measurements. The former analysis leads to an accurate update of the structural data reported in the 1960s, while the latter provides evidence for the mainly electronic character of scattering processes leading to the electrical conductivity. In addition, the electronic properties of TaTe sub 2 have been calculated using the TB-LMTO method. The partial density of states reflects the close connection of the Ta zigzag chains and the Te-Te network. This finding explains the charge transfer in the system in a rather simple way. The orthogonal-orbital character of the bands proved the existence of pi-bonds. The Fermi-surface study supports the interpretation of the experimental resistivity measurements. (author)

  4. NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

    CERN Document Server

    Ladik, János

    1975-01-01

    The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

  5. Highly sensitive quartz crystal microbalance based biosensor using Au dendrite structure

    Science.gov (United States)

    Asai, Naoto; Terasawa, Hideaki; Shimizu, Tomohiro; Shingubara, Shoso; Ito, Takeshi

    2018-02-01

    A Au dendrite structure was obtained by only electroplating under a suitable potential. A blanch like nanostructure was formed along the crystal orientation. In this study, we attempted to fabricate a Au dendrite structure on the electrode of a quartz crystal by electroplating to increase the specific surface area. We estimated the effective surface area by cyclic voltammetry (CV) and monitored the frequency shift induced by antigen–antibody interaction by the quartz crystal microbalance (QCM) method. The dendrite structure with the largest surface area was formed under ‑0.95 V for 5 min. In the measurement of the antigen–antibody interaction, the frequency shifts of 40, 80, and 110 Hz were obtained with the dendrite structured QCM chips formed at the above potential for 1, 1.5, and 2.0 min, respectively. The sensitivity was improved compared with that QCM chip having a flat surface electrode.

  6. Observation of a structural transition for coulomb crystals in a linear Paul trap

    DEFF Research Database (Denmark)

    Kjærgaard, N.; Drewsen, M.

    2003-01-01

    A structural transition for laser cooled ion Coulomb crystals in a linear Paul trap just above the stability limit of parametrically resonant excitation of bulk plasma modes has been observed. In contrast to the usual spheroidal shell structures present below the stability limit, the ions arrange...... in a "string-of-disks" configuration. The spheroidal envelopes of the string-of-disks structures are in agreement with results from cold fluid theory usually valid for ion Coulomb crystals if the ion systems are assumed to be rotating collectively....

  7. Dual curved photonic crystal ring resonator based channel drop filter using two-dimensional photonic crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Chhipa, Mayur Kumar, E-mail: mayurchhipa1@gmail.com [Deptt. of Electronics and Communication Engineering, Government Engineering College Ajmer Rajasthan INDIA (India); Dusad, Lalit Kumar [Rajasthan Technical University Kota, Rajasthan (India)

    2016-05-06

    In this paper channel drop filter (CDF) is designed using dual curved photonic crystal ring resonator (PCRR). The photonic band gap (PBG) is calculated by plane wave expansion (PWE) method and the photonic crystal (PhC) based on two dimensional (2D) square lattice periodic arrays of silicon (Si) rods in air structure have been investigated using finite difference time domain (FDTD) method. The number of rods in Z and X directions is 21 and 20 respectively with lattice constant 0.540 nm and rod radius r = 0.1 µm. The channel drop filter has been optimized for telecommunication wavelengths λ = 1.591 µm with refractive indices 3.533. In the designed structure further analysis is also done by changing whole rods refractive index and it has been observed that this filter may be used for filtering several other channels also. The designed structure is useful for CWDM systems. This device may serve as a key component in photonic integrated circuits. The device is ultra compact with the overall size around 123 µm{sup 2}.

  8. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor

    DEFF Research Database (Denmark)

    Rasmussen, Søren Gøgsig Faarup; Choi, Hee-Jung; Rosenbaum, Daniel M

    2007-01-01

    Structural analysis of G-protein-coupled receptors (GPCRs) for hormones and neurotransmitters has been hindered by their low natural abundance, inherent structural flexibility, and instability in detergent solutions. Here we report a structure of the human beta2 adrenoceptor (beta2AR), which....... These differences may be responsible for the relatively high basal activity and structural instability of the beta2AR, and contribute to the challenges in obtaining diffraction-quality crystals of non-rhodopsin GPCRs....

  9. Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy.

    Science.gov (United States)

    Baias, Maria; Widdifield, Cory M; Dumez, Jean-Nicolas; Thompson, Hugh P G; Cooper, Timothy G; Salager, Elodie; Bassil, Sirena; Stein, Robin S; Lesage, Anne; Day, Graeme M; Emsley, Lyndon

    2013-06-07

    A protocol for the ab initio crystal structure determination of powdered solids at natural isotopic abundance by combining solid-state NMR spectroscopy, crystal structure prediction, and DFT chemical shift calculations was evaluated to determine the crystal structures of four small drug molecules: cocaine, flutamide, flufenamic acid, and theophylline. For cocaine, flutamide and flufenamic acid, we find that the assigned (1)H isotropic chemical shifts provide sufficient discrimination to determine the correct structures from a set of predicted structures using the root-mean-square deviation (rmsd) between experimentally determined and calculated chemical shifts. In most cases unassigned shifts could not be used to determine the structures. This method requires no prior knowledge of the crystal structure, and was used to determine the correct crystal structure to within an atomic rmsd of less than 0.12 Å with respect to the known reference structure. For theophylline, the NMR spectra are too simple to allow for unambiguous structure selection.

