WorldWideScience

Sample records for previous crystal structure

  1. 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.

  2. Crystal structure determination of Efavirenz

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  3. Crystal engineering: structure, property and beyond

    OpenAIRE

    Desiraju, Gautam R.

    2017-01-01

    Crystal engineering, which was considered to be crystal structure engineering, is now transforming into crystal property engineering. The same or similar crystal structures could have different properties while different crystal structures could have similar properties.

  4. 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.

  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. 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

  8. Crystal structure of pseudoguainolide

    Directory of Open Access Journals (Sweden)

    Noureddine Beghidja

    2015-03-01

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

  9. Crystal structure of pymetrozine

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

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

  10. 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.

  11. Nucleation and structural growth of cluster crystals

    International Nuclear Information System (INIS)

    Leitold, Christian; Dellago, Christoph

    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, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds.

  12. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURES ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    The V atoms in the complexes are in octahedral coordination. Thermal stabilities of the complexes have also been studied. KEY WORDS: Oxovanadium complex, Aroylhydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. INTRODUCTION. Coordination chemistry of vanadium has attracted considerable ...

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    Indian Academy of Sciences (India)

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

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

    Indian Academy of Sciences (India)

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

  16. Synthesis, crystal structures, spectroscopic characterization and in ...

    Indian Academy of Sciences (India)

    Both the complexes were structurally characterized by single crystal XRD. The crystal structure of complex 1 displays a distorted square pyramidal geometry in which Schiff base is coordinated to the Cu(II) ion via ONO-donor in the axial mode, whereas, the chelating diamine displays axial and equatorial mode of binding via ...

  17. What makes a crystal structure report valid?

    NARCIS (Netherlands)

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

    2018-01-01

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

  18. 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.

  19. Crystal structure of prethrombin-1

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-11-15

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

  20. Crystal structure resolution by X-rays

    International Nuclear Information System (INIS)

    Jeannin, Y.

    1998-01-01

    This paper deals with the crystal structure analysis by X-rays. It details the different steps of the crystal structure resolution, the measured parameters and the possible errors with appropriate corrections. The presentation includes the x-rays intensity measurement, the structure factor calculus, the Patterson method, the direct methods, the structure analysis, the parameters refinement by least square fit, the temperature factors, disorder and twinning, the primary and secondary extinctions and a absolute configuration determination. (A.L.B.)

  1. 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.

  2. Crystal structure of benzimidazolium salicylate

    Directory of Open Access Journals (Sweden)

    M. Amudha

    2015-10-01

    Full Text Available In the anion of the title molecular salt, C7H7N2+·C7H5O3− (systematic name: 1H-benzimidazol-3-ium 2-hydroxybenzoate, there is an intramolecular O—H...O hydrogen bond that generates an S(6 ring motif. The CO2 group makes a dihedral angle of 5.33 (15° with its attached ring. In the crystal, the dihedral angle between the benzimidazolium ring and the anion benzene ring is 75.88 (5°. Two cations bridge two anions via two pairs of N—H...O hydrogen bonds, enclosing an R44(16 ring motif, forming a four-membered centrosymmetric arrangement. These units are linked via C—H...O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C—H...π and π–π interactions [inter-centroid distances = 3.4156 (7 and 3.8196 (8 Å], forming a three-dimensional structure.

  3. 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.

  4. imide, crystal structure, thermal and dielectric studies

    Indian Academy of Sciences (India)

    Abstract. 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 1H, 13C, 19F NMR,. IR and Raman spectroscopies and its crystal structure is confirmed by single crystal X-ray diffraction ...

  5. Crystal structures of MBP fusion proteins.

    Science.gov (United States)

    Waugh, David S

    2016-03-01

    Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare. © 2016 The Protein Society.

  6. Holmium polysulfide crystals: Structure, shape and composition

    International Nuclear Information System (INIS)

    Belaya, S.V.; Vasilyeva, I.G.; Naumov, D.Yu.; Podberezskaya, N.V.

    2006-01-01

    The variety of morphology, chemical composition and density of holmium polysulfide crystals grown from the flux in different as well as in the same experiments is observed. It was found that the crystals of different habits have the monoclinic structure, P2 1 /m, a=10.95, b=11.45, c=10.97A, β=91.3 o , as already known, and identical composition HoS 1.837 . All the crystals are twinned by the plane (101-bar ). It is shown that the diversity of crystal compositions and density values are due to the constitution of the flux in a crystal and displacement of a crystal in the growth zone. The formation of non-equilibrium growth forms is discussed

  7. Crystal structure prediction accelerated by Bayesian optimization

    Science.gov (United States)

    Yamashita, Tomoki; Sato, Nobuya; Kino, Hiori; Miyake, Takashi; Tsuda, Koji; Oguchi, Tamio

    2018-01-01

    We propose a crystal structure prediction method based on Bayesian optimization. Our method is classified as a selection-type algorithm which is different from evolution-type algorithms such as an evolutionary algorithm and particle swarm optimization. Crystal structure prediction with Bayesian optimization can efficiently select the most stable structure from a large number of candidate structures with a lower number of searching trials using a machine learning technique. Crystal structure prediction using Bayesian optimization combined with random search is applied to known systems such as NaCl and Y2Co17 to discuss the efficiency of Bayesian optimization. These results demonstrate that Bayesian optimization can significantly reduce the number of searching trials required to find the global minimum structure by 30-40% in comparison with pure random search, which leads to much less computational cost.

  8. Liquid crystal light valve structures

    Science.gov (United States)

    Koda, N. J. (Inventor)

    1985-01-01

    An improved photosensor film and liquid crystal light valves embodying said film is provided. The photosensor film and liquid crystal light valve is characterized by a significant lower image retention time while maintaining acceptable photosensitivity. The photosensor film is produced by sputter depositing CdS onto an ITO substrate in an atmosphere of argon/H2S gas while maintaining the substrate at a temperature in the range of about 130 C to about 200 C and while introducing nitrogen gas into the system to the extent of not more than about 1% of plasma mixture. Following sputter deposition of the CdS, the film is annealed in an inert gas at temperatures ranging from about 300 C to about 425 C.

  9. 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.

  10. Single crystal growth and X-ray structure analysis of non-peripheral octahexyl phthalocyanine

    Science.gov (United States)

    Ohmori, Masashi; Nakano, Chika; Higashi, Takuya; Miyano, Tetsuya; Tohnai, Norimitsu; Fujii, Akihiko; Ozaki, Masanori

    2016-07-01

    The single-crystal structure of metal-free non-peripheral octahexyl-substituted phthalocyanine (C6PcH2) has been investigated by single-crystal X-ray structure analysis. Two types of C6PcH2 single crystal, bulk and needle crystals, were separately grown by controlling the recrystallization conditions. The structures of the two types of crystal were determined, and were found to be completely different, that is, C6PcH2 exhibits structural polymorphism. It has been clarified that the C6PcH2 microcrystals in thin films used in previously reported electronic devices have the needle structure.

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

    Science.gov (United States)

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

    2016-04-01

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

  12. Tailoring quantum structures for active photonic crystals

    DEFF Research Database (Denmark)

    Kuznetsova, Nadezda

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

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

    Indian Academy of Sciences (India)

    2.2 X-ray structure determination. Two transparent parallelepipedic crystals with dimensions,. 0.20 × 0.12 × 0.04 and 0.26 × 0.14 × 0.12, were chosen from the preparation. The intensity data were collected on. An APEX II diffractometer with graphite–crystal monochro- mated MoKα radiation (0.71073 Å). Lorentz and polariz-.

  14. Absorption enhancement in graphene photonic crystal structures.

    Science.gov (United States)

    Khaleque, Abdul; Hattori, Haroldo T

    2016-04-10

    Graphene, a single layer of carbon atoms arranged in a honeycomb lattice, is attracting significant interest because of its potential applications in electronic and optoelectronic devices. Although graphene exhibits almost uniform absorption within a large wavelength range, its interaction with light is weak. In this paper, the enhancement of the optical absorption in graphene photonic crystal structures is studied: the structure is modified by introducing scatterers and mirrors. It is shown that the absorption of the graphene photonic crystal structure can be enhanced about four times (nearly 40%) with respect to initial reference absorption of 9.8%. The study can be a useful tool for investigating graphene physics in different optical settings.

  15. Two-dimensional photonic crystal accelerator structures

    Directory of Open Access Journals (Sweden)

    Benjamin M. Cowan

    2003-10-01

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

  16. Crystal structure of enolase from Drosophila melanogaster.

    Science.gov (United States)

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

    2017-04-01

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

  17. 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.

  18. Survey and analysis of crystal polymorphism in organic structures

    Directory of Open Access Journals (Sweden)

    Kortney Kersten

    2018-03-01

    Full Text Available With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components.

  19. 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

  20. 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...

  1. 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.

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

    African Journals Online (AJOL)

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

  3. The crystal structure of thiourea nitrate

    NARCIS (Netherlands)

    Feil, D.; Song Loong, W.

    1968-01-01

    The structure of thiourea nitrate has been determined by three-dimensional X-ray methods. Both Cu Ke and Mo K~ data were obtained with a single-crystal diffractometer and the final R values are 4.9% and 5.5% respectively. The space group is P211m and there are two molecules in the unit cell. All

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

    Indian Academy of Sciences (India)

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

  5. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    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. Synthesis, crystal structure, thermal analysis and dielectric

    Indian Academy of Sciences (India)

    Annual Meetings · Mid Year Meetings · Discussion Meetings · Public Lectures · Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 39; Issue 5. Synthesis, crystal structure, thermal analysis and dielectric properties of two mixed trichlorocadmiates (II).

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

    Indian Academy of Sciences (India)

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

  8. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

    Preferred Customer

    Cg1, Cg2 and Cg3 are the centroids of Mo1-O2-C8-N2-N1, C9-C14 and. C1-C6 benzene rings. Figure 1. Molecular structure of the complex at 30% probability displacement. IR spectra. The hydrazone ligands showed stretching bands attributed to C=O, C=N, C–OH and NH at. 1656, 1637, 1155 and 1237, and 3211 cm–1, ...

  9. 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.

  10. 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.

