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Sample records for crystal structure showed

  1. Liquid Crystal Research Shows Deformation By Drying

    Science.gov (United States)

    2003-01-01

    These images, from David Weitz's liquid crystal research, show ordered uniform sized droplets (upper left) before they are dried from their solution. After the droplets are dried (upper right), they are viewed with crossed polarizers that show the deformation caused by drying, a process that orients the bipolar structure of the liquid crystal within the droplets. When an electric field is applied to the dried droplets (lower left), and then increased (lower right), the liquid crystal within the droplets switches its alignment, thereby reducing the amount of light that can be scattered by the droplets when a beam is shone through them.

  2. Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yong; Wan, Bingbing; Wang, Kevin C.; Cao, Fang; Yang, Yuting; Protacio, Angeline; Dou, Yali; Chang, Howard Y.; Lei, Ming (Michigan-Med); (HHMI)

    2011-09-06

    Ash2L is a core component of the MLL family histone methyltransferases and has an important role in regulating the methylation of histone H3 on lysine 4. Here, we report the crystal structure of the N-terminal domain of Ash2L and reveal a new function of Ash2L. The structure shows that Ash2L contains an atypical PHD finger that does not have histone tail-binding activity. Unexpectedly, the structure shows a previously unrecognized winged-helix motif that directly binds to DNA. The DNA-binding-deficient mutants of Ash2L reduced Ash2L localization to the HOX locus. Strikingly, a single mutation in Ash2L{sub WH} (K131A) breaks the chromatin domain boundary, suggesting that Ash2L also has a role in chromosome demarcation.

  3. Crystal structure and prediction.

    Science.gov (United States)

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  4. Synthesis and Crystal Structure of a Mn(Ⅱ) Complex with Thiosemicarbazone Derivative of Pyridine-3-carbaldehyde Showing Unusual Coordination Mode of Tridentate Thiosemicarbazone

    Institute of Scientific and Technical Information of China (English)

    LI Ming-Xue; ZHOU Jing; WANG Jing-Ping; WANG Zi-Liang

    2006-01-01

    The title complex Mn(HL)4(NCS)2(CH3CH2OH)2 has been achieved via selfassembly by incorporating manganese(Ⅱ) into pyridine-3-carbaldehyde thiosemicarbazonate ligand,and characterized by elemental analysis and single-crystal X-ray diffraction study. The crystal crystallizes in triclinic, space group P1 with a = 8.896(2), b = 9.530(2), c = 14.520(4) (A), α =87.035(4), β= 88.112(4), γ= 69.434(4)°, V= 1150.9(5) (A)3, Z = 1, Mr = 984.17, Dc = 1.420 g/cm3,μ(MoKα) = 0.612 mm-1, F(000) = 511, the final R = 0.0574 and wR = 0.1547 for 2855 observed reflections with I > 2σ(I). The complex contains one six-coordinated manganese ion connected by two thiosemicarbazide ligands, in which the thiosemicarbazone ligand acts as a monodentate ligand and coordinates to the center metal atoms via the pyridyl nitrogen atoms, two ethanol molecules and two isothiocyanic anions to give rise to a mononuclear structure. The coordination of a potentially tridentate thiosemicarbazone in manganese(Ⅱ) complex without using its sulfur and imine nitrogen sites is unusual. Hydrogen bonds existing in the complex link the different components to stabilize the crystal structure.

  5. 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...

  6. Demonstration of Crystal Structure.

    Science.gov (United States)

    Neville, Joseph P.

    1985-01-01

    Describes an experiment where equal parts of copper and aluminum are heated then cooled to show extremely large crystals. Suggestions are given for changing the orientation of crystals by varying cooling rates. Students are more receptive to concepts of microstructure after seeing this experiment. (DH)

  7. Crystal Structures of Furazanes

    OpenAIRE

    Klapötke, Thomas; Schmid, Philipp; Stierstorfer, Jörg

    2015-01-01

    Several nitrogen-rich salts of 3-nitramino-4-nitrofurazane and dinitraminoazoxyfurazane were synthesized and characterized by various spectroscopic methods. The crystal structures were determined by low temperature single crystal X-ray diffraction. Moreover the sensitivities toward thermal and mechanical stimuli were determined by differential thermal analysis (DTA) and BAM (Bundesanstalt für Materialforschung und -prüfung) methods. The standard enthalpies of formation were calculated for all...

  8. 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

  9. Crystal Structures of Furazanes

    Directory of Open Access Journals (Sweden)

    Thomas M. Klapötke

    2015-09-01

    Full Text Available Several nitrogen-rich salts of 3-nitramino-4-nitrofurazane and dinitraminoazoxyfurazane were synthesized and characterized by various spectroscopic methods. The crystal structures were determined by low temperature single crystal X-ray diffraction. Moreover the sensitivities toward thermal and mechanical stimuli were determined by differential thermal analysis (DTA and BAM (Bundesanstalt für Materialforschung und -prüfung methods. The standard enthalpies of formation were calculated for all compounds at the CBS-4M level of theory, and the energetic performance was predicted with the EXPLO5 V6.02 computer code.

  10. Frustrated polymer crystal structures

    Science.gov (United States)

    Lotz, B.; Strasbourg, 67083

    1997-03-01

    Several crystal structures or polymorphs of chiral or achiral polymers and biopolymers with three fold conformation of the helix have been found to conform to a common and -with one exception(Puterman, M. et al, J. Pol. Sci., Pol. Phys. Ed., 15, 805 (1977))- hitherto unsuspected packing scheme. The trigonal unit-cell contains three isochiral helices; the azimuthal setting of one helix differs significantly from that of the other two, leading to a so-called frustrated packing scheme, in which the environment of conformationally identical helices differs. Two variants of the frustrated scheme are analyzed. Similarities with frustrated two dimensional magnetic systems are underlined. Various examples of frustration in polymer crystallography are illustrated via the elucidation or reinterpretation of crystal phases or polymorphs of polyolefins, polyesters, cellulose derivatives and polypeptides. Structural manifestations (including AFM evidence) and morphological consequences of frustration are presented, which help diagnose the existence of this original packing of polymers.(Work done with L. Cartier, D. Dorset, S. Kopp, T. Okihara, M. Schumacher, W. Stocker.)

  11. Structural colours through photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    McPhedran, R.C.; Nicorovici, N.A.; McKenzie, D.R.; Rouse, G.W.; Botten, L.C.; Welch, V.; Parker, A.R.; Wohlgennant, M.; Vardeny, V

    2003-10-01

    We discuss two examples of living creatures using photonic crystals to achieve iridescent colouration. The first is the sea mouse (Aphroditidae, Polychaeta), which has a hexagonal close packed structure of holes in its spines and lower-body felt, while the second is the jelly fish Bolinopsis infundibulum, which has an oblique array of high index inclusions in its antennae. We show by measurements and optical calculations that both creatures can achieve strong colours despite having access only to weak refractive index contrast.

  12. 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.

  13. Crystal structure of ruthenocenecarbonitrile

    Directory of Open Access Journals (Sweden)

    Frank Strehler

    2015-04-01

    Full Text Available The molecular structure of ruthenocenecarbonitrile, [Ru(η5-C5H4C[triple-bond]N(η5-C5H5], exhibits point group symmetry m, with the mirror plane bisecting the molecule through the C[triple-bond]N substituent. The RuII atom is slightly shifted from the η5-C5H4 centroid towards the C[triple-bond]N substituent. In the crystal, molecules are arranged in columns parallel to [100]. One-dimensional intermolecular π–π interactions [3.363 (3 Å] between the C[triple-bond]N carbon atom and one carbon of the cyclopentadienyl ring of the overlaying molecule are present.

  14. Crystal structure of propaquizafop

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2014-12-01

    Full Text Available The title compound, C22H22ClN3O5 {systematic name: 2-(propan-2-ylideneaminooxyethyl (R-2-[4-(6-chloroquinoxalin-2-yloxyphenoxy]propionate}, is a herbicide. The asymmetric unit comprises two independent molecules in which the dihedral angles between the phenyl ring and the quinoxaline ring plane are 75.93 (7 and 82.77 (8°. The crystal structure features C—H...O, C—H...N, and C—H...Cl hydrogen bonds, as well as weak π–π interactions [ring-centroid separation = 3.782 (2 and 3.5952 (19 Å], resulting in a three-dimensional architecture.

  15. Photonic Crystal Laser Accelerator Structures

    Energy Technology Data Exchange (ETDEWEB)

    Cowan, Benjamin M

    2003-05-21

    Photonic crystals have great potential for use as laser-driven accelerator structures. A photonic crystal is a dielectric structure arranged in a periodic geometry. Like a crystalline solid with its electronic band structure, the modes of a photonic crystal lie in a set of allowed photonic bands. Similarly, it is possible for a photonic crystal to exhibit one or more photonic band gaps, with frequencies in the gap unable to propagate in the crystal. Thus photonic crystals can confine an optical mode in an all-dielectric structure, eliminating the need for metals and their characteristic losses at optical frequencies. We discuss several geometries of photonic crystal accelerator structures. Photonic crystal fibers (PCFs) are optical fibers which can confine a speed-of-light optical mode in vacuum. Planar structures, both two- and three-dimensional, can also confine such a mode, and have the additional advantage that they can be manufactured using common microfabrication techniques such as those used for integrated circuits. This allows for a variety of possible materials, so that dielectrics with desirable optical and radiation-hardness properties can be chosen. We discuss examples of simulated photonic crystal structures to demonstrate the scaling laws and trade-offs involved, and touch on potential fabrication processes.

  16. 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.

  17. The crystal structure of the streptococcal collagen-like protein 2 globular domain from invasive M3-type group A Streptococcus shows significant similarity to immunomodulatory HIV protein gp41.

    Science.gov (United States)

    Squeglia, Flavia; Bachert, Beth; De Simone, Alfonso; Lukomski, Slawomir; Berisio, Rita

    2014-02-21

    The arsenal of virulence factors deployed by streptococci includes streptococcal collagen-like (Scl) proteins. These proteins, which are characterized by a globular domain and a collagen-like domain, play key roles in host adhesion, host immune defense evasion, and biofilm formation. In this work, we demonstrate that the Scl2.3 protein is expressed on the surface of invasive M3-type strain MGAS315 of Streptococcus pyogenes. We report the crystal structure of Scl2.3 globular domain, the first of any Scl. This structure shows a novel fold among collagen trimerization domains of either bacterial or human origin. Despite there being low sequence identity, we observed that Scl2.3 globular domain structurally resembles the gp41 subunit of the envelope glycoprotein from human immunodeficiency virus type 1, an essential subunit for viral fusion to human T cells. We combined crystallographic data with modeling and molecular dynamics techniques to gather information on the entire lollipop-like Scl2.3 structure. Molecular dynamics data evidence a high flexibility of Scl2.3 with remarkable interdomain motions that are likely instrumental to the protein biological function in mediating adhesive or immune-modulatory functions in host-pathogen interactions. Altogether, our results provide molecular tools for the understanding of Scl-mediated streptococcal pathogenesis and important structural insights for the future design of small molecular inhibitors of streptococcal invasion.

  18. THE CRYSTAL STRUCTURE OF DIPHENYLTELLURIUM DIBROMIDE,

    Science.gov (United States)

    TELLURIUM COMPOUNDS, *ORGANOMETALLIC COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , BROMIDES, SYMMETRY(CRYSTALLOGRAPHY), X RAY DIFFRACTION, FOURIER ANALYSIS, LEAST SQUARES METHOD, MOLECULAR STRUCTURE, CHEMICAL BONDS.

  19. REFINEMENT OF THE CRYSTAL STRUCTURE OF GUANIDINIUM ALUMINUM SULFATE HEXAHYDRATE.

    Science.gov (United States)

    FERROELECTRIC CRYSTALS, * CRYSTAL STRUCTURE ), (*GUANIDINES, CRYSTAL STRUCTURE ), (*ALUMINUM COMPOUNDS, CRYSTAL STRUCTURE ), SULFATES, HYDRATES, X RAY DIFFRACTION, CHROMIUM COMPOUNDS, CRYSTAL LATTICES, CHEMICAL BONDS

  20. 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.

  1. The crystal structure of a ternary complex of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa Provides new insight into the reaction mechanism and shows a novel binding mode of the 2'-phosphate of NADP+ and a novel cation binding site.

    Science.gov (United States)

    González-Segura, Lilian; Rudiño-Piñera, Enrique; Muñoz-Clares, Rosario A; Horjales, Eduardo

    2009-01-16

    In the human pathogen Pseudomonas aeruginosa, the NAD(P)(+)-dependent betaine aldehyde dehydrogenase (PaBADH) may play the dual role of assimilating carbon and nitrogen from choline or choline precursors--abundant at infection sites--and producing glycine betaine and NADPH, potentially protective against the high-osmolarity and oxidative stresses prevalent in the infected tissues. Disruption of the PaBADH gene negatively affects the growth of bacteria, suggesting that this enzyme could be a target for antibiotic design. PaBADH is one of the few ALDHs that efficiently use NADP(+) and one of the even fewer that require K(+) ions for stability. Crystals of PaBADH were obtained under aerobic conditions in the presence of 2-mercaptoethanol, glycerol, NADP(+) and K(+) ions. The three-dimensional structure was determined at 2.1-A resolution. The catalytic cysteine (C286, corresponding to C302 of ALDH2) is oxidized to sulfenic acid or forms a mixed disulfide with 2-mercaptoethanol. The glutamyl residue involved in the deacylation step (E252, corresponding to E268 of ALDH2) is in two conformations, suggesting a proton relay system formed by two well-conserved residues (E464 and K162, corresponding to E476 and K178, respectively, of ALDH2) that connects E252 with the bulk water. In some active sites, a bound glycerol molecule mimics the thiohemiacetal intermediate; its hydroxyl oxygen is hydrogen bonded to the nitrogen of the amide groups of the side chain of the conserved N153 (N169 of ALDH2) and those of the main chain of C286, which form the "oxyanion hole." The nicotinamide moiety of the nucleotide is not observed in the crystal, and the adenine moiety binds in the usual way. A salt bridge between E179 (E195 of ALDH2) and R40 (E53 of ALDH2) moves the carboxylate group of the former away from the 2'-phosphate of the NADP(+), thus avoiding steric clashes and/or electrostatic repulsion between the two groups. Finally, the crystal shows two K(+) binding sites per subunit

  2. Crystal structure of meteoritic schreibersites: determination of absolute structure

    Science.gov (United States)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  3. Structure of crystals of hard colloidal spheres

    Energy Technology Data Exchange (ETDEWEB)

    Pusey, P.N.; van Megen, W.; Bartlett, P.; Ackerson, B.J.; Rarity, J.G.; Underwood, S.M. (Royal Signals and Radar Establishment, Malvern, WR14 3PS, United Kingsom (GB) Department of Applied Physics, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia School of Chemistry, Bristol University, Bristol, BS8 1TS, United Kingdom Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078)

    1989-12-18

    We report light-scattering measurements of powder diffraction patterns of crystals of essentially hard colloidal spheres. These are consistent with structures formed by stacking close-packed planes of particles in a sequence of permitted lateral positions, {ital A},{ital B},{ital C}, which shows a high degree of randomness. Crystals grown slowly, while still containing many stacking faults, show a tendency towards face-centered-cubic packing: possible explanations for this observation are discussed.

  4. 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.

  5. Crystal structure of pseudoguainolide

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    Noureddine Beghidja

    2015-03-01

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

  6. Pattern information extraction from crystal structures

    Science.gov (United States)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  7. Crystal structure of nuarimol

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available The title compound [systematic name: (RS-(2-chlorophenyl(4-fluorophenyl(pyrimidin-5-ylmethanol], C17H12ClFN2O, is a pyrimidine fungicide. The asymmetric unit comprises two independent molecules, A and B, in which the dihedral angles between the plane of the pyrimidine ring and those of the chlorophenyl and fluorophenyl rings are 71.10 (6 and 70.04 (5° in molecule A, and 73.24 (5 and 89.30 (5° in molecule B. In the crystal, O—H...N hydrogen bonds link the components into [010] chains of alternating A and B molecules. The chains are cross-linked by C—H...F hydrogen bonds and weak C—H...π and C—Cl...π [Cl...ring centroid = 3.7630 (8 Å] interactions, generating a three-dimensional network.

  8. Crystal structure refinement with SHELXL.

    Science.gov (United States)

    Sheldrick, George M

    2015-01-01

    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 refinement with SHELXL

    Energy Technology Data Exchange (ETDEWEB)

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  10. Crystal structure of pymetrozine

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

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

  11. Determining crystal structures through crowdsourcing and coursework

    OpenAIRE

    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 pla...

  12. Determining crystal structures through crowdsourcing and coursework

    OpenAIRE

    Horowitz, Scott; Koepnick, Brian; Jain, Neha; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Koldewey, Philipp; Hettler, Stephen

    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 pla...

  13. Crystal Structure of Human Enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-04-08

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

  14. THE CRYSTAL STRUCTURE OF ANTIMONY (III) SULFOBROMIDE, SBSBR,

    Science.gov (United States)

    ANTIMONY COMPOUNDS, *SULFUR COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , BROMIDES, SYMMETRY(CRYSTALLOGRAPHY), FOURIER ANALYSIS, MOLECULAR STRUCTURE, CRYSTAL LATTICES, CHEMICAL BONDS, X RAY DIFFRACTION.

  15. Crystal structure of the eukaryotic ribosome.

    Science.gov (United States)

    Ben-Shem, Adam; Jenner, Lasse; Yusupova, Gulnara; Yusupov, Marat

    2010-11-26

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.

  16. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

    LEI XianRong; YANG JianHua; LIN Xiang; DAI Qin; CHENG Qiang; GUO LingHong; LI Hui

    2009-01-01

    Optimum resolution data of powder X-ray diffraction (PXRD) for Jatrorrhizine (Jat) were collected by an X' Pert Pro MPD diffractometer with an X'celerator detector under the stepwise scanning condition as 8.255 ms and 0.00836°per step,2θrange of 50°-80° and total scanning period of 8-10 min. Indexing of the crystal system and a search of the space group from the powder X-ray diffraction data were conducted by the computational crystallography method. The pilot crystal models of Jat were globally optimized with Monte Carlo method and then refined with the Rietveld method. In parallel with PXRD test,single crystals of Jat were cultured in an aqueous solution by a slow-decreasing temperature method,then its crystal structure was determined by single crystal X-ray diffraction (SCXRD). Both crystal structures from PXRD and SCXRD are identical. The results show that the crystal structure of Jat belongs to a monoclinic system and the space group P21/c. The parameters of cell dimensions from PXRD are a=7.69(A),b= 12.55(A),c=20.89(A),β=106.53°,Z=4,and V=1933.4(A)3,meanwhile the parameters from SCXRD are a=7.72(A),b=12.61(A),c=20.99(A),β=106.38°,Z=4,and V=1961.3(A)3.

  17. Pattern information extraction from crystal structures

    OpenAIRE

    Okuyan, Erhan

    2005-01-01

    Cataloged from PDF version of article. Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. This work provides a tool that will extract crystal parameters such as primitive vect...

  18. Crystal structure of gold hydride

    Energy Technology Data Exchange (ETDEWEB)

    Degtyareva, Valentina F., E-mail: degtyar@issp.ac.ru

    2015-10-05

    Highlights: • Volume expansion of metal hydrides is due to the increase in the s-band filling. • AuH structure is similar to that of Hg having one more s electron compared to Au. • Structure stability of both Hg and AuH is governed by the Hume-Rothery rule. - Abstract: A number of transition metal hydrides with close-packed metal sublattices of fcc or hcp structures with hydrogen in octahedral interstitial positions were obtained by the high-pressure-hydrogen technique described by Ponyatovskii et al. (1982). In this paper we consider volume increase of metals by hydrogenation and possible crystal structure of gold hydride in relation with the structure of mercury, the nearest neighbor of Au in the Periodic table. Suggested structure of AuH has a basic tetragonal body-centered cell that is very similar to the mercury structure Hg-t I 2. The reasons of stability for this structure are discussed within the model of Fermi sphere–Brillouin zone interactions.

  19. Crystal structure of N-(4-hydroxybenzylacetone thiosemicarbazone

    Directory of Open Access Journals (Sweden)

    Saray Argibay-Otero

    2017-09-01

    Full Text Available The structure of the title compound, C11H15N3OS, shows the flexibility due to the methylene group at the thioamide N atom in the side chain, resulting in the molecule being non-planar. The dihedral angle between the plane of the benzene ring and that defined by the atoms of the thiosemicarbazide arm is 79.847 (4°. In the crystal, the donor–acceptor hydrogen-bond character of the –OH group dominates the intermolecular associations, acting as a donor in an O—H...S hydrogen bond, as well as being a double acceptor in a centrosymmetric cyclic bridging N—H...O,O′ interaction [graph set R22(4]. The result is a one-dimensional duplex chain structure, extending along [111]. The usual N—H...S hydrogen-bonding association common in thiosemicarbazone crystal structures is not observed.

  20. Crystal Structures of New Ammonium 5-Aminotetrazolates

    Directory of Open Access Journals (Sweden)

    Martin Lampl

    2014-11-01

    Full Text Available The crystal structures of three salts of anionic 5-aminotetrazole are described. The tetramethylammonium salt (P forms hydrogen-bonded ribbons of anions which accept weak C–H···N contacts from the cations. The cystamine salt (C2/c shows wave-shaped ribbons of anions linked by hydrogen bonds to screw-shaped dications. The tetramethylguanidine salt (P21/c exhibits layers of anions hydrogen-bonded to the cations.

  1. Crystal Structure of a New Cembranolide Diterpene

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new cembranoide deterpene was isolated from the soft coral Sinularia Tenella. The crystal and chemical structure of the title compound were determined by means of spectroscopic methods and X-ray diffraction analysis as (1R* , 4R* , 5S* , 12S* , 12R* )-9-acetoxy-cembr-8E, 15 (17)-dien-16,4-olide. It shows a moderate cytotoxicity against P 388 and L 1210 cell lines.

  2. Crystal structure of fiber structured pentacene thin films

    OpenAIRE

    2007-01-01

    This PhD thesis presents a technique based on the grazing incidence crystal truncation rod (GI-CTR) X-ray diffraction method used to solve the crystal structure of substrate induced fiber structured organic thin films. The crystal structures of pentacene thin films grown on technologically relevant gate dielectric substrates are reported. It is widely recognized, that the intrinsic charge transport properties in organic thin film transistors (OTFTs) depend strongly on the crystal structur...

  3. Crystal growth and structural analysis of zirconium sulphoselenide single crystals

    Indian Academy of Sciences (India)

    K R Patel; R D Vaidya; M S Dave; S G Patel

    2008-08-01

    A series of zirconium sulphoselenide (ZrSSe3–, where = 0, 0.5, 1, 1.5, 2, 2.5, 3) single crystals have been grown by chemical vapour transport technique using iodine as a transporting agent. The optimum condition for the growth of these crystals is given. The stoichiometry of the grown crystals were confirmed on the basis of energy dispersive analysis by X-ray (EDAX) and the structural characterization was accomplished by X-ray diffraction (XRD) studies. The crystals are found to possess monoclinic structure. The lattice parameters, volume, particle size and X-ray density have been carried out for these crystals. The effect of sulphur proportion on the lattice parameter, unit cell volume and X-ray density in the series of ZrSSe3– single crystals have been studied and found to decrease in all these parameters with rise in sulphur proportion. 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 sulphur content in the ZrSSe3– series. The electrical resistivity parallel to c-axis as well as perpendicular to -axis have been carried out in the temperature range 303–423 K. The results obtained are discussed in detail.

  4. 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

    of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles......This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework......, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics...

  5. Influence of microgravity on protein crystal structures

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Structural determination and comparison of microgravity and ground grown protein crystals have been carried out in order to investigate the effect of microgravity on the structure of protein crystals. Following the structural studies on the hen egg-white lysozyme cystals grown in space and on the ground, the same kind of comparative studies was performed with acidic phospholipase A2 crystals grown in different gravities. Based on the results obtained so far, a conclusion could be made that microgravity might not be strong enough to change the conformation of polypeptide chain of proteins, but it may improve the bound waters' structure, and this might be an important factor for microgravity to improve the protein crystal quality. In addition, the difference in the improvement between the two kinds of protein crystals may imply that the degree of improvement of a protein crystal in microgravity may be related to the solvent content in the protein crystal.

  6. Predicting crystal structures of organic compounds.

    Science.gov (United States)

    Price, Sarah L

    2014-04-07

    Currently, organic crystal structure prediction (CSP) methods are based on searching for the most thermodynamically stable crystal structure, making various approximations in evaluating the crystal energy. The most stable (global minimum) structure provides a prediction of an experimental crystal structure. However, depending on the specific molecule, there may be other structures which are very close in energy. In this case, the other structures on the crystal energy landscape may be polymorphs, components of static or dynamic disorder in observed structures, or there may be no route to nucleating and growing these structures. A major reason for performing CSP studies is as a complement to solid form screening to see which alternative packings to the known polymorphs are thermodynamically feasible.

  7. Crystal Structure Refinement of Synthetic Pure Gyrolite

    Directory of Open Access Journals (Sweden)

    Arūnas Baltušnikas

    2015-03-01

    Full Text Available Pure calcium silicate hydrate – gyrolite was prepared under the saturated steam pressure at 473 K temperature in rotating autoclave. The crystal structure of synthetic gyrolite was investigated by X-ray diffraction and refined using Le Bail, Rietveld and crystal structure modelling methods. Background, peak shape parameters and verification of the space group were performed by the Le Bail full pattern decomposition. Peculiarities of interlayer sheet X of gyrolite unit cell were highlighted by Rietveld refinement. Possible atomic arrangement in interlayer sheet X was solved by global optimization method. Most likelihood crystal structure model of gyrolite was calculated by final Rietveld refinement. It was crystallographically showed, that cell parameters are: a = 0.9713(2 nm, b = 0.9715(2 nm, c = 2.2442(3 nm and alfa = 95.48(2 º, beta = 91.45(2 °, gamma = l20.05(3 °.DOI: http://dx.doi.org/10.5755/j01.ms.21.1.5460

  8. Crystal structure analysis of intermetallic compounds

    Science.gov (United States)

    Conner, R. A., Jr.; Downey, J. W.; Dwight, A. E.

    1968-01-01

    Study concerns crystal structures and lattice parameters for a number of new intermetallic compounds. Crystal structure data have been collected on equiatomic compounds, formed between an element of the Sc, Ti, V, or Cr group and an element of the Co or Ni group. The data, obtained by conventional methods, are presented in an easily usable tabular form.

  9. High-speed prediction of crystal structures for organic molecules

    Science.gov (United States)

    Obata, Shigeaki; Goto, Hitoshi

    2015-02-01

    We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.

  10. 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.

  11. THE CRYSTAL STRUCTURE OF ALPHA-DIMETHYLTELLURIUM DICHLORIDE,

    Science.gov (United States)

    TELLURIUM COMPOUNDS, *ORGANOMETALLIC COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , CHLORIDES, SYMMETRY(CRYSTALLOGRAPHY), MOLECULAR STRUCTURE, CHEMICAL BONDS, X RAY DIFFRACTION, ANISOTROPY, FOURIER ANALYSIS.

  12. SiBr4--prediction and determination of crystal structures.

    Science.gov (United States)

    Wolf, Alexandra K; Glinnemann, Jürgen; Schmidt, Martin U; Tong, Jianwei; Dinnebier, Robert E; Simon, Arndt; Köhler, Jürgen

    2009-06-01

    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol(-1) above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature beta phase crystallizes in P2(1)/c, the high-temperature alpha phase in Pa3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  13. SiBr4 - Prediction and Determination of Crystal Structures

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, A.; Glinnemann, J; Schmidt, M; Tong, J; Dinnebier, R; Simon, A; Kohler, J

    2009-01-01

    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol-1 above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature [beta] phase crystallizes in P21/c, the high-temperature [alpha] phase in Pa overline3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  14. Crystal Structure of Isoquinoline Derivatives

    Institute of Scientific and Technical Information of China (English)

    LUO Mei; ZHANG Jia-Hai; ZHOU Shi-Ming; SUN Jie; YIN Hao; HU Ke-Liang

    2011-01-01

    The chiral compound 5H-imidazol[2,3-b]isoquinoline-l-ethanol-5-one-1,2, 3, 10b-tetrahydro- β(S)-phenyl-3(S)-phenyl was synthesized from the direct condensation of 2- cyanophenyacetonitrile with optically active (S)-(+)-2-phenylglycinol in chlorobenzene under dry, anaerobic conditions. ZnCl2 was used as a Lewis acid catalyst in this reaction, and the structure of this compound was determined by X-ray diffraction, NMR, MS and IR. Crystal data of the title compound: C25H22N2O2, Mr = 382.45, P 21 21 21, a = 5.341(5), b = 16.735(5), c = 22.129(5) A, γ = 90°, V = 1978(2)A^3, Z = 4, Dc = 1.284 g/cm^3, the final R = 0.0321 for 2269 observed reflections with I 〉 2 σ(I) and Rw = 0.0771 for all data.

  15. 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.

  16. 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.

  17. 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.......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....

  18. 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...... consumption for on-chip and chip-to-chip optical communication. In order to develop metal-organic vapor phase epitaxial selective area etching and growth, a mask was fabricated in the HSQ e-beam resist including optimization of exposure and development conditions. By use of CBr4 as an etchant, in situ etching...... area and between the structures oriented along the [0-1-1] and [0-11] directions. Strong wavelength dependence with variations of the mask width of a few μm and opening sizes of hundreds of nanometers was observed. Incorporation of an active medium into PhC structures has showed promising results...

  19. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    Science.gov (United States)

    Manikandan, M. R.; Vijayaprasath, G.; babu, G. Anandha; Bhagavannarayan, G.; Vijayan, N.; Ravi, G.

    2012-06-01

    Single crystals of cadmium manganese thiocyanate (CMTC) have been synthesized successfully and grown by slow evaporation method. The structural perfection of the grown crystals has been analyzed by High resolution X-ray diffraction (HRXRD), which shows the crystalline perfection of the grown crystal is quite good. Optical behavior was assessed by UV-Vis analysis and found that no absorption in the UV visible region and it may be useful for second harmonic applications. The mechanical hardness of the grown crystals was studied and Vicker's microhardness, Stiffness constant was calculated.

  20. 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.

  1. synthesis, characterization and crystal structure of a ...

    African Journals Online (AJOL)

    Preferred Customer

    Crystal and molecular structure of the complex ... Coordination chemistry of molybdenum(VI) has attracted considerable attention due to its biochemical significance [1-3] as well as for the efficient catalytic properties in several organic.

  2. Photonic-crystal fibre: Mapping the structure

    DEFF Research Database (Denmark)

    Markos, Christos

    2015-01-01

    The demonstration of real-time and non-destructive Doppler-assisted tomography of the internal structure of photonic-crystal fibres could aid the fabrication of high-quality fibres with enhanced performance.......The demonstration of real-time and non-destructive Doppler-assisted tomography of the internal structure of photonic-crystal fibres could aid the fabrication of high-quality fibres with enhanced performance....

  3. Structures of cyano-biphenyl liquid crystals

    Science.gov (United States)

    Chu, Yuan-Chao; Tsang, Tung; Rahimzadeh, E.; Yin, L.

    1989-01-01

    The structures of p-alkyl- p'-cyano- bicyclohexanes, C(n)H(2n+1) (C6H10)(C6H10) CN (n-CCH), and p-alkyl- p'-cyano- biphenyls, C(n)H(2n+1) (C6H4)(C6H4) CN (n-CBP), were studied. It is convenient to use an x ray image intensification device to search for symmetric x ray diffraction patterns. Despite the similarities in molecular structures of these compounds, very different crystal structures were found. For the smectic phase of 2CCH, the structure is close to rhombohedral with threefold symmetry. In contrast, the structure is close to hexagonal close-packed with two molecules per unit cell for 4CCH. Since intermolecular forces may be quite weak for these liquid crystals systems, it appears that crystal structures change considerably when the alkyl chain length is slightly altered. Different structures were also found in the crystalline phase of n-CBP for n = 6 to 9. For n = 7 to 9, the structures are close to monclinic. The structures are reminiscent of the smectic-A liquid crystal structures with the linear molecules slightly tilted away from the c-axis. In contrast, the structure is quite different for n = 6 with the molecules nearly perpendicular to the c-axis.

  4. Nucleation and structural growth of cluster crystals

    CERN Document Server

    Leitold, Christian

    2016-01-01

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n=4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply-occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, w...

  5. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...... by the theory, the predicted crystal structures are in accord with experiment in all cases except 79Au. In addition, they have investigated the effect of pressure upon the alkali metals (3Li, 11Na, 37Rb, 55Cs) and selected lanthanide metals (57La, 58Ce, 71Lu) and actinide metals (90Th, 91Pa). In these cases...

  6. Structure of initial crystals formed during human amelogenesis

    Science.gov (United States)

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

    1992-02-01

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

  7. Crystal Structure of Macrocalyxin J

    Institute of Scientific and Technical Information of China (English)

    HE Shan; WU Bin; SHI Hao; SUN Cui-Rong

    2007-01-01

    The title compound, (1α,6β, 1 1β, 14α)-1,7:6,20-diepoxy-6,1 1-dihydroxy- 6,7-secoent- kaur-1 6-ene-7,15-dione-14-acetate (macrocalyxin J), is a diterpenoid which was isolated from the leaves of Rabdosia macrocalyx and characterized by single-crystal X-ray diffraction. It crystallizes in orthorhombic, spac e group P212121 with a = 9.3608(8), b = 14.9787(12), c = 15.5750(13)(A), Z = 4, V = 2183.8(3) (A)3, C22H30O9, Mr = 438.46, Dc = 1.334 g/m3, μ(MoKα) = 0.103 mm-1,F(000) = 936, the final R = 0.0532 and wR = 0.1262 for 2252 observed reflections (I > 2σ(I)). In the molecule, three six-membered rings adopt chair, boat and slightly distorted boat conformations,respectively, while both five-membered rings have approximate envelope conformations.

  8. Extraction and Crystal Structure of Karounidiol

    Institute of Scientific and Technical Information of China (English)

    巢志茂; 王诚

    2003-01-01

    The title compound of karounidiol (C30H48O2), a main active triterpene component of snakegourd seed, was isolated from unsaponifiable matter of the seed oil of Trichosanthes kirilowii Maxim., and characterized by X-ray diffraction analysis. It crystallizes in orthorhombic system, space group P212121 with C30H48O2·CH3OH·H2O (C31H54O4), a = 7.515(1), b = 14.407(1), c = 27.799(2) (A。), V = 3009.8(5)(A。)3, Z = 4, Dx = 1.087 g/cm3, Mr = 490.77, F(000) = 1088 and μ = 0.086 mm-1. The final R = 0.0840 and wR = 0.2289 for 2752 observed reflections (|F|2 ≥ 2σ|F|2). The molecular crystal structure of karounidiol shows relative stereochemistry of (3α,13α,14β, 20α)-3,29-dihydroxy-13-methyl-26-norolean-7,9(11)-diene. The molecule is composed of five six- membered rings with ring junctures of A/B trans, C/D trans and D/E cis.

  9. 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.

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

    Science.gov (United States)

    Marx, Ailie; Adir, Noam

    2013-03-01

    X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels 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) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed.

  11. 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.

  12. Crystal structure of 3-(hydroxymethylchromone

    Directory of Open Access Journals (Sweden)

    Yoshinobu Ishikawa

    2015-07-01

    Full Text Available In the title compound, C10H8O3 (systematic name 3-hydroxymethyl-4H-chromen-4-one, the fused-ring system is slightly puckered [dihedral angle between the rings = 3.84 (11°]. The hydroxy O atom deviates from the heterocyclic ring by 1.422 (1 Å. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generate R22(12 loops. The dimers are linked by aromatic π–π stacking [shortest centroid–centroid distance = 3.580 (3 Å], and C—H...O hydrogen bonds, generating a three-dimensional network.

  13. Crystal structure of 9-methacryloylanthracene

    Directory of Open Access Journals (Sweden)

    Aditya Agrahari

    2015-04-01

    Full Text Available In the title compound, C18H14O, with systematic name 1-(anthracen-9-yl-2-methylprop-2-en-1-one, the ketonic C atom lies 0.2030 (16 Å out of the anthryl-ring-system plane. The dihedral angle between the planes of the anthryl and methacryloyl moieties is 88.30 (3° and the stereochemistry about the Csp2—Csp2 bond in the side chain is transoid. In the crystal, the end rings of the anthryl units in adjacent molecules associate in parallel–planar orientations [shortest centroid–centroid distance = 3.6320 (7 Å]. A weak hydrogen bond is observed between an aromatic H atom and the O atom of a molecule displaced by translation in the a-axis direction, forming sheets of parallel-planar anthryl groups packing in this direction.