  10. A proton wire and water channel revealed in the crystal structure of isatin hydrolase

    DEFF Research Database (Denmark)

    Bjerregaard-Andersen, Kaare; Sommer, Theis; Jensen, Jan Kristian

    2014-01-01

    The high resolution crystal structures of isatin hydrolase from Labrenzia aggregata in the apo and the product state, are described. These are the first structures of a functionally characterized metal-dependent hydrolase of this fold. Isatin hydrolase converts isatin to isatinate and belongs to ...

  11. The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti.

    Science.gov (United States)

    Chu, Huy Nhat; Kobayashi, Jun; Mikami, Bunzo; Yagi, Toshiharu

    2011-01-01

    Pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway I of pyridoxine, a vitamin B(6) compound. Its crystal structure was elucidated for the first time. Molecular replacement with (S)-1-phenylthanol dehydrogenase (PDB code 2EW8) was adopted to determine the tertiary structure of the NAD(+)-bound enzyme.

  12. Crystal structures of meso-tetrakis (2′, 6′/3′, 5′-difluorophenyl ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 4. Crystal structures of meso-tetrakis(2′,6′/3′,5′-difluorophenyl)porphyrins and their metal complexes: Influence of position of the fluoro groups on their structural properties. Bhyrappa Puttaiah Karuppaiah Karunanithi. Regular Articles Volume 128 ...

  13. Acetate Ligands Determine the Crystal Structure of CdSe Nanoplatelets - a Density Functional Theory study

    NARCIS (Netherlands)

    Koster, R.S.; Fang, C.M.; van Blaaderen, A.; Dijkstra, M.; van Huis, M.A.

    2016-01-01

    Cadmium selenide (CdSe) nanoplatelets of a few atomic layers thick exhibit extremely sharp photoluminescence peaks and are synthesized in the zinc blende crystal structure, whereas the most stable bulk polymorph of CdSe is the wurtzite structure. These platelets can be synthesized very

  14. Crystal structure transformation of TiO2 in presence of Fe2O3 and ...

    Indian Academy of Sciences (India)

    Unknown

    267–273. © Indian Academy of Sciences. 267. Crystal structure transformation of TiO2 in presence of ... and found that transformation occurs at higher tem- perature than that for pure anatase. The rate of trans- ... structure, which causes an increase in density, decrease in cell volume, mechanical strain and decrease in ...

  15. Crystal structure and charge distribution of pyrazine: effects of extinction, thermal diffuse scattering and series termination

    NARCIS (Netherlands)

    de With, G.; Harkema, Sybolt; Feil, D.

    1976-01-01

    The crystal structure and electronic charge distribution of pyrazine (1,4-diazabenzene) has been determined at 184 K by X-ray methods. The structural results of Wheatley [Acta Cryst. (1957), 10, 182-187] have been confirmed. A clear indication of bonding effects is obtained. Neither positional and

  16. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Kristensen, Ole

    2012-01-01

    The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a ß-sheet and three a-helices forming...

  17. Development of photonic crystal structures for on-board optical communication

    NARCIS (Netherlands)

    Khan, M.U.; Justice, J.; Boersma, A.; Mourad, M.; Ee, R.J. van; Blaaderen, A. van; Wijnhoven, J.; Corbett, B.

    2014-01-01

    We present designs for sharp bends in polymer waveguides using colloidal photonic crystal (PhC) structures. Both silica (SiO2) sphere based colloidal PhC and core-shell colloidal PhC structures having a titania (TiO 2) core inside silica (SiO2) shells are simulated. The simulation results show that

  18. METHODS OF RECEIVING OF FINE-GRAINED STRUCTURE OF CASTINGS AT CRYSTALLIZATION

    Directory of Open Access Journals (Sweden)

    N. K. Tolochko

    2012-01-01

    Full Text Available The article deals with methods for fine-grained structure of ingots during crystallization depending on the used foundry technologies. It is shown that by using modern scientific and technological advances may improve the traditional and the development of new casting processes, providing production of cast parts with over fine-grained structure and enhanced properties.

  19. Revision of the Crystal Structure of the First Molecular Polymorph in History

    DEFF Research Database (Denmark)

    Johansson, Kristoffer E.; Van De Streek, Jacco

    2016-01-01

    computational crystal structure prediction (CSP) method based on dispersion-corrected density functional theory, we correctly predict the stable form I with the lowest energy among all sampled structures and its polytypic form III with slightly higher energy. From Rietveld refinement of selected CSP models...