  11. The Surface Structure of Ground Metal Crystals

    Science.gov (United States)

    Boas, W.; Schmid, E.

    1944-01-01

    The changes produced on metallic surfaces as a result of grinding and polishing are not as yet fully understood. Undoubtedly there is some more or less marked change in the crystal structure, at least, in the top layer. Hereby a diffusion of separated crystal particles may be involved, or, on plastic material, the formation of a layer in greatly deformed state, with possible recrystallization in certain conditions. Czochralski verified the existence of such a layer on tin micro-sections by successive observations of the texture after repeated etching; while Thomassen established, roentgenographically by means of the Debye-Scherrer method, the existence of diffused crystal fractions on the surface of ground and polished tin bars, which he had already observed after turning (on the lathe). (Thickness of this layer - 0.07 mm). Whether this layer borders direct on the undamaged base material or whether deformed intermediate layers form the transition, nothing is known. One observation ty Sachs and Shoji simply states that after the turning of an alpha-brass crystal the disturbance starting from the surface, penetrates fairly deep (approx. 1 mm) into the crystal (proof by recrystallization at 750 C).

  12. Crystal structure of riboflavin synthase

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-05

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

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

    Science.gov (United States)

    Cottingham, Patrick; Brutchey, Richard L

    2016-04-18

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

  14. 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...... 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...

  15. Solving crystal structures from neutron diffraction data

    International Nuclear Information System (INIS)

    Wilson, C.C.

    1987-07-01

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

  16. 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.

  17. Crystal growth, crystal structure and physical characterization of CeMo/sub 6/S/sub 8/

    International Nuclear Information System (INIS)

    Pena, O.; Geantet, C.; Hortyn, R.; Potel, M.; Padiou, J.; Sergent, M.

    1987-01-01

    Single crystals of Ce/sub x/Mo/sub 6/S/sub 8/ were grown using two methods of crystal growth. Refinement of the crystal structure shows an upper stoichiometry of x = 1.0. The cerium atom occupies the origin site of the hexagonal-rhombohedral unit-cell, with no visible delocalization. Crystals were characterized through their susceptibility and transport properties. A.c. susceptibility shows a smooth ''shoulder'' at 2.4 K, due to a magnetic order. The resistivity of a single crystal presents a minimum at 19 K, followed by a small logarithmic increase with decreasing temperature, and a sharp decrease between 2.7 and 2.4 K. These results on single crystals are discussed in comparison with previous reports on sintered powder

  18. Observations on structural features and characteristics of biological apatite crystals. 4. Observation on ultrastructure of human bone crystals.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-06-01

    In a series of studies to investigate the structural features of the biological crystals such as the tooth and bone, following the previous observations of the tooth crystal using an electron microscope, we examined the ultrastructure of the human bone crystals at near atomic resolution through the cross and longitudinal sections of the crystals. The materials used for this study were the normal bone tissue obtained from the buccal alveolar compact bone of the human mandible in the portion of the lower first molar. The small cubes of the bone tissue were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with the HITACHI H-800 type transmission electron microscope operated at 200 kV. Each crystal was observed at the initial magnification of 300,000 times and at the final magnification of 10,000,000 times and over. Using this approach, we showed the configuration of the hydroxyapatite structure in the cross and longitudinal sections of the bone crystals deposited within and between the collagen fibrils (intrafibrillar and interfibrillar crystals) in the bone tissue. Furthermore, using the same approach, we observed the crystal lattices of the hydroxyapatite structure appearing in the cross and longitudinal sections. We sincerely believe that the electron micrographs shown in this report are the first atomic images from the section obtained from the hydroxyapatite crystal from the human alveolar bone.

  19. Predicting polymeric crystal structures by evolutionary algorithms

    Science.gov (United States)

    Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy

    2014-10-01

    The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.

  20. Extracting Crystal Chemistry from Amorphous Carbon Structures.

    Science.gov (United States)

    Deringer, Volker L; Csányi, Gábor; Proserpio, Davide M

    2017-04-19

    Carbon allotropes have been explored intensively by ab initio crystal structure prediction, but such methods are limited by the large computational cost of the underlying density functional theory (DFT). Here we show that a novel class of machine-learning-based interatomic potentials can be used for random structure searching and readily predicts several hitherto unknown carbon allotropes. Remarkably, our model draws structural information from liquid and amorphous carbon exclusively, and so does not have any prior knowledge of crystalline phases: it therefore demonstrates true transferability, which is a crucial prerequisite for applications in chemistry. The method is orders of magnitude faster than DFT and can, in principle, be coupled with any algorithm for structure prediction. Machine-learning models therefore seem promising to enable large-scale structure searches in the future. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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)

  2. Identification and Characterization of Three Previously Undescribed Crystal Proteins from Bacillus thuringiensis subsp. jegathesan

    Science.gov (United States)

    Sun, Yunjun; Zhao, Qiang; Ding, Xuezhi; Hu, Quanfang; Federici, Brian A.

    2013-01-01

    The total protoxin complement in the parasporal body of mosquitocidal strain, Bacillus thuringiensis subsp. jegathesan 367, was determined by use of a polyacrylamide gel block coupled to mass spectrometry. A total of eight protoxins were identified from this strain, including five reported protoxins (Cry11Ba, Cry19Aa, Cry24Aa, Cry25Aa, and Cyt2Bb), as well as three previously undescribed (Cry30Ca, Cry60Aa, and Cry60Ba) in this isolate. It was interesting that the encoding genes of three new protoxins existed as cry30Ca-gap-orf2 and cry60Ba-gap-cry60Aa. The cry30Ca and a downstream orf2 gene were oriented in the same direction and separated by 114 bp, and cry60Ba was located 156 bp upstream from and in the same orientation to cry60Aa. The three new protoxin genes were cloned from B. thuringiensis subsp. jegathesan and expressed in an acrystalliferous strain under the control of cyt1A gene promoters and the STAB-SD stabilizer sequence. Recombinant strain containing only cry30Ca did not produce visible inclusion under microscope observation, while that containing both cry30Ca and orf2 could produce large inclusions. Cry60Aa and Cry60Ba synthesized either alone or together in the acrystalliferous host could yield large inclusions. In bioassays using the fourth-instar larvae of Culex quinquefasciatus, Cry60Aa and Cry60Ba alone or together had estimated 50% lethal concentrations of 2.9 to 7.9 μg/ml; however, Cry30Ca with or without ORF2 was not toxic to this mosquito. PMID:23524673

  3. Crystal structure of natural phaeosphaeride A

    Directory of Open Access Journals (Sweden)

    Victoria V. Abzianidze

    2015-08-01

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

  4. 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...

  5. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

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

    2016-09-01

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

  6. Crystal structure of Cryptosporidium parvum pyruvate kinase.

    Directory of Open Access Journals (Sweden)

    William J Cook

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

  7. Crystal structure of the human primase.

    Science.gov (United States)

    Baranovskiy, Andrey G; Zhang, Yinbo; Suwa, Yoshiaki; Babayeva, Nigar D; Gu, Jianyou; Pavlov, Youri I; Tahirov, Tahir H

    2015-02-27

    DNA replication in bacteria and eukaryotes requires the activity of DNA primase, a DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for RNA primer synthesis. Understanding of RNA synthesis priming in eukaryotes is currently limited due to the lack of crystal structures of the full-length primase and its complexes with substrates in initiation and elongation states. Here we report the crystal structure of the full-length human primase, revealing the precise overall organization of the enzyme, the relative positions of its functional domains, and the mode of its interaction with modeled DNA and RNA. The structure indicates that the dramatic conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis. The presence of a long linker between the N- and C-terminal domains of p58 provides the structural basis for the bulk of enzyme's conformational flexibility. Deletion of most of this linker affected the initiation and elongation steps of the primer synthesis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. 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.)

  9. Crystal Structure and Physical Properties of U3T3Sn4 (T = Ni, Cu) Single-Crystals

    OpenAIRE

    Shlyk, L.; Estrela, P.; Waerenborgh, J. C.; De Long, L. E.; de Visser, A.; Rojas, D. P.; Gandra, F.; Almeida, M.

    2000-01-01

    Heat capacity experiments, crystal structure determination and transmission electron microscopy have been carried out on U3Cu3Sn4 single-crystals. U3Cu3Sn4 was confirmed to be a heavy-fermion antiferromagnet (TN=13(1) K) with a low temperature electronic heat capacity coefficient gamma=390 mJ/molUK2. Low temperature heat capacity experiments on a U3Ni3Sn4 single-crystal indicate that below 0.4 K there is a crossover between the previously observed non-Fermi liquid behavior and a Fermi liquid ...

  10. Hydrothermal syntheses and crystal structure of NH

    International Nuclear Information System (INIS)

    Kang, Z. J.; Wang, Y. X.; You, F. T.; Lin, J. H.

    2001-01-01

    Ammonium rare earth fluorides NH(sub 4)Ln(sub 3)F(sub 10) (Ln=Dy, Ho, Y, Er, Tm) were synthesized by a hydrothermal method. Two polymorphs, of the hexagonal(beta)-KYb(sub 3)F(sub 10) and the cubic(gamma)-KYb(sub 3)F(sub 10) structure types, were formed under hydrothermal conditions for most of the rare earth fluorides except NH(sub 4)Dy(sub 3)F(sub 10), for which only the cubic -phase was obtained. The crystal structures of MLn(sub 3)F(sub 10) (M=alkaline metal, NH(sup+4) and Ln=rare earth) show a strong correlation to the ratio of ionic radii (R(sub M)/R(sub Ln)), which has been expressed in a structure phase diagram of the ionic radii of univalent and rare earth cations

  11. The Crystal Structures of Potentially Tautomeric Compounds

    Science.gov (United States)

    Furmanova, Nina G.