  14. The crystal structure and crystal chemistry of fernandinite and corvusite

    Science.gov (United States)

    Evans, H.T.; Post, J.E.; Ross, D.R.; Nelen, J.A.

    1994-01-01

    Using type material of fernandinite from Minasragra, Peru, and corvusite from the Jack Claim, La Sal Mountains, Utah, the properties and crystal chemistry of these minerals have been determined by Rietveld analysis of the powder X-ray-diffraction patterns. The crystal structure of both species is isotypic with the V2O5 -type layer first found for ??-Ag0.68V2O5; it consists of chains of VO6 octahedra linked by opposite corners (parallel to b) condensed by edge-sharing to form the layer. The vanadium has average valence 4.8, and the resulting layer-charge is balanced by varying amounts of Ca, Na, and K in the interlayer region accompanied by labile water. This study has confirmed the validity of fernandinite as a unique mineral species. It is closely related to corvusite, from which it is distinguished on the basis of the dominant interlayer cation: Ca for fernandinite, Na for curvusite. -Authors

  15. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

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

    2017-01-01

    structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full......-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...

  16. Anisotropic crystal structure of magnetized neutron star crust

    Science.gov (United States)

    Baiko, D. A.; Kozhberov, A. A.

    2017-09-01

    Although crystallized neutron star crust is responsible for many fascinating observational phenomena, its actual microscopic structure in tremendous gravitational and magnetic fields is not understood. Here we show that in a non-uniform magnetic field, three-dimensional ionic Coulomb crystals comprising the crust may stretch or shrink while their electrostatic pressure becomes anisotropic. The pressure depends non-linearly on the magnitude of the stretch, so that a continuous magnetic field evolution may result in an abrupt crystal elongation or contraction. This may provide a trigger for magnetar activity. A phonon mode instability is revealed, which sets the limits of magnetic field variation beyond which the crystal is destroyed. These limits sometimes correspond to surprisingly large deformations. It is not known what happens to crust matter subject to a pressure anisotropy exceeding these limits. We hypothesize that the ion system then possesses a long-range order only in one or two dimensions, that is becomes a liquid crystal.

  17. Crystal structure of putrescine aspartic acid complex

    OpenAIRE

    Ramaswamy, S.; Murthy, MRN

    1990-01-01

    Polyamines, putrescine, spermidine and spermine are ubiquitous biogenic cations believed to be important for a variety of cellular processes. In order to obtain structural information on the interaction of these amines with other biomolecules, the structure of a complex of putrescine with aspartic acid was determined using single crystal X-ray diffraction methods. The crystals belong monoclinic space group $C_2$ with $a = 21.504 \\AA$, $b = 4.779 \\AA$, $c = 8.350 \\AA$ and $\\beta = {97.63}^{\\ci...

  18. Crystal structure of canagliflozin hemihydrate

    Directory of Open Access Journals (Sweden)

    Kai-Hang Liu

    2016-05-01

    Full Text Available There are two canagliflozin molecules (A and B and one water molecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R-2-(3-{[5-(4-fluorophenylthiophen-2-yl]methyl}-4-methylphenyl-6-(hydroxymethyl-3,4,5,6-tetrahydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methylbenzene and thiophene rings are 115.7 (4 and 111.7 (4°, while the dihedral angles between the fluorobenzene and thiophene rings are 24.2 (6 and 20.5 (9° in molecules A and B, respectively. The hydropyran ring exhibits a chair conformation in both canagliflozin molecules. In the crystal, the canagliflozin molecules and lattice water molecules are connected via O—H...O hydrogen bonds into a three-dimensional supramolecular architecture.

  19. Crystal structure of canagliflozin hemihydrate.

    Science.gov (United States)

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-05-01

    There are two canagliflozin mol-ecules (A and B) and one water mol-ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro-phen-yl)thio-phen-2-yl]meth-yl}-4-methylphen-yl)-6-(hy-droxy-meth-yl)-3,4,5,6-tetra-hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl-benzene and thio-phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro-benzene and thio-phene rings are 24.2 (6) and 20.5 (9)° in mol-ecules A and B, respectively. The hydro-pyran ring exhibits a chair conformation in both canagliflozin mol-ecules. In the crystal, the canagliflozin mol-ecules and lattice water mol-ecules are connected via O-H⋯O hydrogen bonds into a three-dimensional supra-molecular architecture.

  20. Crystal Structure of 8-Demethoxyrunanine

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Ling

    2008-01-01

    A new hasubanane-type alkaloid, 8-demethoxyrunanine, was isolated from Sino- menium acutum and characterized by melting point, HREIMS, 1H NMR, and X-ray diffraction analysis. X-ray diffraction reveals that the title compound crystallizes in the orthorhombic system, space group P212121 with a = 7.308(1), b = 21.742(5), c = 22.893(4) ?, V = 3637.5(11) ?3, Z = 8, Dx = 1.254 g/cm3, F(000) = 1472, μ(MoKα) = 0.087 mm-1, the final R = 0.0438 and wR = 0.0575 for 4497 independent reflections with Rint = 0.0192 and 2091 observed reflections with I > 2σ(I). Four rings (ring A: one benzene ring, ring B: one hexagon carbon ring in a half-chair conformation, ring C: one hexagon carbon ring with α,β-unsaturated ketone segment (-CR2=CR1-C=O) in a screw-boat conformation, and ring D: one nonplanar tetrahydropyrrole) form a hasubanane-type alkaloid.

  1. The different conformations and crystal structures of dihydroergocristine

    Science.gov (United States)

    Mönch, B.; Kraus, W.; Köppen, R.; Emmerling, F.

    2016-02-01

    The identification of different forms of dihydroergocristine (DHEC) was carried out by crystallization from different organic solvents. DHEC was identified as potential template for molecularly imprinted polymers (MIPs) for the epimeric specific analysis of ergot alkaloids (EAs) in food. DHEC was crystallized from different solvents in order to mimic the typical MIP synthesis conditions. Four new solvatomorphs of DHEC were obtained. All solvatomorphs contain a water molecule in the crystal structure, whereas three compounds contain an additional solvent molecule. Based on the conformation of DHEC a comparison with typical EA molecules was possible. The analysis showed that DHEC is a suitable template for MIPs for EAs.

  2. 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 c...

  3. 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.

  4. Structure analysis on synthetic emerald crystals

    Science.gov (United States)

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

    2013-05-01

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

  5. Troublesome Crystal Structures: Prevention, Detection, and Resolution.

    Science.gov (United States)

    Harlow, Richard L

    1996-01-01

    A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures.

  6. THE CRYSTAL STRUCTURE OF 2,7-DIACETOXYTRANS-15,16-DIMETHYL-15,16-DIHYDROPYRENE,

    Science.gov (United States)

    AROMATIC COMPOUNDS, CRYSTAL STRUCTURE ), (*POLYCYCLIC COMPOUNDS, CRYSTAL STRUCTURE ), (* CRYSTAL STRUCTURE , POLYCYCLIC COMPOUNDS), ESTERS, MOLECULAR STRUCTURE, CHEMICAL BONDS, X RAY DIFFRACTION, SCINTILLATION COUNTERS, CANADA

  7. 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.

  8. Synthesis and Crystal Structure of Dehydroandrographolide Dipolycyclophosphate

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The title compound was synthesized and characterized by IR, NMR, H R S I-M S and MS, and its crystal structure was determined by single-crystal X-ray diffraction. The crystal is of orthorhombic system (C4oH52O11P2, Mr= 770.76), space group P21212, with a = 22.562(5), b =29.224(6), c = 7.1953(14) A, V = 4744.2(16) A3, Z = 4, Dc = 1.079 g/cm3, F(000) = 1640 andμ =0.141 mm-1. The final R = 0.0758 and wR = 0.1778 for 2794 observed reflections with I > 2o(I).Intermolecular hydrogen bonds are found between the O atom of carbonyl group and H atoms of olefinic carbon. The absolute configuration of this molecule was confirmed by comparison with that of the original material.

  9. Crystal structure of low-symmetry rondorfite

    Science.gov (United States)

    Rastsvetaeva, R. K.; Zadov, A. E.; Chukanov, N. V.

    2008-03-01

    The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca16[Mg2(Si7Al)(O31OH)]Cl4 from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Å, b = 15.110(2) Å, c = 15.092(2) Å, α = 90.06(1)°, β = 90.01(1)°, γ = 89.93(1)°, Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3σ( F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group ( a = 15.105 Å, sp. gr. Fd overline 3 , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3σ( F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

  10. 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)

  11. The Crystal Structure of a Ternary Complex of Betaine Aldehyde Dehydrogenase from Pseudomonas aeruginosa Provides New Insight Into the Reaction Mechansim and Shows A Novel Binding Mode of the 2'-Phosphate of NADP+ and A Novel Cation Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Segura, L.; Rudino-Pinera, E; Munoz-Clares, R; Horjales, E

    2009-01-01

    In the human pathogen Pseudomonas aeruginosa, the NAD(P)+-dependent betaine aldehyde dehydrogenase (PaBADH) may play the dual role of assimilating carbon and nitrogen from choline or choline precursors-abundant at infection sites-and producing glycine betaine and NADPH, potentially protective against the high-osmolarity and oxidative stresses prevalent in the infected tissues. Disruption of the PaBADH gene negatively affects the growth of bacteria, suggesting that this enzyme could be a target for antibiotic design. PaBADH is one of the few ALDHs that efficiently use NADP+ and one of the even fewer that require K+ ions for stability. Crystals of PaBADH were obtained under aerobic conditions in the presence of 2-mercaptoethanol, glycerol, NADP+ and K+ ions. The three-dimensional structure was determined at 2.1-A resolution. The catalytic cysteine (C286, corresponding to C302 of ALDH2) is oxidized to sulfenic acid or forms a mixed disulfide with 2-mercaptoethanol. The glutamyl residue involved in the deacylation step (E252, corresponding to E268 of ALDH2) is in two conformations, suggesting a proton relay system formed by two well-conserved residues (E464 and K162, corresponding to E476 and K178, respectively, of ALDH2) that connects E252 with the bulk water. In some active sites, a bound glycerol molecule mimics the thiohemiacetal intermediate; its hydroxyl oxygen is hydrogen bonded to the nitrogen of the amide groups of the side chain of the conserved N153 (N169 of ALDH2) and those of the main chain of C286, which form the 'oxyanion hole.' The nicotinamide moiety of the nucleotide is not observed in the crystal, and the adenine moiety binds in the usual way. A salt bridge between E179 (E195 of ALDH2) and R40 (E53 of ALDH2) moves the carboxylate group of the former away from the 2?-phosphate of the NADP+, thus avoiding steric clashes and/or electrostatic repulsion between the two groups. Finally, the crystal shows two K+ binding sites per subunit. One is

  12. Structure sensitive properties of KTP-type crystals

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Adding various dopants during the growth of the parent KTiOPO4 (KTP) crystal has given rise to an extensive series of KTP-type crystals. The doped KTP or KTP-type crystals often have very subtle structural variations from pure KTP crystals. As a result of these structural changes the KTP-type crystals often exhibit different physical properties, which may be referred to as structure sensitive properties. It is possible to fine-tune the nonlinear optical properties of KTP crystals through doping. This results in a broad range of applications for KTP-type crystals.

  13. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

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

    2017-01-01

    synaptic transmission and modulate network excitability by regulating neurotransmitter release. Dysfunction of kainate receptors has been implicated in several neurological disorders such as epilepsy, schizophrenia and depression. Here we provide a review on the current understanding of kainate receptor...... structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full...

  14. 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.

  15. Ultrasonography shows disappearance of monosodium urate crystal deposition on hyaline cartilage after sustained normouricemia is achieved.

    Science.gov (United States)

    Thiele, Ralf G; Schlesinger, Naomi

    2010-02-01

    This study aimed at determining whether lowering serum urate (SU) to less than 6 mg/dl in patients with gout affects ultrasonographic findings. Seven joints in five patients with monosodium urate (MSU) crystal proven gout and hyperuricemia were examined over time with serial ultrasonography. Four of the five patients were treated with urate lowering drugs (ULDs) (allopurinol, n = 3; probenecid, n = 1). One patient was treated with colchicine alone. Attention was given to changes in a hyperechoic, irregular coating of the hyaline cartilage in the examined joints (double contour sign or "urate icing"). This coating was considered to represent precipitate of MSU crystals. Index joints included metacarpophalangeal (MCP) joints (n = 2), knee joints (n = 3), and first metatarsophalangeal (MTP) joints (n = 2). The interval between baseline and follow-up images ranged from 7 to 18 months. Serial SU levels were obtained during the follow-up period. During the follow-up period, three patients treated with ULD (allopurinol, n = 2; probenecid, n = 1) achieved a SU level of or =7 mg/dl. In one patient treated with allopurinol, SU levels improved from 13 to 7 mg/dl during the follow-up period. Decrease, but not resolution of the hyperechoic coating was seen in this patient. In the patient treated with colchicine alone, SU levels remained >8 mg/dl, and no sonographic change was observed. In our patients, sonographic signs of deposition of MSU crystals on the surface of hyaline cartilage disappeared completely if sustained normouricemia was achieved. This is the first report showing that characteristic sonographic changes are influenced by ULDs once SU levels remain < or =6 mg/dl for 7 months or more. Sonographic changes of gout correlate with SU levels and may be a non-invasive means to track changes in the uric acid pool. Larger prospective studies are needed to further assess these potentially important findings.

  16. Crystal structure of an archaeal actin homolog.

    Science.gov (United States)

    Roeben, Annette; Kofler, Christine; Nagy, István; Nickell, Stephan; Hartl, F Ulrich; Bracher, Andreas

    2006-04-21

    Prokaryotic homologs of the eukaryotic structural protein actin, such as MreB and ParM, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid DNA. In contrast to these bacterial actin homologs, little is known about the archaeal counterparts. As a first step, we expressed a predicted actin homolog of the thermophilic archaeon Thermoplasma acidophilum, Ta0583, and determined its crystal structure at 2.1A resolution. Ta0583 is expressed as a soluble protein in T.acidophilum and is an active ATPase at physiological temperature. In vitro, Ta0583 forms sheets with spacings resembling the crystal lattice, indicating an inherent propensity to form filamentous structures. The fold of Ta0583 contains the core structure of actin and clearly belongs to the actin/Hsp70 superfamily of ATPases. Ta0583 is approximately equidistant from actin and MreB on the structural level, and combines features from both eubacterial actin homologs, MreB and ParM. The structure of Ta0583 co-crystallized with ADP indicates that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. However, the conformation of the nucleotide observed in complex with Ta0583 clearly differs from that in complex with actin, but closely resembles the conformation of ParM-bound nucleotide. On the basis of sequence and structural homology, we suggest that Ta0583 derives from a ParM-like actin homolog that was once encoded by a plasmid and was transferred into a common ancestor of Thermoplasma and Ferroplasma. Intriguingly, both genera are characterized by the lack of a cell wall, and therefore Ta0583 could have a function in cellular organization.

  17. Lessons from crystal structures of kainate receptors.

    Science.gov (United States)

    Møllerud, Stine; Frydenvang, Karla; Pickering, Darryl S; Kastrup, Jette Sandholm

    2017-01-01

    Kainate receptors belong to the family of ionotropic glutamate receptors. These receptors assemble from five subunits (GluK1-5) into tetrameric ion channels. Kainate receptors are located at both pre- and postsynaptic membranes in the central nervous system where they contribute to excitatory synaptic transmission and modulate network excitability by regulating neurotransmitter release. Dysfunction of kainate receptors has been implicated in several neurological disorders such as epilepsy, schizophrenia and depression. Here we provide a review on the current understanding of kainate receptor structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full-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 questions and challenges in front of us. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'.

  18. Effect of Crystal Growth Direction on Domain Structure of Mn-Doped (Na,K)NbO3 Crystal

    Science.gov (United States)

    Tsuchida, Kohei; Kakimoto, Ken-ichi; Kagomiya, Isao

    2013-09-01

    Single crystals of (Na0.55K0.45)(Nb0.995Mn0.005)O3 have been grown by a floating zone method in N2 and decompression atmosphere to avoid alkaline metal volatilization on the SrTiO3 material base. The variation of their ferroelectric domain structure and the chemical composition of the grown crystal in the growth direction were evaluated. In the crystal grown in N2 atmosphere, the Na and K are not distributed homogeneously. In addition, the phase transition temperature TC and TO-T showed different values between the grown crystal and raw material. By using laser scanning confocal microscope, the domain structures of the grown crystal revealed random patterns in the initial growth stage and lamellar patterns in the progressing crystal growth. In decompression atmosphere, the TC and TO-T values of the grown crystal were similar to those of the raw material and the domain structures showed a constant domain size. The electrical property of the crystal became stable and the domain structure was easily switched against applied electrical field because the oriented lamellar domain was created during cooling of the crystal.

  19. A DIRECT DETERMINATION OF THE CRYSTAL STRUCTURE OF 2,3,4,6-TETRANITROANILINE,

    Science.gov (United States)

    ORGANIC NITROGEN COMPOUNDS, CRYSTAL STRUCTURE ), (* CRYSTAL STRUCTURE , EXPLOSIVES), (*EXPLOSIVES, CRYSTAL STRUCTURE ), AROMATIC COMPOUNDS, AMINES, NITRATES, LEAST SQUARES METHOD, FOURIER ANALYSIS, CHEMICAL BONDS.

  20. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  1. THE CRYSTAL STRUCTURE OF 2-(4’-AMINO-5’AMINO PYRIMIDY) -2-PENTENE-4-ONE.

    Science.gov (United States)

    NITROGEN HETEROCYCLIC COMPOUNDS, CRYSTAL STRUCTURE ), (*AMINES, CRYSTAL STRUCTURE ), (*KETONES, CRYSTAL STRUCTURE ), CRYSTAL LATTICES, FOURIER ANALYSIS, LEAST SQUARES METHOD, MOLECULAR STRUCTURE, PYRIMIDINES, CHEMICAL BONDS

  2. 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.

  3. Synthesis and structural characterization of a single-crystal to single-crystal transformable coordination polymer.

    Science.gov (United States)

    Tian, Yuyang; Allan, Phoebe K; Renouf, Catherine L; He, Xiang; McCormick, Laura J; Morris, Russell E

    2014-01-28

    A single-crystal to single-crystal transformable coordination polymer compound was hydrothermally synthesized. The structural rearrangement is induced by selecting a ligand that contains both strong and weaker coordinating groups. Both hydrated and dehydrated structures were determined by single crystal X-ray analysis.

  4. Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?

    Science.gov (United States)

    Hylton, Rebecca K; Tizzard, Graham J; Threlfall, Terence L; Ellis, Amy L; Coles, Simon J; Seaton, Colin C; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L

    2015-09-02

    Mandelic acids are prototypic chiral molecules where the sensitivity of crystallized forms (enantiopure/racemic compound/polymorphs) to both conditions and substituents provides a new insight into the factors that may allow chiral separation by crystallization. The determination of a significant number of single crystal structures allows the analysis of 13 enantiopure and 30 racemic crystal structures of 21 (F/Cl/Br/CH3/CH3O) substituted mandelic acid derivatives. There are some common phenyl packing motifs between some groups of racemic and enantiopure structures, although they show very different hydrogen-bonding motifs. The computed crystal energy landscape of 3-chloromandelic acid, which has at least two enantiopure and three racemic crystal polymorphs, reveals that there are many more possible structures, some of which are predicted to be thermodynamically more favorable as well as slightly denser than the known forms. Simulations of mandelic acid dimers in isolation, water, and toluene do not differentiate between racemic and enantiopure dimers and also suggest that the phenyl ring interactions play a major role in the crystallization mechanism. The observed crystallization behavior of mandelic acids does not correspond to any simple "crystal engineering rules" as there is a range of thermodynamically feasible structures with no distinction between the enantiopure and racemic forms. Nucleation and crystallization appear to be determined by the kinetics of crystal growth with a statistical bias, but the diversity of the mandelic acid crystallization behavior demonstrates that the factors that influence the kinetics of crystal nucleation and growth are not yet adequately understood.

  5. 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.

  6. 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.

  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. 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.

  9. Crystal structure and stereochemistry study of 2-substituted benzoxazole derivatives.

    Science.gov (United States)

    Mabied, Ahmed F; Shalaby, Elsayed M; Zayed, Hamdia A; El-Kholy, Esmat; Farag, Ibrahim S A; Ahmed, Naima A

    2014-01-01

    The structure of 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I), has triclinic ([Formula: see text]) symmetry. The structure displays N-H ⋯ N hydrogen bonding. The structure of 2-[(arylidene) cyanomethyl] benzoxazoles, C17H10N2O3 (II), has triclinic ([Formula: see text]) symmetry. The structure displays C-H ⋯ N, C-H ⋯ C hydrogen bonding. In (I), the chlorophenyl and benzoxazole groups adopt a trans configuration with respect to the central cyanomethyle hydrazone moiety. Compound (II) crystallized with two molecules in the asymmetric unit shows cisoid conformation between cyano group and benzoxazole nitrogen, contrary to (I). In (II) the benzodioxole has an envelope conformation (the C17 atom is the flap atom). The molecular geometry obtained using molecular mechanics (MM) calculations has been discussed along with the results of single crystal analysis.

  10. Microprobe of structure of crystal/liquid interface boundary layers

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The molecular structures and its evolutive regularities within the boundary layers in the crystal growth of KDP and DKDP have been studied in real time by using holography and Raman microprobe. The experiments show that the molecular structure of mother solution within the boundary layers is distinctly different from that of the solutions alone. In this paper, the effects of cations within the boundary layers on the structure of solution are considered. Within the characteristic boundary layers, the effects of cations cause the changes in O-P-O bond angle, electronic density redistribution of the phosphate groups, and significant changes in the bond intensity, thus leading to the breaking of partial hydrogen bonds of the phosphate associations, the readjustment of geometry of anionic phosphate groups and desolvation, and the forming of the smectic ordering structure of the anions_cations. Finally, the crystallization unit of anion_cation should be formed at the proximate interface.

  11. A unified picture of the crystal structures of metals

    Science.gov (United States)

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

    1995-04-01

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

  12. Crystal structure prediction from first principles: The crystal structures of glycine

    Science.gov (United States)

    Lund, Albert M.; Pagola, Gabriel I.; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2015-04-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the genetic algorithms search implemented in MGAC, modified genetic algorithm for crystals, coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.

  13. Isolation and Crystal Structure of Horminone

    Institute of Scientific and Technical Information of China (English)

    陈晓; 廖仁安; 翁林红; 谢庆兰; 邓锋杰

    2000-01-01

    The horminone (C20H28O4, Mr= 332.85) was first isolated from the leaves of Rabdosia Serra (Maxim) Hara and its crystal structure was determined by X-ray diffraction method. Horminone is orthorhombic with space group P21P21P21, a=7.7186(7), b=9.5506(9), c=24.227(2) A, V=1785.9(3) A3, Z=4, Dc=1.236g/cm3, λ=0. 71073 A , μ(MoKα)=0. 085mm-1, F(000)=720. The structure was refined to R=0. 0369, wR=0.0978 for 2446 reflections with I>2σ(Ⅰ). X-ray diffraction analysis reveals that there are three six-membered rings in the title molecule. Ring A is in the chair conformation, ring C has the structure of quinone and there are two intermolecular hydrogen bonds between two molecules.

  14. 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.

  15. [Crystal and molecular structure of cytisine salts].

    Science.gov (United States)

    Niedźwiecka, Julia; Przybył, Anna K; Kubicki, Maciej

    2012-01-01

    Cytisine is an alkaloid of plant origin. It is a toxic substance, obtained on an industrial scale from Laburnum anagyroides also known as common laburnum. Today is used in the preparation of anti-smoking products as an agonist of nicotinic receptors nAChR-alpha4beta2. Thanks to crystallographic methods we can examine and describe with high accuracy the actual structure of complex chemical compounds. This work aims to present a series of tests carried out on crystals of cytisine salts, after a prior isolation of cytisine from the seeds of laburnum anagyroides.

  16. Crystal structure of hexaaquadichloridoytterbium(III chloride

    Directory of Open Access Journals (Sweden)

    Kevin M. Knopf

    2015-06-01

    Full Text Available The crystal structure of the title compound, [YbCl2(H2O6]Cl, was determined at 110 K. Samples were obtained from evaporated acetonitrile solutions containing the title compound, which consists of a [YbCl2(H2O6]+ cation and a Cl− anion. The cations in the title compound sit on a twofold axis and form O—H...Cl hydrogen bonds with the nearby Cl− anion. The coordination geometry around the metal centre forms a distorted square antiprism. The ytterbium complex is isotypic with the europium complex [Tambrornino et al. (2014. Acta Cryst. E70, i27].

  17. Crystal Structure of Marburg Virus VP24

    OpenAIRE

    Zhang, Adrianna P. P.; Bornholdt, Zachary A.; Abelson, Dafna M.; Saphire, Erica Ollmann

    2014-01-01

    The VP24 protein plays an essential, albeit poorly understood role in the filovirus life cycle. VP24 is only 30% identical between Marburg virus and the ebolaviruses. Furthermore, VP24 from the ebolaviruses is immunosuppressive, while that of Marburg virus is not. The crystal structure of Marburg virus VP24, presented here, reveals that although the core is similar between the viral genera, Marburg VP24 is distinguished by a projecting β-shelf and an alternate conformation of the N-terminal p...

  18. Crystal structure of Marburg virus VP24.

    Science.gov (United States)

    Zhang, Adrianna P P; Bornholdt, Zachary A; Abelson, Dafna M; Saphire, Erica Ollmann

    2014-05-01

    The VP24 protein plays an essential, albeit poorly understood role in the filovirus life cycle. VP24 is only 30% identical between Marburg virus and the ebolaviruses. Furthermore, VP24 from the ebolaviruses is immunosuppressive, while that of Marburg virus is not. The crystal structure of Marburg virus VP24, presented here, reveals that although the core is similar between the viral genera, Marburg VP24 is distinguished by a projecting β-shelf and an alternate conformation of the N-terminal polypeptide.

  19. Elasticity of some mantle crystal structures. II.

    Science.gov (United States)

    Wang, H.; Simmons, G.

    1973-01-01

    The single-crystal elastic constants are determined as a function of pressure and temperature for rutile structure germanium dioxide (GeO2). The data are qualitatively similar to those of rutile TiO2 measured by Manghnani (1969). The compressibility in the c direction is less than one-half that in the a direction, the pressure derivative of the shear constant is negative, and the pressure derivative of the bulk modulus has a relatively high value of about 6.2. According to an elastic strain energy theory, the negative shear modulus derivative implies that the kinetic barrier to diffusion decreases with increasing pressure.

  20. Crystal structure of a DNA catalyst.

    Science.gov (United States)

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.

  1. Syntheses and Crystal Structures of Pyrazoline Derivants

    Institute of Scientific and Technical Information of China (English)

    SHI Hai-Bin; JI Shun-Jun; ZHANG Yong

    2005-01-01

    Two pyrazoline derivants 1-(2-benzothiazole)-3-phenyl-5-(3-thiophene)-2- pyrazoline (BPTP) and 1-(2-benzothiazole)-3-(2-thiophene)-5-phenyl-2-pyrazoline (BTPP) have been synthe- sized and their crystal structures were determined by X-ray single-crystal diffraction.Crystal of BPTP belongs to triclinic, space group P with a = 9.4430(11), b = 9.9384(13), c = 9.9394(13) (A), α = 83.107(10), β = 79.947(10), γ = 70.221(7)o, V = 862.42(19) (A)3, Z = 2, Dc = 1.392 g/cm3, μ(MoKα) = 0.316 mm-1, F(000) = 376, λ = 0.71070 (A), (Δρ)max = 0.348, (Δρ)min = -0.481 e/(A)3, the final R = 0.0407 and wR = 0.1055 for 2844 observed reflections with I > 2σ(I).Crystal of BTPP is of monoclinic, space group P21/c with a = 11.6158(17), b = 11.2796(18), c = 13.082(2) (A), α = 90, β = 91.087(4), γ = 90o, V = 1713.7(5) (A)3, Z = 4, Dc = 1.401 g/cm3, μ(MoKα) = 0.318 mm-1, Mr = 361.07, F(000) = 752, λ = 0.71070 (A), (Δρ)max = 0.322, (Δρ)min = -0.330 e/(A)3, the final R = 0.0563 and wR = 0.1058 for 3434 observed reflections with I > 2σ(I).

  2. Structural considerations on acridine/acridinium derivatives: Synthesis, crystal structure, Hirshfeld surface analysis and computational studies

    Science.gov (United States)

    Wera, Michał; Storoniak, Piotr; Serdiuk, Illia E.; Zadykowicz, Beata

    2016-02-01

    This article describes a detailed study of the molecular packing and intermolecular interactions in crystals of four derivatives of acridine, i.e. 9-methyl-, 9-ethyl, 9-bromomethyl- and 9-piperidineacridine (1, 2, 3 and 4, respectively) and three 10-methylacridinium salts containing the trifluoromethanesulphonate anion and 9-vinyl-, 9-bromomethyl, and 9-phenyl-10-methylacridinium cations (5, 6 and 7, respectively). The crystal structures of all of the compounds are stabilized by long-range electrostatic interactions, as well as by a network of short-range C-HṡṡṡO (in hydrates and salts 3 and 5-7, respectively), C-Hṡṡṡπ, π-π, C-Fṡṡṡπ and S-Oṡṡṡπ (in salts 5-7) interactions. Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, graphically exhibiting the differences in spatial arrangements of the acridine/acridinium derivatives under scrutiny here. Additionally, computational methods have been used to compare the intermolecular interactions in the crystal structures of the investigated compounds. Computations have confirmed the great contribution of dispersive interactions for crystal lattice stability in the case of 9-substituted acridine and electrostatic interactions for the crystal lattice stability in the case of 9-substituted 10-methylacridinium trifluoromethanesulphonates. The value of crystal lattice energy and the electrostatic contribution in the crystal lattice energy of monohydrated acridine derivatives have confirmed that these compounds have behave as acridinium derivatives.

  3. Band structure characteristics of T-square fractal phononic crystals

    Institute of Scientific and Technical Information of China (English)

    Liu Xiao-Jian; Fan You-Hua

    2013-01-01

    The T-square fractal two-dimensional phononic crystal model is presented in this article.A comprehensive study is performed for the Bragg scattering and locally resonant fractal phononic crystal.We find that the band structures of the fractal and non-fractal phononic crystals at the same filling ratio are quite different through using the finite element method.The fractal design has an important impact on the band structures of the two-dimensional phononic crystals.

  4. 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.

  5. Modeling of photonic crystal waveguide structures

    Science.gov (United States)

    Richter, Ivan; Kwiecien, Pavel; Šiňor, Milan; Haiduk, Adam

    2007-05-01

    Photonic crystal (PhC) structures and photonic structures based on them represent nowadays very promising structures of artificial origin. Since they exhibit very specific properties and characteristics that can be very difficult (or even impossible) to realize by other means, they represent a significant part of new artificially made metamaterial classes. For studying and modeling properties of PhC structures, we have applied, implemented and partially improved various complementary techniques: the 2D plane wave expansion (PWE) method, and the 2D finite-difference time-domain (FDTD) method with perfectly matched layers. Also, together with these in-house methods, other tools available in the field have been applied, including, e.g. MIT MPB (PWE), F2P (FDTD) and CAMFR (bidirectional expansion and propagation mode matching method) packages. We have applied these methods to several PhC waveguide structure examples, studying the effects of varying the key parameters and geometry. Such a study is relevant for proper understanding of physical mechanisms and for optimization and fabrication recommendations. Namely, in this contribution, we have concentrated on several examples of PhC waveguide structure simulations, of two types of guides (dielectric-rode type and air-hole type), with several geometries: rectangular lattice with either rectangular or chessboard inclusions. The modeling results are compared and discussed.

  6. Temperature dependent spin structures in Hexaferrite crystal

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Y.C. [Center for Condensed Matter Sciences, National Taiwan University, Taipei 106, Taiwan (China); Lin, J.G., E-mail: jglin@ntu.edu.tw [Center for Condensed Matter Sciences, National Taiwan University, Taipei 106, Taiwan (China); Chun, S.H.; Kim, K.H. [Department of Physics and Astronomy, Seoul National University, Seoul 151-747 (Korea, Republic of)

    2016-01-01

    In this work, the Hexaferrite Ba{sub 0.5}Sr{sub 1.5}Zn{sub 2}Fe{sub 12}O{sub 22} (BSZFO) is studied due to its interesting characteristics of long-wavelength spin structure. Ferromagnetic resonance (FMR) is used to probe the magnetic states of BSZFO single crystal and its temperature dependence behavior is analyzed by decomposing the multiple lines of FMR spectra into various phases. Distinguished phase transition is observed at 110 K for one line, which is assigned to the ferro(ferri)-magnetic transition from non-collinear to collinear spin state. - Highlights: • For the first time Ferromagnetic Resonance is used to probe the local magnetic structure of Ba{sub 0.5}Sr{sub 1.5}Zn{sub 2}Fe{sub 12}O{sub 22.} • The multiphases in the single crystal is identified, which provides important information toward its future application for the magnetoelectric devices.

  7. Photonic crystal type structure in bivalve ligament of Pinctada maxima

    Institute of Scientific and Technical Information of China (English)

    ZHANG GangSheng

    2007-01-01

    The dry ligament of Pinctada maxima normally appears black; however, it can exhibit striking blue structural colors after being wetted by water. The field-mission SEM investigation shows that the ligament is made of lamellae, which, about 35 μm thick, are made of proteins and aragonite fibers of about 78 nm in diameter. In each single lamella, the fibers are highly aligned characterized by a 2D photonic crystal type structure. According to measured reflective spectra and theoretical simulations, the dry and wet ligaments possess photonic stop band at ultraviolet and blue wavelengths, respectively, which are responsible for structural colorations of ligament.

  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. Improved 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 and robust structure for realizing asymmetric Fano transmission characteristics in photonic crystal waveguide-cavity structures. The use of Fano resonances for optical switching is analyzed using temporal coupled mode theory in combination with three-dimensional finite...... difference time domain simulations taking into account the signal bandwidth. The results suggest a significant energy reduction by employing Fano resonances compared to more well established Lorentzian resonance structures. A specific example of a Kerr nonlinearity shows an order of magnitude energy...

  10. Crystal structure of hexagonal RE(CO{sub 3})OH

    Energy Technology Data Exchange (ETDEWEB)

    Michiba, Kiyonori; Tahara, Takeshi; Nakai, Izumi [Tokyo Univ. of Science, Shinjuku (Japan). Faculty of Science; Miyawaki, Ritsuro; Matsubara, Satoshi [National Museum of Nature and Science, Tokyo (Japan). Dept. of Geology and Paleontology

    2011-07-01

    Hexagonal rare earth carbonate hydroxides, RE(CO{sub 3})OH, where RE = La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, and Er, were hydrothermally synthesized from formic acid and hydroxide gels of rare earth elements. The crystals exhibited bicephalous hexagonal prisms with lengths of several tens of micrometers. The crystal structures of a series of hexagonal RE(CO{sub 3})OH were solved using the single crystal CCD-XRD intensity data sets. The space groups of the synthetic hexagonal RE(CO{sub 3})OH crystals are all P- anti 6. The present study has cast doubt upon the space group P- anti 62c previously reported for the natural Ce(CO{sub 3})OH, hydroxylbastnaesite-(Ce). The cell parameters decreased linearly with decreases in the ionic radii of the rare earth elements. La(CO{sub 3})OH showed the largest unit cell (a = 12.6752(6), c = 10.0806(10) A), while Er(CO{sub 3})OH showed the smallest (a = 11.8977(4), c = 9.6978(8) A). The rare earth atoms are in ninefold coordination with oxygen atoms to form a tricapped trigonal prism. The structure consists of layers of {sup 2}{infinity}[(OH)RE{sub 3/3}]{sup 2+} ions linked by carbonate ions. Raman spectra indicate the presence of carbonate and hydroxide groups. An evolutionary shift was observed from La to Er towards higher frequency, which was associated with a decreasing RE-O bond length. (orig.)

  11. 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.

  12. 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.

  13. 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.