  20. Crystal-Structure Contribution to the Solid Solubility in Transition Metal Alloys

    DEFF Research Database (Denmark)

    Ruban, Andrei; Skriver, Hans Lomholt; Nørskov, Jens Kehlet

    1998-01-01

    The solution energies of 4d metals in other 4d metals as well as the bcc-hcp structural energy differences in random 4d alloys are calculated by density functional theory. It is shown that the crystal structure of the host plays a crucial role in the solid solubility. A local virtual bond...

  1. Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.; Schwalbe, C.H.

    2012-01-01

    A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two

  2. Crystal structure of the high-alkaline serine protease PB92 from Bacillus alcalophilus

    NARCIS (Netherlands)

    van der Laan, J.M.; Teplyakov, A.V.; Kelders, H.; Kalk, K.H.; Misset, O.; Mulleners, L.J.S.M.; Dijkstra, B.W.

    The crystal structure of a serine protease from the alkalophilic strain Bacillus alcalophilus PB92 has been determined by X-ray diffraction at 1.75 Å resolution. The structure has been solved by molecular replacement using the atomic model of subtilisin Carlsberg. The model of the PB92 protease has

  3. Crystal growth, structural, optical, thermal and dielectric properties of lithium hydrogen oxalate monohydrate single crystal

    Science.gov (United States)

    Chandran, Senthilkumar; Paulraj, Rajesh; Ramasamy, P.

    2017-11-01

    The vibrational groups of the lithium hydrogen oxalate monohydrate have been investigated by FTIR and FT- Raman analyses. It has low absorbance in the UV-Vis-NIR region. The laser damage threshold study confirms that the material withstands upto 30 mJ with time of 7 s, after that circular dot damage is seen on the surface. The dark region of the surface damage spot occurs due to the thermal effects. The material is thermally stable upto 93 °C and there is no weight loss below this temperature. The dielectric studies were carried out at the frequency regions of 1 kHz-1 MHz and different temperatures from 40 °C to 80 °C. Semi-organic non-linear optical (NLO) single crystal lithium hydrogen oxalate monohydrate has been grown by slow evaporation solution growth technique. The Hirshfeld surface analysis was performed to understand the different intermolecular interactions in the title compound. The fingerprint plots contain the highest portion of H⋯O/O⋯H (48.3%) interactions.

  4. Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data

    DEFF Research Database (Denmark)

    Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M

    2012-01-01

    Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal...... structure of tri-p-benzamide. The same procedure is then applied to solve the previously unknown crystal structure of tetra-p-benzamide. In the crystal structure of tetra-p-benzamide, an unusual hydrogen-bonding scheme is realised; the hydrogen-bonding scheme is, however, in perfect agreement with solid...

  5. Crystal structure of 3,4-dichloroanilinium hydrogen phthalate

    Directory of Open Access Journals (Sweden)

    Muhammad Shahid

    2015-07-01

    Full Text Available In the title salt, C6H6Cl2N+·C8H5O4−, the carboxylic acid and carboxylate groups of the anion form dihedral angles of 20.79 (19 and 74.76 (14°, respectively, with the plane of the benzene ring. In the crystal, molecules are assembled into a two-dimensional polymeric network parallel to (100 via N—H...O and O—H...O hydrogen bonds. In addition, within the layer, there are π–π stacking interactions between the benzene rings of the cation and the anion [centroid–centroid distance = 3.6794 (17 Å]. A weak C—H...O interaction is also observed.

  6. Crystal structure of febuxostat–acetic acid (1/1

    Directory of Open Access Journals (Sweden)

    Min Wu

    2015-05-01

    Full Text Available The asymmetric unit of the title compound [systematic name: 2-(3-cyano-4-isobutyloxyphenyl-4-methylthiazole-5-carboxylic acid–acetic acid (1/1], C16H16N2O3S·CH3COOH, contains a febuxostat molecule and an acetic acid molecule. In the febuxostat molecule, the thiazole ring is nearly coplanar with the benzene ring [dihedral angle = 3.24 (2°]. In the crystal, the febuxostat and acetic acid molecules are linked by O—H...O, O—H...N hydrogen bonds and weak C—H...O hydrogen bonds, forming supramolecular chains propagating along the b-axis direction. π–π stacking is observed between nearly parallel thiazole and benzene rings of adjacent molecules; the centroid-to-centroid distances are 3.8064 (17 and 3.9296 (17 Å.

  7. Crystal structure of a bioactive sesquiterpene isolated from Artemisia reticulata

    Directory of Open Access Journals (Sweden)

    A. K. Bauri

    2016-04-01

    Full Text Available The title compound, C15H24O2 {systematic name: 1-[6-hydroxy-7-(propan-2-yl-4-methylidene-2,3,3a,4,5,6,7,7a-octahydro-1H-inden-1-yl]ethanone} was isolated from A. reticulata by column chromatography over silica gel by gradient solvent elution. The molecule comprises a bicyclo[4.3.0]nonane ring bearing acetoxy, hydroxy and isopropyl substituents, and an exocyclic double bond on the cyclohexane ring. In the bicyclic skeleton, the cyclohexane ring adopts a chair conformation ring and the cyclopentane ring is in an envelope conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains along [010]. These chains are cross-linked by C—H...O hydrogen bonds.