    1981-08-01

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

  12. Crystal structure of sodium dihydrogen arsenate

    Directory of Open Access Journals (Sweden)

    Joseph Ring

    2017-10-01

    Full Text Available Single crystals of the title compound, Na(H2AsO4, were obtained by partial neutralization of arsenic acid with sodium hydroxide in aqueous solution. The crystal structure of Na(H2AsO4 is isotypic with the phosphate analogue and the asymmetric unit consists of two sodium cations and two tetrahedral H2AsO4− anions. Each of the sodium cations is surrounded by six O atoms of five H2AsO4− groups, defining distorted octahedral coordination spheres. In the extended structure, the sodium cations and dihydrogen arsenate anions are arranged in the form of layers lying parallel to (010. Strong hydrogen bonds [range of O...O distances 2.500 (3–2.643 (3 Å] between adjacent H2AsO4− anions are observed within and perpendicular to the layers. The isotypic structure of Na(H2PO4 is comparatively discussed.

  13. 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.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  15. 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.

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

    African Journals Online (AJOL)

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

  17. 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.

  18. 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.

  19. 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.

  20. Crystal structure of pure ZrO2 nanopowders

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  1. 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.

  2. 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.

  3. Structural perfection and residual electric resistance of tungsten single crystals

    International Nuclear Information System (INIS)

    Tagirova, D.M.; Dyakina, V.P.; Startsev, V.E.; Esin, V.O.

    1997-01-01

    A study was made into residual relative resistance (RRR) and structural perfection (SP) of tungsten single crystals, grown by electron beam zone melting using seeding crystals of several orientations, namely, , , , . The single crystals were of 99.98 and 99.9995 wt.% purity. The RRR value is found to depend on crystallographic orientation of an axis of crystal growth and to correlate with SP. Single crystals of different purity are differ in the nature of orientational dependences. It is shown that the correlation between RRR and SP of crystals is mainly due to conduction electron scattering by subgrain boundaries (internal size effect)

  4. Niobium hyperfine structure in crystal calcium tungstate

    Science.gov (United States)

    Tseng, D. L.; Kikuchi, C.

    1972-01-01

    A study of the niobium hyperfine structure in single crystal calcium tungstate was made by the combination of the technique of electron paramagnetic resonance and electron nuclear double resonance (EPR/ENDOR). The microwave frequency was about 9.4 GHz and the radio frequency from 20MHz to 70 MHz. The rare earth ions Nd(3+), U(3+), or Tm(3+) were added as the charge compensator for Nb(5+). To create niobium paramagnetic centers, the sample was irradiated at 77 deg K with a 10 thousand curie Co-60 gamma source for 1 to 2 hours at a dose rate of 200 K rads per hour and then transferred quickly into the cavity. In a general direction of magnetic field, the spectra showed 4 sets of 10 main lines corresponding to 4 nonequivalent sites of niobium with I = 9/2. These 4 sets of lines coalesced into 2 sets of 10 in the ab-plane and into a single set of 10 along the c-axis. This symmetry suggested that the tungsten ions are substituted by the niobium ions in the crystal.

  5. Tailoring the Crystal Structure Toward Optimal Super Conductors

    Science.gov (United States)

    2016-06-23

    AFRL-AFOSR-VA-TR-2016-0210 TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS Emilia Morosan WILLIAM MARSH RICE UNIV HOUSTON TX Final...TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS 5a. CONTRACT NUMBER FA9550-11-1-0023 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...Form 298 Back (Rev. 8/98) DISTRIBUTION A: Distribution approved for public release. TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS

  6. Crystal structure of a snake venom cardiotoxin

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  7. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Benedikt Ley

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

  10. Crystal structure of Deep Vent DNA polymerase.

    Science.gov (United States)

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

    2017-01-29

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

  11. Stochastic generation of complex crystal structures combining group and graph theory with application to carbon

    Science.gov (United States)

    Shi, Xizhi; He, Chaoyu; Pickard, Chris J.; Tang, Chao; Zhong, Jianxin

    2018-01-01

    A method is introduced to stochastically generate crystal structures with defined structural characteristics. Reasonable quotient graphs for symmetric crystals are constructed using a random strategy combined with space group and graph theory. Our algorithm enables the search for large-size and complex crystal structures with a specified connectivity, such as threefold sp2 carbons, fourfold sp3 carbons, as well as mixed sp2-sp3 carbons. To demonstrate the method, we randomly construct initial structures adhering to space groups from 75 to 230 and a range of lattice constants, and we identify 281 new sp3 carbon crystals. First-principles optimization of these structures show that most of them are dynamically and mechanically stable and are energetically comparable to those previously proposed. Some of the new structures can be considered as candidates to explain the experimental cold compression of graphite.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    A high-resolution X-ray crystallographic study of the effects of solvent deuteration on the crystallization of proteinase K shows negligibly small degradations of the crystals owing to solvent deuteration and small structural differences between nondeuterated and deuterated crystals of proteinase K. 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

  13. Crystal structures of five 6-mercaptopurine derivatives

    Science.gov (United States)

    Gomes, Lígia R.; Low, John Nicolson; Magalhães e Silva, Diogo; Cagide, Fernando; Borges, Fernanda

    2016-01-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(3-meth­oxy­phen­yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-meth­oxy­phen­yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-chloro­phen­yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-bromo­phen­yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth­oxy­phen­yl)-2-[(9H-purin-6-yl)sulfan­yl]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. PMID:27006794

  14. Crystal Structure of Human Kynurenine Aminotransferase ll*

    Energy Technology Data Exchange (ETDEWEB)

    Han,Q.; Robinson, H.; Li, J.

    2008-01-01

    Human kynurenine aminotransferase II (hKAT-II) efficiently catalyzes the transamination of knunrenine to kynurenic acid (KYNA). KYNA is the only known endogenous antagonist of N-methyl-d-aspartate (NMDA) receptors and is also an antagonist of 7-nicotinic acetylcholine receptors. Abnormal concentrations of brain KYNA have been implicated in the pathogenesis and development of several neurological and psychiatric diseases in humans. Consequently, enzymes involved in the production of brain KYNA have been considered potential regulatory targets. In this article, we report a 2.16 Angstroms crystal structure of hKAT-II and a 1.95 Angstroms structure of its complex with kynurenine. The protein architecture of hKAT-II reveals that it belongs to the fold-type I pyridoxal 5-phosphate (PLP)-dependent enzymes. In comparison with all subclasses of fold-type I-PLP-dependent enzymes, we propose that hKAT-II represents a novel subclass in the fold-type I enzymes because of the unique folding of its first 65 N-terminal residues. This study provides a molecular basis for future effort in maintaining physiological concentrations of KYNA through molecular and biochemical regulation of hKAT-II.

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

    Science.gov (United States)

    Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M; Brunklaus, Gunther; Kolb, Ute

    2012-04-01

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

  16. 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…

  17. Synthesis, crystal structure, optical and electrochemical properties of ...

    Indian Academy of Sciences (India)

    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 ...

  18. 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.

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

    KAUST Repository

    Shi, Xueliang

    2015-01-01

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

  20. Redetermination of the Crystal Structure of Al2Br6

    DEFF Research Database (Denmark)

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

    1997-01-01

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

  1. 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.

  2. Crystal structure of Li3Ga(BO32

    Directory of Open Access Journals (Sweden)

    Robert W. Smith

    2017-03-01

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

  3. 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)

  4. Spirallike structure in the conoscopic figures of optically active crystals

    Science.gov (United States)

    Pikul', O. Yu.; Rudoi, K. A.; Livashvili, A. I.; Doronin, V. I.; Stroganov, V. I.

    2005-02-01

    This paper discusses a spirallike structure in the conoscopic figures of optically active crystals, differing from the Airy figure. The cause of the appearance of the spirallike structure is circularly polarized radiation.

  5. Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts.

    Science.gov (United States)

    Mohamed, Sharmarke; Karothu, Durga Prasad; Naumov, Panče

    2016-08-01

    The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol(-1) of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of a Z' = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.

  6. 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...

  7. 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.

  8. 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.

  9. Band structures in fractal grading porous phononic crystals

    Science.gov (United States)

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

    2018-05-01

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

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

    Science.gov (United States)

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

    2017-04-05

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

  11. Synthesis, crystal structure and properties of magnesium and ...

    Indian Academy of Sciences (India)

    2015-04-01

    Apr 1, 2015 ... 2.3 X-ray crystal structure determination. Single crystal X-ray analysis of compounds 1 and 2 was done at the Sophisticated Analytical Instrument. Table 1. Crystal data and selected refinement results for (1) and (2). Empirical formula. C16H30MgO14 (1). C16H16CaO7 (2). Formula weight (g mol−1). 470.71.

  12. 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.

  13. 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...

  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. Structural, spectral and mechanical studies of bimetallic crystal: cadmium manganese thiocyanate single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Manikandan, M.; Vijaya Prasath, G.; Mahalingam, T.; Ravi, G. [Alagappa University, Department of Physics, Karaikudi (India); Bhagavannarayan, G.; Vijayan, N. [National Physical Laboratory, Materials Characterization Division, New Delhi (India)

    2012-09-15

    A nonlinear optical bimetallic thiocyanate complex crystal, cadmium manganese thiocyanate (CMTC) has been successfully synthesized. The growth of single crystals of cadmium manganese thiocyanate has been accomplished from aqueous solution using slow evaporation method. The presence of manganese and cadmium in the synthesized material was confirmed through energy dispersive spectrum (EDS) analysis. Structural analysis was carried out using powder X-ray diffractometer (PXRD) and crystalline perfection of the grown crystals was ascertained by high-resolution X-ray diffraction (HRXRD) analysis. Fourier transform infrared (FTIR) spectrum was taken to confirm the functional groups. The transmittance spectrum of the crystal in the UV-visible region has been recorded and the cutoff wavelength has been determined. The dielectric measurements for the crystals were performed for various frequencies and temperatures. The mechanical properties were evaluated by Vickers microhardness testing, which reveals hardness and stiffness constant of the crystals. (orig.)

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  17. 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.

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

    Science.gov (United States)

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

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

  19. 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...

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

    Indian Academy of Sciences (India)

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

  1. Colloidal hard dumbbells under gravity: structure and crystallization

    NARCIS (Netherlands)

    Marechal, M.A.T.; Dijkstra, M.