  14. The Crystal Structure of Human Argonaute2

    Energy Technology Data Exchange (ETDEWEB)

    Schirle, Nicole T.; MacRae, Ian J. (Scripps)

    2012-07-18

    Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.

  15. Structural Transitions in Cholesteric Liquid Crystal Droplets

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-01

    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.

  16. Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.

    Science.gov (United States)

    Sun, Siyang; Xiang, Ye; Akahata, Wataru; Holdaway, Heather; Pal, Pankaj; Zhang, Xinzheng; Diamond, Michael S; Nabel, Gary J; Rossmann, Michael G

    2013-04-02

    A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.

  17. 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.

  18. Structural templating in a nonplanar phthalocyanine using single crystal copper iodide

    OpenAIRE

    Rochford, L. A. (Luke A.); Ramadan, Alexandra J.; Keeble, Dean S.; Ryan, Mary P.; Heutz, Sandrine; Jones, T S

    2015-01-01

    Solution-grown copper iodide crystals are used as substrates for the templated growth of the nonplanar vanadyl phthalocyanine using organic molecular beam deposition. Structural characterization reveals a single molecular orientation produced by the (111) Miller plane of the copper iodide crystals. These fundamental measurements show the importance of morphology and structure in templating interactions for organic electronics applications.

  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

    , evaporation rate can be controlled or adjusted in this method during the crystallization process to favor either nucleation or growing processes for optimizing crystallization process. The protein crystals gotten by this method were experimentally proven to possess high x-ray diffraction qualities. Finally, we crystallized human lactate dehydrogenase 1 (H4) complexed with NADH and determined its structure by x-ray crystallography. The structure of LDH/NADH displays a significantly different structural feature, compared with LDH/NADH/inhibitor ternary complex structure, that subunits in LDH/NADH complex show open conformation or two conformations on the active site while the subunits in LDH/NADH/inhibitor are all in close conformation. Multiple LDH/NADH crystals were obtained and used for x-ray diffraction experiments. Difference in subunit conformation was observed among the structures independently solved from multiple individual LDH/NADH crystals. Structural differences observed among crystals suggest the existence of multiple conformers in solution.

  20. 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.

  1. Crystal and molecular structure of aflatrem

    Directory of Open Access Journals (Sweden)

    Bruno N. Lenta

    2015-11-01

    Full Text Available The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the molecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabicyclo[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabicyclo[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the molecule exhibits a tilt of 2.02 (1° between its two rings. In the crystal, O—H...O hydrogen bonds connect molecules into chains along [010]. Weak N—H...π interactions connect these chains, forming sheets parallel to (10-1.

  2. The crystal structure Escherichia coli Spy.

    Science.gov (United States)

    Kwon, Eunju; Kim, Dong Young; Gross, Carol A; Gross, John D; Kim, Kyeong Kyu

    2010-11-01

    Escherichia coli spheroplast protein y (EcSpy) is a small periplasmic protein that is homologous with CpxP, an inhibitor of the extracytoplasmic stress response. Stress conditions such as spheroplast formation induce the expression of Spy via the Cpx or the Bae two-component systems in E. coli, though the function of Spy is unknown. Here, we report the crystal structure of EcSpy, which reveals a long kinked hairpin-like structure of four α-helices that form an antiparallel dimer. The dimer contains a curved oval shape with a highly positively charged concave surface that may function as a ligand binding site. Sequence analysis reveals that Spy is highly conserved over the Enterobacteriaceae family. Notably, three conserved regions that contain identical residues and two LTxxQ motifs are placed at the horizontal end of the dimer structure, stabilizing the overall fold. CpxP also contains the conserved sequence motifs and has a predicted secondary structure similar to Spy, suggesting that Spy and CpxP likely share the same fold.

  3. Crystal structure of zirconia by Rietveld refinement

    Institute of Scientific and Technical Information of China (English)

    王大宁; 郭永权; 梁开明; 陶琨

    1999-01-01

    The crystal structures and phase transformation of zirconia ceramics have been investigated by means of X-ray powder diffraction and Rietveld powder diffraction profile fitting technique. A structural transition from monoclinic to tetragonal occurs when Y2O3 and CeO2 are doped into zirconia. The space group of the tetragonal structure is P42/nmc, Z=2. The lattice parameters are α=0.362 6(5) nm, c=0.522 6(3)nm for CeO2 doped zirconia and α=0. 360 2(8)nm, c=0. 517 9(1)nm for Y2O3 doped zirconia, respectively. In each unit cell, there are two kinds of equivalent positions, i. e. 2b and 4d, which are occupied by Zr4+, M(M=Y3+, Ce4+) cations and O2- anions, respectively. The crystallographic correlation among the cubic, tetragonal and monoclinic structures of ZrO2 is discussed.

  4. Isolation and Crystal Structure of Xanthones from Swertia Chirayita

    Institute of Scientific and Technical Information of China (English)

    史高峰; 鲁润华; 杨云裳; 李春雷; 杨爱梅; 蔡立祥

    2004-01-01

    In order to study the relationship between biological and pharmacological activities with their structures, a series of tri- and tetra-oxygenated xanthones including 1-hydroxyl-2,3,4,7- tetramethoxy xanthone 1, 1-hydroxyl-2,3,4,5-tetramethoxyl xanthone 2, 1-hydroxyl-3,5-dimethoxy- xanthone 3, 1,8-dihydroxyl-3,5-dimethoxyl xanthone 4 and 1,5,8-trihydroxyl-3-methoxy xanthone 5 have been isolated from Swertia chirayita. Their structures were established on the basis of spectral and chemical evidences. The crystal structure of 5 was also investigated by single-crystal X-ray diffraction analysis. It crystallizes in the triclinic system, space group Pī with a = 7.1540(10), b = 7.520(2), c = 10.671(2) (A), V = 562.7(2) (A)3 , α = 86.50(3), β = 80.06(3) , γ = 85.00(3)°, Z = 2, Dc = 1.618 g/m3, R = 0.0405, wR = 0.1028 and F(000) = 284. The molecular structure of 5 is nearly planar and four substituents are much closer to the plane. Compound 5 contains three intermolecular hydro- gen bonds. A recent study shows that phenolic hydroxyls in xanthones are the main active groups capable of scavenging ·OH and O2·.

  5. Crystal structure of phenyl N-(4-nitrophenylcarbamate

    Directory of Open Access Journals (Sweden)

    Y. AaminaNaaz

    2015-12-01

    Full Text Available The asymmetric unit of the title compound, C13H10N2O4, contains two independent molecules (A and B. The dihedral angle between the aromatic rings is 48.18 (14° in molecule A and 45.81 (14° in molecule B. The mean plane of the carbamate N—C(=O—O group is twisted slightly from the attached benzene and phenyl rings, making respective dihedral angles of 12.97 (13 and 60.93 (14° in A, and 23.11 (14 and 59.10 (14° in B. In the crystal, A and B molecules are arranged alternately through N—H...O hydrogen bonds and C—H...π interactions, forming chains along the a axis. The chains are further linked by C—H...O hydrogen bonds into a double-chain structure.

  6. New Tricks of the Trade for Crystal Structure Refinement.

    Science.gov (United States)

    Li, Jinjin; Abramov, Yuriy A; Doherty, Michael F

    2017-07-26

    Accurate crystal structures and their experimental uncertainties, determined by X-ray diffraction/neutron diffraction techniques, are vital for crystal engineering studies, such as polymorph stability and crystal morphology calculations. Because of differences in crystal growth and data measurement conditions, crystallographic databases often contain multiple entries of varying quality of the same compound. The choice of the most reliable and best quality crystal structure from many very similar structures remains an unresolved problem, especially for nonexperts. In addition, while crystallographers can make use of some professional software (i.e., Materials Studio) for structure refinement, noncrystallographers may not have access to it. In the present paper, we propose a simple method to study the sensitivity of the crystal lattice energy to changes in the structural parameters, which creates a diagnostic tool to test the quality of crystal structure files and to improve the low-quality structures based on lattice energy distribution. Thus, noncrystallographers could take the proposed idea and program/optimize crystal structure by themselves. They can have their in-house program to determine the reliability of the selected crystal data and then use the best quality data or carry out structural optimization for low-quality data. The proposed method will benefit a broad cross-section of scientific researchers, especially those in solid-state and physical chemistry.

  7. Stability of orientationally disordered crystal structures of colloidal hard dumbbells.

    Science.gov (United States)

    Marechal, Matthieu; Dijkstra, Marjolein

    2008-06-01

    We study the stability of orientationally disordered crystal phases in a suspension of colloidal hard dumbbells using Monte Carlo simulations. For dumbbell bond length L/sigmafcc structure for a large part of the stable plastic crystal regime. In addition, we study the stability of an orientationally disordered aperiodic crystal structure in which the spheres of the dumbbells are on a random-hexagonal-close-packed lattice, and the dumbbells are formed by taking random pairs of neighboring spheres. Using free-energy calculations, we determine the fluid-aperiodic crystal and periodic-aperiodic crystal coexistence regions for L/sigma>0.88 .

  8. Affine structures and a tableau model for E_6 crystals

    CERN Document Server

    Jones, Brant

    2009-01-01

    We provide the unique affine crystal structure for type E_6^{(1)} Kirillov-Reshetikhin crystals corresponding to the multiples of fundamental weights s Lambda_1, s Lambda_2, and s Lambda_6 for all s \\geq 1 (in Bourbaki's labeling of the Dynkin nodes, where 2 is the adjoint node). Our methods introduce a generalized tableaux model for classical highest weight crystals of type E and use the order three automorphism of the affine E_6^{(1)} Dynkin diagram. In addition, we provide a conjecture for the affine crystal structure of type E_7^{(1)} Kirillov-Reshetikhin crystals corresponding to the adjoint node.

  9. A 3D MOF showing unprecedented solvent-induced single-crystal-to-single-crystal transformation and excellent CO2 adsorption selectivity at room temperature.

    Science.gov (United States)

    Qin, Tao; Gong, Jun; Ma, Junhan; Wang, Xin; Wang, Yonghua; Xu, Yan; Shen, Xuan; Zhu, Dunru

    2014-12-28

    A water stable porous 3D metal-organic framework, [Cu3L2(μ3-OH)2(μ2-H2O)]·2DMA (1, mother crystal, H2L = 2,2'-dinitrobiphenyl-4,4'-dicarboxylic acid, DMA = N,N-dimethylacetamide), shows unprecedented irreversible solvent-induced substitutions of bridging aqua ligands and guest-exchanges in single-crystal-to-single-crystal (SCSC) transformations at room temperature (RT), producing quantitatively three daughter crystals, [Cu3L2(μ3-OH)2]·2S (2: 2A, S = acetone; 2B, S = 2-propanol; 2C, S = 2-butanol), which exhibit reversible interconversion by guest-exchanges at RT in SCSC transformations. MOF 1 shows excellent separation selectivity (128) of CO2/N2 at RT and is a better sorbent of micro-solid-phase extraction (μ-SPE) than currently known benchmark ZIF-8.

  10. First-Principles Study on Electronic Structures and Optical Properties of Doped Ag Crystal

    Institute of Scientific and Technical Information of China (English)

    CAO Can; CHEN Ling-Na; JIA Shu-Ting; ZHANG Dan; XU Hui

    2012-01-01

    By using the first-principles calculation based on density functional theory,we investigate the electronic structures and optical properties of Cl-doped Ag crystal. The results show that the electronic structure of Cl-doped Ag crystal depends on the doped concentration and the site of impurity defect.Interestingly,the calculated adsorption spectra of Cl-doped Ag crystal show isotropy or anisotropy coincide with the symmetry of Ag crystal. These features are discussed to provide guidance to experimental efforts for Ag-based nanoeletronic devices.

  11. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    Science.gov (United States)

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  12. Crystal Structure of an Ammonia-Permeable Aquaporin

    DEFF Research Database (Denmark)

    Kirscht, Andreas; Kaptan, Shreyas S; Bienert, Gerd Patrick;

    2016-01-01

    the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals...... an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity...

  13. Crystal structure of 3-bromo-2-hydroxybenzoic acid

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2015-05-01

    Full Text Available Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a central R22(8 ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the short a axis observed in the title structure are frequent packing motifs in this set.

  14. Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.

    Science.gov (United States)

    Hong, Y. S.; And Others

    1980-01-01

    Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)

  15. Structure and properties of Li-rich Zn-doped LiNbO3 Crystal

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The Li-rich Zn-doped LiNbO3 (LN) crystals were grown by the Czochralski method. The structure of the crystals was measured by ultraviolet-visible absorption spectra. The results indicated that the Li-rich Zn-doped LN crystals had the same characteristics as the pure LN crystal. After Zn2+ entered into the lattice of Li-rich Zn-doped LN crystal, it replaced NbLi firstly. When there was no NbLi, Zn2+ replaced Li+ then. The second harmonic generation (SHG) property of Li-rich Zn-doped LiNbO3 crystal was measured. The results showed that the SHG conversation efficiency of Li-rich Zn-doped LiNbO3 crystals was higher than that of Zn-doped LiNbO3 crystals.

  16. Structural study on few co-crystals and a salt of quinoline derivatives having amide bond

    Science.gov (United States)

    Karmakar, Anirban; Kalita, Dipjyoti; Baruah, Jubaraj B.

    2009-10-01

    The N-[2-(4-Methoxy-phenyl)-ethyl]-2-(quinolin-8-yloxy)-acetamide forms 1:1 co-crystals with aromatic diols namely 1,4-dihydroxybenzene, 1,5-dihydroxynaphthalene. In the later case co-crystal is formed in hydrated form. The hydrated form of co-crystal with 1,5-naphthalenediol has two symmetry independent host molecules in its unit cell, whereas such phenomenon in the co-crystal 1,4-dihydroxybenzene is not observed. The crystal structure of perchloric acid salt of (Quinolin-8-ylamino)-acetic acid is determined and this salt also shows two symmetry independent parent molecules in unit cell.

  17. Structure of desheptapeptide (B24-B30) insulin in a new crystal form

    Institute of Scientific and Technical Information of China (English)

    包素锦; 张季平; 常文瑞; 梁栋材

    1999-01-01

    The structure of desheptapeptide (B24-B30) insulin (DHPI) in a new crystal form (form B) has been determined and refined to 0.2 nm resolution. The crystals were obtained under the same crystallization condition as previously reported crystal form (form A). The overall structures of the two crystal forms are similar but obvious differences can be observed in crystal packing and local conformation. The crystal structures of the two forms show that the two independent molecules in an asymmetric unit from a DHPI dimer, and the dimer formation buries more than 18.20 and 16.95 nm~2 of solvent accessible surfaces for form A and form B DHPI, respectively, the largest among insulin and insulin analogs ever reported. Close examination at crystal packing shows that the dimer-forming surface of DHPI, namely Surface Ⅱ, is normally present in the association of insulin and insulin analogs in their crystal structures. The results demonstrate that Surface Ⅱ is crucially important for the formation of two crystal form

  18. Crystal structural studies of destripeptide (B28-B30) insulin

    Institute of Scientific and Technical Information of China (English)

    叶军; 茅毓新; 桂璐璐; 常文瑞; 梁栋材

    2000-01-01

    Single crystals of destripeptide (B28-B30) insulin (DTRI) in three forms were obtained by hanging-drop vapor diffusion method. Form 1 belongs to P21 space group with cell parameters a-4.77 nm, b=6.19 nm, c=6.12 nm, β=110.3°. Form 2 belongs to P4122 or P4322 space group with cell parameters a= 6.45 nm, c=12.07 nm. Form 3 belongs to P212121 space group with cell parameters a=4.98 nm, b=5.16 nm, c=10.06 nm. The structure of form 1 crystal was determined by molecular replacement method and refined at 0.23 nm resolution. The R-factor of the final model is 18.8% with r.m.s. deviations of 0.001 5 nm and 3.3?for the bond lengths and the bond angles, respectively. Studies on the crystal structure show that the removal of B28 Pro has brought DTRI structural changes which made it dissociate more easily than native insulin although DTRI can still form a hexamer.

  19. Polymorphic crystal structures of an all-AT DNA dodecamer.

    Science.gov (United States)

    Acosta-Reyes, Francisco J; Subirana, Juan A; Pous, Joan; Sánchez-Giraldo, Raquel; Condom, Núria; Baldini, Roberto; Malinina, Lucy; Campos, J Lourdes

    2015-03-01

    In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.

  20. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    Science.gov (United States)

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  1. Fourier transform infrared transmission microspectroscopy of photonic crystal structures.

    Science.gov (United States)

    Kilby, Gregory R; Gaylord, Thomas K

    2009-07-01

    The detailed microscopic characterization of photonic crystal (PC) structures is challenging due to their small sizes. Generally, only the gross macroscopic behavior can be determined. This leaves in question the performance at the basic structure level. The single-incident-angle plane-wave transmittances of one-dimensional photonic crystal (PC) structures are extracted from multiple-incident-angle, focused-beam measurements. In the experimental apparatus, an infrared beam is focused by a reflecting microscope objective to produce an incident beam. This beam can be modeled as multiple, variable-intensity plane waves incident on the PC structure. The transmittance of the structure in response to a multiple-incident-angle composite beam is measured. The composite beam measurement is repeated at various incident angle orientations with respect to the sample normal so that, at each angular orientation, the included set of single-angle plane-wave components is unique. A set of measurements recorded over a range of angular orientations results in an underspecified matrix algebra problem. Regularization techniques can be applied to the problem to extract the single-angle plane-wave response of the structure from the composite measurements. Experimental results show very good agreement between the measured and theoretical single-angle plane-wave transmittances.

  2. Crystal structure refinement a crystallographers guide to SHELXL

    CERN Document Server

    2006-01-01

    A crystallographers guide to SHELXL, covering various aspects of practical crystal structure refinement, from the treatment of hydrogen atoms to the assignment of atom types, and more. After an introduction to SHELXL, a brief survey of crystal structure refinement is provided.

  3. The Crystal Structure of Cu4Bi4Se9

    DEFF Research Database (Denmark)

    Makovicky, E.; Søtofte, Inger; Karup-Møller, S.

    2002-01-01

    The crystal structure Of Cu4Bi4Se9,, synthesized at 400 degreesC, was determined from single crystal X-ray diffraction data and refined to the R, value of 0.05. The compound is orthorhombic, with a = 32.692 Angstrom, b = 4.120 Angstrom, and c = 12.202 Angstrom, space group Pnma. The structure...

  4. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    Science.gov (United States)

    Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

    2014-01-01

    Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

  5. The Crystal Structure of Cu4Bi4Se9

    DEFF Research Database (Denmark)

    Makovicky, E.; Søtofte, Inger; Karup-Møller, S.

    2002-01-01

    The crystal structure Of Cu4Bi4Se9,, synthesized at 400 degreesC, was determined from single crystal X-ray diffraction data and refined to the R, value of 0.05. The compound is orthorhombic, with a = 32.692 Angstrom, b = 4.120 Angstrom, and c = 12.202 Angstrom, space group Pnma. The structure...

  6. 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.

  7. A structural approach in networks: showing patterns, possibilities and pitfalls

    Directory of Open Access Journals (Sweden)

    Carlos Alberto Alves

    2010-01-01

    Full Text Available In recent years there has been a noticeable shift in evaluation paradigms away from positivist, individualist and atomistic explanations of phenomena to those seeking a more relational, contextual and systemic understanding. This growing shift in interest to the interrelationships or networks of connections between entities is apparent in fields as organizations in networks, knowledge transmission between social groups and so. A growing theoretical and methodological base is providing enhanced capacities to uncover the actual topologies or patterns of connections between entities, elements, people, organizations or communities and deliver a more fine grained analysis of their elements. In this way network analysis differs from conventional evaluation and research modes since its focus is on the interrelationships of entities not the characteristics of individuals. In this paper, we review and analyze the emerging capacity of the network paradigm as an evaluation method and show how this model can be applied t a range of evaluation arenas. In doing so, we outline a framework to guide network evaluation, establish some key network indicators and highlight key methodological aspects and pitfalls.

  8. 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....

  9. Use of Pom Pons to Illustrate Cubic Crystal Structures.

    Science.gov (United States)

    Cady, Susan G.

    1997-01-01

    Describes a method that uses olefin pom pons to illustrate cubic crystal structure. Facilitates hands-on examination of different packing arrangements such as hexagonal close-packed and cubic close-packed structures. (JRH)

  10. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules.

    Science.gov (United States)

    Janjić, Goran V; Ninković, Dragan B; Zarić, Snezana D

    2013-08-01

    Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

  11. Morphology, crystal structure and hydration of calcined and modified anhydrite

    Institute of Scientific and Technical Information of China (English)

    Xiao-qing Niu; Ji-chun Chen

    2014-01-01

    The effects of calcination and modification on the morphology (shapes and textures) and crystal structure of anhydrite powders were studied. The results show that, calcination at 100°C causes anhydrite to disintegrate into smaller crystals, accompanied by a slight in-crease in d-spacing. Without calcination and modification, the solidification time and curing time of anhydrite are 15 and 77 h, respectively. After the treatment, however, the solidification time and curing time are shortened significantly to 9.5 and 14 min, respectively. The com-pressive and flexural strengths of hydration products made from the treated anhydrite reach 10.2 and 2.0 MPa, respectively. The much shorter solidification and curing time make it possible to use anhydrite as a building and construction material.

  12. Evolutionary crystal structure prediction and novel high-pressure phases

    OpenAIRE

    Oganov, A. R.; Ma, Y.; Lyakhov, A. O.; Valle, M.; C. Gatti

    2010-01-01

    Prediction of stable crystal structures at given pressure-temperature conditions, based only on the knowledge of the chemical composition, is a central problem of condensed matter physics. This extremely challenging problem is often termed "crystal structure prediction problem", and recently developed evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography) made an important progress in solving it, enabling efficient and reliable prediction of structures with up...

  13. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    Science.gov (United States)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  14. 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 reg...

  15. Crystal structure of Clostridium difficile toxin A

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-11

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

  16. Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

    Science.gov (United States)

    Konnert, J.A.; Evans, H.T.

    1987-01-01

    The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

  17. Anisotropic domain structure of KTiOPO4 crystals

    Science.gov (United States)

    Urenski, P.; Lesnykh, M.; Rosenwaks, Y.; Rosenman, G.; Molotskii, M.

    2001-08-01

    Highly anisotropic ferroelectric domain structure is observed in KTiOPO4 (KTP) crystals reversed by low electric field. The applied Miller-Weinreich model for sidewise motion of domain walls indicates that this anisotropy results from the peculiarities of KTP crystal lattice. The domain nuclei of dozen nanometer size, imaged by atomic force microscopy method, demonstrate regular hexagonal forms. The orientation of domain walls of the elementary nuclei coincides with the orientation of the facets of macroscopic KTP crystals. The observed strong domain elongation along one principal crystal axis allows us to improve tailoring of ferroelectric domain engineered structures for nonlinear optical converters.

  18. Spectroscopic, thermal and structural studies on manganous malate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, J., E-mail: smartlabindia@gmail.com; Lincy, A., E-mail: lincymaria@gmail.com; Mahalakshmi, V.; Saban, K. V. [Smart Materials Analytic Research and Technology (SMART), Department of Physics, St. Berchmans College (India)

    2013-01-15

    Prismatic crystals of manganous malate have been prepared by controlled ionic diffusion in hydrosilica gel. The structure was elucidated using single crystal X-ray diffraction. The crystals are orthorhombic with space group Pbca. Vibrations of the functional groups were identified by the FTIR spectrum. Thermogravimetric and differential thermal analyses (TG-DTA) were carried out to explore the thermal decomposition pattern of the material. Structural information derived from FTIR and TG-DTA studies is in conformity with the single crystal XRD data.

  19. Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthrones.

    Science.gov (United States)

    Schmidt, Martin U; Paulus, Erich F; Rademacher, Nadine; Day, Graeme M

    2010-10-01

    The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P2(1)/c, Z = 2, the dichloro derivative in P1, Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes in P2(1)/c, Z = 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom-atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom-atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph.

  20. 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.

  1. The early crystal nucleation process in hard spheres shows synchronised ordering and densification

    Science.gov (United States)

    Berryman, Joshua T.; Anwar, Muhammad; Dorosz, Sven; Schilling, Tanja

    2016-12-01

    We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first "solid-like" particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions and also provide evidence against any separation of translational and orientational order on the relevant lengthscales.

  2. Chiral crystal of a C2v-symmetric 1,3-diazaaulene derivative showing efficient optical second harmonic generation

    KAUST Repository

    Ma, Xiaohua

    2011-03-01

    Achiral nonlinear optical (NLO) chromophores 1,3-diazaazulene derivatives, 2-(4â€-aminophenyl)-6-nitro-1,3-diazaazulene (APNA) and 2-(4â€-N,N-diphenylaminophenyl)-6-nitro-1,3-diazaazulene (DPAPNA), were synthesized with high yield. Despite the moderate static first hyperpolarizabilities (β0) for both APNA [(136 ± 5) à - 10-30 esu] and DPAPNA [(263 ± 20) à - 10-30 esu], only APNA crystal shows a powder efficiency of second harmonic generation (SHG) of 23 times that of urea. It is shown that the APNA crystallization driven cooperatively by the strong H-bonding network and the dipolar electrostatic interactions falls into the noncentrosymmetric P2 12121 space group, and that the helical supramolecular assembly is solely responsible for the efficient SHG response. To the contrary, the DPAPNA crystal with centrosymmetric P-1 space group is packed with antiparalleling dimmers, and is therefore completely SHG-inactive. 1,3-Diazaazulene derivatives are suggested to be potent building blocks for SHG-active chiral crystals, which are advantageous in high thermal stability, excellent near-infrared transparency and high degree of designing flexibility. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011 Optical crystals based on 1,3-diazaazulene derivatives are reported as the first example of organic nonlinear optical crystal whose second harmonic generation activity is found to originate solely from the chirality of their helical supramolecular orientation. The strong H-bond network forming between adjacent choromophores is found to act cooperatively with dipolar electrostatic interactions in driving the chiral crystallization of this material. Copyright © 2011 Wiley Periodicals, Inc.

  3. Origin and structure of polar domains in doped molecular crystals

    Science.gov (United States)

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-11-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals.

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

    Science.gov (United States)

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

    2017-02-09

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

  5. Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

    Energy Technology Data Exchange (ETDEWEB)

    Cordes, Timothy J.; Worzalla, Gregory A.; Ginster, Aaron M.; Forest, Katrina T. (UW)

    2012-09-07

    Virulence factor regulator (Vfr) enhances Pseudomonas aeruginosa pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prvents the growth of P. aeruginosa.

  6. 9R structure in drawn industrial single crystal copper wires

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian; YAN Wen; FAN Xin-hui

    2009-01-01

    By using transmission electron microscopy, the microstructures of drawn industrial single crystal copper wires produced by Ohno Continuous Casting(OCC) process were analyzed. The results show that the typical microstructures in the wires mainly include extended planar dislocation boundaries, a small fraction of twins and some dislocation cells sharing boundaries parallel to drawn direction. Besides the typical microstructures, 9R structure configurations were observed in the wires. The formation of 9R polytypes may be caused by the coupled emission of Shockley dislocations from a boundary.

  7. Novel photonic crystal cavities and related structures.

    Energy Technology Data Exchange (ETDEWEB)

    Luk, Ting Shan

    2007-11-01

    The key accomplishment of this project is to achieve a much more in-depth understanding of the thermal emission physics of metallic photonic crystal through theoretical modeling and experimental measurements. An improved transfer matrix technique was developed to enable incorporation of complex dielectric function. Together with microscopic theory describing emitter radiative and non-radiative relaxation dynamics, a non-equilibrium thermal emission model is developed. Finally, experimental methodology was developed to measure absolute emissivity of photonic crystal at high temperatures with accuracy of +/-2%. Accurate emissivity measurements allow us to validate the procedure to treat the effect of the photonic crystal substrate.

  8. Crystal fingerprint space--a novel paradigm for studying crystal-structure sets.

    Science.gov (United States)

    Valle, Mario; Oganov, Artem R

    2010-09-01

    The initial aim of the crystal fingerprint project was to solve a very specific problem: to classify and remove duplicate crystal structures from the results generated by the evolutionary crystal-structure predictor USPEX. These duplications decrease the genetic diversity of the population used by the evolutionary algorithm, potentially leading to stagnation and, after a certain time, reducing the likelihood of predicting essentially new structures. After solving the initial problem, the approach led to unexpected discoveries: unforeseen correlations, useful derived quantities and insight into the structure of the overall set of results. All of these were facilitated by the project's underlying idea: to transform the structure sets from the physical configuration space to an abstract, high-dimensional space called the fingerprint space. Here every structure is represented as a point whose coordinates (fingerprint) are computed from the crystal structure. Then the space's distance measure, interpreted as structure 'closeness', enables grouping of structures into similarity classes. This model provides much flexibility and facilitates access to knowledge and algorithms from fields outside crystallography, e.g. pattern recognition and data mining. The current usage of the fingerprint-space model is revealing interesting properties that relate to chemical and crystallographic attributes of a structure set. For this reason, the mapping of structure sets to fingerprint space could become a new paradigm for studying crystal-structure ensembles and global chemical features of the energy landscape.

  9. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    OpenAIRE

    2013-01-01

    We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomicall...

  10. 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...

  11. 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,

  12. The crystal structure and superconducting properties of monatomic bromine.

    Science.gov (United States)

    Duan, Defang; Meng, Xing; Tian, Fubo; Chen, Changbo; Wang, Liancheng; Ma, Yanming; Cui, Tian; Liu, Bingbing; He, Zhi; Zou, Guangtian

    2010-01-13

    The crystal structure and superconducting properties of monatomic bromine under high pressure have been studied by first-principles calculations. We have found the following phase transition sequence with increasing pressure: from body-centered orthorhombic (bco, phase II) to body-centered tetragonal structure (bct, phase III) at 126 GPa, then to face-centered cubic structure (fcc, phase IV) at 157 GPa, which is stable at least up to 300 GPa. The calculated superconducting critical temperature T(c) = 1.46 K at 100 GPa is consistent with the experimental value of 1.5 K. In addition, our results of T(c) decrease with increasing pressure in all the monatomic phases of bromine, similar to monatomic iodine. Further calculations show that the decrease of λ with pressure in phase IV is mainly attributed to the weakening of the 'soft' vibrational mode caused by pressure.

  13. 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.

  14. 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.

  15. Functional substitution of coordination polyhedron in crystal structure of silicates

    Institute of Scientific and Technical Information of China (English)

    叶大年; 马哲生; 赫伟; 李哲; 施倪承; D.Pushcharovsky

    2002-01-01

    On the bases of the study of comparative crystal chemistry of silicates it has been concluded that the octahedra and square pyramids of Ti-0 and Zr-O play functional role of tetrahedra of Si-O in the construction of crystal structures. Therefore, those silicates may be named titano-and zircono-silicates. Because of the functional similarity of coordination polyhedra, the structures of cristobalite and feldspar have been compared with those of perovskite and garnet, respectively. As a new concept, the functional replacement of tetrahedra by octahedra and/or pyramids is defined by the authors of this paper for favorable comparison of relative crystal structures.

  16. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

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

    2012-01-01

    , such as body-centered cubic and face-centered cubic, can be suppressed by a proper choice of the potential depth and periodicity. Furthermore, by varying the harmonic trap parameters and/or the optical potential in time, controlled transitions between crystal structures can be obtained with close to unit......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...

  17. 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)

  18. Missing strings of residues in protein crystal structures.

    Science.gov (United States)

    Djinovic-Carugo, Kristina; Carugo, Oliviero

    2015-01-01

    A large fraction of the protein crystal structures deposited in the Protein Data Bank are incomplete, since the position of one or more residues is not reported, despite these residues are part of the material that was analyzed. This may bias the use of the protein crystal structures by molecular biologists. Here we observe that in the large majority of the protein crystal structures strings of residues are missing. Polar residues incline to occur in missing strings together with glycine, while apolar and aromatic residues tend to avoid them. Particularly flexible residues, as shown by their extremely high B-factors, by their exposure to the solvent and by their secondary structures, flank the missing strings. These data should be a helpful guideline for crystallographers that encounter regions of flat and uninterpretable electron density as well as end-users of crystal structures.

  19. Growth morphology and structural characteristic of C70single crystals

    Institute of Scientific and Technical Information of China (English)

    周维亚; 解思深; 吴源; 常保和; 王刚; 钱露茜

    1999-01-01

    Large size C70 single crystals with the dimension of more than 5 mm are grown from the vapor phase by controlling nucleation. X-ray diffraction and electron diffraction confirm that in the C70 single crystal a phase of the hexagonal close-packed (hcp) structure coexists with a minor face-center-cubic (fcc) phase at room temperature. The morphologies and their formation mechanism of the C70 single crystals are investigated by means of scanning electron microscopy and optical microscopy. The influence of growth conditions on the morphologies of C70 single crystals is discussed.

  20. Structure, Hydrodynamics, and Phase Transition of Freely Suspended Liquid Crystals

    Science.gov (United States)

    Clark, Noel A.

    2000-01-01

    Kosterlitz Thouless phase transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profile and have been used to show that the interlayer interactions in anti-ferroelectric tilted smectics do not extend significantly beyond nearest neighbors. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments wherein the intermolecular coupling is effectively reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the position of the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, several potentially interesting microgravity free film experiments have been identified.

  1. Crystal structure of Ca5Nb5O17

    Science.gov (United States)

    Guevarra, J.; van Smaalen, S.; Rotiroti, N.; Paulmann, C.; Lichtenberg, F.

    2005-09-01

    The crystal structure of Ca5Nb5O17, an n=5 member of the homologous series AnBnO, at room temperature has been determined by single-crystal X-ray diffraction using synchrotron radiation with a CCD area detector. The structure is monoclinic with spacegroup P21/c ( b unique) and lattice parameters a=7.7494(3) Å, b=5.4928(1) Å, c=32.241(1) Å, and β=96.809(4)∘. It consists of perovskite-like slabs of corner-sharing NbO6 octahedra separated by an interslab region, where the octahedra on opposite sides of the gap do not share oxygen atoms resulting in an extra layer of oxygen atoms with respect to the ideal perovskite structure. The slabs are five octahedra wide. Ca atoms within the slabs occupy 12-fold coordinated sites whereas those at the borders show irregular coordination environments. The distortion of the octahedra increases from the center to the borders of the slabs. The computed valences for the Nb ions are very close to 5 at the borders while smaller values were obtained for sites in the middle of the slabs which suggests that the electrical conduction takes place predominantly in the middle of the slabs.

  2. Crystal structure of Mg3Pd from first-principles calculations

    Institute of Scientific and Technical Information of China (English)

    DENG Yong-he; WANG Tao-fen; ZHANG Wei-bing; TANG Bi-yu; ZENG Xiao-qin; DING Wen-jiang

    2008-01-01

    Crystal structure of Mg3Pd alloy was studied by first-principles calculations based on the density functional theory. The total energy, formation heat and cohesive energy of the two types of Mg3Pd were calculated to assess the stability and the preferentiality. The results show that Mg3Pd alloy with Cu3P structure is more stable than Na3As structure, and Mg3Pd alloy is preferential to Cu3P structure. The obtained densities of states and charge density distribution for the two types of crystal structure were analyzed and discussed in combination with experimental findings for further discussion of the Mg3Pd structure.

  3. 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.

  4. 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.

  5. Molecular and Crystal Structures of Three Berberine Derivatives

    OpenAIRE

    Jiří Dostál; Zdirad Žák; Marek NeÄÂas; Milan PotáÄÂek; Stanislav Man

    2001-01-01

    Berberine azide, berberine thiocyanate, and 8-cyano-8H-berberine were prepared from berberine chloride, a quaternary protoberberine alkaloid. The molecular and crystal structures of all compounds are reported and discussed.

  6. Determination of channeling perspectives for complex crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Allen, W.R.

    1993-03-01

    Specification of the atomic arrangement for axes and planes of high symmetry is essential for crystal alignment using Rutherford backscattering and for studies of the lattice location of impurities in single crystals. By rotation of an inscribed orthogonal coordinate system, a visual image for a given perspective of a crystal structure can be specified. Knowledge of the atomic arrangement permits qualitative channeling perspectives to be visualized and calculation of continuum potentials for channeling. Channeling angular-yield profiles can then be analytically modeled and, subsequently, shadowing by host atoms of positions within the unit cell predicted. Software to calculate transformed atom positions for a channeling perspective in a single crystal are described and illustrated for the spinel crystal structure.