  8. Crystal Structure-Ionic Conductivity Relationships in Doped Ceria Systems

    DEFF Research Database (Denmark)

    Omar, Shobit; Wachsman, Eric D.; Jones, Jacob L.

    2009-01-01

    lattice strain of 10 mol% trivalent cation-doped ceria systems at the same temperatures. A consistent set of ionic conductivity data is developed, where the samples are synthesized under similar experimental conditions. On comparing the grain ionic conductivity, Nd0.10Ce0.90O2−δ exhibits the highest ionic...... conductivity among other doped ceria systems. The grain ionic conductivity is around 17% higher than that of Gd0.10Ce0.90O2−δ at 500°C, in air. X-ray diffraction profiles are collected on the sintered powder of all the compositions, from room temperature to 600°C, in air. From the lattice expansion data...... crystal structure–ionic conductivity relationship based on minimum elastic strain is not sufficient to explain the ionic conductivity behavior in ceria-based system....

  9. Crystal structure of N,N′-dibenzylpyromellitic diimide

    Directory of Open Access Journals (Sweden)

    Hansu Im

    2016-12-01

    Full Text Available The title compound, C24H16N2O4 [systematic name: 2,6-dibenzylpyrrolo[3,4-f]isoindole-1,3,5,7(2H,6H-tetraone], consists of a central pyromellitic diimide moiety with terminal benzyl groups at the N-atom positions. The molecule is located about an inversion centre, so the asymmetric unit contains one half-molecule. In the molecule, both terminal phenyl groups, tilted by 72.97 (4° with respect to the mean plane of the central pyromellitic diimide moiety (r.m.s. deviation = 0.0145 Å, are oriented away from each other, forming an elongated S-shaped conformation. In the crystal, molecules are connected via weak C—H...O hydrogen bonds and C—H...π interactions, resulting in the formation of supramolecular layers extending parallel to the ab plane.

  10. Crystal structure of an apremilast ethanol hemisolvate hemihydrate solvatomorph

    Directory of Open Access Journals (Sweden)

    Yun-Deng Wu

    2017-06-01

    Full Text Available The title compound, C22H24N2O7S·0.5C2H5OH·0.5H2O {systematic name: (S-4-acetamido-2-[1-(3-ethoxy-4-methoxyphenyl-2-(methylsulfonylethyl]isoindoline-1,3-dione ethanol hemisolvate hemihydrate}, is a novel solvatomorph of apremilast (AP, which is an inhibitor of phosphodiesterase 4 (PDE4 and is indicated for the treatment of adult patients with active psoriatic arthritis. The asymmetric unit contains one molecule of AP and disordered molecules of ethanol and water, both with half occupancy. The dihedral angle between the planes of the phenyl ring and the isoindole ring is 67.9 (2°. Extensive intra- and intermolecular hydrogen bonds help to stabilize the molecular conformation and sustain the crystal packing.

  11. Crystal structure of iron(III perchlorate nonahydrate

    Directory of Open Access Journals (Sweden)

    Erik Hennings

    2014-12-01

    Full Text Available Since the discovery of perchlorate salts on Mars and the known occurrence of ferric salts in the regolith, there is a distinct possibility that the title compound could form on the surface of Mars. [Fe(H2O6](ClO43·3H2O was crystallized from aqueous solutions at low temperatures according to the solid–liquid phase diagram. It consists of Fe(H2O6 octahedra (point group symmetry -3. and perchlorate anions (point group symmetry .2 as well as non-coordinating water molecules, as part of a second hydrogen-bonded coordination sphere around the cation. The perchlorate appears to be slightly disordered, with major–minor component occupancies of 0.773 (9:0.227 (9.

  12. Crystal structure of N-carbamothioyl-2-methylbenzamide

    Directory of Open Access Journals (Sweden)

    Farook Adam

    2015-06-01

    Full Text Available There are two molecules in the asymmetric unit of the title compound, C9H10N2OS. In one, the dihedral angle between the aromatic ring and the carbamothioyl group is 52.31 (7° and in the other it is 36.16 (6°. Each molecule features an intramolecular N—H...O hydrogen bond, which generates an S(6 ring and the O and S atoms have an anti disposition. In the crystal, molecules are linked by N—H...S and N—H...O hydrogen bonds, generating separate [130] and [1-30] infinite chains. Weak C—H...O and C—H...S interactions are also observed.

  13. Tunable band structures in digital oxides with layered crystal habits

    Science.gov (United States)

    Shin, Yongjin; Rondinelli, James M.

    2017-11-01

    We use density functional calculations to show that heterovalent cation-order sequences enable control over band-gap variations up to several eV and band-gap closure in the bulk band insulator LaSrAlO4. The band-gap control originates from the internal electric fields induced by the digital chemical order, which induces picoscale band bending; the electric-field magnitude is mainly governed by the inequivalent charged monoxide layers afforded by the layered crystal habit. Charge transfer and ionic relaxations across these layers play secondary roles. This understanding is used to construct and validate a descriptor that captures the layer-charge variation and to predict changes in the electronic gap in layered oxides exhibiting antisite defects and in other chemistries.