    2011-01-01

    We study the structure and phase behavior of hard dumbbells under gravity. The fluid shows layering near the wall, where subsequent layers of dumbbells align alternatingly parallel or perpendicular to the wall. We observe coexistence of a fluid with a plastic crystal (PC) and an aligned crystal

  2. Mathematical aspects of Rietveld refinement and crystal structure ...

    Indian Academy of Sciences (India)

    Administrator

    Abstract. The core mathematics, goodness-of-fit parameters of Rietveld refinement technique is introduced for structural analysis of crystalline materials not available as single crystals. X-ray diffraction (XRD) pat- terns of PbTiO3 compound prepared by following solid-state route, suggests it to be in single crystal form. All.

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

    Czech Academy of Sciences Publication Activity Database

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

    2006-01-01

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

  4. Synthesis, Characterization, Crystal Structure and Keto-enol Kinetics

    African Journals Online (AJOL)

    A crystal structure determination of Hbth (orthorhombic, Pbca, Z=8, R=0.0290) shows asymmetrical enolization on the side of the phenyl group. The preferred enol isomer of β-diketones containing more than one aromatic moiety that crystallizes in the solid state is determined by the resonance driving force stabilization of the ...

  5. Nucleation of colloidal crystals on configurable seed structures

    NARCIS (Netherlands)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chongyuan Wang

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

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

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2015-11-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  9. Redetermination of the crystal structure of K2Hg(SCN4

    Directory of Open Access Journals (Sweden)

    Jascha Bandemehr

    2017-07-01

    Full Text Available Single crystals of K2Hg(SCN4 [dipotassium tetrathiocyanatomercurate(II] were grown from aqueous solutions of potassium thiocyanate and mercury(II thiocyanate and studied by single-crystal X-ray diffraction. In comparison with the previously reported structure model [Zvonkova (1952. Zh. Fiz. Khim. 26, 1798–1803], all atoms in the crystal structure were located, with lattice parameters and fractional coordinates determined to a much higher precision. In the (crystal structure, the HgII atom is located on a twofold rotation axis and is coordinated in the form of a distorted tetrahedron by four S atoms of the thiocyanate anions. The K+ cation shows a coordination number of eight.

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  11. Crystal structure of ?-d,l-psicose

    OpenAIRE

    Ishii, Tomohiko; Sakane, Genta; Yoshihara, Akihide; Fukada, Kazuhiro; Senoo, Tatsuya

    2015-01-01

    The title compound, C6H12O6, a C-3 position epimer of fructose, was crystallized from an aqueous solution of equimolar mixture of d- and l-psicose (1,3,4,5,6-penta?hydroxy?hexan-2-one, ribo-2-hexulose, allulose), and it was confirmed that d-psicose (or l-psicose) formed ?-pyran?ose with a 2 C 5 (or 5 C 2) conformation. In the crystal, an O?H?O hydrogen bond between the hy?droxy groups at the C-3 and C-2 positions connects homochiral mol?ecules into a column along the b axis. The columns are l...

  12. 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....

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

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

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

  14. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 5. Synthesis and crystal structure of a wheel-shaped supramolecular coordination complex. Deepak Gupta Palanisamy Rajakannu Bhaskaran Shankar Firasat Hussain Malaichamy Sathiyendiran. Special issue on Chemical Crystallography Volume 126 ...

  15. 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.

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  17. Synthesis crystal structure, photoluminescence and photocatalytic ...

    Indian Academy of Sciences (India)

    photoluminescence and photocatalytic properties of 1 were also been investigated. Keywords. Zinc; 5-(pyridyl)tetrazolato (PTZ); Single-Crystal X-Ray Crystallography. 1. Introduction. In last few years tetrazole ligands have been widely used to synthesize metal–organic and H-bonded frameworks of various topologies.1–5 ...

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

    Indian Academy of Sciences (India)

    64

    SHELXL-97 programs included in WINGX package [6, 7, and 8]. ... Elmer software. 2.6. Absorption and photoluminescence measurements. A PerkinElmer LS 55 spectrometer and exciting with 350 nm radiation were used to record ..... [8] Farrugia LJ, 1999, WinGX suite for small-molecule single-crystal crystallography. J.of.

  19. Formation of structured nanophases in halide crystals

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

  20. 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/sigmadumbbell and sigma the diameter of the spheres, we determine the difference in Helmholtz free energy of a plastic crystal with a hexagonal-close-packed (hcp) and a face-centered-cubic (fcc) structure using thermodynamic integration and the lattice-switch Monte Carlo method. We find that the plastic crystal with the hcp structure is more stable than the one with the fcc 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 .

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    African Journals Online (AJOL)

    NICO

    The structures are compared to expected solution species under the same conditions. The crystal structure of complex 1 exhibits a seven coordinate structure which contains a protonated picolinic acid ligand that bonds bidentately to the cadmium ion via both carboxylate oxygens. Two nitrates coordinate to the metal centre ...

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2017-05-05

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

  5. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

    Directory of Open Access Journals (Sweden)

    Aramburu Ander

    2010-11-01

    Full Text Available Abstract Background Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored. Results We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP and sensitivity (ST of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results. Conclusions The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.

  6. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-07-13

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

  8. Synthesis, crystal structures, hydrogen bonding graph-sets and ...

    African Journals Online (AJOL)

    Synthesis, crystal structures, hydrogen bonding graph-sets and theoretical studies of nickel (+II) co-ordinations with pyridine-2,6-dicarboxamide oxime. ... which crystallized in the monoclinic space group C2/c with a = 14.915(2), b = 0.895(2), c = 8.205(1) Å, β = 114.69(1), and Z = 4. The complex consists of discrete cations ...

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

    Indian Academy of Sciences (India)

    Administrator

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

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

    Indian Academy of Sciences (India)

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

  11. Synthesis and crystal structure of [chlorobis(triphenylphospino) (p ...

    Indian Academy of Sciences (India)

    X-ray Structure of new copper(I)-thiosemicarbazone complex. 187. Table 1. Crystallographic data of complex 3. Empirical Formula. C44H38Cl2CuN3P2S. Formula Weight. 837.21. Temperature (K). 293(2). Wavelength (Å). 0.71073. Crystal system. Triclinic. Crystal size (mm). 0.3 x 0.2 x 0.2. Space group. P-1. Z, calculated. 2.

  12. Crystal structure and theoretical studies on quinoline phosphate

    Science.gov (United States)

    Ben Issa, T.; Ghalla, H.; Marzougui, S.; Benhamada, L.

    2017-12-01

    The crystal structure of (C9H7N) H3PO4 (QP) was determined from single crystals obtained by slow evaporation methods (space group Pī; a = 7.5508(3) Å, b = 7.9705(3) Å, c = 8.6849(3) Å; α = 77.3725(18)°, β = 82.6225(19)°, γ = 74.9829(19)°). The crystal structure of QP is built up from infinite hydrogen bonding inorganic chains of (H3PO4)n lay parallel to the an axis, which are also connected to the quinoline rings through hydrogen bonds in a 3D arrangement. The structure was examined through atoms in molecules (AIM) topological and Hirshfeld surface (HS) analyses and its molecular structure optimized by theoretical density functional (DFT) calculations. The QP observed IR absorptions between 4000 and 400 cm-1 were assigned on the basis of the calculated theoretical vibrational modes.

  13. The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains.

    Science.gov (United States)

    Parker, Michelle L; Houston, Simon; Wetherell, Charmaine; Cameron, Caroline E; Boulanger, Martin J

    2016-01-01

    Treponema pallidum subspecies pallidum is the causative agent of syphilis, a chronic, multistage, systemic infection that remains a major global health concern. The molecular mechanisms underlying T. pallidum pathogenesis are incompletely understood, partially due to the phylogenetic divergence of T. pallidum. One aspect of T. pallidum that differentiates it from conventional Gram-negative bacteria, and is believed to play an important role in pathogenesis, is its unusual cell envelope ultrastructure; in particular, the T. pallidum peptidoglycan layer is chemically distinct, thinner and more distal to the outer membrane. Established functional roles for peptidoglycan include contributing to the structural integrity of the cell envelope and stabilization of the flagellar motor complex, which are typically mediated by the OmpA domain-containing family of proteins. To gain insight into the molecular mechanisms that govern peptidoglycan binding and cell envelope biogenesis in T. pallidum we report here the structural characterization of the putative OmpA-like domain-containing protein, Tp0624. Analysis of the 1.70 Å resolution Tp0624 crystal structure reveals a multi-modular architecture comprised of three distinct domains including a C-terminal divergent OmpA-like domain, which we show is unable to bind the conventional peptidoglycan component diaminopimelic acid, and a previously uncharacterized tandem domain unit. Intriguingly, bioinformatic analysis indicates that the three domains together are found in all orthologs from pathogenic treponemes, but are not observed together in genera outside Treponema. These findings provide the first structural insight into a multi-modular treponemal protein containing an OmpA-like domain and its potential role in peptidoglycan coordination and stabilization of the T. pallidum cell envelope.

  14. 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.

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  16. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    Science.gov (United States)

    Payne, Stephen A.; Kway, Wayne L.; DeLoach, Laura D.; Krupke, William F.; Chai, Bruce H. T.

    1994-01-01

    Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.

  17. On the influence of crystal structure on the electromagnetic shower development in the lead tungstate crystals

    Science.gov (United States)

    Baryshevsky, V. G.; Haurylavets, V. V.; Korjik, M. V.; Lobko, A. S.; Mechinsky, V. A.; Sytov, A. I.; Tikhomirov, V. V.; Uglov, V. V.

    2017-07-01

    The development of high-energy electromagnetic showers in long oriented lead tungstate crystals, accelerated by the effects induced by the strong field of atomic strings, is simulated for the first time. For that the characteristics of pair production and gamma-radiation by electrons or positrons were first simulated by the direct application of Baier-Katkov formulae in a thin PWO crystal to derive the scaling coefficients of the corresponding Bethe-Heitler cross sections to be incorporated into GEANT4 for the simulation of the electromagnetic shower development in a long crystal. Simulation results demonstrate the significant influence of the crystal structure on the e± and gamma-quanta registration processes in the existing homogeneous electromagnetic calorimeters and gamma-telescopes as well as wide possibilities of improving their performance in future developments.