  7. Crystal structure of S-(4-methylbenzyl piperidinedithiocarbamate

    Directory of Open Access Journals (Sweden)

    Z. A. Rahima

    2015-09-01

    Full Text Available The title compound, C14H19NS2, crystallizes in the thione form with the presence of a C=S bond. The piperidine ring adopts a chair conformation. The dihedral angle between the essentially planar dithiocarbamate and p-tolyl fragments is 74.46 (10°

  8. Crystal structure of the fibrinogen-like recognition domain of FIBCD1

    DEFF Research Database (Denmark)

    Møller, Jesper Bonnet; Schlosser, Anders; Sørensen, Grith Lykke;

    The high resolution crystal structures of a recombinant fragment of the C-terminal fibrinogen-related domain of FIBCD1, a vertebrate chitin receptor, have been determined. The overall structure shows similarity in structure and aggregation to the homologous innate immune protein tachylectin 5A...

  9. Synthesis and crystal structure of PdSnTe

    Energy Technology Data Exchange (ETDEWEB)

    Laufek, F. [Czech Geological Survey, Geologicka 6, 152 00 Praha 5 (Czech Republic)], E-mail: frantisek.laufek@geology.cz; Vymazalova, A. [Czech Geological Survey, Geologicka 6, 152 00 Praha 5 (Czech Republic); Navratil, J. [Joint Laboratory of Solid State Chemistry of IMC AS CR and University of Pardubice, Studentska 84, 532 10 Pardubice (Czech Republic); Drabek, M. [Czech Geological Survey, Geologicka 6, 152 00 Praha 5 (Czech Republic); Plasil, J. [Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2 (Czech Republic); Plechacek, T. [Joint Laboratory of Solid State Chemistry of IMC AS CR and University of Pardubice, Studentska 84, 532 10 Pardubice (Czech Republic)

    2009-01-22

    The compound with composition PdSnTe was prepared by heating of stoichiometric amount of Pd, Sn and Te in silica glass tube at 400 deg. C. Its crystal structure was refined by Rietveld method using conventional X-ray powder diffraction data. PdSnTe shows orthorhombic symmetry, space group Pbca with unit cell parameters a = 6.5687(2), b = 6.6028(2), c = 12.8849(4) A, V = 558.8(1) A{sup 3} and Z = 8. The title compound can be viewed as a ternary-ordered variant of {alpha}-NiAs{sub 2}-type structure, it is isostructural with PtSiTe. Temperature dependence of electrical conductivity and Hall coefficient are presented, it suggests semimetallic or strongly degenerated semiconductor behaviour of the prepared compound.

  10. 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.

  11. Crystal structures at high pressures and temperatures

    Science.gov (United States)

    Caldwell, Wendel Alexander

    2000-10-01

    The diamond anvil cell (DAC) is a unique instrument that can generate pressures equivalent to those inside planetary interiors (pressures on the order of 1 million atmospheres) under sustained conditions. When combined with a bright source of collimated x-rays, the DAC can be used to probe the structure of materials in-situ at ultra-high pressures. An understanding of the high-pressure structure of materials is important in determining what types of processes may take place in the Earth at great depths. Motivated by previous studies showing that xenon becomes metallic at pressures above ˜1 megabar (100 GPa), we examined the stable structures and reactivity of xenon at pressures approaching that of the core-mantle boundary in the Earth. Our findings indicate the transformation of xenon from face-centered cubic (fcc) to hexagonal close-packed (hcp) structures is kinetically hindered at room temperature, with the equilibrium fcc--hcp phase boundary at 21 (+/-3) gigapascals, a pressure lower than was previously thought. Additionally, we find no tendency on the part of xenon to form a metal alloy with iron or platinum to at least 100 to 150 gigapascals, making it unlikely that the Earth's core serves as a reservoir for primordial xenon. Measurements of the compressibility of natural (Mg.75,Fe .25)2SiO4 gamma-spinel at pressures of the Earth's transition zone yield a pressure derivative of the bulk modulus K0 ' = 6.3 (+/-0.3). As gamma-spinel is considered to be a dominant mineral phase of the transition-zone of the Earth's mantle (400--670 km depth), the relatively high value of K0' for gamma-spinel may help explain the rapid increase with depth of seismic velocities through the transition zone. The thermodynamics, mechanisms and kinetics of pressure-induced amorphization are not well understood. We report here new studies indicating little or no entropy difference between the crystalline and glassy states of Ca(OH) 2 (portlandite). Additional work on the pressure

  12. Preparation and structure characteristics of nano-Bi2O3 powders with mixed crystal structure

    Institute of Scientific and Technical Information of China (English)

    LI Wei

    2005-01-01

    The nano-Bi2 O3 powders were prepared by a chemical precipitation method with Bi(NO3)3, H NO3 and NaOH as reactants. The structural characteristics and morphology of nano-Bi2O3 powders were investigated by X-ray diffraction and transmission electron microscopy, respectively. The results show that under the optimum condition that 300 g/L Bi(NO3)3 reacts at 90 ℃ for 2 h, the Bi2O3 powders with 60 nm on the average and 99.5% in purity are obtained. The prepared nano-Bi2 O3 powders contain a mixed crystal structure of monoclinic and triclinic in stead of traditional structure of monoclinic α-Bi2 O3. And the mixed crystal structure is stable in air. The reason for the appearance of the mixed crystal structure may be that the ionic radius ratio of Bi3+ to O2- changes easily during the formation of nano-Bi2 O3 particles by a chemical precipitation method.

  13. 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...

  14. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    Science.gov (United States)

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

  15. Structure and Dynamics of Freely Suspended Liquid Crystals

    Science.gov (United States)

    Clark, Noel A.

    2004-01-01

    transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profiles and have been used to show that the interlayer interactions in antiferroelectric tilted smectics do not extend significantly beyond nearest neighbors. Freely suspended films played a pivotal role in the recent discovery of macroscopic chiral-polar ordering in fluids of achiral molecules. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments, in which the intermolecular coupling is effectively further reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, a class of experiments on the behavior of 1D interfaces in 2D films have been pursued with results that point to potentially quite interesting effects in microgravity.

  16. Crystal Structure of a Marine Natural Compound, Anhydrofusarubin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    One marine natural compound, anhydrofusarubin, was isolated from the endophytic fungus No.B77 from the mangrove tree on the South China Sea coast.It was the first time that such a compound was isolated from marine fungus.The structure was identified by NMR data and mass spectrometry (MS).In addition, its structure was determined by single-crystal X-ray diffraction analysis.It crystallizes in triclinic, space group P1- with a = 8.3185(15), b = 12.397(2), c = 13.767(3)(A), α= 65.692(3), β= 79.266(3), γ= 75.692(3)°, C15H12O6, Mr= 288.24, V = 1248.0(4)(A)3, Z = 4, Dc = 1.534 g/cm3, F(000) = 600,/μ = 0.120 mm-1, the final R = 0.0459 and wR = 0.1184 for 5360 observed reflections (1>2σ(I)).In the primary bioassay, the title compound shows strong inhibitory activity against Gram-positive bacteria Staphyococcus aureus (ATCC27154) with the MIC value of 12.5μg/mL.

  17. Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant.

    Science.gov (United States)

    Kawato, Tatsuya; Mizohata, Eiichi; Shimizu, Yohei; Meshizuka, Tomohiro; Yamamoto, Tomohiro; Takasu, Noriaki; Matsuoka, Masahiro; Matsumura, Hiroyoshi; Kodama, Tatsuhiko; Kanai, Motomu; Doi, Hirofumi; Inoue, Tsuyoshi; Sugiyama, Akira

    2015-01-01

    The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for natural biocytin. Here, we design a bivalent iminobiotin analog that shows 1000-fold higher affinity than before, and determine its crystal structure complexed with the mutant protein.

  18. Homodiselenacalix[4]arenes: Molecules with Unique Channelled Crystal Structures.

    Science.gov (United States)

    Thomas, Joice; Dobrzańska, Liliana; Van Meervelt, Luc; Quevedo, Mario Alfredo; Woźniak, Krzysztof; Stachowicz, Marcin; Smet, Mario; Maes, Wouter; Dehaen, Wim

    2016-01-18

    A synthetic route towards homodiselenacalix[4]arene macrocycles is presented, based on the dynamic covalent chemistry of diselenides. The calixarene inner rim is decorated with either alkoxy or tert-butyl ester groups. Single-crystal X-ray analysis of two THF solvates with methoxy and ethoxy substituents reveals the high similarity of their molecular structures and alterations on the supramolecular level. In both crystal structures, solvent channels are present and differ in both shape and capacity. Furthermore, the methoxy-substituted macrocycle undergoes a single-crystal-to-single-crystal transformation during which the molecular structure changes its conformation from 1,3-alternate (loaded with THF/water) to 1,2-alternate (apohost form). Molecular modelling techniques were applied to explore the conformational and energetic behaviour of the macrocycles.

  19. Chiral Liquid Crystals: Structures, Phases, Effects

    Directory of Open Access Journals (Sweden)

    Ingo Dierking

    2014-06-01

    Full Text Available The introduction of chirality, i.e., the lack of mirror symmetry, has a profound effect on liquid crystals, not only on the molecular scale but also on the supermolecular scale and phase. I review these effects, which are related to the formation of supermolecular helicity, the occurrence of novel thermodynamic phases, as well as electro-optic effects which can only be observed in chiral liquid crystalline materials. In particular, I will discuss the formation of helical superstructures in cholesteric, Twist Grain Boundary and ferroelectric phases. As examples for the occurrence of novel phases the Blue Phases and Twist Grain Boundary phases are introduced. Chirality related effects are demonstrated through the occurrence of ferroelectricity in both thermotropic as well as lyotropic liquid crystals. Lack of mirror symmetry is also discussed briefly for some biopolymers such as cellulose and DNA, together with its influence on liquid crystalline behavior.

  20. Effect of antimony incorporation on structural properties of CuInS{sub 2} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Ben Rabeh, M., E-mail: mohamedbenrabeh@yahoo.f [Laboratoire de Photovoltaique et Materiaux Semi-Conducteurs - ENIT BP 37, Le belvedere, 1002 Tunis (Tunisia); Chaglabou, N., E-mail: nadia_chaglabou@yahoo.f [Laboratoire de Photovoltaique et Materiaux Semi-Conducteurs - ENIT BP 37, Le belvedere, 1002 Tunis (Tunisia); Kanzari, M., E-mail: Mounir.Kanzari@ipeit.rnu.t [Laboratoire de Photovoltaique et Materiaux Semi-Conducteurs - ENIT BP 37, Le belvedere, 1002 Tunis (Tunisia)

    2010-02-15

    CuInS{sub 2} (CIS) single crystals doped with 1, 2, 3 and 4 atomic percent (at.%) of antimony (Sb) were grown by the horizontal Bridgman method. The effect of Sb doping on the structural properties of CIS crystal was studied by means of X-ray diffraction (XRD), energy dispersive X-ray analysis (EDAX), scanning electron microscopy (SEM) and PL measurements. X-ray diffraction data suggests that the doping of Sb in the CIS single crystals does not affect the tetragonal (chalcopyrite) crystal structure and exhibited a (1 1 2) preferred orientation. In addition, with increasing Sb concentration, the X-ray diffraction analysis show that Sb doped CIS crystals are more crystallized and the diffraction peaks of the CuInS{sub 2} phase were more pronounced in particular the (1 1 2) plane. EDAX study revealed that Sb atoms can occupy the indium site and/or occupying the sulfur site to make an acceptor. PL spectra of undoped and Sb doped CIS crystals show two emission peaks at 1.52 and 1.62 eV, respectively which decreased with increasing atomic percent antimony. Sb doped CIS crystals show p-type conductivity.

  1. Synthesis and Crystal Structure of a New Manganese Complex

    Institute of Scientific and Technical Information of China (English)

    WANG Jian; LIU Ping; CHEN Yun

    2003-01-01

    @@ In order to study the relationship between the manganese ion and the biological coordination agent, the role ofmanganese ion in the active sites and the structure of the active sites in the manganese enzymes, small molecule complexes are often applied to modeling the structure and the properties of reaction in the active centers. In this pa per, we will report the synthesis and crystal structure of a new manganese(Ⅱ) complex, catena[ aqua-(p-methoxybenzoato- O, O′ ) - (p-methoxybenzoato- O )- (2,2′-bipyridine)-manganese (Ⅱ) ] (p-methoxybenzoic acid). The crystal structure was confirmeded by X-ray crystallography analysis.

  2. Formation of crystal-like structures and branched networks from nonionic spherical micelles

    Science.gov (United States)

    Cardiel, Joshua J.; Furusho, Hirotoshi; Skoglund, Ulf; Shen, Amy Q.

    2015-12-01

    Crystal-like structures at nano and micron scales have promise for purification and confined reactions, and as starting points for fabricating highly ordered crystals for protein engineering and drug discovery applications. However, developing controlled crystallization techniques from batch processes remain challenging. We show that neutrally charged nanoscale spherical micelles from biocompatible nonionic surfactant solutions can evolve into nano- and micro-sized branched networks and crystal-like structures. This occurs under simple combinations of temperature and flow conditions. Our findings not only suggest new opportunities for developing controlled universal crystallization and encapsulation procedures that are sensitive to ionic environments and high temperatures, but also open up new pathways for accelerating drug discovery processes, which are of tremendous interest to pharmaceutical and biotechnological industries.

  3. Atomic structure and crystallization processes of amorphous (Co,Ni)–P metallic alloy

    Energy Technology Data Exchange (ETDEWEB)

    Modin, Evgeny B., E-mail: modin.eb@dvfu.ru [Far Eastern Federal University, Shukhanova 8, Vladivostok 690950 (Russian Federation); Pustovalov, Evgeny V.; Fedorets, Aleksander N.; Dubinets, Aleksander V.; Grudin, Boris N.; Plotnikov, Vladimir S. [Far Eastern Federal University, Shukhanova 8, Vladivostok 690950 (Russian Federation); Grabchikov, Sergey S. [Scientific and Practical Centre of Material Science, Belarus National Academy of Sciences, P. Brovki 19, Minsk 220072 (Belarus)

    2015-08-25

    Highlights: • The CoP–CoNiP amorphous alloys were studied by the Cs-corrected high resolution transmission electron microscopy. • In situ heating experiments showed that crystallization starts at 200–250 °C on the network frame and cell boundaries. • Crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. • Adding nickel to the CoP alloy leads to higher thermal stability. • At the beginning of crystallization there are high diffusion coefficients, 1.2–2.4 ∗ 10{sup −18} m{sup 2}/s at 250 °C. - Abstract: This work concerns the in situ investigation of the atomic structure of (Co,Ni)–P alloys during relaxation and crystallization by high resolution transmission electron microscopy. The CoP–CoNiP alloys, in the initial state, have a hierarchical network-like disordered structure. Crystallization starts at 200–250 °C on the network frame and cell boundaries. In the early stages, crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. The diffusion coefficient at the start of crystallization is 1.2–2.4 × 10{sup −18} m{sup 2}/s at 250 °C and we assume that the high diffusion speed is due to surface diffusion.

  4. 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...

  5. Investigation on growth, structure and characterization of succinate salt of 8-hydroxyquinoline: an organic NLO crystal.

    Science.gov (United States)

    Thirumurugan, R; Babu, B; Anitha, K; Chandrasekaran, J

    2015-04-05

    8-Hydroxyquinolinium succinate (8-HQSU) has been synthesized and single crystals were grown from ethanol solvent by employing the technique of slow evaporation at room temperature. The structure of the grown crystal has been elucidated by single crystal X-ray diffraction analysis. It reveals that 8-HQSU crystallizes in monoclinic system with non-centro symmetric space group P2(1). FTIR, 1H and 13C NMR spectral investigations have been carried out to identify the vibrational modes of various functional groups and placement of proton and carbon in the 8-HQSU compound, respectively. UV-vis-NIR transmission spectrum shows the cutoff wavelength around 357 nm. In addition, a photoluminescence spectral analysis was carried out for 8-HQSU crystals. The thermal properties of crystals were evaluated from TGA and DTA techniques and the crystal was found to be stable up to 145°C. The dielectric studies show that the dielectric constant and dielectric loss decrease exponentially with frequency at different temperatures. Photoconductivity studies were carried out on the grown crystals it reveals the positive photo conducting nature. Powder second harmonic generation property of the crystal was confirmed by Kurtz and Perry powder SHG technique and it is found to be 1.3 times greater than that of KDP. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Single-Crystal Structure of a Covalent Organic Framework

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, YB; Su, J; Furukawa, H; Yun, YF; Gandara, F; Duong, A; Zou, XD; Yaghi, OM

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 degrees C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 degrees C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  7. Crystal structure of 4-(4-methoxyphenoxybenzaldehyde

    Directory of Open Access Journals (Sweden)

    Andreas Schäfer

    2015-12-01

    Full Text Available The title compound, C14H12O3, was synthesized via the nucleophilic addition of 4-methoxyphenol to 4-fluorobenzaldehyde. The dihedral angle between the least-squares planes of the benzene rings is 71.52 (3° and the C—O—C angle at the central O atom is 118.82 (8°. In the crystal, weak C—H...O hydrogen bonds link the molecules to generate supramolecular layers in the bc plane. The layers are linked by weak C—H...π interactions.

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

    Directory of Open Access Journals (Sweden)

    Alberto Cabrera

    2015-12-01

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

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

    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.

  12. Protein dynamics derived from clusters of crystal structures.

    OpenAIRE

    van Aalten, D M; Conn, D A; de Groot, B L; Berendsen, H J; Findlay, J B; 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 describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results ...

  13. Crystal Structure of the Vanadate-Inhibited Ca2+-ATPase

    DEFF Research Database (Denmark)

    Clausen, Johannes D.; Bublitz, Maike; Arnou, Bertrand Jean-Paul;

    2016-01-01

    Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca2+-ATPase with bound vanadate in the absence of Ca2+. Vanadate is bound...

  14. Optimization of liquid crystal structures for real time holography applications.

    Science.gov (United States)

    Sahraoui, B; Anczykowska, A; Bartkiewicz, S; Mysliwiec, J

    2011-11-21

    In this paper we present results of experiments designed to increase our understanding of the photorefractive effect occurring during processes of dynamic hologram generation in Hybrid Photorefractive Liquid Crystal Structures (HPLCS). We also propose equivalent mathematical model which can be used to optimize those structures in order to obtain the highest diffraction efficiency in possibly shortest time.

  15. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds.

    Science.gov (United States)

    Jungblut, Swetlana; Dellago, Christoph

    2016-09-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure.

  16. Low-energy nuclear reactions in crystal structures

    Science.gov (United States)

    Bagulya, A. V.; Dalkarov, O. D.; Negodaev, M. A.; Rusetskii, A. S.

    2017-09-01

    Results of studying low-energy nuclear reactions at the HELIS facility (LPI) are presented. Investigations of yields from DD reactions in deuterated crystal structures at deuteron energies of 10 to 25 keV show a considerable enhancement effect. It is shown that exposure of the deuterated targets to the H+ (proton) and Ne+ beams with energies from 10 to 25 keV and an X-ray beam with the energy of 20 to 30 keV stimulates DD reaction yields. For the CVD diamond target, it is shown that its orientation with respect to the deuteron beam affects the neutron yield. The D+ beam is shown to cause much higher heat release in the TiDx target than the H+ and Ne+ beams, and this heat release depends on the deuterium concentration in the target and the current density of the deuteron beam.

  17. 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.

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

    Science.gov (United States)

    Torres-Larios, Alfredo; Swinger, Kerren K; Krasilnikov, Andrey S; Pan, Tao; Mondragón, Alfonso

    2005-09-22

    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 A 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.

  19. Crystal structure of iron-oxide nanoparticles synthesized from ferritin

    Energy Technology Data Exchange (ETDEWEB)

    Krispin, Michael, E-mail: michael.krispin@physik.uni-augsburg.de; Ullrich, Aladin, E-mail: aladin.ullrich@physik.uni-augsburg.de; Horn, Siegfried, E-mail: horn@physik.uni-augsburg.de [University of Augsburg, Institute of Physics (Germany)

    2012-02-15

    We have investigated the crystal structure of nanosized iron-oxide by X-ray diffraction (XRD), extended X-ray absorption fine structure measurements at the iron K-edge as well as by transmission electron microscopy (TEM). Iron-oxide nanoparticles were produced by thermal treatment of horse spleen ferritin molecules. The structure of these particles was compared to {alpha}-Fe{sub 2}O{sub 3} and {gamma}-Fe{sub 2}O{sub 3} nanopowder references. The thermal treatment of a submonolayer film of ferritin molecules results in pure {gamma}-Fe{sub 2}O{sub 3} nanoparticles, while for films above a certain thickness {alpha}-Fe{sub 2}O{sub 3} and {gamma}-Fe{sub 2}O{sub 3} coexist, exhibiting two different crystallite sizes. TEM shows a characteristic particle diameter of {approx}7 nm for {gamma}-Fe{sub 2}O{sub 3} resulting from thermal treatment of monolayers, consistent with the crystallite size of the {gamma}-phase as obtained from XRD measurements on multi-layered samples. XRD shows the {alpha}-Fe{sub 2}O{sub 3} phase to be characterized by a crystallite size of {approx}34 nm.

  20. Crystal structure of sulfotransferase STF9 from Mycobacterium avium.

    Science.gov (United States)

    Hossain, Md Murad; Moriizumi, Yuuji; Tanaka, Shotaro; Kimura, Makoto; Kakuta, Yoshimitsu

    2012-02-01

    Sulfotransferases catalyze the sulfate conjugation of a wide variety of endogenous and exogenous molecules. Human pathogenic mycobacteria produce numerous sulfated molecules including sulfolipids which are well related to the virulence of several strains. The genome of Mycobacterium avium encodes eight putative sulfotransferases (stf1, stf4-stf10). Among them, STF9 shows higher similarity to human heparan sulfate 3-O-sulfotransferase isoforms than to the bacterial STs. Here, we determined the crystal structure of sulfotransferase STF9 in complex with a sulfate ion and palmitic acid at a resolution of 2.6 Å. STF9 has a spherical structure utilizing the classical sulfotransferase fold. STF9 exclusively possesses three N-terminal α-helices (α1, α2, α3) parallel to the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) binding motif. The sulfate ion binds to the PAPS binding structural motif and the palmitic acid molecule binds in the deep cleft of the predicted substrate binding site suggesting the nature of endogenous acceptor substrate of STF9 resembles palmitic acid. The substrate binding site is covered by a flexible loop which may have involvement in endogenous substrate recognition. Based on the mutational study (Hossain et al., Mol Cell Biochem 350:155-162; 2011) and structural resemblance of STF9-sulfate ion-palmitic acid complex to the hHS3OST3 complex with PAP (3'-phosphoadenosine-5'-phosphate) and an acceptor sugar chain, Glu170 and Arg96 are appeared to be catalytic residues in STF9 sulfuryl transfer mechanism.

  1. 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.

  2. Finite particle size drives defect-mediated domain structures in strongly confined colloidal liquid crystals

    Science.gov (United States)

    Gârlea, Ioana C.; Mulder, Pieter; Alvarado, José; Dammone, Oliver; Aarts, Dirk G. A. L.; Lettinga, M. Pavlik; Koenderink, Gijsje H.; Mulder, Bela M.

    2016-06-01

    When liquid crystals are confined to finite volumes, the competition between the surface anchoring imposed by the boundaries and the intrinsic orientational symmetry-breaking of these materials gives rise to a host of intriguing phenomena involving topological defect structures. For synthetic molecular mesogens, like the ones used in liquid-crystal displays, these defect structures are independent of the size of the molecules and well described by continuum theories. In contrast, colloidal systems such as carbon nanotubes and biopolymers have micron-sized lengths, so continuum descriptions are expected to break down under strong confinement conditions. Here, we show, by a combination of computer simulations and experiments with virus particles in tailor-made disk- and annulus-shaped microchambers, that strong confinement of colloidal liquid crystals leads to novel defect-stabilized symmetrical domain structures. These finite-size effects point to a potential for designing optically active microstructures, exploiting the as yet unexplored regime of highly confined liquid crystals.

  3. Crystal structure of 1-(4-formylbenzylidenethiosemicarbazone

    Directory of Open Access Journals (Sweden)

    Rosa Carballo

    2014-09-01

    Full Text Available The asymmetric unit of the title compound, C9H9N3OS, contains two approximately planar molecules (r.m.s. deviations for 14 non-H atoms = 0.094 and 0.045 Å, with different conformations. In one of them, the C=O group is syn to the S atom and in the other it is anti. Each molecule features an intramolecular N—H...N hydrogen bond, which generates an S(5 ring. In the crystal, molecules are linked by N—H...O and N—H...S hydrogen bonds, generating discrete networks; the syn molecules form [010] chains and the anti molecules form (100 sheets.

  4. 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.

  5. 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.

  6. 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.

  7. Photonic Band Gap Structures with Periodically Arranged Atoms in a Two-Dimensional Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    LI Zhi-Yu; CHEN Fang; ZHOU Jian-Ying

    2005-01-01

    @@ Linear transmission, reflection and absorption spectra for a new two-dimensional photonic crystal with periodically arranged resonant atoms are examined. Numerical results show that a twin-gap structure with forbidden bands displaced from a non-doped bandgap structure can be produced as a result of atomic polarization. The absorption spectrum is also significantly altered compared to the single atom entity.

  8. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan [Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)

    2015-10-27

    The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

  10. 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-...

  11. Influence of crystal structure on the compaction properties of n-alkyl 4-hydroxybenzoate esters (parabens).

    Science.gov (United States)

    Feng, Yushi; Grant, David J W

    2006-07-01

    The aim of the study is to examine the influence of slip planes on the nanoindentation hardness and compaction properties of methyl, ethyl, n-propyl, and n-butyl 4-hydroxybenzoate (parabens). Molecular modeling calculations, embodying the attachment energy concept, were performed to predict the slip planes in the crystal lattices, whereas the nanoindentation hardness of the crystals and the tensile strength of directly compressed compacts were measured. Unlike the other three parabens, methyl paraben has no slip planes in its crystal lattice, and its crystals showed greater nanoindentation hardness, corresponding to lower plasticity, whereas its tablets exhibited substantially lower tensile strength than those of ethyl, propyl, or butyl paraben. The nanoindentation hardness of the crystals and the tensile strength of directly compressed tablets were each found to correlate directly with the absence or presence of slip planes in the crystal structures of the parabens because slip planes confer greater plasticity. This work presents a molecular insight into the influence of crystal structural features on the tableting performance of molecular crystals in general and of crystalline pharmaceuticals in particular.

  12. Functional substitution of coordination polyhedron in crystal structure of silicates

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    On the bases of the study of comparative crystal chemistry of silicates it has been concluded that the octahedra and square pyramids of Ti-O and Zr-O play functional role of tetrahedra of Si-O in the construction of crystal structures.Therefore,those silicates may be named titano- and zircono-silicates.Because of the functional similarity of coordination polyhedra,the structures of cristobalite and feldspar have been compared with those of perovskite and garnet,respectively.As a new concept,the functional replacement of tetrahedra by octahedra and/or pyramids is defined by the authors of this paper for favorable comparison of relative crystal structures.

  13. Electron Crystallographic Study on Structure Determination for Minute Crystals

    Institute of Scientific and Technical Information of China (English)

    LI Fanghua; FAN Haifu; WAN Zhenghua; HU Jianjun; TANG Dong

    2007-01-01

    @@ In the 1970s the development of high-resolution electron microscopy (HREM) provided a new approach to structure determination for minute crystals, which is thoroughly different from the diffraction methods.However, the previous method of trial and error has its own limits, such as some preliminary structural information must be known in advance; the crystals must be sufficient strong under the electron beam irradiation;and not all atoms can be seen in the image. Two ideas were proposed to initiate the present research project:one is to transform an arbitrary image into the crystal structure map, and the other is to enhance the image resolution by combining the information contained in the image and the corresponding electron diffraction pattern. These ideas have been realized via the combination of electron microscopy and diffraction crystallography.

  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. 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 a

  16. Strain gradient crystal plasticity: A continuum mechanics approach to modeling micro-structural evolution

    DEFF Research Database (Denmark)

    El-Naaman, Salim Abdallah; Nielsen, Kim Lau; Niordson, Christian Frithiof

    2015-01-01

    In agreement with dislocation theory, recent experiments show, both quantitatively and qualitatively, how geometrically necessary dislocations (GNDs) distribute in dislocation wall and cell structures. Hence, GND density fields are highly localized with large gradients and discontinuities occurring...... between the cells. This behavior is not typical for strain gradient crystal plasticity models. The present study employs a higher order extension of conventional crystal plasticity theory in which the viscous slip rate is influenced by the gradients of GND densities through a back stress...

  17. Strain gradient crystal plasticity: A continuum mechanics approach to modeling micro-structural evolution

    DEFF Research Database (Denmark)

    El-Naaman, Salim Abdallah; Nielsen, Kim Lau; Niordson, Christian Frithiof

    2015-01-01

    In agreement with dislocation theory, recent experiments show, both quantitatively and qualitatively, how geometrically necessary dislocations (GNDs) distribute in dislocation wall and cell structures. Hence, GND density fields are highly localized with large gradients and discontinuities occurring...... between the cells. This behavior is not typical for strain gradient crystal plasticity models. The present study employs a higher order extension of conventional crystal plasticity theory in which the viscous slip rate is influenced by the gradients of GND densities through a back stress...

  18. Change in crystal structure and physical properties of the Multiferroics YMnO3 single crystals by Strong gravitational field

    Science.gov (United States)

    Tokuda, M.; Weijian, M.; Hayami, S.; Yoshiasa, A.; Mashimo, T.

    2017-04-01

    Many researchers have studied the multiferroicity of the hexagonal RMnO3 (R: rare-earth element) for both applications and fundamental studies. To investigate the relationship between the structure and physical properties of materials, some people apply the chemical pressure effect. The procedure of chemical pressure effect involves substituting rare-earth elements for ones which have a different ionic radius. Mashimo et al. have developed a high-temperature ultracentrifuge apparatus that can generate extended duration strong gravitational field in excess of 106 G under a wide range of temperatures (up to 500°C). Strong gravitational fields directly act on each atom as a different body force. This can cause the change in crystal structure. Thus, we subjected YMnO3 single crystal to strong gravity experiments (0.78×106 G, 400°C, 2 h) and investigated the resulting changes in the crystal structure and physical properties of the gravity sample. The single crystal four-circle X-ray diffraction measurements revealed the change in the nearest neighboring Mn-Mn and M-O bond distances. The temperature dependence of magnetic susceptibility by SQUID showed the change in the magnetic anisotropy of gravity sample.

  19. Polymorph identification and crystal structure determination by a combined crystal structure prediction and transmission electron microscopy approach.

    Science.gov (United States)

    Eddleston, Mark D; Hejczyk, Katarzyna E; Bithell, Erica G; Day, Graeme M; Jones, William

    2013-06-10

    Electron diffraction offers advantages over X-ray based methods for crystal structure determination because it can be applied to sub-micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo-inositol and theophylline. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

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

  1. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

  3. Synthesis and Crystal Structure of Metronidazole-derived Compound

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A MET-OH derivative, MET-OTs 1, was designed, prepared and structurally charac- terized by single-crystal X-ray diffraction. X-ray structure analysis reveals that 1 crystallizes in the monoclinic system, space group P21/c, with a = 16.1178(14), b = 7.5473(6), c = 13.4161(11) (A), V = 1520.3(2) (A)3, β = 111.3210(10)o, Z = 4, Dc = 1.421 g/cm3 and F(000) = 680.

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  5. Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine.

    Science.gov (United States)

    Noble, Christian G; Li, Shi-Hua; Dong, Hongping; Chew, Sock Hui; Shi, Pei-Yong

    2014-11-01

    Flavivirus methyltransferase is a genetically-validated antiviral target. Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. This raises a possibility that SAM is an integral structural component required for the folding of dengue virus (DENV) methyltransferase. Here we exclude this possibility by solving the crystal structure of DENV methyltransferase without SAM. The SAM ligand was removed from the enzyme through a urea-mediated denaturation-and-renaturation protocol. The crystal structure of the SAM-depleted enzyme exhibits a vacant SAM-binding pocket, with a conformation identical to that of the SAM-enzyme co-crystal structure. Functionally, equivalent enzymatic activities (N-7 methylation, 2'-O methylation, and GMP-enzyme complex formation) were detected for the SAM-depleted and SAM-containing recombinant proteins. These results clearly indicate that the SAM molecule is not an essential component for the correct folding of DENV methyltransferase. Furthermore, the results imply a potential antiviral approach to search for inhibitors that can bind to the SAM-binding pocket and compete against SAM binding. To demonstrate this potential, we have soaked crystals of DENV methyltransferase without a bound SAM with the natural product Sinefungin and show that preformed crystals are capable of binding ligands in this pocket.

  6. Structural aspects of dog allergies: the crystal structure of a dog dander allergen Can f 4.

    Science.gov (United States)

    Niemi, Merja H; Rytkönen-Nissinen, Marja; Jänis, Janne; Virtanen, Tuomas; Rouvinen, Juha

    2014-09-01

    Four out of six officially recognized dog allergens are members of the lipocalin protein family. So far, a three-dimensional structure has been determined for only one dog allergen, Can f 2, which is a lipocalin protein. We present here the crystal structure of a second lipocalin allergen from dog, a variant of Can f 4. Moreover, we have compared and analyzed the structures of these two weakly homologous (amino acid identity 21%) dog allergens. The size and the amino acid composition of the ligand-binding pocket indicate that Can f 4 is capable of binding only relatively small hydrophobic molecules which are different from those that Can f 2 is able to bind. The crystal structure of Can f 4 contained both monomeric and dimeric forms of the allergen, suggesting that Can f 4 is able to form transient (weak) dimers. The existence of transient dimers in solution was confirmed by use of native mass spectrometry. The dimeric structure of Can f 4 is formed when the ends of four β-strands are packed against the same strands from the second monomer. The residues in the interface are mainly hydrophobic and the formation of the dimer is similar to the major horse allergen Equ c 1. Interestingly, the crystal structure of dog Can f 2 has been reported to show a different type of dimer formation. The capability of these allergens to form dimers may be important for the development of immediate allergic reaction (mast cell activation) because oligomeric allergens can effectively present multivalent epitopes.

  7. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy.

    Science.gov (United States)

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu

    2017-01-23

    An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by (129) Xe NMR spectroscopy. The high sensitivity of the (129) Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

  8. High resolution crystal structure of human β-glucuronidase reveals structural basis of lysosome targeting

    National Research Council Canada - National Science Library

    Hassan, Md Imtaiyaz; Waheed, Abdul; Grubb, Jeffery H; Klei, Herbert E; Korolev, Sergey; Sly, William S

    2013-01-01

    ...). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases...

  9. High Resolution Crystal Structure of Human [beta]-Glucuronidase Reveals Structural Basis of Lysosome Targeting

    National Research Council Canada - National Science Library

    Hassan, Md; Waheed, Abdul; Grubb, Jeffery; Klei, Herbert; Korolev, Sergey; Sly, William

    2013-01-01

    ...). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases...

  10. Synthesis, crystal structure, crystal growth and physical properties of N,N-diethyl anilinium picrate

    Science.gov (United States)

    Subramaniyan @ Raja, R.; Anandha Babu, G.; Ramasamy, P.

    2011-11-01

    Crystalline substance of N,N-diethyl anilinium picrate (NNDEAP) has been synthesized and single crystals of NNDEAP were successfully grown for the first time by the slow evaporation solution growth technique at room temperature with dimensions 14×10×10 mm3. The formation of the new crystal has been confirmed by single crystal X-ray diffraction studies. The structural perfection of the grown crystal was analyzed by high resolution X-ray diffraction (HRXRD) measurements. The functional groups of NNDEAP have been identified by Fourier transform infrared spectral studies. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) have also been carried out and the thermal behavior of NNDEAP has been studied. The UV-vis-NIR studies have been carried out to identify the optical transmittance and the cut off wavelength of NNDEAP is identified. The dielectric loss and the dielectric constant as a function of frequency and temperature were measured for the grown crystal and the nature of variation of dielectric constant εr and dielectric losses (tan δ) were studied. Vicker's hardness test has been carried out on NNDEAP to measure the load dependent hardness. The laser induced surface damage threshold for the grown crystal was measured using Nd:YAG laser.

  11. 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.