  14. Crystal structure of 2-nitro-N-(2-nitrophenylbenzamide

    Directory of Open Access Journals (Sweden)

    Rodolfo Moreno-Fuquen

    2015-06-01

    Full Text Available In the title compound, C13H9N3O5, the mean plane of the non-H atoms of the central amide fragment C—N—C(=O—C [r.m.s. deviation = 0.0442 Å] forms dihedral angles of 71.76 (6 and 24.29 (10° with the C-bonded and N-bonded benzene rings, respectively. In the crystal, molecules are linked by N—H...O hydrogen bonds forming C(4 chains along [100]. Weak C—H...O contacts link the molecules into (100 sheets containing edge-fused R44(30 rings. Together, the N—H...O and C—H...O hydrogen bonds generate a three-dimensional network.

  15. Crystal structure of 3-benzyl-1-[(cyclohexylideneamino]thiourea

    Directory of Open Access Journals (Sweden)

    Shaaban K. Mohamed

    2015-12-01

    Full Text Available The conformation of the title compound, C14H19N3S, is partially determined by an intramolecular N—H...N hydrogen-bond interaction, although the N—H...N angle of 108° is quite small. The cyclohexylidene ring has a chair conformation and its mean plane is inclined to the benzene ring by 46.30 (8°. In the crystal, molecules are linked by pairs of N—H...S hydrogen bonds, forming inversion dimers, with an R22(8 ring motif. The dimers are reinforced by pairs of C—H...S hydrogen bonds, and are linked by further weak C—H...S hydrogen bonds, forming chains propagating along [100].

  16. Crystal structure of 4-(dimethylaminopyridinium 4-aminobenzoate dihydrate

    Directory of Open Access Journals (Sweden)

    A. Thirunavukkarasu

    2015-01-01

    Full Text Available In the title hydrated molecular salt, C7H11N2+·C7H6NO2−·2H2O, the cation is protonated at the pyridine N atom and the dihedral angle between the benzene ring and the CO2− group in the anion is 8.5 (2°. In the crystal, the cation forms an N—H...O hydrogen bond to the anion and the anion forms two N—H...O hydrogen bonds to adjacent water molecules. Both water molecules form two O—H...O hydrogen bonds to carboxylate O atoms. In combination, these hydrogen bonds generate a three-dimensional network and two weak C—H...π interactions are also observed.

  17. Understanding the Influence of the Electronic Structure on the Crystal Structure of a TTF-PTM Radical Dyad.

    Science.gov (United States)

    Vela, Sergi; Souto, Manuel; Ratera, Imma; Rovira, Concepció; Veciana, Jaume

    2016-12-29

    The understanding of the crystal structure of organic compounds, and its relationship to their physical properties, have become essential to design new advanced molecular materials. In this context, we present a computational study devoted to rationalize the different crystal packing displayed by two closely related organic systems based on the TTF-PTM dyad (TTF = tetrathiafulvalene, PTM = polychlorotriphenylmethane) with almost the same molecular structure but a different electronic one. The radical species (1), with an enhanced electronic donor-acceptor character, exhibits a herringbone packing, whereas the nonradical protonated analogue (2) is organized forming dimers. The stability of the possible polymorphs is analyzed in terms of the cohesion energy of the unit cell, intermolecular interactions between pairs, and molecular flexibility of the dyad molecules. It is observed that the higher electron delocalization in radical compound 1 has a direct influence on the geometry of the molecule, which seems to dictate its preferential crystal structure.

  18. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    Science.gov (United States)

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

  19. Comparing quantum-chemical calculation methods for structural investigation of zeolite crystal structures by solid-state NMR spectroscopy.

    Science.gov (United States)

    Brouwer, Darren H; Moudrakovski, Igor L; Darton, Richard J; Morris, Russell E

    2010-12-01

    Combining quantum-chemical calculations and ultrahigh-field NMR measurements of (29)Si chemical shielding (CS) tensors has provided a powerful approach for probing the fine details of zeolite crystal structures. In previous work, the quantum-chemical calculations have been performed on 'molecular fragments' extracted from the zeolite crystal structure using Hartree-Fock methods (as implemented in Gaussian). Using recently acquired ultrahigh-field (29) Si NMR data for the pure silica zeolite ITQ-4, we report the results of calculations using recently developed quantum-chemical calculation methods for periodic crystalline solids (as implemented in CAmbridge Serial Total Energy Package (CASTEP) and compare these calculations to those calculated with Gaussian. Furthermore, in the context of NMR crystallography of zeolites, we report the completion of the NMR crystallography of the zeolite ITQ-4, which was previously solved from NMR data. We compare three options for the 'refinement' of zeolite crystal structures from 'NMR-solved' structures: (i) a simple target-distance based geometry optimization, (ii) refinement of atomic coordinates in which the differences between experimental and calculated (29)Si CS tensors are minimized, and (iii) refinement of atomic coordinates to minimize the total energy of the lattice using CASTEP quantum-chemical calculations. All three refinement approaches give structures that are in remarkably good agreement with the single-crystal X-ray diffraction structure of ITQ-4. Copyright © 2010 John Wiley & Sons, Ltd.