  18. The crystal structure of tRNA

    Indian Academy of Sciences (India)

    Madhu

    determination of the 3D structure of the tRNA (in 1974) has not been recognized with such distinction. ... structure: these being led by Aaron Klug at the MRC. Laboratory of Molecular Biology (LMB), Cambridge, UK, ..... by-product of the tRNAPhe structure was the first detailed chemical picture of a G–U base pair in a double ...

  19. 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. © 2011 International Union of Crystallography. All rights reserved.

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

    Science.gov (United States)

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

    1999-08-03

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

  1. Nematic liquid crystal director structures in rectangular regions

    Science.gov (United States)

    Walton, J.; Mottram, N. J.; McKay, G.

    2018-02-01

    We consider a shallow rectangular well of nematic liquid crystal subject to weak anchoring on the sides of the well. By considering weak anchoring instead of infinitely strong anchoring, we are able to analyze nematic equilibria in the well without the need to exclude point defects at the corners, as done in previous work in the area. For relatively weak anchoring, we are able to derive analytic expressions for the director alignment angle in terms of an infinite series of modes, involving roots of a transcendental equation. The analytic forms of the director configuration are then used to calculate critical anchoring strengths at which uniform and distorted director structures exchange stability. We also consider the asymptotic behavior of the director structure and energy for very strong anchoring. We show that in both cases—for the transitions from uniform to distorted states and the limit of infinitely strong anchoring—the approximate analytic expansions agree very well with corresponding numerical calculations of the full model.

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

    Indian Academy of Sciences (India)

    Abstract. Coordination polymer of Cu(II) bridged by o-phthalic acid alone is not known. The reaction of. CuCl2.2H2O with (2-butoxycarbonyl)benzoic acid yielded three dimensional coordination polymer bridged by o-phthalic acid. X-ray crystal structure shows structure with monoclinic P21/c space group. o-Phthalic acid.

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

    Indian Academy of Sciences (India)

    Single crystal X-ray structural characterization revealsthat the side arm carboxylate group of the coordinated Schiff base exhibits a μ 1 , 3 -bridging mode and connectsthe neighbouring copper(II) ions leading to a zigzag 1D chain structure where the copper(II) ions displaydistorted square pyramidal geometries. Variable ...

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

    Indian Academy of Sciences (India)

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

  5. Crystal structure and ionic conductivity of a new bismuth tungstate,

    Indian Academy of Sciences (India)

    Unknown

    43. Dedicated to Prof J Gopalakrishnan on his 62nd birthday. *For correspondence. Crystal structure and ionic conductivity of a new bismuth tungstate,. Bi3W2O10⋅5. B MUKTHA and T N GURU ROW*. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012 e-mail: ssctng@sscu.iisc.ernet.in.

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

    Indian Academy of Sciences (India)

    WINTEC

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

  7. Band structure peculiarities of magnetic photonic crystals

    Science.gov (United States)

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

    2017-10-01

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

  8. 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.

  9. Cambridge Structural Database as a tool for studies of general structural features of organic molecular crystals

    International Nuclear Information System (INIS)

    Kuleshova, Lyudmila N; Antipin, Mikhail Yu

    1999-01-01

    The review surveys and generalises data on the use of the Cambridge Structural Database (CSD) for studying and revealing general structural features of organic molecular crystals. It is demonstrated that software and facilities of the CSD allow one to test the applicability of a number of known concepts of organic crystal chemistry (the principle of close packing, the frequency of occurrence of space groups, the preferred formation of centrosymmetrical molecular crystals, etc.) on the basis of abundant statistical data. Examples of the use of the Cambridge Structural Database in engineering of molecular crystals and in the systematic search for compounds with specified properties are given. The bibliography includes 122 references.

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

    Science.gov (United States)

    Mtioui-Sghaier, Olfa; Mendoza-Meroño, Rafael; Ktari, Lilia; Dammak, Mohamed; García-Granda, Santiago

    2015-07-01

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

  11. 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-...

  12. Static and Dynamic Structure Analyses of Polymer Crystals

    Science.gov (United States)

    Tashiro, Kohji

    Recent development in static and dynamic structure analyses of polymer crystals has been reviewed. Various methods were developed to enhance the reliability of static structure analysis. Usage of synchrotron high-energy X-ray beam allowed us to increase the total number of observed X-ray reflections by one order. Wide-angle neutron diffraction revealed the hydrogen atomic positions accurately, making it possible to evaluate the mechanical property of polymer crystals quantitatively. Time-resolved measurements of wide-angle and small-angle X-ray scatterings as well as infrared and Raman spectra have revealed the structural revolution processes as seen in the studies of isothermal crystallization and mechanical deformation processes.

  13. Static and dynamic structure analyses of polymer crystals

    International Nuclear Information System (INIS)

    Tashiro, Kohji

    2011-01-01

    Recent development in static and dynamic structure analyses of polymer crystals has been reviewed. Various methods were developed to enhance the reliability of static structure analysis. Usage of synchrotron high-energy X-ray beam allowed us to increase the total number of observed X-ray reflections by one order. Wide-angle neutron diffraction revealed the hydrogen atomic positions accurately, making it possible to evaluate the mechanical property of polymer crystals quantitatively. Time-resolved measurements of wide-angle and small-angle X-ray scatterings as well as infrared and Raman spectra have revealed the structural revolution processes as seen in the studies of isothermal crystallization and mechanical deformation processes. (author)

  14. Crystal structure of TlU3OF11 oxyfluoride

    International Nuclear Information System (INIS)

    Hsini, S.; Caignol, E.; Metin, J.; Avignant, D.; Cousseins, J.C.

    1986-01-01

    The TlU 3 OF 11 oxyfluoride crystallizes in the monoclinic system with unit-cell parameters a=14.051, A, b=8.106, A, c=8.389, A, β=90.00 and space group Cm (No.8), Z=4. Its crystal structure has been determined from single crystal X-ray diffraction data collected with a Nonius Cad 4 automatic diffractometer and refined to a conventional R=0.060 from 1526 independent reflections. The structure consists of double layers of edge-shared and corner-shared UOF 8 distorted tricapped trigonal prisms running perpendicularly to the c axis. This stacking delimits channels within lie the Tl + ions. The structure analysis using different methods for evaluating the valence-bond distributions has been carried out and has shown an ordered oxygen-fluorine distribution within the anionic sublattice [fr

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

    International Nuclear Information System (INIS)

    Schuster, M.

    2001-08-01

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

  16. 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...

  17. 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 ...

  18. The crystal structure of urea nitrate

    NARCIS (Netherlands)

    Harkema, Sybolt; Feil, D.

    1969-01-01

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

  19. 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

  20. 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.

  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. The crystal structure of GXGD membrane protease FlaK

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya (Yale-MED)

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  3. The Crystal Structure of GXGD Membrane Protease FlaK

    Energy Technology Data Exchange (ETDEWEB)

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  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. 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)

  6. On structure of some laminated crystals with organic molecules

    International Nuclear Information System (INIS)

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

    1982-01-01

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

  7. 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.

  8. Systematic analysis of crystal and molecular structures

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Dohnálek, Jan

    2012-01-01

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

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    2017-06-01

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

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

    International Nuclear Information System (INIS)

    Song Ruiying; Wu Congfeng; He Xiaodong; Dong Sai

    2007-01-01

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

  13. Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in [Department of Physics, Agni College of Technology, Thalambur, Chennai-603103 (India); Perumal, Rajesh Narayana [Department of Physics, SSN College of Engineering, Kalavakkam, Chennai-603110 (India)

    2014-04-24

    Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

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

    Science.gov (United States)

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

    2002-01-01

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

  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...

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

    Indian Academy of Sciences (India)

    performed on complex 1 to rationalize its experimental absorption spectra. Complex 1 exhibits luminescence in EtOH ... potential applications in biological systems like, devel- opment of structural and functional models for ... to react with [WOnS4−n] (n = 0-2).11,12 These reactions result in the formation of a large number of ...

  17. Rufinamide: Crystal structure elucidation and solid state characterization.

    Science.gov (United States)

    Salunke, Nita; Thipparaboina, Rajesh; Chavan, Rahul B; Lodagekar, Anurag; Mittapalli, Sudhir; Nangia, Ashwini; Shastri, Nalini R

    2018-02-05

    Rufinamide (R) is a triazole derivative approved for the management of partial seizures and seizures associated with Lennox-Gastaut Syndrome, in November 2007. Crystal structure, solid state characterization, drug-excipient compatibility and solubility play a pivotal role in formulation development. This work deals with the crystal structure elucidation of R by single crystal X-ray diffraction and solid state characterization by thermal, spectroscopic and crystallographic techniques. Drug- excipient compatibility was assessed by differential scanning calorimetry (DSC). New RP-HPLC method for quantification of R was developed with improved retention time. Solubility and dissolution of drug in different media was determined. Additionally, the flow behavior of the drug was evaluated by measuring Carr's index and Hausner's ratio, while the compressibility behavior was studied using Well's protocol. R crystallized from dimethylformamide (R-DMF) was utilized for single crystal analysis. The drug crystallized in triclinic crystal system with P-1 space group. Asymmetric unit cell consists of two molecules of R held by intermolecular hydrogen bond (connected by NH⋯O, which forms the catemeric chain). Analytical outcomes from DSC, thermogravimetric analysis (TGA) and powder X-ray diffraction (PXRD) revealed that the drug was present in pure crystalline form and was devoid of any polymorphic or pseudopolymorphic impurities. Influence of pH on the solubility and dissolution of R-DMF was found to be insignificant. The drug exhibited poor aqueous solubility, which was improved nearly 4.6 fold with the addition of 2% sodium lauryl sulphate (SLS). The drug exhibits poor flow and elastic compression nature. Excipients such as poly ethylene glycol (PEG) 8000, SLS, lactose monohydrate, starch and Hydroxypropyl methylcellulose (HPMC) E15 were incompatible with R-DMF as identified by thermal analysis. It is envisaged that these information regarding solid state properties of R

  18. 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.

  19. Crystal structures and atomic model of NADPH oxidase

    NARCIS (Netherlands)

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

    2017-01-01

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

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

    International Nuclear Information System (INIS)

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

    1977-12-01

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

  1. Refining of crystal structures of macromolecules with molecular dynamics

    International Nuclear Information System (INIS)

    Mascarenhas, Y.P.