  12. Synthesis and Crystal Structure of Isosteviol Derivatives

    Institute of Scientific and Technical Information of China (English)

    Tao Jing-Chao; Tian Guo-Qiang; Zhang Yan-Bing; Wu Ya; Liu Hong-Min

    2004-01-01

    Isosteviol (ent-16-ketobeyeran-19-oic acid, I) is a tetracyclic diterpenoid with a beyerane skeleton obtained by acid hydrolysis of stevioside.1 Several tetracyclic diterpenoids, specially the kaurenes, have important biological activities. Recent studies on the microbial transformation of isosteviol have revealed that it is metabolized by Cunninghamella bainieri, Actinoplanes sp., Mucor recurvatus, and Cunninghamella blackesleeana to yield five new metabolites.2 The hydroxylation pattern of these bioactive compounds may influence their binding on to the receptors, as was proposed for the Rabdosia diterpenoids. Therefore, the introduction of hydroxyl groups or unsaturated bonds in saturated and non-hydroxylated diterpenoids, like isosteviol, may enhance existing properties or lead to new biological activities. Although some beyeranes have been subjected to biotransformations by fungi,4 there are few report in the literature related the chemical transformation of Isosteviol. In the present study, we try to develop the chemical transformation of isosteviol and other beyeranes in order to obtaining some bioactive compounds with beyerane skeleton. Seven isosteviol derivatives, Ⅱ-Ⅷ, were therefore synthesized and characterized. The X-ray crystal strcture of H(R = H) was also determined.

  13. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase ll)

    Energy Technology Data Exchange (ETDEWEB)

    Collard, F.; Zhang, J; Nemet, I; Qanungo, K; Monnier, V; Yee, V

    2008-01-01

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6{angstrom} resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12{angstrom} deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  14. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)

    Energy Technology Data Exchange (ETDEWEB)

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C. (Case Western)

    2009-01-12

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6{angstrom} resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12{angstrom} deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  15. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)*

    Science.gov (United States)

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2008-01-01

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6Å resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12Å deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates. PMID:18667417

  16. Crystal structure of the deglycating enzyme fructosamine oxidase (amadoriase II).

    Science.gov (United States)

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R; Monnier, Vincent M; Yee, Vivien C

    2008-10-03

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6A resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12A deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  17. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ubizskii, S.B.; Vasylechko, L.O.; Savytskii, D.I.; Matkovskii, A.O.; Syvorotka, I.M. [Res. Production Amalgamation Carat, L' viv (Ukraine)

    1994-10-01

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

  19. 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.

  20. 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.

  1. STRUCTURE FORMATION OF COLLOIDS IN NEMATIC LIQUID CRYSTALS

    Directory of Open Access Journals (Sweden)

    B.I.Lev

    2003-01-01

    Full Text Available We investigated the behaviour of colloidal particles suspended in nematic liquid crystals. These colloidal particles interact through elastic deformation of the nematic director field which can result in nontrivial collective behavior, leading to the formation of spatially modulated structures. In this paper, the formation of lattice structures is described both by computer simulations and by analytical theory. Effective interactions of the pairs of spherical macroparticles suspended in nematic liquid crystals have been suggested by many authors. Using these pairwise interactions, spatial structures are obtained by means of dynamic simulations. We have suggested a number of possible structures, which may be formed in multi-macroparticle systems. Regions of temperatures and concentrations are determined in which such a structure might appear.

  2. The crystal structure of samarosporin I at atomic resolution.

    Science.gov (United States)

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  3. New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.

    Science.gov (United States)

    Thach, Trung Thanh; Lee, Sangho

    2014-11-01

    Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a=73.5, b=54.3, c=62.7 Å, β=118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cα atoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate (Ap5A) belonged to space group P1, with unit-cell parameters a=53.9, b=62.3, c=63.0 Å, α=101.9, β=112.6, γ=89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

  4. Temperature dependence of crystal structure and digestibility of roasted diaspore

    Institute of Scientific and Technical Information of China (English)

    周秋生; 李小斌; 彭志宏; 刘桂华

    2004-01-01

    Through X-ray diffraction patterns and scanning electronic micrographs, temperature dependence of the crystal structure of roasted diasporic bauxite at different temperatures and the digestibility of roasting production were investigated systematically. The lattice parameters of unit cell for chemically purified diaspore and unequilibrium alumina-contained oxide obtained from the diaspore roasted at different temperatures were determined. It is found that, with roasting temperature increasing, the roasting production changes from the original dense and perfect diaspore crystal into imperfect corundum with many microcracks and small pores on its surface and then into perfect corundum with low digestibility. The optimum roasting temperature with best digestibility is approximately 525 ℃ when residence time is about 25 min. It is thought that the change of crystal structure, formation of microcracks and small pores in the temperature field are the main essential reasons for improving digestibility of diasporic bauxite and its roasting production.

  5. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    Science.gov (United States)

    Kozlov, M. E.; Murthy, N. S.; Udod, I.; Khayrullin, I. I.; Baughman, R. H.; Zakhidov, A. A.

    2007-03-01

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO2 sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO2 lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time.

  6. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kozlov, M.E.; Baughman, R.H.; Zakhidov, A.A. [The University of Texas at Dallas, NanoTech Institute, Richardson, TX (United States); Murthy, N.S. [University of Vermont, Department of Physics, Burlington, VT (United States); Udod, I. [Teva Pharmaceuticals USA, Fairfield, NJ (United States); Khayrullin, I.I. [eMagin Corporation, Hopewell Junction, NY (United States)

    2007-03-15

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO{sub 2} sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO{sub 2} lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time. (orig.)

  7. Crystal Structure Representations for Machine Learning Models of Formation Energies

    CERN Document Server

    Faber, Felix; von Lilienfeld, O Anatole; Armiento, Rickard

    2015-01-01

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

  8. Synthesis and crystal structures of three new benzotriazolylpropanamides

    Directory of Open Access Journals (Sweden)

    Donna S. Amenta

    2017-06-01

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

  9. 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.

  10. Influence of crystal structure on the optically stimulated luminescence properties of feldspars

    DEFF Research Database (Denmark)

    Poolton, N.R.J.; Bøtter-Jensen, L.; Ypma, P.J.M.

    1994-01-01

    Work is presented showing that the crystal structure of feldspar plays an important role in determining the energy positions at which optically stimulated luminescence transitions can occur, their thermo-optical behavior, the transport properties of charge in the conduction and valence bands, and......, and the time decay characteristics of the luminescence. First-order calculations of these effects are presented, and comparison is made with experimental results.......Work is presented showing that the crystal structure of feldspar plays an important role in determining the energy positions at which optically stimulated luminescence transitions can occur, their thermo-optical behavior, the transport properties of charge in the conduction and valence bands...

  11. Growth, Band Structure and Optical Properties of LiSrBO3 Crystal

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The bulk crystal of LiSrBO3(8.39 g) with a size of 21mm × 20mm × 15mm was grown by high temperature solution growth method. The relationship between growth habit and crystal structure was discussed. The transmission spectrum shows an UV absorption edge at about 300 nm. The melting temperature of this crystal was determined to be 942 ℃ by DTA-TG measurement. The band structure of the LiSrBO3 crystal was studied by means of the first principle method. An indirect band gap was found to be about 4.0 eV, and a low dielectric constant was estimated to be about 1.9 in terms of theoretical results.

  12. High-Pressure Crystal Structure, Lattice Vibrations, and Band Structure of BiSbO4.

    Science.gov (United States)

    Errandonea, Daniel; Muñoz, Alfonso; Rodríguez-Hernández, Placida; Gomis, Oscar; Achary, S Nagabhusan; Popescu, Catalin; Patwe, Sadeque J; Tyagi, Avesh K

    2016-05-16

    The high-pressure crystal structure, lattice-vibrations, and electronic band structure of BiSbO4 were studied by ab initio simulations. We also performed Raman spectroscopy, infrared spectroscopy, and diffuse-reflectance measurements, as well as synchrotron powder X-ray diffraction. High-pressure X-ray diffraction measurements show that the crystal structure of BiSbO4 remains stable up to at least 70 GPa, unlike other known MTO4-type ternary oxides. These experiments also give information on the pressure dependence of the unit-cell parameters. Calculations properly describe the crystal structure of BiSbO4 and the changes induced by pressure on it. They also predict a possible high-pressure phase. A room-temperature pressure-volume equation of state is determined, and the effect of pressure on the coordination polyhedron of Bi and Sb is discussed. Raman- and infrared-active phonons were measured and calculated. In particular, calculations provide assignments for all the vibrational modes as well as their pressure dependence. In addition, the band structure and electronic density of states under pressure were also calculated. The calculations combined with the optical measurements allow us to conclude that BiSbO4 is an indirect-gap semiconductor, with an electronic band gap of 2.9(1) eV. Finally, the isothermal compressibility tensor for BiSbO4 is given at 1.8 GPa. The experimental (theoretical) data revealed that the direction of maximum compressibility is in the (0 1 0) plane at ∼33° (38°) to the c-axis and 47° (42°) to the a-axis. The reliability of the reported results is supported by the consistency between experiments and calculations.

  13. Crystal structure of nitrogen regulatory protein IIANtr from Neisseria meningitidis

    Directory of Open Access Journals (Sweden)

    Stammers David K

    2005-08-01

    Full Text Available Abstract Background The NMB0736 gene of Neisseria meningitidis serogroup B strain MC58 encodes the putative nitrogen regulatory protein, IIANtr (abbreviated to NM-IIANtr. The homologous protein present in Escherichia coli is implicated in the control of nitrogen assimilation. As part of a structural proteomics approach to the study of pathogenic Neisseria spp., we have selected this protein for structure determination by X-ray crystallography. Results The NM-IIANtr was over-expressed in E. coli and was shown to be partially mono-phosphorylated, as assessed by mass spectrometry of the purified protein. Crystals of un-phosphorylated protein were obtained and diffraction data collected to 2.5 Å resolution. The structure of NM-IIANtr was solved by molecular replacement using the coordinates of the E. coli nitrogen regulatory protein IIAntr [PDB: 1A6J] as the starting model. The overall fold of the Neisseria enzyme shows a high degree of similarity to the IIANtr from E. coli, and the position of the phosphoryl acceptor histidine residue (H67 is conserved. The orientation of an adjacent arginine residue (R69 suggests that it may also be involved in coordinating the phosphate group. Comparison of the structure with that of E. coli IIAmtl complexed with HPr [PDB: 1J6T] indicates that NM-IIANtr binds in a similar way to the HPr-like enzyme in Neisseria. Conclusion The structure of NM-IIANtr confirms its assignment as a homologue of the IIANtr proteins found in a range of other Gram-negative bacteria. We conclude that the NM- IIANtr protein functions as part of a phosphorylation cascade which, in contrast to E. coli, shares the upstream phosphotransfer protein with the sugar uptake phosphoenolpyruvate:sugar phosphotransferase system (PTS, but in common with E. coli has a distinct downstream effector mechanism.

  14. Crystal structure engineering for improved performance of emerging nanoscale devices

    Science.gov (United States)

    Chimalgi, Vinay Uday

    Recent advances in growth techniques and increasing number of experimental studies have made nanostructures grown along different crystallographic directions a reality. These new structures could not only benefit the electronic devices used in mainstream information technology but also show great promise for applications in lasers, solid-state lighting, near-field photolithography, free-space quantum cryptography, consumer displays, quantum computation, as well as diagnostic medicine and imaging. However, only few theoretical investigations have been performed on these structures due to the complex nature of the interplay of atomicity, structural fields, polarization, and quantum size-quantization, all strong function of the crystallographic direction. The objective of this work is mainly four-fold: (1) Integrate a computational framework employing a combination of fully atomistic valence force-field molecular mechanics and 20-band sp3s*d5-SO tight-binding based electronic band­structure models, and numerically investigate the effects of internal fields on the electronic and optical properties of zincblende InAs/GaAs quantum dots grown on (100), (110), and (111) orientated substrates. (2) Augment/extend the open source NEMO 3-D bandstructure simulator by incorporating a recently proposed first principles based model to gauge the importance of nonlinear piezoelectricity on the single-particle electronic states and interband optical transitions in emerging In(Ga)N/GaN disk-in-wire LED structures having c-plane and m-plane wurtzite crystal symmetry. (3) Coupling the NEMO 3-D software toolkit with a commercial TCAD simulator to determine the terminal electrical and optical characteristics of InGaN/GaN disk-in-wire LEDs; and (4) Finding an optimum crystallographic device for InGaN/GaN disk-in-wire LEDs to achieve improved internal quantum efficiency (IQE).

  15. Single crystal surface structure by bragg scattering

    DEFF Research Database (Denmark)

    Nielsen, Mogens

    1985-01-01

    X-ray diffraction is becoming an important tool in the measurements of surface structures. Single crystalline samples are used as in Low Energy Electron Diffraction (LEED)-studies. The X-ray technique is somewhat more involved due to the need of bright, collimated photon sources, in general...... synchrotron X-rays, and of very accurate angular settings in the ultrahigh-vacuum environment of the sample. We present the technique and discuss examples of experimental results....

  16. Electronic structure and first hyperpolarizability of poly(2-L-alanine-3-sodium nitrate (I)) crystals

    Indian Academy of Sciences (India)

    A Duarte Moller

    2014-10-01

    Poly(2-L-alanine-3-sodium nitrate (I)), -LASN, crystals have been grown by slow evaporation at room temperature. The nominal size of the crystals obtained by the method was of 500 nm. The UV–Vis spectrum shows a wide range, where absorption is lacking around 532 nm, which is required in order to have the second harmonic emission, when an incident radiation of 1064 nm strikes on the crystal. This guarantees the possible use of the crystal in visible light applications. The transparent nature of the crystal in the visible and infrared regions within the transmission spectrum confirms the nonlinear optical properties of the crystal. Additionally, Fourier transform infrared spectroscopy displays its functional groups which correspond to the poly(2-L-alanine-3-sodium nitrate (I)), where the presence of nitrates in the lattice generally can be identified by their characteristic signature within the 1660–1625, 1300–1255, 870–833 and 763–690 cm-1 range. Single crystal diffraction was carried out in order to determine atomic structure and lattice parameter. Structural parameters were = 5.388(9) Å, = 9.315(15) Å and = 13.63(2) Å. The structure of poly(2-Lalanine-3-sodium nitrate (I)) shown by single crystal diffraction shows an asymmetric unit consisting of one sodium and one nitrate ion and one L-alanine molecule. The coordination geometry around the sodium atom was trigonal bipyramidal, with three bidentate nitrate anions coordinating through their oxygen atoms and two L-alanine molecules, each coordinating through one carboxyl oxygen atom. Electronic structure was obtained by using the Becke–Lee–Yang–Part and Hartree–Fock approximations with hybrid exchangecorrelation three-parameter functional and G-311**G() basis set. Theoretical and experimental results were compared and discussed as having an excellent agreement among them.

  17. 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 ...

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  19. Crystal and molecular structure of lancerodiol-p-hydroxybenzoate

    Directory of Open Access Journals (Sweden)

    Mohamed H Abd El-Razek

    2010-01-01

    Full Text Available Lancerodiol-p-hydroxybenzoate was isolated from the leaves of Ferula sinaica L. (Apiaceae as light needle crystals. This work reports for the first time the molecular structure and relative configuration of compound 1, established by X-ray analysis.

  20. 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

  1. Topology optimization for transient response of photonic crystal structures

    DEFF Research Database (Denmark)

    Matzen, René; Jensen, Jakob Søndergaard; Sigmund, Ole

    2010-01-01

    An optimization scheme based on topology optimization for transient response of photonic crystal structures is developed. The system response is obtained by a finite-element time-domain analysis employing perfectly matched layers as an absorbing boundary condition. As an example a waveguide...

  2. Redetermination of the Crystal Structure of Al2Br6

    DEFF Research Database (Denmark)

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

    1997-01-01

    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....

  3. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.

    NARCIS (Netherlands)

    Sprogoe, D.; Broek, van den L.A.M.; Mirza, O.; Kastrup, J.S.; Voragen, A.G.J.; Gajhede, M.; Skov, L.K.

    2004-01-01

    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 a-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphoryla

  4. Crystal structure of the sodium-potassium pump

    DEFF Research Database (Denmark)

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

    2007-01-01

    The Na+,K+-ATPase generates electrochemical gradients for sodium and potassium that are vital to animal cells, exchanging three sodium ions for two potassium ions across the plasma membrane during each cycle of ATP hydrolysis. Here we present the X-ray crystal structure at 3.5 A resolution of the...

  5. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

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

    2012-01-01

    , such as body-centered cubic and face-centered cubic, can be suppressed by a proper choice of the potential depth and periodicity. Furthermore, by varying the harmonic trap parameters and/or the optical potential in time, controlled transitions between crystal structures can be obtained with close to unit...

  6. Materials research at Stanford University. [composite materials, crystal structure, acoustics

    Science.gov (United States)

    1975-01-01

    Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.

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

    Science.gov (United States)

    Douglas, Bodie

    2009-01-01

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

  8. VO{sub 2} (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Rao Popuri, Srinivasa [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France); National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara (Romania); Artemenko, Alla [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France); Labrugere, Christine [CeCaMA, University of Bordeaux 1, ICMCB, 87 Avenue du Dr. A. Schweitzer, F-33608 Pessac (France); Miclau, Marinela [National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara (Romania); Villesuzanne, Antoine [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France); Pollet, Michaël, E-mail: pollet@icmcb-bordeaux.cnrs.fr [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France)

    2014-05-01

    Well crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal reaction in the presence of V{sub 2}O{sub 5} and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO{sub 2} (A) micro rods. The structural and electronic transitions in VO{sub 2} (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO{sub 2} (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO{sub 2} (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO{sub 2} (M1) are described. - Graphical abstract: Using a single step and template free hydrothermal synthesis, well crystallized VO{sub 2} (A) microrods were prepared and the P4/ncc space group was assigned to the room temperature crystal structure. Reversible and irreversible phase transitions among different VO{sub 2} polymorphs were identified and their progressive nature was highlighted. Attempts to increase the microrods size, involving layer by layer formation mechanisms, are presented. - Highlights: • Highly crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal process. • The P4/ncc space group was determined for VO{sub 2} (A) at room temperature. • The electronic structure and progressive nature of the structural phase transition were investigated. • A weak coupling between structural and electronic phase transitions was identified. • Different crystallite morphologies were discussed in relation with growth mechanisms.

  9. Crystal structure and magnetization of a Co3B2O6 single crystal

    Science.gov (United States)

    Kazak, N. V.; Platunov, M. S.; Ivanova, N. B.; Knyazev, Yu. V.; Bezmaternykh, L. N.; Eremin, E. V.; Vasil'ev, A. D.; Bayukov, O. A.; Ovchinnikov, S. G.; Velikanov, D. A.; Zubavichus, Ya. V.

    2013-07-01

    The crystal structure and magnetic properties of Co3B2O6 single crystals are studied. Orthorhombic symmetry with space group Pnnm is detected at room temperature. The measurements of static magnetization and dynamic magnetic susceptibility reveal two magnetic anomalies at T 1 = 33 K and T 2 = 10 K and an easy-axis magnetic anisotropy. The effective magnetic moment indicates a high-spin state of the Co2+ ion. A spin-flop transition is found at low temperatures and H sf = 23 kOe. EXAFS spectra of the K-edge absorption of Co are recorded at various temperatures, the temperature-induced changes in the parameters of the local environment of cobalt are analyzed, and the effective Co-Co and Co-O distances are determined. The magnetic interactions in the crystal are analyzed in terms of an indirect coupling model.

  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. Crystal Structure of an Ammonia-Permeable Aquaporin.

    Science.gov (United States)

    Kirscht, Andreas; Kaptan, Shreyas S; Bienert, Gerd Patrick; Chaumont, François; Nissen, Poul; de Groot, Bert L; Kjellbom, Per; Gourdon, Pontus; Johanson, Urban

    2016-03-01

    Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants, allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia. Here, we report the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity filter region are sufficient to convert a strictly water-specific human aquaporin into an AtTIP2;1-like ammonia channel. A flexible histidine and a novel water-filled side pore are speculated to deprotonate ammonium ions, thereby possibly increasing permeation of ammonia. The molecular understanding of how aquaporins facilitate ammonia flux across membranes could potentially be used to modulate ammonia losses over the plasma membrane to the atmosphere, e.g., during photorespiration, and thereby to modify the nitrogen use efficiency of plants.

  12. Structural modification of tantalum crystal induced by nitrogen ion implantation

    Indian Academy of Sciences (India)

    A H RAMEZANI; M R HANTEHZADEH; M GHORANNEVISS; E DARABI

    2016-06-01

    This paper investigates the effect of nitrogen ion implantation on tantalum surface structure. In this experiment, nitrogen ions which had an energy of 30 keV and doses of $1 \\times 10^{17}$ to $10 \\times 10^{17}$ ions cm$^{−2}$ were used. X-ray diffraction analysis (XRD) was applied for both the metallic Ta substrate and the study of new structures that have been created through the nitrogen ion implantation. Atomic force microscopy (AFM) was also used tocheck the roughness variations prior to and also after the implantation phase. The experimental results show the formation of hexagonal tantalum nitride (TaN$_{0.43}$) in addition to the fact that by increasing the ion dose, the nitrogen atoms occupy more interstitial spaces in the target crystal. The nitride phase also seen for $3\\times 10^{17}$ and $5\\times 10^{17}$ ions cm$^{−2}$, while it disappeared for higher dose of $7\\times 10^{17}$ and $1\\times 10^{18}$ ions cm$^{−2}$. The FWHM of the dominant peak of tantalum nitride suggest the growth of the crystallite’s size, which is in agreement with the AFM results ofthe grains.

  13. Large scale structures in liquid crystal/clay colloids

    Energy Technology Data Exchange (ETDEWEB)

    Duijneveldt, Jeroen S van [School of Chemistry, Cantock' s Close, University of Bristol, Bristol BS8 1TS (United Kingdom); Klein, Susanne [HP Laboratories, Filton Road, Stoke Gifford, Bristol BS34 8QZ (United Kingdom); Leach, Edward [HP Laboratories, Filton Road, Stoke Gifford, Bristol BS34 8QZ (United Kingdom); Pizzey, Claire [School of Chemistry, Cantock' s Close, University of Bristol, Bristol BS8 1TS (United Kingdom); Richardson, Robert M [H H Wills Physics Laboratory, Tyndall Avenue, University of Bristol, Bristol BS8 1TL (United Kingdom)

    2005-04-20

    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.

  14. Crystal Structure of an Ammonia-Permeable Aquaporin.

    Directory of Open Access Journals (Sweden)

    Andreas Kirscht

    2016-03-01

    Full Text Available Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants, allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia. Here, we report the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity filter region are sufficient to convert a strictly water-specific human aquaporin into an AtTIP2;1-like ammonia channel. A flexible histidine and a novel water-filled side pore are speculated to deprotonate ammonium ions, thereby possibly increasing permeation of ammonia. The molecular understanding of how aquaporins facilitate ammonia flux across membranes could potentially be used to modulate ammonia losses over the plasma membrane to the atmosphere, e.g., during photorespiration, and thereby to modify the nitrogen use efficiency of plants.

  15. Crystal Structure of Cold Compressed Graphite

    Science.gov (United States)

    Amsler, Maximilian; Flores-Livas, José A.; Lehtovaara, Lauri; Balima, Felix; Ghasemi, S. Alireza; Machon, Denis; Pailhès, Stéphane; Willand, Alexander; Caliste, Damien; Botti, Silvana; San Miguel, Alfonso; Goedecker, Stefan; Marques, Miguel A. L.

    2012-02-01

    Through a systematic structural search we found an allotrope of carbon with Cmmm symmetry which we predict to be more stable than graphite for pressures above 10 GPa. This material, which we refer to as Z-carbon, is formed by pure sp3 bonds and it provides an explanation to several features in experimental x-ray diffraction and Raman spectra of graphite under pressure. The transition from graphite to Z-carbon can occur through simple sliding and buckling of graphene sheets. Our calculations predict that Z-carbon is a transparent wide band-gap semiconductor with a hardness comparable to diamond.

  16. TUNABLE Band Structures of 2d Multi-Atom Archimedean-Like Phononic Crystals

    Science.gov (United States)

    Xu, Y. L.; Chen, C. Q.; Tian, X. G.

    2012-06-01

    Two dimensional multi-atom Archimedean-like phononic crystals (MAPCs) can be obtained by adding "atoms" at suitable positions in primitive cells of traditional simple lattices. Band structures of solid-solid and solid-air MAPCs are computed by the finite element method in conjunction with the Bloch theory. For the solid-solid system, our results show that the MAPCs can be suitably designed to split and shift band gaps of the corresponding traditional simple phononic crystal (i.e., with only one scatterer inside a primitive cell). For the solid-air system, the MAPCs have more and wider band gaps than the corresponding traditional simple phononic crystal. Numerical calculations for both solid-solid and solid-air MAPCs show that the band gap of traditional simple phononic crystal can be tuned by appropriately adding "atoms" into its primitive cell.

  17. Single Crystal Structure Determination of Alumina to 1 Mbar

    Science.gov (United States)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  18. Thermodynamics of sublimation, crystal lattice energies, and crystal structures of racemates and enantiomers: (+)- and (+/-)-ibuprofen.

    Science.gov (United States)

    Perlovich, German L; Kurkov, Sergey V; Hansen, Lars Kr; Bauer-Brandl, Annette

    2004-03-01

    Thermodynamic differences between ibuprofen (IBP) racemate and the (+)-enantiomer were studied by X-ray diffraction, thermoanalysis, and crystal energy calculations. The thermodynamic functions of sublimation (as a measure of crystal lattice energy) were obtained by the transpiration method. The sublimation enthalpies (DeltaH(sub)) of (+/-)-IBP and (+)-IBP are 115.8 +/- 0.6 and 107.4 +/- 0.5 kJ. mol(-1), respectively. Using the temperature dependency of the saturated vapor pressure, the relative fractions of enthalpy and entropy of the sublimation process were calculated, and the sublimation process for both the racemate and the enantiomer was found to be enthalpy driven (62%). Two different force fields, Mayo et al. (M) and Gavezzotti (G), were used for comparative analysis of crystal lattice energies. Both force fields revealed that the van der Waals term contributes more to the packing energy in (+)-IBP than in (+/-)-IBP. The hydrogen bonding energy, however, contributes at 29.7 and 32.3% to the total crystal lattice energy in (+)-IBP and (+/-)-IBP (M), respectively. Furthermore, different structure fragments of the IBP molecule were analyzed with respect to their contribution to nonbonded van der Waals interactions. The effect of the C-H distance on the van der Waals term of the crystal lattice energy was also studied.

  19. 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.

  20. 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.

  1. Tailor-made force fields for crystal-structure prediction.

    Science.gov (United States)

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

  2. Magnetic and structural transitions in crystals with a structure of the NaCl type

    Science.gov (United States)

    Kassan-Ogly, F. A.; Filippov, B. N.

    2009-04-01

    A model of simultaneous magnetic and structural first-order transitions in antiferromagnets with a strong cubic magnetic anisotropy has been constructed on the basis of a synthesis of magnetic modified 6-state and 8-state Potts models and the theoretical model of structural phase transitions in cubic crystals. A revised scheme has been suggested for the derivation of possible magnetic structures in the fcc lattice with allowance for competing interactions between the nearest and next-nearest neighbors. A calculation of the temperature evolution of high-temperature diffuse magnetic scattering of neutrons has been carried out to show that the mechanism of a magnetic transition at the Néel point is caused by the transformation of diffuse magnetic scattering into magnetic Bragg peaks.

  3. High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K.

    Science.gov (United States)

    Chatake, Toshiyuki; Ishikawa, Takuya; Yanagisawa, Yasuhide; Yamada, Taro; Tanaka, Ichiro; Fujiwara, Satoru; Morimoro, Yukio

    2011-11-01

    Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H(2)O) with heavy water (D(2)O) prior to neutron diffraction experiments in order to diminish background noise. The effects of solvent deuteration on the crystallization of proteinase K (PK) with polyethylene glycol as a precipitant were investigated using high-resolution X-ray crystallography. In previous studies, eight NO(3)(-) anions were included in the PK crystal unit cell grown in NaNO(3) solution. In this study, however, the PK crystal structure did not contain NO(3)(-) anions; consequently, distortions of amino acids arising from the presence of NO(3)(-) anions were avoided in the present crystal structures. High-resolution (1.1 Å) X-ray diffraction studies showed that the degradation of PK crystals induced by solvent deuteration was so small that this degradation would be negligible for the purpose of neutron protein crystallography experiments at medium resolution. Comparison of the nonhydrogen structures of nondeuterated and deuterated crystal structures demonstrated very small structural differences. Moreover, a positive correlation between the root-mean-squared differences and B factors indicated that no systematic difference existed.

  4. Crystal structure of alpha poly-p-xylylene.

    Science.gov (United States)

    Kubo, S.; Wunderlich, B.

    1971-01-01

    A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

  5. Modulation mechanism and disorder structure in hollandite-type crystals

    Energy Technology Data Exchange (ETDEWEB)

    Wu Xiaojing; Fujiki, Yoshiki; Horiuchi, Shigeo (National Inst. for Research in Inorganic Materials, Ibaraki (Japan)); Ishigame, Mareo (Research Inst. for Scientific Measurements, Tohoku Univ., Sendai (Japan))

    1991-07-01

    The structural modulation in some hollandite-type crystals is explained by a vacancy-displacive modulation model. In this model the large cations located in the tetragonal channels along the c axis deviate from the average position to form a modulation wave. Three types of disorder in the initial phase of the modulation wave have been introduced to interpret apparently different diffraction patterns in hollandite-type crystals. A mathematical analysis as well as optical diffraction give results similar to those experimentally observed. High-resolution transmission electron microscope images have been observed to confirm the discussion further. (orig.).

  6. 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.

  7. Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs

    OpenAIRE

    Merritt, Ethan A.; Arakaki, Tracy L; Gillespie, J Robert; Larson, Eric T.; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J.; Kim, Jessica; Li ZHANG; Verlinde, Christophe L M J; Fan, Erkang; Zucker, Frank; Buckner, Frederick S.; Van Voorhis, Wesley C.; Hol, Wim G. J.

    2010-01-01

    Crystal structures of histidyl-tRNA synthetase from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme, and reveal differences from bacterial homologs. Histidyl-tRNA synthetases in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three dimensional topology of this domain is very different in b...

  8. Synthesis of 2,6-diaminopyridine substituted -oxoketene ,-acetals: Crystal structure and hydrogen bonding interactions

    Indian Academy of Sciences (India)

    Okram Mukherjee Singh; Laishram Ronibala Devi; Neeladri Das

    2013-09-01

    Polyaza -oxoketene ,-acetals can exist as either enamino or imino tautomeric forms. Based on the spectroscopic data and structural analysis of one of the ,-acetals, the stereochemistry was unambiguously assigned as an all--configuration. The crystal structure confirms the enamino structure and shows extensive use of C-H…X (X = N, O, and S) weak hydrogen bonding interactions, thereby generating a 3-dimensional network in solid state.

  9. Modeling liquid crystal bilayer structures with minimal surfaces.

    Science.gov (United States)

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W

    2004-01-22

    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  10. The body-centered cubic structure of methyllithium tetramer crystal: staggered methyl conformation by electrostatic stabilization via intratetramer multipolarization.

    Science.gov (United States)

    Ohta, Yusuke; Demura, Akimitsu; Okamoto, Takuya; Hitomi, Haruko; Nagaoka, Masataka

    2006-06-29

    The methyllithium tetramer (CH3Li)4 structure in the bcc crystal has been theoretically optimized with the use of density functional theory calculations under the periodic boundary condition. The X-ray structure shows that the methyl-group conformation in tetramer in crystal takes the staggered form rather than the eclipsed form that is taken in the isolated tetramer, i.e., the crystal packing effect, and this has been reproduced for the first time. It is concluded that the staggered form is advantageous in crystal, as a whole, due to the larger electrostatic stabilization via the induced intratetramer multipolarization, although it should cause, simultaneously, smaller destabilization in intratetramer electronic energy.

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

    Directory of Open Access Journals (Sweden)

    Anuruddha Rajapakse

    2014-11-01

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

  12. Crystal structure and density of helium to 232 kbar

    Science.gov (United States)

    Mao, H. K.; Wu, Y.; Jephcoat, A. P.; Hemley, R. J.; Bell, P. M.; Bassett, W. A.

    1988-01-01

    The properties of helium and hydrogen at high pressure are topics of great interest to the understanding of planetary interiors. These materials constitute 95 percent of the entire solar system. A technique was presented for the measurement of X-ray diffraction from single-crystals of low-Z condenses gases in a diamond-anvil cell at high pressure. The first such single-crystal X-ray diffraction measurements on solid hydrogen to 26.5 GPa were presented. The application of this technique to the problem of the crystal structure, equation of state, and phase diagram of solid helium is reported. Crucial for X-ray diffraction studies of these materials is the use of a synchrotron radiation source which provides high brillance, narrow collimation of the incident and diffracted X-ray beams to reduce the background noise, and energy-dispersive diffraction techniques with polychromatic (white) radiation, which provides high detection efficiency.

  13. Crystal structure of bis(1-ethylpyridinium dioxonium hexacyanidoferrate(II

    Directory of Open Access Journals (Sweden)

    Rikako Tanaka

    2017-02-01

    Full Text Available The title compound, (C7H10N2(H3O2[Fe(CN6] or (Etpy2(H3O2[Fe(CN6] (Etpy+ is 1-ethylpyridinium, crystallizes in the space group Pnnm. The FeII atom of the [Fe(CN6]4− anion lies on a site with site symmetry ..2/m, and has an octahedral coordination sphere defined by six cyanido ligands. Both the Etpy+ and the oxonium cations are located on a mirror plane. In the crystal, electron-donor anions of [Fe(CN6]4− and electron-acceptor cations of Etpy+ are each stacked parallel to the b axis, resulting in a columnar structure with segregated moieties. The crystal packing is stabilized by a three-dimensional O—H...N hydrogen-bonding network between the oxonium ions and the cyanide ligands of [Fe(CN6]4−.

  14. Crystal Growth, Structure and Morphology of Rifapentine Methanol Solvate

    Institute of Scientific and Technical Information of China (English)

    周堃; 李军; 罗建洪; 金央

    2012-01-01

    Rifapentine, an important antibiotic, was crystallized from methanol solvent in the form of its methanol solvate. The crystal structure of rifapentine methanol solvate belongs to monoclinic, space group P21, with the unit cell parameters of a = 1.2278(3) nm, b = 1.9768(4) rim, c = 1.2473(3) nm, Z= 2, and β = 112.35(3). The parallelepiped.morphology was also predicted by Materials Studio simulation program.. The influence of intermolecular in-teraction was taken into account in the attachment energy model. The crystal shape fits the calculated morphology well, which was performed on the potential energy minimized model using a generic DREIDING 2.21 force fieldand developed minimization protocol with derived'partial charges.

  15. Synthesis and Crystal Structure of Tetranuclear Zinc Benzoate

    Institute of Scientific and Technical Information of China (English)

    YIN Ming-cai; WANG Chi-wei; AI Chang-chun; YUAN Liang-jie; SUN Ju-tang

    2004-01-01

    A tetranuclear zinc benzoate Zn4O(C6H5CO2)6 was synthesized and characterized by X-ray single crystal determination. It crystallizes in cubic, space group Ia-3d. Its crystal cell is very large, a=4.100 63(18) nm, V=68.953(5) nm3 and Z = 48. The structure is composed of discrete Zn4O(C6H5CO2)6 molecules. In each molecule, four zinc atoms are held together by a central oxygen atom, which results in the formation of a regular tetrahedron. All benzoate ligands coordinate to zinc atoms in a bidentate bridging mode. Each zinc atom is in a slightly distorted tetrahedral geometry, coordinated by three benzoate oxygen atoms and the central oxygen atom. The intermolecular interactions result in the formation of a three-dimensional supramolecular framework, with non-intersecting parallel channels.

  16. Crystal structure and physical properties of a dithiolene complex crystal with adamantane supramolecular rotator

    OpenAIRE

    Yan, Yin-Nan; Kubo, Kazuya; Noro, Shin-ichiro; Akutagawa, Tomoyuki; Nakamura, Takayoshi

    2014-01-01

    Supramolecular cation salt of adamantane rotator with a dithiolene complex, (fluoroadamantylammonium(+))([18]-crown-6)[Ni(dmit)(2)](-) (1) was synthesized. The fluorine atom of the adamantane unit showed a large thermal factor elongated latitudinally, suggesting molecular rotation in the solid state. Crystal 1 exhibited a large dielectric response by applying an AC field along the a axis.

  17. 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.