  20. 1.5-NM PROJECTION STRUCTURE OF HELA-CELL PROSOME-MCP (PROTEASOME) PROVIDED BY 2-DIMENSIONAL CRYSTALS

    NARCIS (Netherlands)

    PERKINS, GA; BERGSMASCHUTTER, W; KEEGSTRA, W; ARNBERG, AC; COUX, O; SCHERRER, K

    1994-01-01

    We grew two-dimensional crystals of HeLa cell prosomes, also called multicatalytic proteinases (MCP) and proteasomes, for a structure determination by electron microscopy. The molecules were arranged in side views in these crystals. The crystals have p21 plane group symmetry with one particle per

  1. The crystal structure of Kirkiite, Pb10Bi3As3S19

    DEFF Research Database (Denmark)

    Makovicky, Emil; Balic Zunic, Tonci; Karanovic, Ljiljana

    2006-01-01

    layers parallel to (083) of kirkiite; the slabs are unit-cell-twinned on (010) refl ection planes. The structure contains one split As position, and two additional sites that could accommodate both As and Bi. The As,Bi distribution over these two sites is determined by the trapezoidal distortion......The crystal structure of kirkiite has been solved using single-crystal data (MoKa X-ray diffraction, CCD area detector) to the conventional R-factor R1 = 0.069. It crystallizes in space group P21/m, with a 8.621(4), b 26.03(1), c 8.810(4) Å, ß 119.21(1)° and Z = 2. A crystal-structure determination....... The crystal structure of kirkiite can be described as (010) slabs of octahedra, three octahedra thick and related mutually by a refl ection plane situated in the intervening prismatic layer. In another interpretation, it is composed of slabs based on a transitional PbS-SnS archetype, with tightly bonded...

  2. Crystal structure study and investigation of solid-state cyclization for AMG 222, a channel hydrate.

    Science.gov (United States)

    Kiang, Y-H; Nagapudi, Karthik; Liu, Jodi; Staples, Richard J; Jona, Janan

    2013-01-30

    In this study, we investigate the solid-state structure and stability of AMG 222 (5-(2-[2-(2-cyano-pyrrolidin-1-yl)-2-oxo-ethylamino]-propyl)-5-(1H-tetrazol-5-yl)-10,11-dihydro-5H-dibenzo[a,d]cycloheptene-2,8 dicarboxylic acid bisdimethylamide), a small molecule DPP-IV inhibitor. Crystal structure of AMG 222 has been solved from single crystal X-ray analysis. Crystallographic data are as follows: monoclinic, P2(1) (no. 4), a=9.0327(5)Å, b=18.6177(8)Å, c=21.4927(10)Å, β=90.126(3)°, V=3614.4(3)Å(3), Z=4. Based on single crystal structure, AMG 222 is a pentahydrate with the water molecules sitting in channels formed by the drug framework. There are three distinct crystal structures of AMG 222 between 0 and 95% relative humidity (RH), namely the anhydrate, hemihydrate, and pentahydrate forms. Solid-state stability of the GMP batch showed a high level of cyclized degradation product. It was postulated that the degradation was promoted by increased amorphous content generated as a result of excessive drying that was employed to remove residual crystallization solvent. Material produced using a modified procedure using a humidified nitrogen purge had lower amorphous content and lower levels of cyclic degradation when compared to the GMP batch. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Crystallization and structural studies of components of the protein-synthesizing system from Thermus thermophilus

    Science.gov (United States)

    Garber, M.; Davydova, N.; Eliseikina, I.; Fomenkova, N.; Gryaznova, O.; Gryshkovskaya, I.; Nevskaya, N.; Nikonov, S.; Rak, A.; Sedelnikova, S.; Serganov, A.; Shcherbakov, D.; Tishchenko, S.; Vysotskaya, V.; Zheltonosova, J.; Liljas, A.; Aevarsson, A.; Al-Karadaghi, S.

    1996-10-01

    A long-term program on crystallization and structural studies of the protein synthesis machinery components from an extreme thermophile Thermus thermophilus was set up at the Institute of Protein Research (Russia) about 15 years ago. These studies have recently revealed the structures of elongation factor G, aspartyl-tRNA synthetase and ribosomal proteins S6 and L1. Different components of the protein synthesis machinery from T.thermophilus are also being investigated in other groups and many important results have been obtained recently. Here we describe only some special problems on crystal handling and non-isomorphism that have been overcome during structural studies of EF-G and ribosomal proteins in our group. This paper presents also new data on the crystallization of ribosomal proteins S7, S8, S15, L22 and leucyl-tRNA synthetase from T.thermophilus.

  4. Crystal structure and hydrogen-bonding patterns in 5-fluorocytosinium picrate

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2017-03-01

    Full Text Available In the crystal structure of the title compound, 5-fluorocytosinium picrate, C4H5FN3O+·C6H2N3O7−, one N heteroatom of the 5-fluorocytosine (5FC ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11° with the ring of the picrate (PA− anion. In the crystal, the 5FC+ cation interacts with the PA− anion through three-centre N—H...O hydrogen bonds, forming two conjoined rings having R21(6 and R12(6 motifs, and is extended by N—H...O hydrogen bonds and C—H...O interactions into a two-dimensional sheet structure lying parallel to (001. Also present in the crystal structure are weak C—F...π interactions.