    1988-01-01

    In this work, the refining of crystal structures of macromolecules is discussed. The annealing method is employed and it can be previewed that, this method, will be largely used in the future for protein crystallography. (A.C.A.S.) [pt

  2. BiFeO3 Crystal Structure at Low Temperatures

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  3. Crystal structure of the sodium-potassium pump

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  4. The crystal and molecular structure of 2,3-diazanaphthalene

    NARCIS (Netherlands)

    Huiszoon, C.; van de Waal, B.W.; van Egmond, A.B.; Harkema, Sybolt

    1972-01-01

    The structure of 2,3-diazanaphthalene (phthalazine) has been determined by X-ray methods. Cell constants and intensity data were obtained with a single-crystal diffractometer. The space group is Pbca. Cell constants are 13.695, 10.557 and 9.285 A. There are eight nearly planar molecules in the unit

  5. The crystal and molecular structure of 2,7-diazanaphthalene

    NARCIS (Netherlands)

    Huiszoon, C.; van Hummel, G.J.; van den Ham, D.M.W.

    1977-01-01

    X-ray diffraction data were collected at 20°C on a computer-controlled Philips diffractometer (PW 1100). The structure was solved by direct methods and refined by the full-matrix least-squares method to an R of 0.065 (weighted R 0.046). The molecule in the crystal is of lower symmetry than C2,.. The

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

    Indian Academy of Sciences (India)

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

  9. Crystal structure and bio-mimicking of Catecholase activity

    Indian Academy of Sciences (India)

    Unprecedented hetero-geometric discrete copper(II) complexes: Crystal structure and bio-mimicking of Catecholase activity. ABHRANIL DE DHANANJAY DEY HARE RAM YADAV MILAN MAJI VINAYAK RANE R M KADAM ANGSHUMAN ROY CHOUDHURY BHASKAR BISWAS. Regular Article Volume 128 Issue 11 ...

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

    Indian Academy of Sciences (India)

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

  11. Magnetic structure of URhSi single crystal

    Czech Academy of Sciences Publication Activity Database

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

    2003-01-01

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

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

    NARCIS (Netherlands)

    Li, Y

    2017-01-01

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

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 6. Synthesis, crystal structure and catecholase activity of a Ni(II) complex derived from a tetradentate Schiff base ligand. Pradipta Kumar Basu Merry Mitra Amrita Ghosh Latibuddin Thander Chia -Her Lin Rajarshi Ghosh. Rapid Communications Volume 126 ...

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

    Indian Academy of Sciences (India)

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

  15. Crystal structure of 2,2′-bipyrrole

    Directory of Open Access Journals (Sweden)

    Christopher A. Michaels

    2017-10-01

    Full Text Available The complete molecule of the title compound, C8H8N2, is generated by a crystallographic center of symmetry. In the crystal, short N—H...π [H...π = 2.499 (19 Å] interactions link the molecules into a herringbone structure.

  16. Effect of crystal structure on photoinduced superhydrophilicity of ...

    Indian Academy of Sciences (India)

    on the film surfaces during irradiation and storage in a dark place was measured by a contact angle analyser. The results indicate that copper grafted titanium dioxide brookite thin film showed higher hydrophilicity than copper grafted titania rutile thin film. Keywords. Copper grafted TiO2; crystal structure; superhydrophilicity.

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

    African Journals Online (AJOL)

    NICO

    The salt undergoes melting followed by decomposition to give gaseous products. KEYWORDS. Hydrazine, succinic acid, hydrazinium hydrogensuccinate, crystal structure, thermal studies. 1. Introduction. Dibasic acids are known to form N2H5HA, (N2H5)2A and. N2H5HA.H2A type salts (H2A = dibasic acid) with hydrazine.

  18. Synthesis, crystal structure and characterization of new biologically ...

    Indian Academy of Sciences (India)

    Sulfonamide; Cu(II) complexes; crystal structure; oxidative DNA cleavage; cytotoxic activity. 1. Introduction. The continuous demand for new ... between the base stacks of double-stranded DNA, thus showing cytotoxic effects on several ... proteins.11,12 The toxicity of Cu(II) complexes seems to be lower than classic cancer ...

  19. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    Synthesis and crystal structure of a wheel-shaped supramolecular coordination complex. DEEPAK GUPTA, PALANISAMY RAJAKANNU, BHASKARAN SHANKAR,. FIRASAT HUSSAIN and MALAICHAMY SATHIYENDIRAN. ∗. Department of Chemistry, University of Delhi, Delhi 110 007, India e-mail: mvdiran@yahoo.com; ...

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

    African Journals Online (AJOL)

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

  1. The crystal structure of the phosphatidylinositol 4-kinase II alpha

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

    Roč. 15, č. 10 (2014), s. 1085-1092 ISSN 1469-221X R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : crystal structure * kinase * membrane * Monte Carlo simulations * phosphatidyl inositol Subject RIV: CE - Biochemistry Impact factor: 9.055, year: 2014

  2. Quasi-crystal structures with neutron diffraction

    International Nuclear Information System (INIS)

    Janot, C.

    1992-01-01

    Long-range order in materials can be aperiodic. This paper reports on quasi-periodic lattices that are mathematically derived from cross sections of objects that are periodically arranged in a higher dimensional space. Experimental investigations of these structures require the specification of more parameters than for classical crystallography. Neutron diffraction, with the special technique of contrast variation, allows a reasonable approach to this problem

  3. A unified picture of the crystal structures of metals

    International Nuclear Information System (INIS)

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

    1995-01-01

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

  4. 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.

  5. Band structures in Sierpinski triangle fractal porous phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Vasily F. Shabanov

    2013-08-01

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

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

    DEFF Research Database (Denmark)

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

    specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures...... form the 3'-end of mRNA, is normally the first and also rate-limiting step in cellular mRNA degradation and therefore a key process in the control of eukaryotic mRNA turnover. Since Ccr4p is believed to be the main deadenylase the precise role of Pop2p in the complex is less clear. Nevertheless, Pop2p...

  8. 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.

  9. TE-polarized graphene modes sustained by photonic crystal structures.

    Science.gov (United States)

    Degli-Eredi, I; Sipe, J E; Vermeulen, N

    2015-05-01

    We present the design of a supporting photonic crystal structure that would allow for the excitation of the predicted transverse electric (TE) polarized excitation in a single layer of graphene. We show that it is possible to measure this excitation at room temperature, and that adding an extra layer of dielectric material on top of the structure would further facilitate the experimental observation of the graphene mode.

  10. Protein crystal structure analysis using synchrotron radiation at atomic resolution

    International Nuclear Information System (INIS)

    Nonaka, Takamasa

    1999-01-01

    We can now obtain a detailed picture of protein, allowing the identification of individual atoms, by interpreting the diffraction of X-rays from a protein crystal at atomic resolution, 1.2 A or better. As of this writing, about 45 unique protein structures beyond 1.2 A resolution have been deposited in the Protein Data Bank. This review provides a simplified overview of how protein crystallographers use such diffraction data to solve, refine, and validate protein structures. (author)

  11. Solving crystal structures of metal and chemical hydrides

    OpenAIRE

    Cerny, Radovan

    2008-01-01

    The methods of structural characterization of metal and chemical hydrides are reviewed. The existing difficulties and problems are outlined and possible solutions presented. It is shown that powder diffraction, and especially the Direct Space Method, is essential component of hydride research. Crystal structures containing as many as 55 independent atoms (including hydrogen) have been fully characterized using powder diffraction. This is of great importance, because rapid collection of powder...

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

    Indian Academy of Sciences (India)

    It is well known that domains and crystal structure control the physical properties of ferroelectrics. The ex-situelectric field-dependent structural study, carried out in unpoled/poled crushed powder and bulk samples for (Li 0.5 Nd 0.5 ) 2 + modified 0.95Bi 0.5 Na 0.5 TiO 3 −0.05BaTiO 3 solid solution, established a correlation ...

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

    Science.gov (United States)

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

    2017-12-01

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

  14. Hyperfine structure of positronium energy levels in a crystal

    International Nuclear Information System (INIS)

    Bondarev, I.V.; Kuten, S.A.

    1993-07-01

    Hyperfine structure of positronium energy levels in crystal solids with noncubic lattice is considered. It is shown that due to the hyperfine interaction between the electron and the positron positronium atom in a crystal can have effective quadrupole moment and tensor polarizability. In such a case the effective quadrupole interaction with intracrystalline fields leads to the quadrupole splitting of triplet level and also to the positronium magnetic quenching anisotropy in the presence of external magnetic field. The possibilities of experimental observation of such anisotropy are discussed. (author). 26 refs, 1 fig

  15. Crystal field and crossover effects in the scheelite structure

    Energy Technology Data Exchange (ETDEWEB)

    Kazei, Z.A. [Physics Department, Moscow State University, 119992 Moscow (Russian Federation)]. E-mail: kazei@plms.phys.msu.su; Snegirev, V.V. [Physics Department, Moscow State University, 119992 Moscow (Russian Federation); Andreenko, A.S. [Physics Department, Moscow State University, 119992 Moscow (Russian Federation); Kondratiev, O.D. [Physics Department, Moscow State University, 119992 Moscow (Russian Federation)

    2006-05-15

    The Zeeman effect, magnetization and differential magnetic susceptibility of a DyLiF{sub 4} crystal are investigated experimentally and theoretically in pulsed magnetic fields. Energy level crossing of the Dy{sup 3+} ion is found for H-parallel [0 0 1], resulting in peaks of the differential magnetic susceptibility dM/dH and inflection points in the magnetization curves M(H) at low temperatures. Magnetic anomalies at the crossover in DyLiF{sub 4} are shown to be sensitive to the electron structure of the Dy{sup 3+} ion, which allows this effect to be used for refining the crystal field parameters.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Christopher S. Frampton

    2017-03-01

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

  18. Field-controlled structures in ferromagnetic cholesteric liquid crystals.

    Science.gov (United States)

    Medle Rupnik, Peter; Lisjak, Darja; Čopič, Martin; Čopar, Simon; Mertelj, Alenka

    2017-10-01

    One of the advantages of anisotropic soft materials is that their structures and, consequently, their properties can be controlled by moderate external fields. Whereas the control of materials with uniform orientational order is straightforward, manipulation of systems with complex orientational order is challenging. We show that a variety of structures of an interesting liquid material, which combine chiral orientational order with ferromagnetic one, can be controlled by a combination of small magnetic and electric fields. In the suspensions of magnetic nanoplatelets in chiral nematic liquid crystals, the platelet's magnetic moments orient along the orientation of the liquid crystal and, consequently, the material exhibits linear response to small magnetic fields. In the absence of external fields, orientations of the liquid crystal and magnetization have wound structure, which can be either homogeneously helical, disordered, or ordered in complex patterns, depending on the boundary condition at the surfaces and the history of the sample. We demonstrate that by using different combinations of small magnetic and electric fields, it is possible to control reversibly the formation of the structures in a layer of the material. In such a way, different periodic structures can be explored and some of them may be suitable for photonic applications. The material is also a convenient model system to study chiral magnetic structures, because it is a unique liquid analog of a solid helimagnet.