  18. Crystal structure of cytotoxin protein suilysin from Streptococcus suis.

    Science.gov (United States)

    Xu, Lingfeng; Huang, Bo; Du, Huamao; Zhang, Xuejun C; Xu, Jianguo; Li, Xuemei; Rao, Zihe

    2010-01-01

    Cholesterol-dependent cytolysins (CDC) are pore forming toxins. A prototype of the CDC family members is perfringolysin O (PFO), which directly binds to the cell membrane enriched in cholesterol, causing cell lysis. However, an exception of this general observation is intermedilysin (ILY) of Streptococcus intermedius, which requires human CD59 as a receptor in addition to cholesterol for its hemolytic activity. A possible explanation of this functional difference is the conformational variation between the C-terminal domains of the two toxins, particularly in the highly conserved undecapeptide termed tryptophan rich motif. Here, we present the crystal structure of suilysin, a CDC toxin from the infectious swine pathogen Streptococcus suis. Like PFO, suilysin does not require a host receptor for hemolytic activity; yet the crystal structure of suilysin exhibits a similar conformation in the tryptophan rich motif to ILY. This observation suggests that the current view of the structure-function relationship between CDC proteins and membrane association is far from complete.

  19. Properties, theoretical study and crystal structure of 3-benzothiazole-9-ethyl carbazole.

    Science.gov (United States)

    Gu, Yingchun; Lin, Dayong; Fei, Xuening; Wang, Cuihong; Li, Ling; Tang, Yalin; Zhou, Jianguo

    2016-09-01

    The title compound of 3-benzothiazole-9-ethyl carbazole was synthesized by the reaction of 3-aldehyde-9-ethyl carbazole and 2-aminothiophenol. The compound was characterized by (1) H nuclear magnetic resonance (NMR) and mass spectrometry (MS). Its crystal structure was obtained and determined by single crystal X-ray diffraction. The results showed that the crystal belongs to the orthorhombic crystal system and the cell parameters of space group P2(1)2(1)2(1) were a = 5.6626 (12) Å, b = 12.606 (3) Å, c = 22.639 (5) Å, α = 90°, β = 90°, γ = 90°, V = 1616.0 (6) Å(3) , Z = 4, Dc = 1.350 mg/m(3) . The UV-vis and fluorescence spectra were also studied preliminarily. The fluorescence spectra of the title compound with bovine serum albumin (BSA) showed that BSA could be marked with the compound and the stability constant between them was 0.82 × 10(7)  M(-1) . Meanwhile, the crystal and molecule were theoretically surveyed by density functional tight-binding (DFTB). The results showed that there was an orbital overlap for lowest unoccupied molecular orbital (LUMO) between the neighbouring molecules for the crystal, which is different from the molecule structure. It was also showed that the crystal structure is a non-conductor. Copyright © 2016 John Wiley & Sons, Ltd.

  20. 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...

  1. Crystal Structure and Electronic Structure of a Luminescent Compound 2-(2-Pyridyl) Benzimidazole

    Institute of Scientific and Technical Information of China (English)

    岳淑美; 苏忠民; 马建方; 廖奕; 阚玉和; 张恒君

    2003-01-01

    The crystal structure of 2-(2-pyridyl) benzimidazole was determined by singlecrystal X-ray diffraction at 193(2) K. It crystallizes in orthorhombic system, space group Pbca with unit cell constants a = 10.6204(7), b = 10.1407(4), c = 18.6327(8) A, Z= 8, V= 2006.7(2) A3, Dc. =1.292 g/cm3, F(000) = 816 andμ(MoKα) = 0.081 mm-1. The structure was refined to R = 0.0317 and wR = 0.0454 for 795 observed reflections with Ⅰ> 2σ(Ⅰ). In the solid state, it has an emission maximum at 369 nm, while in solution (DMSO), the maximum excitation is at 372 nm. Quantum chemistry calculation was performed by the method of density functional theory. Theoretical results show that atom N is the reactive site when coordinating with a metal, and the electronic structure of the title compound presents excellent carrier transport properties.

  2. Crystal Structures of Fe2+ Dioxygenase Superoxo, Alkylperoxo, and Bound Product Intermediates

    OpenAIRE

    Kovaleva, Elena G.; Lipscomb, John D.

    2007-01-01

    We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The X-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been p...

  3. Subtleties in crystal structure solution from powder diffraction data using simulated annealing: ranitidine hydrochloride.

    Science.gov (United States)

    Huq, Ashfia; Stephens, P W

    2003-02-01

    Recent advances in crystallographic computing and availability of high-resolution diffraction data have made it relatively easy to solve crystal structures from powders that would have traditionally required single crystal samples. The success of direct space methods depends heavily on starting with an accurate molecular model. In this paper we address the applicability of using these methods in finding subtleties such as disorder in the molecular conformation that might not be known a priori. We use ranitidine HCl as our test sample as it is known to have a conformational disorder from single crystal structural work. We redetermine the structure from powder data using simulated annealing and show that the conformational disorder is clearly revealed by this method.

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

    Energy Technology Data Exchange (ETDEWEB)

    Devaud, G. (Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States)); Furcinitti, P.S. (Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309 (United States)); Fleming, J.C.; Lyon, M.K.; Douglas, K. (Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States))

    1992-09-01

    We have examined the structure of S-layers isolated from {ital Sulfolobus} {ital 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 related to the organization of units within each crystal domain. Projection maps from TEM images have shown that there are significant differences in the final average maps, depending on which side of the sample is adsorbed to the carbon support film. Comparison of AFM images to TEM projection maps has allowed us to relate high magnification views obtained by AFM to the relatively high resolution information obtained by electron microscopy and image processing.

  5. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

    DEFF Research Database (Denmark)

    van de Streek, Jacco; Neumann, Marcus A

    2014-01-01

    is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.......In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published...... minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom...

  6. Structural engineering of three-dimensional phononic crystals

    Science.gov (United States)

    Delpero, Tommaso; Schoenwald, Stefan; Zemp, Armin; Bergamini, Andrea

    2016-02-01

    Artificially-structured materials are attracting the research interest of a growing community of scientists for the possibility to develop novel materials with advantageous properties that arise from the ability to tailor the propagation of elastic waves, and thus energy, through them. In this work, we propose a three-dimensional phononic crystal whose unit cell has been engineered to obtain a strong wave-attenuation band in the middle of the acoustic frequency range. The combination of its acoustic properties with the dimensions of the unit cell and its static mechanical properties makes it an interesting material for possibly several applications in civil and mechanical engineering, for instance as the core of an acoustically insulating sandwich panel. A sample of this crystal has been manufactured and experimentally tested with respect to its acoustic transmissibility. The performance of the phononic crystal core is remarkable both in terms of amplitude reduction in the transmissibility and width of the attenuation band. A parametric study has been finally conducted on selected geometrical parameters of the unit cell and on their effect on the macroscopic properties of the crystal. This work represents an application-oriented example of how the macroscopic properties of an artificially-structured material can be designed, according to specific needs, by a conventional engineering of its unit cell.

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

    Science.gov (United States)

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

    2016-11-01

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

  8. Experimental demonstration of a four-port photonic crystal cross-waveguide structure

    DEFF Research Database (Denmark)

    Yu, Yi; Heuck, Mikkel; Ek, Sara;

    2012-01-01

    We report the design and fabrication of a four-port InP photonic crystal cavity-waveguide structure in which two crossing waveguides intersect in a cavity. Transmission measurements show that by exploiting mode-gap effects, high cross-talk suppression between the two waveguides can be obtained...

  9. Analysis of liquid crystal properties for photonic crystal fiber devices

    DEFF Research Database (Denmark)

    Weirich, Johannes; Lægsgaard, Jesper; Wei, Lei

    2009-01-01

    We analyze the bandgap structure of Liquid Crystal infiltrated Photonic Crystal Fibers depending on the parameters of the Liquid Crystals by means of finite element simulations. For a biased Liquid Crystal Photonic Crystal Fiber, we show how the tunability of the bandgap position depends...... on the Liquid Crystal parameters....

  10. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao (Hebei); (Toronto); (Huazhong)

    2012-06-28

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

  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

    2015-11-14

    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.

  12. 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.

  13. STRUCTURAL CHARACTERIZATION OF POLYETHYLENES BY DSC ANALYSIS AFTER CRYSTALLIZATION SEGREGATION

    Institute of Scientific and Technical Information of China (English)

    Yu Ma; Mao Xu

    2000-01-01

    The molecular structure of polyethylene (PE) samples with various comonomers including propylene, 1-butene and 1-hexene was investigated by DSC and 13C-NMR techniques. The density of the samples varies from 0.948 g/cm3 to 0.917 g/cm3, and the molecular weight determined by the GPC method is in the range of 1~2 × 105. The branch point content of the samples was determined by 13C-NMR measurements and was found to be less than 20 per 1000 C atoms along the main chain. Crystallization segregation DSC technique (CSDSC) was used to characterize the branch point distribution or the segment length distribution of PEs. The crystallization segregation was performed in a successive annealing process at decreasing temperatures. The interval of two successive annealing temperatures was 6 K, and the time length of each annealing step was 2.5 h. The CSDSC results clearly indicate that all the PE samples used, including some metallocene PEs,more or less exhibit their non-uniformity in segment length distribution, and bimodal or multimodal CSDSC curves were usually observed. For quantitative characterization of the CSDSC curves and the segment length distribution two parameters,the average melting point, TmAV, and the root-mean-square deviation of melting temperature, (ATm2AV)1/2, were proposed.TmAV is corresponding to the average segment length due to branching and (ATm2AV)1/2 gives information about the width of the segment length distribution. Experimental results show that both the degree of average melting temperature depression and the width of the distribution seem to increase with increasing the branching content and are dependent on the type of comonomers. Very good reproducibility and additivity of the CSDSC method were evidenced experimentally. It was concluded that the CSDSC technique is a sensitive and convenient method for characterizing the segment length distribution of branched polyethylenes and will be of great interest in structure-property relationship

  14. Electronic and crystal structures of thermoelectric CaMgSi intermetallic compound

    Energy Technology Data Exchange (ETDEWEB)

    Miyazaki, Hidetoshi, E-mail: miyazaki@nitech.ac.jp [Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Inukai, Manabu [Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Soda, Kazuo [Department of Quantum Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan); Miyazaki, Nobufumi; Adachi, Nozomu; Todaka, Yoshikazu [Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi 441-8580 (Japan); Nishino, Yoichi [Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555 (Japan)

    2016-01-15

    Highlights: • We report the electronic and crystal structures of the TiNiSi-type CaMgSi compound. • CaMgSi has a semiconductor-like electronic structure with a small band gap. • CaMgSi is a Mott-type insulator owing to strongly correlated electrons effect. - Abstract: We investigated the electronic and crystal structures of a new thermoelectric material, CaMgSi compound, by using synchrotron radiation photoemission spectroscopy (SR-PES), synchrotron radiation X-ray powder diffraction (SR-XRD) measurements, and electronic band structure calculation to understand the way leading to improvement in the thermoelectric properties of this material. Electronic band structure calculation of the CaMgSi compound using the crystal structure determined from SR-XRD measurement showed a semi-metallic electronic structure with a pseudo-gap at the Fermi level. In contrast to the predicted semi-metallic electronic structure, the SR-PES results showed a small semiconductor-like gap at the Fermi level. This result revealed that the CaMgSi compound is a Mott-type insulator owing to strongly correlated electrons effect in the Ca 3d and Mg 3p states being well hybridized with those in the Si 3p states. The observed electronic structure of the CaMgSi compound suggests that an optimal carrier doping exists to best control the n- and p-type thermoelectric properties and enhance the power factors.

  15. ReSe2: a reassessment of crystal structure and thermal analysis

    Science.gov (United States)

    Jariwala, Bhakti; Thamizhavel, Arumugum; Bhattacharya, Arnab

    2017-02-01

    The rhenium-based layered dichalcogenide ReSe2 crystallizes in a distorted triclinic structure which results in unique, anisotropic electronic and optical properties. This, along with a weak layer-dependence of band gap has made ReSe2 a subject of intense contemporary research interest. However, there has been no agreement on the exact crystal structure of this material, or knowledge of its thermal properties like the melting point. In this work, we perform single crystal, Laue, and powder diffraction measurements on high-quality ReSe2 crystals synthesized using a modified Bridgman technique. We confirm the presence of triclinic symmetry (P\\bar{1} -space group) and support the view that that ReSe2 has a distorted CdCl2-type structure (rather than Cd(OH)2 as initially proposed) and obtain lattice parameter values of a  =  6.5791(8) Å, b  =  6.6897(10) Å, and c  =  6.7013(11) Å. Further, thermal measurements on these crystals show a clear endothermic peak at around 1115 °C pointing to a melting transition, and show no other phase transitions up to 1300 °C.

  16. 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.

  17. Crystal Structure of a Potassium Ion Transporter TrkH

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; H Huang; M Getahun Derebe; E Levin; V Kabaleeswaran; Y Pan; M Punta; J Love; et al.

    2011-12-31

    The TrkH/TrkG/KtrB proteins mediate K{sup +} uptake in bacteria and probably evolved from simple K{sup +} channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K{sup +} channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K{sup +} and Rb{sup +} over smaller ions such as Na{sup +} or Li{sup +}. Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K{sup +} flux. These results reveal the molecular basis of K{sup +} selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.

  18. The crystal structure of synthetic kutinaite, Cu14Ag6As7

    DEFF Research Database (Denmark)

    Karanovic, Ljiljana; Poleti, Dejan; Makovicky, Emil;

    2002-01-01

    kutinaite, X-ray diffraction, powder method, crystal structure, icosahedral alloy, arsenide, metal clusters......kutinaite, X-ray diffraction, powder method, crystal structure, icosahedral alloy, arsenide, metal clusters...

  19. 'Weird' crystal structures of elements at high pressure

    Energy Technology Data Exchange (ETDEWEB)

    Kolobyanina, Tat' yana N [L.F. Vereshchagin Institute of High Pressure Physics, Russian Academy of Sciences, Troitsk, Moscow region (Russian Federation)

    2002-12-31

    New crystal structures, in particular incommensurate composite crystals, discovered in the high-pressure phases of Group I, II, IV, and V elements are described, and their intermetallic and other binary structural analogs are discussed. (reviews of topical problems)

  20. Crystal Structure of the Catalytic Domain of Drosophila [beta]1,4-Galactosyltransferase-7

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Boopathy; Qasba, Pradman K. (NIH)

    2010-11-03

    The {beta}1,4-galactosyltransferase-7 ({beta}4Gal-T7) enzyme, one of seven members of the {beta}4Gal-T family, transfers in the presence of manganese Gal from UDP-Gal to an acceptor sugar (xylose) that is attached to a side chain hydroxyl group of Ser/Thr residues of proteoglycan proteins. It exhibits the least protein sequence similarity with the other family members, including the well studied family member {beta}4Gal-T1, which, in the presence of manganese, transfers Gal from UDP-Gal to GlcNAc. We report here the crystal structure of the catalytic domain of {beta}4Gal-T7 from Drosophila in the presence of manganese and UDP at 1.81 {angstrom} resolution. In the crystal structure, a new manganese ion-binding motif (HXH) has been observed. Superposition of the crystal structures of {beta}4Gal-T7 and {beta}4Gal-T1 shows that the catalytic pocket and the substrate-binding sites in these proteins are similar. Compared with GlcNAc, xylose has a hydroxyl group (instead of an N-acetyl group) at C2 and lacks the CH{sub 2}OH group at C5; thus, these protein structures show significant differences in their acceptor-binding site. Modeling of xylose in the acceptor-binding site of the {beta}4Gal-T7 crystal structure shows that the aromatic side chain of Tyr{sup 177} interacts strongly with the C5 atom of xylose, causing steric hindrance to any additional group at C5. Because Drosophila Cd7 has a 73% protein sequence similarity to human Cd7, the present crystal structure offers a structure-based explanation for the mutations in human Cd7 that have been linked to Ehlers-Danlos syndrome.

  1. How evolutionary crystal structure prediction works--and why.

    Science.gov (United States)

    Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

    2011-03-15

    Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an

  2. Demonstration Show That Promotes and Assesses Conceptual Understanding Using the Structure of Drama

    Science.gov (United States)

    Walter Kerby, Holly; DeKorver, Brittland K.; Cantor, Joanne; Weiland, Marcia J.; Babiarz, Christopher L.

    2016-01-01

    Demonstration shows are a widely used form of Informal Science Education. While there is evidence that the shows are highly enjoyable, little work has been done to investigate the cognitive impacts of these shows. This article describes the development and production of "The Boiling Point," a show that uses the structure of a play to…

  3. Crystal structure of Pb3(IO4(OH22

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-07-01

    Full Text Available The structure of the title compound, trilead(II bis[dihydroxidotetraoxidoiodate(VII], was determined from a crystal twinned by non-merohedry with two twin domains present [twin fraction 0.73 (1:0.27 (1]. It contains three Pb2+ cations and two IO4(OH23− anions in the asymmetric unit. Each of the Pb2+ cations is surrounded by eight O atoms (cut-off value = 3.1 Å in the form of a distorted polyhedron. The octahedral IO4(OH23− anions are arranged in rows extending parallel to [021], forming a distorted hexagonal rod packing. The cations and anions are linked into a framework structure. Although H-atom positions could not be located, O...O distances suggest medium-strength hydrogen-bonding interactions between the IO4(OH2 octahedra, further consolidating the crystal packing.

  4. Solid State Synthesis and Crystal Structure of K3SI

    Institute of Scientific and Technical Information of China (English)

    ZHAO Zhen-Qian; LIU Xi; CHEN Wen-Tong; LI Yan; WU A-Qing; ZENG Hui-Yi; GUO Guo-Cong; HUANG Jin-Shun

    2006-01-01

    A new ternary alkali metal chalcogenide halide, K3SI, has been synthesized by solid state reaction method and structurally characterized by X-ray crystallography. The crystal belongs to hexagonal, space group P63cm with a = 11.699(1), c = 5.8279(9) (A), Mr = 276.26, V = 690.8(1)(A)3, Z = 6, Dc = 3.985 g/cm3, F(000) = 756, μ= 9.913 mm-1, S = 1.004, R = 0.0719 and wR = 0.2204. The title compound is the first example containing S anion in the ternary alkali metal chalcogenide halides family M3QX (M = alkali metal, Q = chalcogenide, X = halide), which crystallizes in the hexagonal anti-perovskite structure type.

  5. Crystal structure of tris-(hydroxyl-ammonium) orthophosphate.

    Science.gov (United States)

    Leinemann, Malte; Jess, Inke; Boeckmann, Jan; Näther, Christian

    2015-11-01

    The crystal structure of the title salt, ([H3NOH](+))3·[PO4](3-), consists of discrete hydroxyl-ammonium cations and ortho-phos-phate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phospho-rus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by inter-molecular 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 inter-actions are observed.

  6. 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.

  7. 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.

  8. Dispersion Based Photonic-Crystal Structures for RF Applications

    Science.gov (United States)

    2006-06-01

    dimensional FDTD simulation. In our experiment, we fabricated the device using a computer numerically controlled ( CNC ) router . A tapered planar structure is...millimeter-wave photonic crystals are fabricated in Rexolite slabs by a computer numerically controlled ( CNC ) micro-milling system. Using the millimeter...loss, and low cost. In particular, it can be fabricated using a CNC micro-milling machine. Also, its low index provides a weaker confinement in the

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

    OpenAIRE

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

    2016-01-01

    Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from...

  10. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    Energy Technology Data Exchange (ETDEWEB)

    Han,Q.; Robinson, H.; Gao, Y.; Vogelaar, N.; Wilson, S.; Rizzi, M.; Li, J.

    2006-01-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  11. Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.

    Science.gov (United States)

    Han, Qian; Robinson, Howard; Gao, Yi Gui; Vogelaar, Nancy; Wilson, Scott R; Rizzi, Menico; Li, Jianyong

    2006-12-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75A high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1A resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  12. High resolution crystal structure of human β-glucuronidase reveals structural basis of lysosome targeting.

    Directory of Open Access Journals (Sweden)

    Md Imtaiyaz Hassan

    Full Text Available Human β-glucuronidase (GUS cleaves β-D-glucuronic acid residues from the non-reducing termini of glycosaminoglycan and its deficiency leads to mucopolysaccharidosis type VII (MPSVII. Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases. The structure revealed several new details including a new glycan chain at Asn272, in addition to that previously observed at Asn173, and coordination of the glycan chain at Asn173 with Lys197 of the lysosomal targeting motif which is essential for phosphotransferase recognition. Analysis of the high resolution structure not only provided new insights into the structural basis for lysosomal targeting but showed significant differences between human GUS, which is medically important in its own right, and E. coli GUS, which can be selectively inhibited in the human gut to prevent prodrug activation and is also widely used as a reporter gene by plant biologists. Despite these differences, both human and E. coli GUS share a high structure homology in all three domains with most of the glycosyl hydrolases, suggesting that they all evolved from a common ancestral gene.

  13. Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants

    Science.gov (United States)

    Noguera, Martín E.; Vazquez, Diego S.; Ferrer-Sueta, Gerardo; Agudelo, William A.; Howard, Eduardo; Rasia, Rodolfo M.; Manta, Bruno; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

    2017-02-01

    Thioredoxin is a ubiquitous small protein that catalyzes redox reactions of protein thiols. Additionally, thioredoxin from E. coli (EcTRX) is a widely-used model for structure-function studies. In a previous paper, we characterized several single-point mutants of the C-terminal helix (CTH) that alter global stability of EcTRX. However, spectroscopic signatures and enzymatic activity for some of these mutants were found essentially unaffected. A comprehensive structural characterization at the atomic level of these near-invariant mutants can provide detailed information about structural variability of EcTRX. We address this point through the determination of the crystal structures of four point-mutants, whose mutations occurs within or near the CTH, namely L94A, E101G, N106A and L107A. These structures are mostly unaffected compared with the wild-type variant. Notably, the E101G mutant presents a large region with two alternative traces for the backbone of the same chain. It represents a significant shift in backbone positions. Enzymatic activity measurements and conformational dynamics studies monitored by NMR and molecular dynamic simulations show that E101G mutation results in a small effect in the structural features of the protein. We hypothesize that these alternative conformations represent samples of the native-state ensemble of EcTRX, specifically the magnitude and location of conformational heterogeneity.

  14. Crystal structure of lead(II tartrate: a redetermination

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2015-01-01

    Full Text Available Single crystals of poly[μ4-tartrato-κ6O1,O3:O1′:O2,O4:O4′-lead], [Pb(C4H4O6]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002. Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H...O hydrogen bonds between the OH groups of one tartrate anion and the carboxylate O atoms of adjacent anions.

  15. Pressure effects on crystal and electronic structure of bismuth tellurohalides

    Science.gov (United States)

    Rusinov, I. P.; Menshchikova, T. V.; Sklyadneva, I. Yu; Heid, R.; Bohnen, K.-P.; Chulkov, E. V.

    2016-11-01

    We study the possibility of pressure-induced transitions from a normal semiconductor to a topological insulator (TI) in bismuth tellurohalides using density functional theory and tight-binding method. In BiTeI this transition is realized through the formation of an intermediate phase, a Weyl semimetal, that leads to modification of surface state dispersions. In the topologically trivial phase, the surface states exhibit a Bychkov-Rashba type dispersion. The Weyl semimetal phase exists in a narrow pressure interval of 0.2 GPa. After the Weyl semimetal-TI transition occurs, the surface electronic structure is characterized by gapless states with linear dispersion. The peculiarities of the surface states modification under pressure depend on the band-bending effect. We have also calculated the frequencies of Raman active modes for BiTeI in the proposed high-pressure crystal phases in order to compare them with available experimental data. Unlike BiTeI, in BiTeBr and BiTeCl the topological phase transition does not occur. In BiTeBr, the crystal structure changes with pressure but the phase remains a trivial one. However, the transition appears to be possible if the low-pressure crystal structure is retained. In BiTeCl under pressure, the topological phase does not appear up to 18 GPa due to a relatively large band gap width in this compound.

  16. Nanoconfinement-induced structures in chiral liquid crystals.

    Science.gov (United States)

    Melle, Michael; Theile, Madlona; Hall, Carol K; Schoen, Martin

    2013-08-28

    We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase.

  17. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Carol K. Hall

    2013-08-01

    Full Text Available We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase.

  18. Crystal structure of lead(II) tartrate: a redetermination.

    Science.gov (United States)

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions.

  19. Structure-mechanical property correlations in mechanochromic luminescent crystals of boron difluoride dibenzoylmethane derivatives.

    Science.gov (United States)

    Krishna, Gamidi Rama; Devarapalli, Ramesh; Prusty, Rajesh; Liu, Tiandong; Fraser, Cassandra L; Ramamurty, Upadrasta; Reddy, Chilla Malla

    2015-11-01

    The structure and mechanical properties of crystalline materials of three boron difluoride dibenzoylmethane (BF2dbm) derivatives were investigated to examine the correlation, if any, among mechanochromic luminescence (ML) behaviour, solid-state structure, and the mechanical behaviour of single crystals. Qualitative mechanical deformation tests show that the crystals of BF2dbm( (t) Bu)2 can be bent permanently, whereas those of BF2dbm(OMe)2 exhibit an inhomogeneous shearing mode of deformation, and finally BF2dbmOMe crystals are brittle. Quantitative mechanical analysis by nano-indentation on the major facets of the crystals shows that BF2dbm( (t) Bu)2 is soft and compliant with low values of elastic modulus, E, and hardness, H, confirming its superior suceptibility for plastic deformation, which is attributed to the presence of a multitude of slip systems in the crystal structure. In contrast, both BF2dbm(OMe)2 and BF2dbmOMe are considerably stiffer and harder with comparable E and H, which are rationalized through analysis of the structural attributes such as the intermolecular interactions, slip systems and their relative orientation with respect to the indentation direction. As expected from the qualitative mechanical behaviour, prominent ML was observed in BF2dbm( (t) Bu)2, whereas BF2dbm(OMe)2 exhibits only a moderate ML and BF2dbmOMe shows no detectable ML, all examined under identical conditions. These results confirm that the extent of ML in crystalline organic solid-state fluorophore materials can be correlated positively with the extent of plasticity (low recovery). In turn, they offer opportunities to design new and improved efficient ML materials using crystal engineering principles.

  20. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    Science.gov (United States)

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

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

    Science.gov (United States)

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

    2014-09-16

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

  2. The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2: Ab Initio Calculations

    Science.gov (United States)

    Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.

    2016-12-01

    Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.

  3. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-02-24

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

  4. Structural studies show energy transfer within stabilized phycobilisomes independent of the mode of rod-core assembly.

    Science.gov (United States)

    David, Liron; Prado, Mindy; Arteni, Ana A; Elmlund, Dominika A; Blankenship, Robert E; Adir, Noam

    2014-03-01

    The major light harvesting complex in cyanobacteria and red algae is the phycobilisome (PBS), comprised of hundreds of seemingly similar chromophores, which are protein bound and assembled in a fashion that enables highly efficient uni-directional energy transfer to reaction centers. The PBS is comprised of a core containing 2-5 cylinders surrounded by 6-8 rods, and a number of models have been proposed describing the PBS structure. One of the most critical steps in the functionality of the PBS is energy transfer from the rod substructures to the core substructure. In this study we compare the structural and functional characteristics of high-phosphate stabilized PBS (the standard fashion of stabilization of isolated complexes) with cross-linked PBS in low ionic strength buffer from two cyanobacterial species, Thermosynechococcus vulcanus and Acaryochloris marina. We show that chemical cross-linking preserves efficient energy transfer from the phycocyanin containing rods to the allophycocyanin containing cores with fluorescent emission from the terminal emitters. However, this energy transfer is shown to exist in PBS complexes of different structures as characterized by determination of a 2.4Å structure by X-ray crystallography, single crystal confocal microscopy, mass spectrometry and transmission electron microscopy of negatively stained and cryogenically preserved complexes. We conclude that the PBS has intrinsic structural properties that enable efficient energy transfer from rod substructures to the core substructures without requiring a single unique structure. We discuss the significance of our observations on the functionality of the PBS in vivo.

  5. Synthesis, crystal structure, optical and electrochemical properties of 9,10-dihydroxybenzo[ℎ]quinoline

    Indian Academy of Sciences (India)

    Kew-Yu Chen; Hsing-Yang Tsai; Wei-Chi Lin; Hou-Hsein Chu; Yu-Ching Weng; Chih-Chieh Chan

    2014-07-01

    9,10-Dihydroxybenzo[ℎ]quinoline (1), a 10-hydroxybenzo[ℎ]quinoline (2) derivative, was synthesized and characterized by 1H NMR, 13C NMR, UV-vis and fluorescence spectra, and single-crystal X-ray diffraction. Compound 1 possesses an intramolecular six-membered-ring hydrogen bond, from which excitedstate intramolecular proton transfer (ESIPT) takes place from the phenolic proton to the pyridinic nitrogen, resulting in a proton-transfer tautomer emission of 650 nm in dichloromethane. Its molecular geometry in the ground state has also been calculated using density functional theory (DFT) at the B3LYP/6-31G∗∗ level and compared with its crystal structure. Results show that the optimized geometry can well reproduce the crystal structure. Furthermore, both absorption and emission spectra of 1 and 2 were calculated using time-dependent DFT (TD-DFT) calculations, and were in good agreement with the experimental results.

  6. Crystal structure, spectrum character and explosive property of a new cocrystal CL-20/DNT

    Science.gov (United States)

    Liu, Ke; Zhang, Gao; Luan, Jieyu; Chen, Zhiqun; Su, Pengfei; Shu, Yuanjie

    2016-04-01

    A new cocrystal explosive of 2,4,6,8,10,12-hexanitrohexaazaiso-wurtzitane(CL-20) and 2,5-dinitrotoluene(DNT) in a molar ratio of 1:2 has been prepared by slow solvent evaporation method. Crystal structure of the cocrystal characterized by single crystal X-ray diffraction (SXRD) reveals that the cocrystal is formed by intermolecular hydrogen bond interactions and belongs to the triclinic system with P-1 group. Moreover, the obivious differences of powder X-ray diffraction (PXRD) patterns, infrared spectroscopy and Raman spectroscopy confirm that the intermolecular interactions have great influence for the crystal structure and formation of cocrystal. The cocrystal exhibits a lower impact height of 44 cm, suggesting a substantial reduction of sensitivity in comparison with CL-20. And thermal test results showed cocrystal obtains a lower melting point than DNT, which means huge advantages in blasting engineering.

  7. Crystal Structure of D-Valine at the Temperature of 293, 270, 223 and 173K

    Institute of Scientific and Technical Information of China (English)

    WANG Wen-Qing; GONG Yan; WANG Zhe-Ming; YAN Chun-Hua

    2003-01-01

    The crystal structure of D-valine has been determined by Mo-Kα (λ = 0.71073 A) X-ray diffraction method for the first time. It crystallizes in monoclinic, space group P21 (Z = 4) with a = 9.6728(5), b = 5.2722(3), c = 12.0425(8) A, β = 90.750(2)° at 293 K. The asymmetric unit contains two crystallographically independent molecules — A (trans form) and B (gauche I form). They are rotational isomers with two kinds of conformations about the Cα -Cβ bond. The results of measurements of crystal structure at 293, 270, 223 and 173 K show a little change in bond lengths and geometries as a function of temperature. No evidence was obtained for the existence of configuration transformation from D- to L-valine.

  8. Synthesis and Crystal Structure of Compound [ZnS6 (C12H8N2)

    Institute of Scientific and Technical Information of China (English)

    陈之荣; 李健晖; 李鸿钧; 苏卫平; 曹荣

    2000-01-01

    The title compound ZnS6(C12H8N2) was obtained by reaction of zinic powder with sulfur and 1,10-phenathtroline in DMF solvent, and its structure has been determined by single crystal X-ray diffraction analysis. The crystal data for the compound: triclinic, P-1, Z = 2, a = 8. 159(2), b = 9. 485(2), c = 11. 997(2)A , α =110. 00(3)°,β = 99.22(3)°, γ = 100.57(3)°, V = 832A3, Dc =1. 748g/cm3, μ(MoKa)=0. 2219 cm-1, F(000)=440. The structure was refined to R = 0. 0723 and Rw = 0. 0865 for 1427 independent observed reflections. The tilte crystal consists of a discrete molecules, in which the core of ZnS2N2 shows a distorted tetrahedral geometry.

  9. Crystal structure determiningof 7-ADCA based on X-raypowder diffraction

    Institute of Scientific and Technical Information of China (English)

    HU Enping; CHENG Qiang; GUO Linghong; LI Hui

    2006-01-01

    Optimum resolution data of X-ray powder diffraction for 7-amino desacetoxy cephalospo- ranic acid(7-ADCA) were collected from an X' Pert Pro MPD diffractometer with the setup of 0.01°/s and 0.01° per step. Indexing to the crystal system and searching space group from the diffraction data were conducted by means of the computational crystallography method. The pilot crystal models of 7-ADCA were then refined by Rietveld method to obtain the exact three-dimensional structure. The results show that the crystal structure of 7-ADCA is monoclinic, space group P21 with unit cell dimensions a=13.50(A) b=6.01(A), c =5.91(A), α=γ=90.00°,β=101.96°, Z=2 and V =469.10(A)3. The fraction coordinate of each atom in the unit cell is well located and reported.

  10. 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.

  11. Unified approach for determining tetragonal tungsten bronze crystal structures.

    Science.gov (United States)

    Smirnov, M; Saint-Grégoire, P

    2014-05-01

    Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the rigid unit modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the TTB-like niobates lends credence to the obtained theoretical predictions.

  12. Holographic liquid crystal polarization grating with Fabry-Perot structure.

    Science.gov (United States)

    Sakamoto, Moritsugu; Yamaguchi, Haruki; Noda, Kohei; Sasaki, Tomoyuki; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2016-03-15

    A holographic liquid crystal polarization grating with a Fabry-Perot structure was developed. Because of its resonant structure, the device offers high levels of control of the diffraction properties of incident-polarized light beams, depending on the resonance conditions. The diffracted light beams are emitted in both the reflection and transmission directions, and the device thus works as a multibranch polarization grating with double optical paths, unlike a conventional polarization grating. These device features were experimentally demonstrated and were also explained theoretically.

  13. 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.

  14. Crystal structure of seleno-l-cystine dihydrochloride

    OpenAIRE

    Carl Henrik Görbitz; Vladimir Levchenko; Jevgenijs Semjonovs; Mohamed Yusuf Sharif

    2015-01-01

    Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar disulfide bridge. The title compound [systematic name: (R,R)-1,1′-dicarboxy-2,2′-(diselanediyl)diethanaminium dichloride], C6H14N2O4Se22+·2Cl−, is the first example of a small molecule structure of the biologically important analogue with a —CH2—Se—Se—CH2— bridging unit. Bon...

  15. 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.

  16. The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry.

    Science.gov (United States)

    Noya, Eva G; Vega, Carlos; Doye, Jonathan P K; Louis, Ard A

    2010-06-21

    The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values of the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centered-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centered-cubic crystal becomes more stable than the body-centered-cubic crystal, and at higher temperatures, a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centered-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centered-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centered-cubic crystal and between the fluid and the diamond crystal show that at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles.

  17. The Cambridge Structural Database: a quarter of a million crystal structures and rising.

    Science.gov (United States)

    Allen, Frank H

    2002-06-01

    The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

  18. Crystal structure of eukaryotic ribosome and its complexes with inhibitors.

    Science.gov (United States)

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  19. Crystal structure of the 80S yeast ribosome.

    Science.gov (United States)

    Jenner, Lasse; Melnikov, Sergey; Garreau de Loubresse, Nicolas; Ben-Shem, Adam; Iskakova, Madina; Urzhumtsev, Alexandre; Meskauskas, Arturas; Dinman, Jonathan; Yusupova, Gulnara; Yusupov, Marat

    2012-12-01

    The first X-ray structure of the eukaryotic ribosome at 3.0Å resolution was determined using ribosomes isolated and crystallized from the yeast Saccharomyces cerevisiae (Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M: The structure of the eukaryotic ribosome at 3.0 A resolution. Science 2011, 334:1524-1529). This accomplishment was possible due to progress in yeast ribosome biochemistry as well as recent advances in crystallographic methods developed for structure determination of prokaryotic ribosomes isolated from Thermus thermophilus and Escherichia coli. In this review we will focus on the development of isolation procedures that allowed structure determination (both cryo-EM and X-ray crystallography) to be successful for the yeast S. cerevisiae. Additionally we will introduce a new nomenclature that facilitates comparison of ribosomes from different species and kingdoms of life. Finally we will discuss the impact of the yeast 80S ribosome crystal structure on perspectives for future investigations.