  5. X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Vitova, Tonya

    2008-02-15

    The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu{sup 1+} and Cu{sup 2+}) and Fe (Fe{sup 2+} and Fe{sup 3+}) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn{sup 2+} and Mn{sup 3+} in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu{sup 1+}) and sixfold (Cu{sup 2+}) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with {sup 3}He{sup 2+} ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

  6. X-ray reflectivity reveals ionic structure at liquid crystal-aqueous interfaces.

    Science.gov (United States)

    Hallett, James E; Hayward, Dominic W; Arnold, Thomas; Bartlett, Paul; Richardson, Robert M

    2017-08-23

    Here X-ray reflectivity has been used to determine the structure of liquid crystal monolayers for different cyanobiphenyl homologues supported on aqueous solutions of two different salt species. Sodium iodide induces homeotropic ordering for all of the monolayer forming liquid crystal homologues studied here, and forms a Stern layer of iodide ions at the liquid crystal cyano headgroup, similar to the case of lipids or surfactants supported on electrolyte solutions. The liquid crystal headgroups were also found to penetrate into the water surface when binding with iodide ions. Sodium bromide, however, does not form the same localisation of ions close to a liquid crystal monolayer, and instead appears to produce no noticeable change in the scattering length density of the liquid crystal monolayer compared to pure water. However, on further compression the X-ray reflectivity dramatically changes, revealing the emergence of the so-called "trilayer" structure for 5CB and 8CB. This transition occurs at a lower areal density for sodium bromide than for pure water, and unlike for the uncompressed film, a layer of bromide ions was found at the trilayer-water interface.

  7. AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

    Science.gov (United States)

    Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

    2002-01-01

    Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

  8. Electromagnetic wave control of ceramic/resin photonic crystals with diamond structure

    Directory of Open Access Journals (Sweden)

    Soshu Kirihara, Mitsuo Takeda, Kazuaki Sakoda and Yoshinari Miyamoto

    2004-01-01

    Full Text Available Millimeter-order photonic crystals with the periodic arrangement of the dielectric constant were fabricated by infiltrating the mixed slurry of ceramics and polyester into the epoxy molds with an inverse form of a diamond structure. The epoxy molds are designed and processed by using a CAD/CAM process of stereolithography. The photonic crystals were prepared to have the diamond structure of the ceramic/polyester composite lattice, which is embedded in the epoxy matrix. The ceramic powders mixed with polyester are TiO2, SrTiO3, and BaTiO3 with high dielectric constant. It is possible to control more freely and widely the dielectric constant of the photonic crystals by this method. These ceramic/resin photonic crystals formed the complete photonic band gaps in the microwave band of 7–11 GHz, which can totally reflect the electromagnetic wave for all crystal directions. Attenuation profiles of the transmission amplitude in the band gaps were controlled with the dielectric constant of the composite lattice. The obtained results fairly agreed with the theoretical simulation of the electromagnetic wave propagation through photonic crystals.

  9. Protein crystal structure from non-oriented, single-axis sparse X-ray data

    Directory of Open Access Journals (Sweden)

    Jennifer L. Wierman

    2016-01-01

    Full Text Available X-ray free-electron lasers (XFELs have inspired the development of serial femtosecond crystallography (SFX as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ∼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases

  10. Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1.

    Science.gov (United States)

    Hosaka, Toshiaki; Okazaki, Masateru; Kimura-Someya, Tomomi; Ishizuka-Katsura, Yoshiko; Ito, Kaori; Yokoyama, Shigeyuki; Dodo, Kosuke; Sodeoka, Mikiko; Shirouzu, Mikako

    2017-09-01

    Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P221 21 , which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P221 21 were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family. © 2017 The Protein Society.

  11. Protein crystal structure from non-oriented, single-axis sparse X-ray data.

    Science.gov (United States)

    Wierman, Jennifer L; Lan, Ti-Yen; Tate, Mark W; Philipp, Hugh T; Elser, Veit; Gruner, Sol M

    2016-01-01

    X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so 'sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ∼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are

  12. Crystal structure of the monoclinic phase (phase IV of bis(tetramethylammonium tetrachloridocuprate(II

    Directory of Open Access Journals (Sweden)

    Gorgui Awa Seck

    2017-03-01

    Full Text Available The crystal structure of the low-temperature monoclinic phase of the title compound, [(CH34N]2[CuCl4], was determined at 120 K. The structure of the room-temperature phase has been determined in the orthorhombic space group Pmcm [Morosin & Lingafelter (1961. J. Phys. Chem. 50–51; Clay et al. (1975. Acta Cryst. B31 289–290]. The asymmetric unit consists of one discrete tetrachloridocuprate anion with a distorted tetrahedral geometry and two tetramethylammonium cations. In the crystal, the cations and the anions are linked via weak C—H...Cl hydrogen bonds.