  19. 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.

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

    KAUST Repository

    Dumbrack, Roland

    2016-01-26

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

  1. Crystal structure and magnetism of UOsAl

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-04-15

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

  2. Band structure and optical properties of diglycine nitrate crystal

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  3. 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.

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

    International Nuclear Information System (INIS)

    Yao, Shuhua; Chen, Yanfeng

    2010-01-01

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

  5. 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...... at the catalytic site as a planar VO3− in complex with water and Mg2+ 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...... nucleotide analogs in the E2·VO3− structure with that in E2·BeF3− (E2P ground state analog) reveals multiple binding modes to the Ca2+-ATPase....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-08-21

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  8. Observations on structural features and characteristics of biological apatite crystals. 7. Observation on lattice imperfection of human tooth and bone crystals II.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-12-01

    In a series of studies to investigate the structural features of the biological crystal, such as the tooth and bone, using an electron microscope, we examined the ultrastructure of the human enamel, dentin, and bone crystals at near atomic resolution and showed the configuration of the hydroxyapatite structure through the cross and longitudinal sections of the enamel, dentin, and bone crystals. Subsequently, based on the results of our observations of the ultrastructure of the tooth and bone crystals, we attempted to clarify the essential structural features and characteristics of the lattice imperfections in the hydroxyapatite structure composing of the human enamel, dentin, and bone crystals from the morphological viewpoint. Therefore, using the same approach, we examined the images of the lattice imperfection of the normal human enamel, dentin, and bone crystals. In this report, following the previous observation of the lattice imperfection on the point defect structure and the dislocations appearing in the inner structure of the crystal, we describe the image of the face defect structure obtained by using the same approach from the sections of the human enamel, dentin, and bone crystals, such as the stacking fault, grain boundary, and others. The materials used for this study were the human enamel, dentin, and bone crystals. The small cubes of the material were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with the HITACHI H-800 H and H-9000 type transmission electron microscopes operated at 200 kV and 300 kV respectively. Each crystal was observed at an initial magnification of 300,000 times and at a final magnification of 10,000,000 times and over. We sincerely believe that the electron micrographs shown in this report are the first to show the images of the lattice imperfections from the sections

  9. 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.

  10. Dynamic Behavior of Helical Structure in Ferroelectric Liquid Crystals

    Science.gov (United States)

    Katayama, Takashi; Uehara, Hiroyuki; Furue, Hirokazu; Hatano, Jun

    2004-09-01

    Ferroelectric liquid crystals (FLCs) take a helical structure which can be unwound by the application of an electric field. Although the static orientational process of FLC molecules is well known, the dynamic modification process of the helical structure is not clearly understood. We formulated equations for simulating the dynamic response in terms of the elastic free-energy density based on the continuum theory, and subsequently was solved the dynamic equations numerically. Furthermore, the conoscopic image was simulated by a 4× 4 matrix method. We investigated the effect of spontaneous polarization and dielectric anisotropy on the dynamic behavior of the helical structure in FLC.

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

    Science.gov (United States)

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

    2015-03-01

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

  12. GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

    Science.gov (United States)

    Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

    2018-04-10

    We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

  13. 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...

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

    African Journals Online (AJOL)

    dihydroisoxazole-4-carboxylate (5) was synthesized and studied by the single crystal X-ray diffraction method. Its structure was confirmed by IR, 1H and 13C NMR spectroscopy, microanalyses, and X-ray single crystal structure determination.

  15. EVO—Evolutionary algorithm for crystal structure prediction

    Science.gov (United States)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

    We present EVO—an evolution strategy designed for crystal structure search and prediction. The concept and main features of biological evolution such as creation of diversity and survival of the fittest have been transferred to crystal structure prediction. EVO successfully demonstrates its applicability to find crystal structures of the elements of the 3rd main group with their different spacegroups. For this we used the number of atoms in the conventional cell and multiples of it. Running EVO with different numbers of carbon atoms per unit cell yields graphite as the lowest energy structure as well as a diamond-like structure, both in one run. Our implementation also supports the search for 2D structures and was able to find a boron sheet with structural features so far not considered in literature. Program summaryProgram title: EVO Catalogue identifier: AEOZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 23488 No. of bytes in distributed program, including test data, etc.: 1830122 Distribution format: tar.gz Programming language: Python. Computer: No limitations known. Operating system: Linux. RAM: Negligible compared to the requirements of the electronic structure programs used Classification: 7.8. External routines: Quantum ESPRESSO (http://www.quantum-espresso.org/), GULP (https://projects.ivec.org/gulp/) Nature of problem: Crystal structure search is a global optimisation problem in 3N+3 dimensions where N is the number of atoms in the unit cell. The high dimensional search space is accompanied by an unknown energy landscape. Solution method: Evolutionary algorithms transfer the main features of biological evolution to use them in global searches. The combination of the "survival of the fittest" (deterministic) and the

  16. Potassium and magnesium succinatouranilates – Synthesis and crystal structure

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-04-15

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

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

    International Nuclear Information System (INIS)

    Wallace, S.T.

    1998-10-01

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

  18. 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.

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

    African Journals Online (AJOL)

    DCC = distance between ring centroids; α perpendicular distance of Cg(I) from ring J;. Cg ring O7N5C4C5N6, O16N11C8C9N12 and O1 thesis and crystal structure of trinuclear potassium(I) complex. Bull. Chem. Soc. Ethiop. 2017, 31(2) anions, and connects with five adjacent OBNF2– anions through seven n bonds ...

  20. The crystal structure of urea oxalic acid (2:1)

    NARCIS (Netherlands)

    Harkema, Sybolt; Bats, J.W.; Weyenberg, A.M.; Feil, D.

    1972-01-01

    The crystal structure of urea oxalic acid, 2[CO(NH2)2].(COOH)2 has been determined using three-dimensional X-ray data, collected on an automatic diffractometer. The space group is P21/c. The lattice constants are: a = 5.058 (3), b = 12.400 (3), c = 6.964 (2) A, fl= 98"13 (7) °. The number of

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 120; Issue 3. Preparation, crystal structure, and characterization of an inorganic-organic hybrid polyoxoniobate [Cu(en)2]3[Cu(en)2(H2O)]1.5[K0.5Nb24O72H14.5]2.25H2O. Jing-Ping Wang Hong-Yu Niu Jing-Yang Niu. Volume 120 Issue 3 May 2008 pp 309-313 ...

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

    Indian Academy of Sciences (India)

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

  3. Structure of REE ethylene diamine tetraacetates in crystals and solutions

    International Nuclear Information System (INIS)

    Ternovaya, T.V.; Shelest, V.P.; Gerasimenko, N.V.; Il'nitskaya, E.L.

    1985-01-01

    Systematic investigations into the structures of REE ethylene diamine tetraacetat complexes in crystals and solutions have been carried out using spectrography, PMR, IR-spectroscopy and thermogravimetric methods. The existence of crystal complexes of similar composition is established for the whole series of REE with the coordination number=9 (in the yttrium group, possibly, 8) and with three coordinated water molecules studied by X-ray diffraction method. Such structures are not realized in solutions, in crystals they are thermodynamically stable in the cerium group and spontaneously disintegrate in the yttrium group to transform to a more stable form KLnEDTAx2H 2 O, analogous in its structure to dissolved. complexes of the group. It is stated that anhydrous complexes don't exist. The EDTA in crystals is always six-dentate and in solutions from La through Nd is five-dentate, from Nd through Tb an equilibrium between two forms is observed with EDTA being five-dentate and six-dentate, and coordination number 8 with a further reduction to 7 and an increase to six-dentant the series end. In the cerium group complexes 3 mol. H 2 O are coordinated in solution, in the middle of the series the form equilibrium with 3 and 2 H 2 O molecules with reduction to 1 H 2 O by the series end, is observed. The isomer number of EDTA and REE complexes (from neodymium to lutetium) is equal to 2. The thermodynamic characteristics of LnEDTA-complexes are completely explained by changes in their structure in the REE series

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

    DEFF Research Database (Denmark)

    Hvam, Jørn Märcher

    ) properties that do not exist in nature. Periodic structuring on the length scale of the wavelength of light as in photonic crystals, on the other hand, dramatically influences the propagation of light as well as the fundamental interaction between light and matter. In this talk, I shall discuss some...... important consequences on spontaneous emission and lasing as well as some aspects of slow light and nonlinear interactions....

  5. Synthesis and crystal structure of [chlorobis (triphenylphospino)(p ...

    Indian Academy of Sciences (India)

    The structure of complex 3 was confirmed by X-ray crystallography. It has been found to crystallize in the triclinic system with space group P-1 and unit cell parameters: a = 10.207(5) Å, b = 13.027(5) Å, c = 16.269(5) Å, = 100.054(5)°, = 99.228(5)° and = 97.234(5)°. This complex has distorted tetrahedral geometry with ...

  6. Crystal structure of the uranyl-oxide mineral rameauite

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

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

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

    Indian Academy of Sciences (India)

    The molecular and crystal structure of the adduct NF3·BF3 was studied computationally using density functional theory. It shows that the adduct exists in the form of a complex but is not ionic. The heats of formation in the gas and the condensed phase of the adduct are −1266.09 and −1276.37 kJ·mol−1, respectively, which ...