  20. From Protein Structure to Function via Single Crystal Optical Spectroscopy

    Directory of Open Access Journals (Sweden)

    Luca eRonda

    2015-04-01

    Full Text Available The more than 100.000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic artifacts, including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density map, thus limiting the relevance of structure determinations. Moreover, for most of these structures no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in the inference for protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5’-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.

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

    Science.gov (United States)

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

    2013-09-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

  3. Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes.

    Science.gov (United States)

    Goldenberg, Barbara L; Young, Victor G; Barany, George

    2015-10-01

    The present paper reports crystallographic studies on three related compounds that were of inter-est as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitro-gen-protecting groups: (N-methyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C3H4Cl3NOS2, (1), (N-benzyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (3). Their mol-ecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent mol-ecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [110], which are linked by short Cl⋯Cl and S⋯O contacts forming sheets parallel to (001). In the crystal of (2), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O⋯Cl contacts forming ribbons along the c-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking.

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

    Science.gov (United States)

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

    2012-06-01

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

  5. Synthesis and Crystal Structure of a New Adamantane Amide Derivative

    Institute of Scientific and Technical Information of China (English)

    ZHOU Ying-Hua; LV Qi-Chun; ZHANG Qian; CHENG Yong; SHENG En-Hong

    2012-01-01

    A novel adamantane acyl amide derivative containing two phthalimido pendant groups(C31H31N3O5) has been synthesized,and its structure was characterized by elemental analysis,IR,1 H NMR spectra,and single-crystal X-ray diffraction.The crystal belongs to triclinic,space group P1 with a=7.3158(10),b=13.2405(18),c=14.378(2),α=72.419(2),β=84.496(2),γ=81.799(2)o,V=1312.0(3)3,Z=2,Dc=1.330 g/cm 3,μ=0.09 mm-1,Mr=525.59,F(000)=556,S=1.001,R=0.0523 and wR=0.0707 for 5901 unique reflections with 2363 observed ones(I〉2σ(I)).π-π stacking interactions(offset face-to-face) exist between the two rings of phthalimides from the neighboring molecules in the title crystal structure.The intermolecular dihedral angle between the two rings of neighboring phthalic amides is 6.26° and the distance is 4.008.

  6. 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].

  7. Effect of crystal packing on the structures of polymeric metallocenes.

    Science.gov (United States)

    Dinnebier, R E; van Smaalen, Sander; Olbrich, F; Carlson, S

    2005-02-21

    The pressure dependencies of the crystal structures of the polymeric metallocenes lithium cyclopentadienide (LiCp) and potassium cyclopentadienide (KCp) have been determined by synchrotron X-ray powder diffraction. The decrease of the volume of LiCp by 34% up to a pressure of p = 12.2 GPa and of KCp by 23% at p = 5.3 GPa as well as the bulk moduli of K = 7.7 GPa for LiCp and 4.9 GPa for KCp indicate a high compressibility for these compounds. The crystal structures of KCp have been determined up to p = 3.9 GPa. An increase of the bend angle is found from 45 degrees at p = 0 GPa up to 51 degrees at p = 3.9 GPa. This variation is completely explained by a model invoking attractive K+ Cp- interaction and repulsive nonbonded carbon-carbon interactions. It is proposed that the bend angle in the polymeric alkali metal metallocenes is the result of the optimization of the crystal packing.

  8. Radial mosaic internal structure of rounded diamond crystals from alluvial placers of Siberian platform

    Science.gov (United States)

    Ragozin, A. L.; Zedgenizov, D. A.; Kuper, K. E.; Shatsky, V. S.

    2016-12-01

    The specific gray to almost black diamonds of rounded morphology are especially typical in alluvial placers of the northeastern part of the Siberian platform. The results of study of internal structure of these diamonds are presented. X-ray topography and birefringence patterns of polished plates of studied diamonds show their radial mosaic structure. Diamonds consists of slightly misorientated (up to 20') subindividuals which are combined to mosaic wedge-shaped sectors. Electron back-scatter diffraction technique has demonstrated that subindividuals are often combined in the single large blocks (subgrains). The whole crystals commonly consist of several large subgrains misoriented up to 5° to one another. The total nitrogen content of these diamonds vary in the range 900-3300 ppm and nitrogen aggregation state (NB/(NB + NA)*100) from 25 to 64 %. Rounded diamond crystals of variety V are suggested to have been formed at the high growth rate caused by the high oversaturation of carbon in the crystallization medium. It may result in the splitting of growing crystal and their radial mosaic structure as a sequence. High content of structural nitrogen defects and the great number of mechanical impurities - various mineral and fluid inclusions may also favor to generation of this structure.

  9. Crystal structures of β-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding.

    Science.gov (United States)

    Tsutsui, Yuko; Ramakrishnan, Boopathy; Qasba, Pradman K

    2013-11-01

    The β-1,4-galactosyltransferase 7 (β4GalT7) enzyme is involved in proteoglycan synthesis. In the presence of a manganese ion, it transfers galactose from UDP-galactose to xylose on a proteoglycan acceptor substrate. We present here the crystal structures of human β4GalT7 in open and closed conformations. A comparison of these crystal structures shows that, upon manganese and UDP or UDP-Gal binding, the enzyme undergoes conformational changes involving a small and a long loop. We also present the crystal structures of Drosophila wild-type β4GalT7 and D211N β4GalT7 mutant enzymes in the closed conformation in the presence of the acceptor substrate xylobiose and the donor substrate UDP-Gal, respectively. To understand the catalytic mechanism, we have crystallized the ternary complex of D211N β4GalT7 mutant enzyme in the presence of manganese with the donor and the acceptor substrates together in the same crystal structure. The galactose moiety of the bound UDP-Gal molecule forms seven hydrogen bonds with the protein molecule. The nonreducing end of the xylose moiety of xylobiose binds to the hydrophobic acceptor sugar binding pocket created by the conformational changes, whereas its extended xylose moiety forms hydrophobic interactions with a Tyr residue. In the ternary complex crystal structure, the nucleophile O4 oxygen atom of the xylose molecule is found in close proximity to the C1 and O5 atoms of the galactose moiety. This is the first time that a Michaelis complex of a glycosyltransferase has been described, and it clearly suggests an SN2 type catalytic mechanism for the β4GalT7 enzyme.

  10. A new crystal structure for (BEDT–TTF)2SbF6 and some of its physical properties

    Indian Academy of Sciences (India)

    G K R Senadeera; T Mori

    2005-02-01

    A new crystal structure for bis(ethylenedithio)tetrathiafulvalene [(BEDT–TTF)2 SbF6] was determined by single crystal X-ray diffraction. The crystal structure was refined in the $P \\overline{1}$ space group at room temperature. Crystal data for new structure are as follows: triclinic, = 8.670 (2) Å, = 8.664 (2) Å, = 16.842 (5) Å, = 89$^\\circ \\cdot$29 (2), = 90$^\\circ \\cdot$71 (3), = 92$^\\circ \\cdot$67 (1), = 1263.64 Å3, = 2, = 2.136 g cm-3, (Mo–K), = 0.7107 Å, = 0.057 for a total of 5517 independent reflections. The donors form a trimerized column, and the band structure calculated by the tight-binding approximation shows band insulator properties. The temperature dependent of the d.c. resistivity shows a semiconducting behaviour with room temperature resistivity along the -axis; $\\rho_{290 K}$ = 5.6 ohm cm.

  11. CMS experiment : animation showing the construction of the main structural components of CMS together

    CERN Multimedia

    2006-01-01

    This 17-minute long animation shows the construction of the main structural components of CMS in the surface hall in Cessy and offers a detailed overview of the installation in the experimental cavern.

  12. CMS experiment : animation showing the construction of the main structural components of CMS together

    CERN Multimedia

    CERN Multimedia Production Unit

    2003-01-01

    This 17-minute long animation shows the construction of the main structural components of CMS in the surface hall in Cessy and offers a detailed overview of the installation in the experimental cavern.

  13. Mafic-crystal distributions, viscosities, and lava structures of some Hawaiian lava flows

    Science.gov (United States)

    Rowland, Scott K.; Walker, George P. L.

    1988-09-01

    The distribution patterns of mafic phenocrysts in some Hawaiian basalt flows are consistent with simple in situ gravitational settling. We use the patterns to estimate the crystal settling velocity and hence viscosity of the lava, which in turn can be correlated with surface structures. Numerical modeling generates theoretical crystal concentration profiles through lava flow units of different thicknesses for differing settling velocities. By fitting these curves to field data, crystal-settling rates through the lavas can be estimated, from which the viscosities of the flows can be determined using Stokes' Law. Lavas in which the crystal settling velocity was relatively high (on the order of 5 × 10 -4 cm/sec) show great variations in phenocryst content, both from top to bottom of the same flow unit, and from one flow unit to another. Such lava is invariably pahoehoe, flow units of which are usually less than 1 m thick. Lavas in which the crystal-settling velocity was low show a small but measurable variation in phenocryst content. These lavas are part of a progression from a rough pahoehoe to toothpaste lava to a'a. Toothpaste lava is characterized by spiny texture as well as the ability to retain surface grooves during solidification, and flow units are usually thicker than 1 m. In the thickest of Hawaiian a'a flows, those of the distal type, no systematic crystal variations are observed, and high viscosity coupled with a finite yield strength prevented crystal settling. The amount of crystal settling in pahoehoe indicates that the viscosity ranged from 600 to 6000 Pa s. The limited amount of settling in toothpaste lava indicates a viscosity greater than this value, approaching 12,000 Pa s. We infer that distal-type a'a had a higher viscosity still and also possessed a yield strength.

  14. 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.

  15. Crystal Structure of Ethanolamine 5-Nitrosalicylic Acid Organic Adduct

    Institute of Scientific and Technical Information of China (English)

    金轶; 车云霞; 魏荣敏; 郑吉民

    2004-01-01

    The title adduct (C18H24N4O12, Mr = 488.41) crystallizes in monoclinic, space group P21/c with a = 4.0514(19), b = 25.193(11), c = 10.751(5)(A), β = 95.070(8)o, V = 1093.0(9)(A)3, Z = 4, Dc = 1.484 g/cm3, F(000) = 512, μ(MoKα) = 1.26 cm-1, T = 293 K, the final R = 0.0593 and wR = 0.0862 for 956 observed reflections with I > 2(I). The compound is a 1:1 adduct of ethanolamine and 5-nitrosalicylic acid. The nitrogen atom of ethanolamine is protonated. In this crystal there exist a number of hydrogen bonds which link the ethanolamine and 5-nitrosalicylic acid molecules to form a three-dimensional infinite network structure.

  16. Synthesis and crystal structure of ethyl benzimidazole-2-yl phosphonate

    Institute of Scientific and Technical Information of China (English)

    HU, Fang-Zhong; WENG, Lin-Hong; YANG, Hua-Zheng; ZOU, Xiao-Mao

    2000-01-01

    When N-cyanoimido- ( O, O-diethyl ) phosphonyl/ S-methyl thiocarbonate (1) was treated with o-phenylenediamine in the presence of Et3N in ethanol, diethyl benzimidazole-2-yl recrys phonate(2) was obtained and hydrolyzed during the recrys tallization in MeOH/H2O, generating ethyl benzimidazole-2-yl phosphonate(3). The crystal structure of compound 3 was determined by X-ray diffraction method. The crystals belong to monoclinic, space rgoup C2/c, a=1.78408(18), b=O. 83725(9), c=1.67401(18) nm, β= 118.997(2)°, v=2. 1870(4) nm3, z=8, Dc=1.374g/cm3, F(000)=944.The final R and wR are 0.0499 and 0.1436, respectively. The mechanism of the above reaction is also discussed.

  17. 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.

  18. 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.

  19. 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.

  20. Average and Local Crystal Structures of (Ga(1-x)Znx)(N(1-x)Ox) Solid Solution Nanoparticles.

    Science.gov (United States)

    Feygenson, Mikhail; Neuefeind, Joerg C; Tyson, Trevor A; Schieber, Natalie; Han, Wei-Qiang

    2015-12-07

    We report a comprehensive study of the crystal structure of (Ga(1-x)Znx)(N(1-x)Ox) solid solution nanoparticles by means of neutron and synchrotron X-ray scattering. In our study, we used four different types of (Ga(1-x)Znx)(N(1-x)Ox) nanoparticles, with diameters of 10-27 nm and x = 0.075-0.51, which show energy band gaps from 2.21 to 2.61 eV. Rietveld analysis of the neutron diffraction data revealed that the average crystal structure is hexagonal wurtzite (space group P63mc) for the larger nanoparticles, while the crystal structure of smaller nanoparticles is disordered hexagonal. Pair-distribution-function analysis found that the intermediate crystal structure retains a "motif" of the average one; however, the local structure is more disordered. The implications of disorder on the reduced energy band gap are discussed.

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

    Science.gov (United States)

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

    2006-05-19

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

  2. Polarizabilities and Shielding Factors of Ions in Cesium Halide Crystals with the Cesium Chloride Structure

    Science.gov (United States)

    Mahbubar, Rahman; Michihiro, Yoshitaka; Nakamura, Koichi; Kanashiro, Tatsuo

    2001-08-01

    The calculated results of the polarizabilities and the quadrupole shielding factor of the ions in cesium halide crystals with the cesium chloride structure are presented. The calculation is done on the basis of the self-consistent field local density approximation and the modified Sternheimer equation. The crystalline potential is treated by the spherical solid model. The size effect is seen in the values of the polarizabilities and the quadrupole shielding factor. The values of the polarizabilities and the quadrupole shielding factor of cesium ion show only slight change in different crystals. The values of chlorine ion show significant reduction and the amount of the reduction is different in the different crystals. The effect of the crystalline environment on the electron states is discussed.

  3. International trade shows: Structure, strategy and performance of exhibitors at individual booths vs. joint booths

    DEFF Research Database (Denmark)

    Hansen, Kåre

    2000-01-01

    This paper examines differences in exhibitors who participate at international trade shows at joint booths and those who participate at individual booths. The structure, strategy, and trade show performance of exhibitors at joint booths and those at individual booths are analysed. The analysis of...... implications for exhibitors at interna-tional trade shows and export marketing programmes and other marketing programmes offering services to international trade show exhibitors....

  4. Shear moduli in bcc-fcc structure transition of colloidal crystals.

    Science.gov (United States)

    Zhou, Hongwei; Xu, Shenghua; Sun, Zhiwei; Zhu, Ruzeng

    2015-10-14

    Shear moduli variation in the metastable-stable structure transition of charged colloidal crystals was investigated by the combination techniques of torsional resonance spectroscopy and reflection spectrometer. Modulus of the system increases with the proceeding of the transition process and it finally reaches the maximum value at the end of the transition. For colloidal crystals in stable state, the experimental moduli show good consistence with theoretical expectations. However, in the transition process, the moduli are much smaller than theoretical ones and this can be chalked up to crystalline imperfection in the transition state.

  5. Shear moduli in bcc-fcc structure transition of colloidal crystals

    Science.gov (United States)

    Zhou, Hongwei; Xu, Shenghua; Sun, Zhiwei; Zhu, Ruzeng

    2015-10-01

    Shear moduli variation in the metastable-stable structure transition of charged colloidal crystals was investigated by the combination techniques of torsional resonance spectroscopy and reflection spectrometer. Modulus of the system increases with the proceeding of the transition process and it finally reaches the maximum value at the end of the transition. For colloidal crystals in stable state, the experimental moduli show good consistence with theoretical expectations. However, in the transition process, the moduli are much smaller than theoretical ones and this can be chalked up to crystalline imperfection in the transition state.

  6. Disordered crystal structure of pentamethylcyclopentadienylsodium as seen by high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Tedesco, C; Dinnebier, R E; Olbrich, F; van Smaalen, S

    2001-10-01

    The crystal structure of pentamethylcyclopentadienylsodium, [NaC10H15] (NaCp*), has been determined from high-resolution X-ray powder diffraction. The compound crystallizes in space group Cmcm with lattice parameters a = 4.61030 (3), b = 16.4621 (3), c = 14.6751 (2) A, V = 1113.77 (4) A(3) (Z = 4). NaCp* forms polymeric multidecker chains along the a axis. The Rietveld refinement (R(p) = 0.050 and R(F) = 0.163) shows that the Cp* moieties occupy, with disorder, two different orientations rotated away from the eclipsed conformation by +/-13.8 degrees.

  7. Study of periodic band gap structure of the magnetized plasma photonic crystals

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hai-feng; MA Li; LIU Shao-bin

    2009-01-01

    The characteristics of the periodic band gaps of the one dimension magnetized plasma photonic crystals are studied with the piecewise linear current density recursive convolution (PLCDRC) finite-differential time-domain (FDTD) method. In fre-quency-domain, the transmission coefficients of electromagnetic Gaussian pulses are computed, and the effects of the periodic structure constant, plasma layer thickness and parameters of plasma on the properties of periodic band gaps of magnetized photonic crystals are analyzed. The results show that the periodic band gaps depend strongly on the plasma parameters.

  8. Fabrication and structure of Langmuir-Blodgett films of ferroelectric liquid crystal

    Institute of Scientific and Technical Information of China (English)

    WEN Zi; JIANG Qing; T.Kenji; O.Yukihiro

    2005-01-01

    The molecular aggregation, orientation, and structure in Langmuir-Blodgett films of ferroelectric liquid crystal were studied by ultraviolet and Fourier transform infrared spectra. The results show that medium strong H-aggregates in the Langmuir-Blodgett films of ferroelectric liquid crystal are formed by chromophores where the alkyl chains are nearly perpendicular to the film surface. Compared with the cast films, the CO stretching bands, due to the rotational isomerism around the O-C axis of the chiral part, can be identified clearly in Langmuir-Blodgett films.

  9. Crystal structure of the tetrameric fibrinogen-like recognition domain of Fibrinogen C domain containing 1 (FIBCD1)

    DEFF Research Database (Denmark)

    Shrive, Annette K; Moeller, Jesper B; Burns, Ian;

    2014-01-01

    The high-resolution crystal structures of a recombinant fragment of the C-terminal fibrinogen-like recognition domain of FIBCD1, a vertebrate receptor that binds chitin, have been determined. The overall tetrameric structure shows similarity in structure and aggregation to the horseshoe crab innate...

  10. Synthesis, Crystal Structure, Vibration Spectral, and DFT Studies of 4-Aminoantipyrine and Its Derivatives

    Directory of Open Access Journals (Sweden)

    Ping Wei

    2013-01-01

    Full Text Available Three compounds derived from 4-aminoantipyrine (AA were synthesized and their structures confirmed by melting point, elemental analysis, FT-IR, and 1H-NMR. The molecular structures of the four compounds were characterized by single-crystal X-ray diffraction and calculated by using the density functional theory (DFT method with 6-31G (d basis set. The calculated molecular geometries and the vibration frequencies of the AA derivatives in the ground state have been compared with the experimental data. The results show that the optimized geometries can reproduce well the crystal structural parameters, and the theoretical vibration frequencies show good agreement with the experimental data, although the experimental data are different from the theoretical ones due to the intermolecular forces. Besides, the molecular electrostatic potential (MEP and the frontier molecular orbital (FMO analysis of the compounds were investigated by theoretical calculations.

  11. 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.

  12. Crystal structure and conformational analysis of angiotensinogen fragments.

    Science.gov (United States)

    Benkoulouche, M; Cotrait, M; Geoffre, S; Precigoux, G

    1989-12-01

    The tripeptide acetyl-L-prolyl-L-phenylalanyl-L-histidine crystallizes in the orthorhombic space group P2(1)2(1)2(1) with eight molecules in a unit cell of dimensions a = 9.028(2), b = 140.54(6) and c = 42.41(1)A. The structure has been solved by direct methods and refined to an R value of 0.056 for 2904 observed reflections. The molecule exists as a zwitterion with terminal (His)CO2- and (imidazole)H+ as charged groups. The two peptide molecules in the structure adopt a type I beta-turn with Pro and Phe as the corner residues. The main conformational difference between the two crystallographically independent molecules is seen to be in the histidine side-chain orientations. The molecules arrange themselves in sheets perpendicular to the c axis. All hydrophobic side chains lie on one side of the sheets thus generated, whereas the hydrophilic groups are located on the other side. An interesting feature of the crystal structure is the existence of a water layer between adjacent peptide sheets. The conformational study of the isolated Ac-His-Pro-Phe-His-MA using energy calculations gives a rather limited number of stable conformers. The most stable corresponds to a type I beta-turn stabilized through two hydrogen bonds, followed by a less stable type II beta-turn (delta E = 2.0 kcal) and a partly helical structure (delta E = 2.6 kcal).

  13. Single crystals of superconducting SmFeAsO Hx : Structure and properties

    Science.gov (United States)

    Pisoni, A.; Katrych, S.; Arakcheeva, A.; Verebélyi, T.; Bokor, M.; Huang, P.; Gaál, R.; Matus, P.; Karpinski, J.; Forró, L.

    2016-07-01

    We report the synthesis, structure, and superconducting properties of single crystals of SmFeAsO Hx . The crystals were grown at high pressure and high temperature using a cubic anvil technique. 1H-NMR studies confirm the presence of H atoms in the samples. Single crystal x-ray diffraction analyses demonstrate a remarkable disorder in the S m2O2 layers induced by hydrogen incorporation and reveal that the H positions are compatible with a H2O -like geometry inside the crystals. We have measured the magnetotransport properties of SmFeAsO Hx single crystals with x =0.07 , 0.11, and 0.16 in magnetic field up to 16 T, oriented along the two main crystallographic directions. The results show an increase of the critical temperature with hydrogen content. The zero-temperature upper critical fields and the magnetic anisotropy are calculated as a function of the hydrogen content. SmFeAsO Hx crystals present significantly higher upper critical fields and magnetic anisotropies compared to SmFeAs O1 -xFx compounds.

  14. The optical Tamm states in a photonic-crystal Structure based on the cholesteric liquid crystal

    CERN Document Server

    Vetrov, Stepan Ya; Timofeev, Ivan V

    2015-01-01

    We investigate the localized surface modes in a structure consisting of the cholesteric liquid crystal layer, a phase plate, and a metal layer. These modes are analogous to the optical Tamm states. The anisotropy of transmission of light propagating the forward and backward directions is established. It is demonstrated that the transmission spectrum can be controlled by external fields acting on the cholesteric and by varying the plane of polarization of the incident light. [The text is presented both in English (pp 1-10) and in Russian (pp 11-20)

  15. The crystal structure of a bimorphinan with highly selective kappa opioid receptor antagonist activity

    Science.gov (United States)

    Urbańczyk-Lipkowska, Zofia; Etter, Margaret C.; Lipkowski, Andrzej W.; Portoghese, Philip S.

    1987-07-01

    The crystal structure of the dihydrobromide heptahydrate of nor-binaltorphimine (17, 17'-bis(cyclopropylmethyl)-6,6',7,7'-tetrahydro-4,5α: 4',5'α-diepoxy-6,6'-imino[7,7' bimorphinan]-3,3',14,14'-tetraol)is presented. This structure is the first reported structure of a rigid bivalent opioid ligand. Two morphinan pharmacophores are connected by a rigid spacer, the pyrrole ring. The nor-binaltorphimine structure itself shows unique, high selectivity as a kappa opioid receptor antagonist. Crystal data: P3 2, Z = 3, a = b = 20.223 (4), c = 9.541(7) Å, α = β = 90°, γ = 120°; R = 0.079 (1765 reflections, Fobs > 1σ( F)).

  16. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis.

    Science.gov (United States)

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-09-21

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts.

  17. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis

    Science.gov (United States)

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

  18. Liquid crystal-based Mueller matrix spectral imaging polarimetry for parameterizing mineral structural organization.

    Science.gov (United States)

    Gladish, James C; Duncan, Donald D

    2017-01-20

    Herein, we discuss the remote assessment of the subwavelength organizational structure of a medium. Specifically, we use spectral imaging polarimetry, as the vector nature of polarized light enables it to interact with optical anisotropies within a medium, while the spectral aspect of polarization is sensitive to small-scale structure. The ability to image these effects allows for inference of spatial structural organization parameters. This work describes a methodology for revealing structural organization by exploiting the Stokes/Mueller formalism and by utilizing measurements from a spectral imaging polarimeter constructed from liquid crystal variable retarders and a liquid crystal tunable filter. We provide results to validate the system and then show results from measurements on a mineral sample.

  19. 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.

  20. Bismuth zinc vanadate, BiZn2VO6 : new crystal structure type and electronic structure.

    OpenAIRE

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

    2015-01-01

    We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn2VO6, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn2VO6 adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO4 tetrahedra, ZnO6 octahedra and VO4 tet...

  1. Study of crystal structure at high temperature phase in KIO sub 3 crystal by synchrotron powder X-ray diffraction

    CERN Document Server

    Kasatani, H; Kuroiwa, Y; Yagi, K; Katayama, R; Terauchi, H

    2003-01-01

    The accurate crystal structure of the I-phase in KIO sub 3 crystal has been obtained at 530 K, for the first time, by the MEM/Rietveld analysis from high-energy X-ray powder-diffraction data. The crystal structure of the I-phase is the rhombohedral perovskite structure (space group R3m; Z=1). The MEM charge-density distributions reveal that the shorter I-O bond exhibits a covalent bonding character and others (I-K, K-O and longer I-O bonds) an ionic.

  2. In situ proteolysis to generate crystals for structure determination: an update.

    Directory of Open Access Journals (Sweden)

    Amy Wernimont

    Full Text Available For every 100 purified proteins that enter crystallization trials, an average of 30 form crystals, and among these only 13-15 crystallize in a form that enables structure determination. In 2007, Dong et al reported that the addition of trace amounts of protease to crystallization trials--in situ proteolysis--significantly increased the number of proteins in a given set that produce diffraction quality crystals. 69 proteins that had previously resisted structure determination were subjected to crystallization with in situ proteolysis and ten crystallized in a form that led to structure determination (14.5% success rate. Here we apply in situ proteolysis to over 270 new soluble proteins that had failed in the past to produce crystals suitable for structure determination. These proteins had produced no crystals, crystals that diffracted poorly, or produced twinned and/or unmanageable diffraction data. The new set includes yeast and prokaryotic proteins, enzymes essential to protozoan parasites, and human proteins such as GTPases, chromatin remodeling proteins, and tyrosine kinases. 34 proteins yielded deposited crystal structures of 2.8 A resolution or better, for an overall 12.6% success rate, and at least ten more yielded well-diffracting crystals presently in refinement. The success rate among proteins that had previously crystallized was double that of those that had never before yielded crystals. The overall success rate is similar to that observed in the smaller study, and appears to be higher than any other method reported to rescue stalled protein crystallography projects.

  3. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Maskaly, Karlene Rosera [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2005-06-01

    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  4. Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

    Science.gov (United States)

    Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

    2014-12-11

    The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

  5. Modulation of calcium oxalate dihydrate growth by selective crystal-face binding of phosphorylated osteopontin and polyaspartate peptide showing occlusion by sectoral (compositional) zoning.

    Science.gov (United States)

    Chien, Yung-Ching; Masica, David L; Gray, Jeffrey J; Nguyen, Sarah; Vali, Hojatollah; McKee, Marc D

    2009-08-28

    Calcium oxalate dihydrate (COD) mineral and the urinary protein osteopontin/uropontin (OPN) are commonly found in kidney stones. To investigate the effects of OPN on COD growth, COD crystals were grown with phosphorylated OPN or a polyaspartic acid-rich peptide of OPN (DDLDDDDD, poly-Asp(86-93)). Crystals grown with OPN showed increased dimensions of the {110} prismatic faces attributable to selective inhibition at this crystallographic face. At high concentrations of OPN, elongated crystals with dominant {110} faces were produced, often with intergrown, interpenetrating twin crystals. Poly-Asp(86-93) dose-dependently elongated crystal morphology along the {110} faces in a manner similar to OPN. In crystal growth studies using fluorescently tagged poly-Asp(86-93) followed by imaging of crystal interiors using confocal microscopy, sectoral (compositional) zoning in COD was observed resulting from selective binding and incorporation (occlusion) of peptide exclusively into {110} crystal sectors. Computational modeling of poly-Asp(86-93) adsorption to COD {110} and {101} surfaces also suggests increased stabilization of the COD {110} surface and negligible change to the natively stable {101} surface. Ultrastructural, colloidal-gold immunolocalization of OPN by transmission electron microscopy in human stones confirmed an intracrystalline distribution of OPN. In summary, OPN and its poly-Asp(86-93) sequence similarly affect COD mineral growth; the {110} crystallographic faces become enhanced and dominant attributable to {110} face inhibition by the protein/peptide, and peptides can incorporate into the mineral phase. We, thus, conclude that the poly-Asp(86-93) domain is central to the OPN ability to interact with the {110} faces of COD, where it binds to inhibit crystal growth with subsequent intracrystalline incorporation (occlusion).

  6. Crystal structure and infrared spectrum of thallium holmium polyphosphate, TIHo(PO3)4

    Institute of Scientific and Technical Information of China (English)

    Karima Horchani-Naifer; Jaouher Amami; Mokhtar Ferid

    2008-01-01

    Crystals of thallium-holmium polyphosphate TIHo(PO3)4 were grown by flux method technique and characterized by single crystal X-ray diffraction. Structure of TIHo(PO3)4 was solved for the first time, and it crystallized in the monoclinic P21/n space group with the following unit-cell dimensions: a=1.02225(3) nm, b=0.88536(2) nm, c=1.09541(4) nm, β=105.888(1)°, V=0.95354(5) nm3 and Z=4. The crystal structure was solved from 2174 independent reflections with final R1(F2)=0.0442 and Rw(F<2)=0.0861 refined with 164 parameters. The atomic arrangement could be described as a long chain polyphosphate organization. Holmium atoms had eighffold coordination. The structure of T1Ho(PO3)4 consisted of HoO8 polyhedra sharing oxygen atoms with phosphoric group PO4. Infrared spectrum was investigated at room temperature in the frequencies range, 350-4000 cm-1, showing some characteristic vibration bands of infinite chain structure of PO4 tetrahedra linked by bridging oxygen.

  7. Challenges and Opportunities for New Protein Crystallization Strategies in Structure-Based Drug Design

    Science.gov (United States)

    Grey, Jessica; Thompson, David

    2010-01-01

    Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process, while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is a iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high-resolution (< 2Å) three-dimensional structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate. The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed. PMID:21116481

  8. Self-Restoration by Smectic Layer Structures of Monostable Ferroelectric Liquid Crystal in Flexible Devices

    Science.gov (United States)

    Fujikake, Hideo; Sato, Hiroto; Isaka, Fumito; Murashige, Takeshi; Kikuchi, Hiroshi; Kurita, Taiichiro; Sato, Fumio

    2004-12-01

    In this paper, we discuss a self-restoration phenomenon affecting smectic layer deformation and molecular alignment in monostable ferroelectric liquid crystals used for flexible displays. First, the mechanical stability of tilted ‘bookshelf’ structures of smectic layers anchored on substrates using alignment layers was examined by precisely shearing two substrates. The microscopic texture of a monostable ferroelectric liquid crystal showed tolerance to shearing and the self-restoration was thought to be due to a smectic layer reconnection phenomenon, whereas a conventional bistable ferroelectric liquid crystal film generated alignment defects due to the tilting of the stable molecular direction. We then fabricated a flexible monostable device containing fine polymer fiber networks, where anchoring of molecularly aligned polymer fibers led to the observation of monostable liquid crystal switching. A uniform liquid crystal alignment was maintained in a 100 mm× 100 mm device even after bending more than 10000 times at a minimum radius of curvature of 20 mm, due to the enhanced shearing tolerance of the smectic layer structure.

  9. Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

    Science.gov (United States)

    Bindel, Thomas H.

    2008-01-01

    A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

  10. Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

    Science.gov (United States)

    Bindel, Thomas H.

    2008-01-01

    A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

  11. Crystal Structure of Borophosphate with 61 Screw Axis Helices

    Institute of Scientific and Technical Information of China (English)

    石恒真; 单永奎; 戴立益; 刘煜炎; 翁林红

    2003-01-01

    A brilliant purple octahedral single crystal is hydrothermally synthesized by the reaction of CoCl2·6H2O, H3BO3 and H3PO4 in NaOH aqueous solution of CH3(CH2)15N(CH3)3Br, and its crystal structure has been characterized by single-crystal X-ray diffraction. The compound, NaCo(H2O)2BP2O8·H2O (Mr = 336.72), belongs to hexagonal, space group P6122 with a = 9.447(5), c = 15.83(1) (A。), V = 1223(1) (A。)3, Dc = 2.742 g/cm3, Z = 6, F(000) = 1002 and β= 2.606 mm-1. The three-dimensional framework in the compound is built up from the linkage tetrahedral ribbons, in which the BO4 and PO4 tetrahedra alternate with CoO6 octahedra. The sodium ions and water molecules are located within the free thread of the helical ribbons.

  12. Structural and magnetic studies on copper succinate dihydrate single crystals

    Indian Academy of Sciences (India)

    M P BINITHA; P P PRADYUMNAN

    2017-09-01

    Single crystals of copper succinate dihydrate were grown in silica gel by slow diffusion of copper chloride tosodium metasilicate gel impregnated with succinic acid. The grown crystal was subjected to single crystal X-ray diffractionstudies. In its structure each copper atom is penta co-ordinated to oxygen atoms of four succinate oxygens and oxygenof co-ordinated water molecule. The four bis-bidendate succinate anions form syn–syn bridges among two copper atomsto form a polymeric two-dimensional chain. From room temperature vibrating sample magnetometer (VSM) studies themagnetic moment of the material is calculated as 1.35 Bohr magneton (BM), indicating antiferromagnetic interaction betweencopper atoms and can be explained as due to the orbital overlap of the bridging ligand and the two copper atoms in syn-synorientation. A strong bonding of the magnetic orbital of equatorially oriented Cu atom on both sides of the exchange pathway(Cu–O-C-O–Cu) leads to the anti-ferromagnetic interaction.

  13. 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.

  14. Crystal structure of the bacteriophage P2 integrase catalytic domain.

    Science.gov (United States)

    Skaar, Karin; Claesson, Magnus; Odegrip, Richard; Högbom, Martin; Haggård-Ljungquist, Elisabeth; Stenmark, Pål

    2015-11-30

    Bacteriophage P2 is a temperate phage capable of integrating its DNA into the host genome by site-specific recombination upon lysogenization. Integration and excision of the phage genome requires P2 integrase, which performs recognition, cleavage and joining of DNA during these processes. This work presents the high-resolution crystal structure of the catalytic domain of P2 integrase, and analysis of the structure-function relationship of several previously identified non-functional P2 integrase mutants. The DNA binding area is characterized by a large positively charged patch, harboring key residues. The structure reveals potential for large dimer flexibility, likely essential for rearrangement of DNA strands upon integration and excision of the phage DNA.

  15. 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).

  16. Potassium and magnesium succinatouranilates - Synthesis and crystal structure

    Science.gov (United States)

    Novikov, S. A.; Grigoriev, M. S.; Serezhkina, L. B.; Serezhkin, V. N.

    2017-04-01

    Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K2[(UO2)2(C4H4O4)3] (1) and [Mg(H2O)6] [(UO2)2(C4H4O4)3]·2H2O (2), where C4H4O42- is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO2)2(C4H4O4)3]2- with the same A2Q023 crystallochemical formula (A=UO22+, Q02=C4O4H42-), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ions is one of the factors, which affects the structure of [(UO2)2(C4H4O4)3]2- anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A2Q023 crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality.

  17. Origins of Water Molecules in the Photosystem II Crystal Structure.

    Science.gov (United States)

    Sakashita, Naoki; Watanabe, Hiroshi C; Ikeda, Takuya; Saito, Keisuke; Ishikita, Hiroshi

    2017-06-20

    The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl(-)2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.

  18. 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.

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

    Science.gov (United States)

    Orlando, Benjamin J; Malkowski, Michael G

    2016-10-01

    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.

  20. Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.

    Science.gov (United States)

    Clausen, Johannes D; Bublitz, Maike; Arnou, Bertrand; Olesen, Claus; Andersen, Jens Peter; Møller, Jesper Vuust; Nissen, Poul

    2016-04-05

    Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase with bound vanadate in the absence of Ca(2+). Vanadate is bound at the catalytic site as a planar VO3(-) in complex with water and Mg(2+) in a dephosphorylation transition-state-like conformation. Validating bound VO3(-) by anomalous difference Fourier maps using long-wavelength data we also identify a hitherto undescribed Cl(-) site near the dephosphorylation site. Crystallization was facilitated by trinitrophenyl (TNP)-derivatized nucleotides that bind with the TNP moiety occupying the binding pocket that normally accommodates the adenine of ATP, rationalizing their remarkably high affinity for E2P-like conformations of the Ca(2+)-ATPase. A comparison of the configurations of bound nucleotide analogs in the E2·VO3(-) structure with that in E2·BeF3(-) (E2P ground state analog) reveals multiple binding modes to the Ca(2+)-ATPase.