  13. Crystal structure of the RNA 2',3'-cyclic phosphodiesterase from Deinococcus radiodurans.

    Science.gov (United States)

    Han, Wanchun; Cheng, Jiahui; Zhou, Congli; Hua, Yuejin; Zhao, Ye

    2017-05-01

    2',3'-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase from Deinococcus radiodurans was crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism.

  14. Photonic crystal Fano structures and their application to ultrafast switching and lasers

    DEFF Research Database (Denmark)

    Yu, Yi; Bekele, Dagmawi Alemayehu; Hu, Hao

    2016-01-01

    We present investigations on photonic-crystal Fano structures based on a cavitywaveguide configuration. We show that the use of Fano resonance can enable great improvements in high-speed low-energy all-optical switching and realizing ultra-fast nanolasers.......We present investigations on photonic-crystal Fano structures based on a cavitywaveguide configuration. We show that the use of Fano resonance can enable great improvements in high-speed low-energy all-optical switching and realizing ultra-fast nanolasers....

  15. Synthesis and Single Crystal Structures of Substituted-1,3-Selenazol-2-amines.

    Science.gov (United States)

    Hua, Guoxiong; Du, Junyi; Slawin, Alexandra M Z; Woollins, J Derek

    2016-12-29

    The synthesis and X-ray single crystal structures of a series of new 4-substituted-1,3-selenazol-2-amines is reported. The efficient preparation of these compounds was carried out by two-component cyclization of the selenoureas with equimolar amounts of α-haloketones. The selenoureas were obtained from the reaction of Woollins' reagent with cyanamides, followed by hydrolysis with water. All new compounds have been characterized by IR spectroscopy, multi-NMR (¹H, 13C, 77Se) spectroscopy, accurate mass measurement and single crystal X-ray structure analysis.

  16. Synthesis and Single Crystal Structures of Substituted-1,3-Selenazol-2-amines

    Directory of Open Access Journals (Sweden)

    Guoxiong Hua

    2016-12-01

    Full Text Available The synthesis and X-ray single crystal structures of a series of new 4-substituted-1,3-selenazol-2-amines is reported. The efficient preparation of these compounds was carried out by two-component cyclization of the selenoureas with equimolar amounts of α-haloketones. The selenoureas were obtained from the reaction of Woollins’ reagent with cyanamides, followed by hydrolysis with water. All new compounds have been characterized by IR spectroscopy, multi-NMR (1H, 13C, 77Se spectroscopy, accurate mass measurement and single crystal X-ray structure analysis.

  17. Crystal structure features in a new compound C4B25Mg1.42

    Science.gov (United States)

    Konovalikhin, S. V.; Ponomarev, V. I.

    2015-09-01

    The composition of C4B25Mg1.42 crystal obtained by self-propagating high-temperature synthesis was determined using X-ray diffraction. This is the first crystalline structure where all boron atoms in the В12 icosahedron occupy crystallographically independent positions; this circumstance allowed us to analyze the effect of substituents on bond lengths in the icosahedron. The crystal structure features, including the channels filled with disordered Mg atoms and the spread of В—В endo- and exo-bond lengths in the icosahedra, are described. A crystallochemical analysis of pair bonds has been performed for the first time.

  18. Azidothymidine: crystal structure and possible functional role of the azido group.

    Science.gov (United States)

    Camerman, A; Mastropaolo, D; Camerman, N

    1987-01-01

    The crystal and molecular structures of the anti-acquired immunodeficiency syndrome agent 3'-azido-3'-deoxythymidine (AZT) have been determined by x-ray diffraction. There are two crystallographically independent AZT molecules in the crystal asymmetric unit; they have similar conformations and differ primarily in the glycosyl torsion angle. Comparisons with a hydrated thymidylate structure indicate that the azido group does not significantly affect the gross conformational preference of the molecule. The comparisons also suggest possible functional roles for the azido group in enzyme binding. PMID:2446321

  19. Band structure computation of polygonal solid-solid phononic crystal with features using frequency domain spectral superelement method

    Science.gov (United States)

    Mukherjee, Sushovan; Gopalakrishnan, S.

    2017-04-01

    Phononic crystals are synthetic materials with a periodic structure having spatial variations of elasto-inertial properties of constituent materials, aimed at developing devices and bulk material with engineered acoustic/ elastic properties. Multi-material structures with sides of a space filling polygonal tessellation, can constitute solid-solid phononic crystal. Coupled with inclusions and features, phononic crystals show rich and varied band structure phenomenon. We use frequency domain spectral superelement method and Bloch theory to efficiently calculate the band structures of such phononic crystals. We particularly investigate hexagonal honeycombs to assess the impacts of joint elasticity, inertia and circular and elliptical holes on band gap behavior.

  20. Purification, crystal structure determination and functional characterization 1 of type III antifreeze proteins from the fish Zoarces viviparus

    DEFF Research Database (Denmark)

    Poulsen, Jens-Christian N.; Ramløv, Hans; Lo Leggio, Leila

    2014-01-01

    , 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...