  1. Photonic crystal digital alloys and their band structure properties.

    Science.gov (United States)

    Lee, Jeongkug; Kim, Dong-Uk; Jeon, Heonsu

    2011-09-26

    We investigated semi-disordered photonic crystals (PCs), digital alloys, and made thorough comparisons with their counterparts, random alloys. A set of diamond lattice PC digital alloys operating in a microwave regime were prepared by alternately stacking two kinds of sub-PC systems composed of alumina and silica spheres of the same size. Measured transmission spectra as well as calculated band structures revealed that when the digital alloy period is short, band-gaps of the digital alloys are practically the same as those of the random alloys. This study indicates that the concept of digital alloys holds for photons in PCs as well.

  2. Crystal structure of pure ZrO{sub 2} nanopowders

    Energy Technology Data Exchange (ETDEWEB)

    Lamas, D.G. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina)]. E-mail: dlamas@citefa.gov.ar; Rosso, A.M. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Anzorena, M. Suarez [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Fernandez, A. [DEICOR - Departamento de Investigaciones en Corrosion, CITEFA, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Bellino, M.G. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Cabezas, M.D. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Walsoee de Reca, N.E. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Craievich, A.F. [Instituto de Fisica, FAP, USP, Travessa R da Rua do Matao, No.187, Cidade Universitaria (05508-900) Sao Paulo (Brazil)

    2006-09-15

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

  3. Crystal structure determination of anti-DNA Fab A52.

    Science.gov (United States)

    Stanfield, Robyn L; Eilat, Dan

    2014-08-01

    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  4. Crystal structure of hexa-aqua-dichlorido-ytterbium(III) chloride.

    Science.gov (United States)

    Knopf, Kevin M; Crundwell, Guy; Westcott, Barry L

    2015-06-01

    The crystal structure of the title compound, [YbCl2(H2O)6]Cl, was determined at 110 K. Samples were obtained from evaporated aceto-nitrile solutions containing the title compound, which consists of a [YbCl2(H2O)6](+) cation and a Cl(-) anion. The cations in the title compound sit on a twofold axis and form O-H⋯Cl hydrogen bonds with the nearby Cl(-) anion. The coordination geometry around the metal centre forms a distorted square anti-prism. The ytterbium complex is isotypic with the europium complex [Tambrornino et al. (2014 ▶). Acta Cryst. E70, i27].

  5. Topological Structure of Knotted Vortex Lines in Liquid Crystals

    Institute of Scientific and Technical Information of China (English)

    DUAN Yi-Shi; ZHAO Li; ZHANG Xin-Hui

    2007-01-01

    In this paper, a novel decomposition expression for the U(1) gauge field in liquid crystals (LCs) is derived.Using this decomposition expression and the φ-mapping topological current theory,.we investigate the topological structure of the vortex lines in LCs in detail. A topological invariant, i.e., the Chern-Simons (CS) action for the knotted vortex lines is presented, and the CS action is shown to be the total sum of all the self-linking and linking numbers of the knot family. Moreover, it is pointed out that the CS action is preserved in the branch processes of the knotted vortex lines.

  6. Synthesis, Crystal Structural Investigations, and DFT Calculations of Novel Thiosemicarbazones

    Directory of Open Access Journals (Sweden)

    Brian J. Anderson

    2016-02-01

    Full Text Available The crystal and molecular structures of three new thiosemicarbazones, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide monohydrate (1, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide (2 and 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide acetonitrile solvate (3, are reported and confirmed by single crystal X-ray diffraction, NMR and UV-vis spectroscopic data. Compound (1, C11H15N3O2S·H2O, crystallizes in the monoclinic with space group P21/c, with cell parameters a = 8.2304(3 Å, b = 16.2787(6 Å, c = 9.9708(4 Å, and β = 103.355(4°. Compound (2, C12H17N3O2S, crystallizes in the C2/c space group with cell parameters a = 23.3083(6 Å, b = 8.2956(2 Å, c = 13.5312(3 Å, β = 91.077(2°. Compound (3, C11H15N3O2S·C2H3N, crystallizes in the triclinic P-1 space group with cell constants a = 8.9384(7 Å, b = 9.5167(8 Å, c = 10.0574(8 Å, α = 110.773(7°, β = 92.413(6°, and γ = 90.654(7°. DFT B3LYP/6-31(G geometry optimized molecular orbital calculations were also performed and frontier molecular orbitals of each compound are displayed. The correlations between the calculated molecular orbital energies (eV for the surfaces of the frontier molecular orbitals to the electronic excitation transitions from the absorption spectra of each compound have been proposed. Additionally, similar correlations observed among three closely related compounds, (4, 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide, (5, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide acetonitrile monosolvate and (6, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide, examining structural differences from the substitution of the methoxy group from the phenyl ring (4, 5, or 6 position and the substitution of the terminal amine (methyl or ethyl to their frontier molecular orbital surfaces and from their Density Functional

  7. Crystal structure and Raman spectra of rubidium hydrogen squarate

    Science.gov (United States)

    Georgopoulos, Stéfanos L.; Diniz, Renata; Rodrigues, Bernardo L.; de Oliveira, Luiz F. C.

    2005-05-01

    Rubidium hydrogen squarate (RbHC 4O 4, RbHSQ) crystallized in monoclinic space group P2 1/ c. This compound form a short asymmetric intermolecular hydrogen bond whose O-O distance is 2.482(4) Å. The hydrogen squarate anions are forming head-to-tail infinite chain hydrogen-bonding motifs. A long interplanar separation (4.15 Å) indicates that a weak π interaction occurs between hydrogen squarate anions in RbHSQ. The hydrogen bond and cation-anion interactions are the predominant driving forces in the crystal packing. The Raman spectrum of RbHSQ shows an average behaviour between squaric acid and squarate dianion, however, the vibrational modes at ca. 1800 cm -1 (CO stretching mode) and in the region 1500-1700 cm -1 (CO+CC stretching modes) are the most affected by the presence of strong hydrogen bonding interactions.

  8. 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.

  9. Structural Characteristics and Crystallization of Metallic Glass Sputtered Films by Using Zr System Target

    Directory of Open Access Journals (Sweden)

    Katsuyoshi Kondoh

    2008-01-01

    Full Text Available Zr-Al-Ni-Cu thin films were deposited by the radio-frequency sputtering method at low substrate temperature using three kinds of targets: Zr55Al10Ni5Cu30 bulk metallic glass target (α-BMG target, crystallized bulk metallic glass target (c-BMG target, and an elemental composite target composed of each Zr, Al, Ni chips, and Cu plate. XRD profiles of the films prepared when using these targets indicated that all of the films showed amorphous structures. While XRD profiles of the films using α- and c-BMG targets revealed a broad peak of 2θ=38 degree in the same way as the α-BMG target indicating amorphous structures, that of the film using elemental composite targets showed a broad peak of 2θ=42 degree, which is higher compared to the latter material. As a result of annealing the films at various temperatures for 900 seconds, the film using the α-BMG target showed a crystallization temperature of 748 K, higher than that of BMG with 723 K, while the other films had lower crystallization temperatures below 723 K. XRD profiles also indicated that the crystallized compounds of the films were different from those of BMG target.

  10. Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

    Science.gov (United States)

    Koley, Biplab; Chatterjee, S.; Jana, Partha P.

    2017-02-01

    A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

  11. Photonic-magnonic crystals: Multifunctional periodic structures for magnonic and photonic applications

    Energy Technology Data Exchange (ETDEWEB)

    Kłos, J. W., E-mail: klos@amu.edu.pl; Krawczyk, M. [Faculty of Physics, Adam Mickiewicz University in Poznań, Umultowska 85, Poznań 61-614 (Poland); Dadoenkova, Yu. S.; Dadoenkova, N. N. [Donetsk Physical and Technical Institute of the National Academy of Sciences of Ukraine, 83114 Donetsk (Ukraine); Lyubchanskii, I. L. [Donetsk Physical and Technical Institute of the National Academy of Sciences of Ukraine, 83114 Donetsk (Ukraine); Faculty of Physics and Technology, Donetsk National University, 83000 Donetsk (Ukraine)

    2014-05-07

    We investigate the properties of a photonic-magnonic crystal, a complex multifunctional one-dimensional structure with magnonic and photonic band gaps in the GHz and PHz frequency ranges for spin waves and light, respectively. The system consists of periodically distributed dielectric magnetic slabs of yttrium iron garnet and nonmagnetic spacers with an internal structure of alternating TiO{sub 2} and SiO{sub 2} layers which form finite-size dielectric photonic crystals. We show that the spin-wave coupling between the magnetic layers, and thus the formation of the magnonic band structure, necessitates a nonzero in-plane component of the spin-wave wave vector. A more complex structure perceived by light is evidenced by the photonic miniband structure and the transmission spectra in which we have observed transmission peaks related to the repetition of the magnetic slabs in the frequency ranges corresponding to the photonic band gaps of the TiO{sub 2}/SiO{sub 2} stack. Moreover, we show that these modes split to very high sharp (a few THz wide) subpeaks in the transmittance spectra. The proposed novel multifunctional artificial crystals can have interesting applications and be used for creating common resonant cavities for spin waves and light to enhance the mutual influence between them.

  12. Structure defect prediction of single crystal turbine blade by dendrite envelope tracking model

    Institute of Scientific and Technical Information of China (English)

    WANG Tong-min; Itsuo OHNAKA; Hideyuki YASUDA; SU Yan-qing; GUO Jing-jie

    2006-01-01

    The structure defects such as stray grains during unidirectional solidification can severely reduce the performance of single crystal turbine blades. A dendrite envelope tracking model is developed for predicting the structure defects of unidirectional solidification turbine blade. The normal vector of dendrite envelope is estimated by the gradient of dendrite volume fraction,and the growth velocity of the dendrite envelope (dendrite tips) is calculated with considering the anisotropy of grain growth. The solute redistribution at dendrite envelope is calculated by introducing an effective solute partition coefficient. Simulation tests show that the solute-build-up due to the rejection at envelope greatly affects grain competition and consequently solidification structure. The model is applied to predict the structure defects (e.g. stray grain) of single crystal turbine blade during unidirectional solidification. The results show that the developed model is reliable and has the following abilities: reproduce the growth competition among the different-preferential-direction grains:predict the stray grain formation:simulate the structure evolution (single crystal or dendrite grains).

  13. Bis-methyl imidazolium methylidene bis(trifluoromethanesulfonyl)imide, crystal structure, thermal and dielectric studies

    Indian Academy of Sciences (India)

    BOUMEDIENE HADDAD; TAQIYEDDINE MOUMENE; DIDIER VILLEMIN; JEAN-FRANÇOIS LOHIER; EL-HABIB BELARBI

    2016-06-01

    A new geminal di-cationic ionic liquid (IL) containing a central cationic unit methylidene capped by a basic functionality (imidazole) is synthesized. The compound was characterized by means of ${}^1$H, ${}^13$C, ${}^19$F NMR, IR and Raman spectroscopies and its crystal structure is confirmed by single crystal X-ray diffraction method. The X-ray studies on ([M(CH$_2$)IM$^{2+}$][2NTf$^−_2$ ]) show that it crystallizes in monoclinic system with space group:P 21/c. Thermal properties were investigated in the temperature range from 0 to 400$^{\\circ}$C by using differential thermal (DTA) and thermogravimetric (TGA) analyses. The frequency-dependent electrical data are discussed using complexdielectric permittivity in the frequency range of ($10^{−2}–10^6$ Hz) and in the temperature range of $−50–20^{\\circ}$C. The outstanding dielectric and thermal properties make this IL as promising candidate for electrochemical devices.

  14. Calculation and analysis of complex band structure in dispersive and dissipative two-dimensional photonic crystals

    CERN Document Server

    Brûlé, Yoann; Gralak, Boris

    2015-01-01

    Numerical calculation of modes in dispersive and absorptive systems is performed using the finite element method. The dispersion is tackled in the frame of an extension of Maxwell's equations where auxiliary fields are added to the electromagnetic field. This method is applied to multi-domain cavities and photonic crystals including Drude and Drude-Lorentz metals. Numerical results are compared to analytical solutions for simple cavities and to previous results of the literature for photonic crystals, showing excellent agreement. The advantages of the developed method lie on the versatility of the finite element method regarding geometries, and in sparing the use of tedious complex poles research algorithm. Hence the complex spectrum of resonances of non-hermitian operators and dissipative systems, like two-dimensional photonic crystal made of absorbing Drude metal, can be investigated in detail. The method is used to reveal unexpected features of their complex band structures.

  15. A fast selenium derivatization strategy for crystallization and phasing of RNA structures

    Science.gov (United States)

    Olieric, Vincent; Rieder, Ulrike; Lang, Kathrin; Serganov, Alexander; Schulze-Briese, Clemens; Micura, Ronald; Dumas, Philippe; Ennifar, Eric

    2009-01-01

    Site-specific 2′-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 2′-OCH3-modified RNA sequences, prior to the replacement of 2′-OCH3 groups with their 2′-SeCH3 counterparts. The method exploits the similar crystallization properties of 2′-OCH3- and 2′-SeCH3-modified RNAs and has been successfully validated for two test cases. In addition, our data show that 2′-SeCH3-modified RNA have an increased resistance to X-ray radiolysis in comparison with commonly used 5-halogen-modified RNA, which permits collection of experimental electron density maps of remarkable quality. PMID:19228585

  16. Single crystal structures of thallium (I) thorium fluorides and crystal chemistry of monovalent tetravalent cation pentafluorides

    Science.gov (United States)

    Oudahmane, Abdelghani; El-Ghozzi, Malika; Jouffret, Laurent; Avignant, Daniel

    2015-12-01

    Two thallium (I) thorium (IV) fluorides, TlTh3F13 and TlThF5 were obtained by solid state synthesis and their crystal structures determined from single crystal X-ray diffraction data recorded at room temperature with an APEX-II CCD diffractometer. TlTh3F13 is orthorhombic, space group Pmc21, with a=8.1801(2) Å, b=7.4479(2) Å, c=8.6375(2) Å, V=526.24(2) Å3, Z=2 and TlThF5 is monoclinic, space group P21/n, with a=8.1128(5) Å, b=7.2250(4) Å, c=8.8493(6) Å, β=116.683(3)°, V=463.46(5) Å3, Z=4. The structure of TlTh3F13 comprises layers of corner and edge-sharing ThF9 polyhedra further linked by chains of trans connected tricapped trigonal prisms ThF9 through corners and edges. The three dimensional thorium frameworks delimits channels parallel to [0 0 1] where the 11-coordinated Tl+ ions are arranged into double columns located in mirror planes of the structure. TlTh3F13 is isotypic with RbTh3F13, RbU3F13 and with one of the two polymorphs of CsTh3F13. The structure of TlThF5 may be regarded as a layer structure built up from the regular succession of 2∞[ M ‧F5 ] - corrugated layers further held by the Tl+ ions along the [1 0 1 ̅] direction. The layers are built up from edge and corner-sharing thorium polyhedra where each (ThF9)5- monocapped square antiprism is connected to five others by sharing three edges and two corners. TlThF5 is isostructural with β-NH4UF5 and with one of the polymorphs of CsThF5. A comparison of the different structural types of MM‧F5 pentafluorides is presented and a diagram of repartition of their structures is given. From the comparison of the Tl structures with their Rb or Cs homologs, where very similar monovalent cation environments are observed it should be concluded to a stereochemically inactivity of the 6s2 lone pair of Tl(I) in both TlTh3F13 and TlThF5, contrary to what is observed in richer Tl(I) content Tl3ThF7 fluorothorate.

  17. Crystal Structure of a Novel Viral Protease with a Serine/Lysine Catalytic Dyad Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Feldman,A.; Lee, J.; Delmas, B.; Paetzel, M.

    2006-01-01

    The blotched snakehead virus (BSNV), an aquatic birnavirus, encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease (VP4) to liberate itself and the viral proteins pVP2, X and VP3. The protein pVP2 is further processed by VP4 to give rise to the capsid protein VP2 and four structural peptides. We report here the crystal structure of a VP4 protease from BSNV, which displays a catalytic serine/lysine dyad in its active site. This is the first crystal structure of a birnavirus protease and the first crystal structure of a viral protease that utilizes a lysine general base in its catalytic mechanism. The topology of the VP4 substrate binding site is consistent with the enzymes substrate specificity and a nucleophilic attack from the si-face of the substrates scissile bond. Despite low levels of sequence identity, VP4 shows similarities in its active site to other characterized Ser/Lys proteases such as signal peptidase, LexA protease and Lon protease. Together, the structure of VP4 provides insights into the mechanism of a recently characterized clan of serine proteases that utilize a lysine general base and reveals the structure of potential targets for antiviral therapy, especially for other related and economically important viruses, such as infectious bursal disease virus in poultry and infectious pancreatic necrosis virus in aquaculture.

  18. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    Directory of Open Access Journals (Sweden)

    Yijin Liu

    2015-12-01

    Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

  19. Photochemical manipulation of colloidal structures in liquid-crystal colloids

    Science.gov (United States)

    Yamamoto, T.; Tabe, Y.; Yokoyama, H.

    2007-05-01

    We investigated photochemical manipulation of physical properties and colloidal structures in liquid-crystal (LC) colloids containing azobenzene compounds. In a LC suspension where polymeric particles were dispersed in a host LC, we achieved photochemical control of light-scattering properties of the suspension. In a nematic phase, when the suspension was sandwiched with two glass plates, the film became opaque. This would be attributable to an appearance of both multidomain structures of LC alignment and mismatches of refractive indices between the materials. The opaque state turned into a transparent one when a nematic-to-isotropic phase transition was induced by the trans-to-cis photoisomerization of the azo-dye. This will result from a disappearance of both the multidomain structures and the refractive-index mismatches in the isotropic phase. The transparent film went back into the initial opaque film when the nematic phase was obtained by the cis-to-trans photoisomerization. In a LC emulsion in which glycerol or water droplets were dispersed in liquid crystals, we examined photochemical change of defect structures and inter-droplet distances by the photochemical manner. At the initial state, Saturn ring and hedgehog defects were formed around the droplets. For the glycerol droplets, we observed structural transformations between Saturn ring and boojums on irradiation with ultra-violet and visible light. For the water droplets, the inter-droplet distances varied by changing defect size on the irradiation. These phenomena would result from modulation of anchoring conditions of the droplets by the photoisomerization of the azo-dyes.

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

    Directory of Open Access Journals (Sweden)

    Jianwei eWang

    2015-06-01

    Full Text Available Materials with apatite crystal structure provide 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 was investigated for iodide incorporation into the channel of the structure using Artificial Neural Network. A total of 86 experimentally determined apatite crystal structures of different compositions were compiled from literature, and 46 of them were used to train the networks and 42 were used to test the performance of the trained networks. The results show that the performances of the networks are satisfactory for predictions of unit cell parameters a and c and channel size of the structure. The trained and tested networks were then used to predict unknown compositions of apatite that incorporates iodide. With a crystal chemistry consideration, chemical compositions that lead to matching the size of the structural channel to the size of iodide were then predicted to be able to incorporate iodide in the structural channel. The calculations suggest that combinations of A site cations of Ag+, K+, Sr2+, Pb2+, Ba2+, and Cs+, and X site cations, mostly formed tetrahedron, of Mn5+, As5+, Cr5+, V5+, Mo5+, Si4+, Ge4+, and Re7+ are possible apatite compositions that are able to incorporate iodide. The charge balance of different apatite compositions can be achieved by multiple substitutions at a single site or coupled substitutions at both A and X sites. The results give important clues for designing experiments to synthesize new apatite compositions and also provide a fundamental understanding how iodide is incorporated in the apatite structure. This understanding can provide important insights for apatite waste forms design by optimizing the chemical composition and synthesis

  1. 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.

  2. Crystal Structure of [Bis(L-AlaninatoDiaqua]Nickel(II Dihydrate

    Directory of Open Access Journals (Sweden)

    Awni Khatib

    2009-01-01

    Full Text Available The title complex, [Ni(C3H6O2N2(H2O2]⋅2H2O, has been prepared from nickel(II chloride in aqueous solution by adding L-alanine and potassium hydroxide. It has been crystallized from aqueous solution, and its structure was determined by X-ray structure analysis. The nickel(II ion adopts distorted octahedral coordination geometry with two bidentate L-alanine molecules and two water molecules. The complex is neutral and dihydrated. The crystal structure shows the hydrogen bonding between water and amide hydrogens within the lattice, and each fragment of the complex contains two water molecules as hydrated water. The L-alaninato ligand skeleton of the compound adopts the most stable trans-III configuration in the solid state. The alternating two five-membered chelate rings are in the stable gauche conformation.

  3. Complex rare-earth aluminum hydrides: mechanochemical preparation, crystal structure and potential for hydrogen storage.

    Science.gov (United States)

    Weidenthaler, Claudia; Pommerin, André; Felderhoff, Michael; Sun, Wenhao; Wolverton, Christopher; Bogdanović, Borislav; Schüth, Ferdi

    2009-11-25

    A novel type of complex rare-earth aluminum hydride was prepared by mechanochemical preparation. The crystal structure of the REAlH(6) (with RE = La, Ce, Pr, Nd) compounds was calculated by DFT methods and confirmed by preliminary structure refinements. The trigonal crystal structure consists of isolated [AlH(6)](3-) octahedra bridged via [12] coordinated RE cations. The investigation of the rare-earth aluminum hydrides during thermolysis shows a decrease of thermal stability with increasing atomic number of the RE element. Rare-earth hydrides (REH(x)) are formed as primary dehydrogenation products; the final products are RE-aluminum alloys. The calculated decomposition enthalpies of the rare-earth aluminum hydrides are at the lower end for reversible hydrogenation under moderate conditions. Even though these materials may require somewhat higher pressures and/or lower temperatures for rehydrogenation, they are interesting examples of low-temperature metal hydrides for which reversibility might be reached.

  4. Reinvestigation of the crystal structure of lautite, CuAsS

    Directory of Open Access Journals (Sweden)

    Paola Bonazzi

    2008-03-01

    Full Text Available The crystal structure of the mineral lautite (copper arsenic sulfide, CuAsS, previously described as either centrosymmetric [Pnma; Marumo & Nowacki (1964. Schweiz. Miner. Petro. Mitt. 44, 439–454] or noncentrosymmetric [Pna21; Craig & Stephenson (1965. Acta Cryst. 19, 543–547], was reinvestigated by means of single-crystal X-ray diffraction. The centrosymmetric structural model reported previously was confirmed, although with improved precision for the atomic coordinates and interatomic distances. Lautite shows a sphalerite-derivative structure with a linking of Cu[AsS3], As[CuAs2S] and S[Cu3As] tetrahedra. All atoms lie on special positions (Wyckoff position 4c, site symmetry m.

  5. Photonic band structure of ZnO photonic crystal slab laser

    CERN Document Server

    Yamilov, A; Cao, H

    2005-01-01

    We recently reported on the first realization of ultraviolet photonic crystal laser based on zinc oxide [Appl. Phys. Lett. {\\bf 85}, 3657 (2004)]. Here we present the details of structural design and its optimization. We develop a computational super-cell technique, that allows a straightforward calculation of the photonic band structure of ZnO photonic crystal slab on sapphire substrate. We find that despite of small index contrast between the substrate and the photonic layer, the low order eigenmodes have predominantly transverse-electric (TE) or transverse-magnetic (TM) polarization. Because emission from ZnO thin film shows strong TE preference, we are able to limit our consideration to TE bands, spectrum of which can possess a complete photonic band gap with an appropriate choice of structure parameters. We demonstrate that the geometry of the system may be optimized so that a sizable band gap is achieved.

  6. Crystal Structure of Human Senescence Marker Protein 30: Insights Linking Structural, Enzymatic, and Physiological Functions

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborti, Subhendu; Bahnson, Brian J. (Delaware)

    2010-05-25

    Human senescence marker protein 30 (SMP30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. The penultimate step in vitamin-C biosynthesis is catalyzed by this enzyme in nonprimate mammals. It has also been implicated as an organophosphate hydrolase, with the ability to hydrolyze diisopropyl phosphofluoridate and other nerve agents. SMP30 was originally identified as an aging marker protein, whose expression decreased androgen independently in aging cells. SMP30 is also referred to as regucalcin and has been suggested to have functions in calcium homeostasis. The crystal structure of the human enzyme has been solved from X-ray diffraction data collected to a resolution of 1.4 {angstrom}. The protein has a 6-bladed {beta}-propeller fold, and it contains a single metal ion. Crystal structures have been solved with the metal site bound with either a Ca{sup 2+} or a Zn{sup 2+} atom. The catalytic role of the metal ion has been confirmed by mutagenesis of the metal coordinating residues. Kinetic studies using the substrate gluconolactone showed a k{sub cat} preference of divalent cations in the order Zn{sup 2+} > Mn{sup 2+} > Ca{sup 2+} > Mg{sup 2+}. Notably, the Ca{sup 2+} had a significantly higher value of K{sub d} compared to those of the other metal ions tested (566, 82, 7, and 0.6 {micro}m for Ca{sup 2+}, Mg{sup 2+}, Zn{sup 2+}, and Mn{sup 2+}, respectively), suggesting that the Ca{sup 2+}-bound form may be physiologically relevant for stressed cells with an elevated free calcium level.

  7. Selective cleavage of periodic mesoscale structures: two-dimensional replication of binary colloidal crystals into dimpled gold nanoplates.

    Science.gov (United States)

    Kuroda, Yoshiyuki; Sakamoto, Yasuhiro; Kuroda, Kazuyuki

    2012-05-23

    Specific crystallographic planes of binary colloidal crystals consisting of silica nanoparticles are two-dimensionally replicated on the surface of gold nanoplates. The selectivity of the surface patterns is explained by the geometrical characteristics of the binary colloidal crystals as templates. The binary colloidal crystals with the AlB(2)- and NaZn(13)-type structures are fabricated from aqueous dispersions of stoichiometrically mixed silica nanoparticles with different sizes. The stoichiometry is precisely controlled on the basis of a seed growth of silica nanoparticles. Dimpled gold nanoplates are formed by the two-dimensional growth of gold between partially cleaved surfaces of templates. The selectivity of the surface patterns is explained using the AlB(2)-type binary colloidal crystal as a template. The surface pattern is determined by the preferential cleavage of the plane with the lowest density of particle-particle connections. The tendency to form well-defined cleavage in binary colloidal crystals is crucial to formation of dimpled gold nanoplates, which is explained using the NaZn(13)-type binary colloidal crystal as a template. Its complex structure does not show well-defined cleavage, and only distorted nanoplates are obtained. Therefore, the mechanism of the two-dimensional replication of binary colloidal crystals is reasonably explained on the basis of their periodic mesoscale structures and crystal-like properties.

  8. Structural peculiarities of single crystal diamond needles of nanometer thickness

    Science.gov (United States)

    Orekhov, Andrey S.; Tuyakova, Feruza T.; Obraztsova, Ekaterina A.; Loginov, Artem B.; Chuvilin, Andrey L.; Obraztsov, Alexander N.

    2016-11-01

    Diamond is attractive for various applications due to its unique mechanical and optical properties. In particular, single crystal diamond needles with high aspect ratios and sharp apexes of nanometer size are demanded for different types of optical sensors including optically sensing tip probes for scanning microscopy. This paper reports on electron microscopy and Raman spectroscopy characterization of the diamond needles having geometrically perfect pyramidal shapes with rectangular atomically flat bases with (001) crystallography orientation, 2-200 nm sharp apexes, and with lengths from about 10-160 μm. The needles were produced by selective oxidation of (001) textured polycrystalline diamond films grown by chemical vapor deposition. Here we study the types and distribution of defects inside and on the surface of the single crystal diamond needles. We show that sp3 type point defects are incorporated into the volume of the diamond crystal during growth, while the surface of the lateral facets is enriched by multiple extended defects. Nitrogen addition to the reaction mixture results in increase of the growth rate on {001} facets correlated with the rise in the concentration of sp3 type defects.

  9. Crystal structure of the ternary compound {gamma}-Al{sub 3}FeSi

    Energy Technology Data Exchange (ETDEWEB)

    Roger, Jerome; Jeanneau, Erwann; Viala, Jean-Claude [UMA CNRS no. 5615, Claude Bernard Lyon 1 Univ., Villeurbanne (France). Lab. des Multimateriaux et Interfaces

    2011-07-01

    Ternary iron silicide aluminide {gamma}-Al{sub 3}FeSi crystals were grown from two Al-Fe-Si melts quenched in cold water. The crystal structures were determined from single-crystal X-ray data: trigonal symmetry, space group R-3 (n 148), unit cell parameters a = 10.2223(2) A, c = 19.6791(4) A (V = 1781 A{sup 3}) for the Si-poorer crystal and a = 10.1987(2) A, c = 19.5320(3) A (V = 1759 A{sup 3}) for the Si-richer one. The structure of {gamma}-Al{sub 3}FeSi may be described in terms of Al-cubes connected together by Al-Al pairs. The structure contains also Al cuboctaedra with one Fe-Al mixed atom in the center. The average chemical formula obtained from the refinements is Al{sub 3}FeSi. This phase shows a partial disorder on the aluminium network because of the substitution of aluminum atoms by silicon. This substitution mechanism is at the origin of the large homogeneity range of this phase. (orig.)

  10. Synthesis and crystal structure of 5-(4'-carboxyphenyl)-10,15,20-tri(4¢-t-butylphenyl)porphinato zinc(II) complex

    Indian Academy of Sciences (India)

    P Bhyrappa; C Arunkumar; J J Vittal

    2005-03-01

    Synthesis and crystal structure of 5-(4'-carboxyphenyl)-10,15,20-tri(4'--butylphenyl)porphinato zinc(II) have been presented. The title complex shows interesting hydrogen-bonded dimeric structure in the solid state.

  11. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith (UC)

    2008-11-12

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 {angstrom} resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an 'arm' structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

  12. Crystal structure of the petal death protein from carnation flower.

    Science.gov (United States)

    Teplyakov, Alexey; Liu, Sijiu; Lu, Zhibing; Howard, Andrew; Dunaway-Mariano, Debra; Herzberg, Osnat

    2005-12-20

    Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase, the enzyme is actually a C-C bond cleaving lyase exhibiting a broad substrate profile. The crystal structure of PDP has been determined at 2.7 A resolution, revealing a dimer-of-dimers oligomeric association. Consistent with sequence homology, the overall alpha/beta barrel fold of PDP is the same as that of other isocitrate lyase/PEP mutase superfamily members, including a swapped eighth helix within a dimer. Moreover, Mg(2+) binds in the active site of PDP with a coordination pattern similar to that seen in other superfamily members. A compound, covalently bound to the catalytic residue, Cys144, was interpreted as a thiohemiacetal adduct resulting from the reaction of glutaraldehyde used to cross-link the crystals. The Cys144-carrying flexible loop that gates access to the active site is in the closed conformation. Models of bound substrates and comparison with the closed conformation of isocitrate lyase and 2-methylisocitrate lyase revealed the structural basis for the broad substrate profile of PDP.

  13. Crystal Structure of 3S-hydroxy-7 Melleine

    Science.gov (United States)

    Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai

    2006-10-01

    A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) Å, b=7.2284(13) Å, c=13.398(2) Å, β=104.217(3)°, C10H10O4·H2O, Mr=212.20, V=1022.2(3) Å3, Z=4, Dc=1.379 mg/m3, F(000)=448, μ=0.112 mm-1, the final R=0.0498, ωR=0.101 for 2407 observed reflections (I>2σ(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 μg/disk in the preliminary test.

  14. Crystal structure of K[Hg(SCN)3] - a redetermination.

    Science.gov (United States)

    Weil, Matthias; Häusler, Thomas

    2014-09-01

    The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ▶). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954 (11), 2.4481 (8) and 2.7653 (6) Å in comparison with values of 2.24, 2.43 and 2.77 Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65 (2) to 154.06 (3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ∞[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926 (2) and 3.051 (3) Å.

  15. Synthesis and Crystal Structure of a New Mononuclear Copper Complex

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new kind of Cu (Ⅱ) complex [Cu(tpmb)2Cl2]@CH3OH@H2O (tpmb = 1,3,5-tri(2- pyrimidinyl)sulfanylmethyl-2,4,6-trimethylbenzene) was synthesized, and its structure has been determined by X-ray single-crystal diffraction. It crystallizes in the triclinic, space group P ī with a = 8.8397(2), b = 13.327(3), c = 13.926(3) (A), ( = 63.27(3), ( = 86.96(3), ( = 80.68(3)°, V = 1445.6(5) (A)3, C49H51Cl2CuN12O2S6, Mr = 1166.82, Z = 1, F(000) = 604, Dc = 1.340 g/cm3, μ = 0.735 mm-1, R = 0.0545 and wR = 0.1575 for 4521 observed reflections (I > 2σ(I)). X-ray analysis reveals that the Cu (Ⅱ) ion is coordinated by two Cl- anions and two nitrogen atoms from different pyrimidine groups, forming a square structure.

  16. Two organoantimony (V) coordination complexes modulated by isomers of trifluoromethylbenzoate ligands: Syntheses, crystal structure, photodegradation properties

    Science.gov (United States)

    Zhang, Xiao-Yin; Cui, Lian-sheng; Zhang, Xia; Jin, Fan; Fan, Yu-Hua

    2017-04-01

    Two organoantimony (V) coordination complexes, namely Ph3Sb(2-tmbc) (1) and Ph3Sb(3-tmbc) (2) (2-tmbc = 2-(trifluoromethyl)benzoic carboxyl, 3-tmbc = 3-(trifluoromethyl)benzoic carboxyl) have been synthesized and characterized by IR spectra, elemental analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. Single-crystal X-ray diffraction analysis reveals that complexes 1 and 2 show different architectures by the intermolecular hydrogen bonds (Csbnd H⋯F), complex 1 displays an 1D straight chain structure, while complex 2 shows an 1D zigzag chain structure. The photodegradation properties of complexes 1 and 2 has been investigated in organic dyes (RhB, MV, MB) the results indicated that the two complexes are good candidates for the photocatalytic degradation of three dyes. The tentative photocatalytic degradations mechanism is discussed.

  17. Photonic Band Gaps in Two-Dimensional Crystals with Fractal Structure

    Institute of Scientific and Technical Information of China (English)

    刘征; 徐建军; 林志方

    2003-01-01

    We simulate the changes of the photonic band structure of the crystal in two dimensions with a quasi-fractal structure when it is fined to a fractal. The result shows that when the dielectric distribution is fined, the photonic band structure will be compressed on the whole and the ground photonic band gap (PBG) closed while the next PBGs shrunk, in conjunction with their position declining in the frequency spectrum. Furthermore, the PBGs in the high zone are much more sensitive than those in low zones.

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

    Science.gov (United States)

    Vognsen, Tina; Kristensen, Ole

    2012-03-30

    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 β-sheet and three α-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

  19. Crystal structure of Hg2SO4 – a redetermination

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-09-01

    Full Text Available The crystal structure of mercury(I sulfate (or mercurous sulfate, Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969. Acta Chem. Scand. 23, 1607–1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg—Hg = 2.5031 (7 compared to 2.500 (3Å]. The structure consists of alternating rows along [001] of Hg22+ dumbbells (generated by inversion symmetry and SO42− tetrahedra (symmetry 2. The dumbbells are linked via short O—Hg—Hg—O bonds to the sulfate tetrahedra into chains extending parallel to [20-1]. More remote O—Hg—Hg—O bonds connect these chains into a three-dimensional framework.

  20. Band structure of absorptive two-dimensional photonic crystals

    Science.gov (United States)

    van der Lem, Han; Tip, Adriaan; Moroz, Alexander

    2003-06-01

    The band structure for an absorptive two-dimensional photonic crystal made from cylinders consisting of a Drude material is calculated. Absorption causes the spectrum to become complex and form islands in the negative complex half-plane. The boundaries of these islands are not always formed by the eigenvalues calculated for Bloch vectors on the characteristic path, and we find a hole in the spectrum. For realistic parameter values, the real part of the spectrum is hardly influenced by absorption, typically less than 0.25%. The employed method uses a Korringa-Kohn-Rostoker procedure together with analytical continuation. This results in an efficient approach that allows these band-structure calculations to be done on a Pentium III personal computer.