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

    African Journals Online (AJOL)

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

  9. Luminescence properties of piezoelectric single crystals with langasite structure

    International Nuclear Information System (INIS)

    Itoh, Minoru; Takagi, Shinya; Kitaura, Mamoru; Fujita, Masami; Endo, Naoyuki

    2007-01-01

    Luminescence properties of single crystals of langasite (LGS), langataite (LGT), and langanite (LGN) are investigated at 5 K by using synchrotron radiation as an exciting light source. Two emission bands are observed at 420 and 500 nm in LGS, at 410 and 460 nm in LGT, and at 500 and 535 nm in LGN. The origin of these bands is discussed by reference to the electronic structure of LGS

  10. 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...

  11. 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.

  12. Revealing Structural Transformations during Crystallization of DNA-Nanoparticle Assemblies

    Science.gov (United States)

    Zhang, Yugang; Lu, Fang; van der Lelie, Daniel; Gang, Oleg

    2013-03-01

    Nanoparticle assembly via sequence-specific DNA recognition emerges as a powerful strategy for the fabrication of nanoparticle (NP)-based crystalline materials. Generally, a delicate thermal annealing is essential for the crystallization of NPs from kinetically trapped disordered states. Due to the complex coupling between interactions, entropic and chain effects in these systems, the crystallization pathway remains an intricate and open question. Herein, we present an experimental study of the crystallization process for DNA-directed nanoparticle assembly systems using synchrotron-based small angle x-ray scattering (SAXS). We demonstrated the effects of two crystallization-dominant factors, namely, temperature and volume fraction, on the structural transformation and order development. By combining a single component and binary systems we uncovered the evolution of global and local particle arrangements, such as correlation length, compositional disorder and coordination number, during the phase transformation. Research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

  13. Synthesis and crystal structure determination of Br2SeIBr ...

    Indian Academy of Sciences (India)

    Unknown

    Abstract. In this paper polyhalogen–chalcogen Br2SeIBr was synthesized and the crystal structure was de- termined by single crystal X-ray diffraction method. This compound was prepared in the temperature range. 150–50°C which was brownish-red in colour and crystallized in monoclinic crystal system and space group.

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

    African Journals Online (AJOL)

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

  15. Crystal structure of (V, Mo)84P49

    International Nuclear Information System (INIS)

    Lomnitskaya, Ya.F.; Orishchin, S.V.; Kuz'ma, Yu.B.; Babizhetskij, V.S.; Geren, R.

    2004-01-01

    New ternary compound (V, Mo) 84 P 49 of the V 3.2 Mo 8.8 P 7.0 composition was synthesized. It is found by means of technique of monocrystal the compound is crystallized as its own structural type: sp.gr. P6-bar, a=2.52015(3), c=0.330070(5) nm; R F =0.054, R ω F=0.058 for 1894 reflexes with F hkl >4.0σ(F hkl ). Parameters of atoms and technique of their distribution in the structure were determined. The (V, Mo) 84 P 49 structure combines in association with the earlier known (Ti, Mo) 36 P 21 structure into the new homologous row, the first member of which is a Cr 12 P 7 structure [ru

  16. Crystal structure of inactive form of Rab3B

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-11-01

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

  18. Crystal Structure of the Yeast Nicotinamidase Pnc1p

    OpenAIRE

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

    2007-01-01

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

  19. 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.

  20. Crystal structure of human protein kinase CK2

    DEFF Research Database (Denmark)

    Niefind, K; Guerra, B; Ermakowa, I

    2001-01-01

    The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalytic...... subunits, which make no direct contact with one another. Each catalytic subunit interacts with both regulatory chains, predominantly via an extended C-terminal tail of the regulatory subunit. The CK2 structure is consistent with its constitutive activity and with a flexible role of the regulatory subunit...

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

    Science.gov (United States)

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

    2017-09-07

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

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

    Science.gov (United States)

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

    2016-04-14

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

  3. 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.

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

    Science.gov (United States)

    Yusupova, Gulnara; Yusupov, Marat

    2017-01-01

    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’. PMID:28138070

  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...... contains three square pyramidal Bi sites, an octahedrally coordinated Bi site as well as two tetrahedrally and two irregularly coordinated Cu sites. The structure is an intergrowth of PbS-like slabs with irregularly configured slabs of Bi pyramids and Cu tetrahedra. It contains covalently bonded Se-2...... groups. Isotypy with Cu4Bi4S9 is connected with substantial changes in coordination details for two out of five distinct Cu sites. Modular relationships to the structures of the cuprobismutite series of Cu-Bi sulfo-salts cart be expressed as different ways of recombination of the same large structural...

  6. 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.

  7. 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].

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Sam Horrell

    2018-05-01

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

  13. 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.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    Science.gov (United States)

    Clark, Noel A.

    2000-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enable the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable condensed phase fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new liquid crystal physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and

  16. Structure and Growth Control of Organic–Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals

    Science.gov (United States)

    Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong

    2016-01-01

    Recently, organic–inorganic halide perovskites have sparked tremendous research interest because of their ground‐breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light‐emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high‐quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three‐dimensional large sized single crystals, two‐dimensional nanoplates, one‐dimensional nanowires, to zero‐dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high‐performance (opto)electronic devices. PMID:27812463

  17. Structure and Growth Control of Organic-Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals.

    Science.gov (United States)

    Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong; Liang, Ziqi

    2016-04-01

    Recently, organic-inorganic halide perovskites have sparked tremendous research interest because of their ground-breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light-emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high-quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three-dimensional large sized single crystals, two-dimensional nanoplates, one-dimensional nanowires, to zero-dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high-performance (opto)electronic devices.

  18. Crystal structure of mimivirus uracil-DNA glycosylase.

    Directory of Open Access Journals (Sweden)

    Eunju Kwon

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

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

    Science.gov (United States)

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

    2018-04-01

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

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

    Science.gov (United States)

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

    2012-02-01

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

  1. 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.

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

    Science.gov (United States)

    Yang, Yong; Kawazoe, Yoshiyuki

    2018-03-01

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

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

    Science.gov (United States)

    Rajkumar, M.; Chandramohan, A.

    2017-12-01

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

  4. 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…

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

    Indian Academy of Sciences (India)

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

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

    Science.gov (United States)

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

    2011-07-01

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

  7. Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii

    Science.gov (United States)

    Wang, Ganggang; Guo, Rong; Bartlam, Mark; Yang, Haitao; Xue, Hong; Liu, Yiwei; Huang, Li; Rao, Zihe

    2003-01-01

    The Sac10b family consists of a group of highly conserved DNA binding proteins from both the euryarchaeotal and the crenarchaeotal branches of Archaea. The proteins have been suggested to play an architectural role in the chromosomal organization in these organisms. Previous studies have mainly focused on the Sac10b proteins from the crenarchaeota. Here, we report the 2.0 Å resolution crystal structure of Mja10b from the euryarchaeon Methanococcus jannaschii. The model of Mja10b has been refined to an R-factor of 20.9%. The crystal structure of an Mja10b monomer reveals an α/β structure of four β-strands and two α-helices, and Mja10b assembles into a dimer via an extensive hydrophobic interface. Mja10b has a similar topology to that of its crenarchaeota counterpart Sso10b (also known as Alba). Structural comparison between the two proteins suggests that structural features such as hydrophobic inner core, acetylation sites, dimer interface, and DNA binding surface are conserved among Sac10b proteins. Structural differences between the two proteins were found in the loops. To understand the structural basis for the thermostability of Mja10b, the Mja10b structure was compared to other proteins with similar topology. Our data suggest that extensive ion-pair networks, optimized accessible surface area and the dimerization via hydrophobic interactions may contribute to the enhanced thermostability of Mja10b. PMID:14627741

  8. Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland.

    Science.gov (United States)

    Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O'Grady, Martin; Mariani, Stefano; Phillimore, Albert

    2014-03-01

    We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Ireland, Britain and continental Europe. A total of 752 pike ( Esox lucius ) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two 'waves', the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species.

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

    Science.gov (United States)

    Narihiro, Takashi; Tamaki, Hideyuki; Akiba, Aya; Takasaki, Kazuto; Nakano, Koichiro; Kamagata, Yoichi; Hanada, Satoshi; Maji, Taizo

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

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

  11. Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland

    Science.gov (United States)

    Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O’Grady, Martin; Mariani, Stefano; Phillimore, Albert

    2014-01-01

    Aim We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Location Ireland, Britain and continental Europe. Methods A total of 752 pike (Esox lucius) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Results Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Main conclusions Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two ‘waves’, the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies

  12. Crystal structure of the DNA sequence d(CGTGAATTCACG)2 with DAPI.

    Science.gov (United States)

    Sbirkova-Dimitrova, Hristina I; Shivachev, Boris

    2017-09-01

    The structure of 4',6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space group P2 1 2 1 2 1 by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA-DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A-T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  15. Structure and Chemical Durability of Lead Crystal Glass.

    Science.gov (United States)

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

    2016-11-01

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

  16. Crystal Structure of Three Compounds Related to Triphenylene and Tetracyanoquinodimethane

    DEFF Research Database (Denmark)

    Andresen, T.L.; Krebs, Frederik C; Larsen, M.

    1999-01-01

    The crystal structures of a charge-transfer complex of triphenylene with 1,3,5-tris(2,2-dicyanovinyl) benzene (1), a complex of 2,3,6,7,10,11-hexamethoxytriphenylene with 2,5-dichlorotetracyanoquinodimethane (2) and also 2,5-dichlorotetracyanoquinodimethane itself (3) have been determined. Compou...... = 83.73(3), gamma = 66.06(3)degrees. Compound 3 is monoclinic, space group I2/a (C2/c), with a = 13.692(3), b = 7.7183(15), c = 16.391(3) Angstrom, beta = 99.47(3)degrees. The structures of 1 and 2 consist of mixed stacks of donors and accepters. The structures of 2 and 3 both include 1...

  17. 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).

  18. Crystal structure of the yeast nicotinamidase Pnc1p.

    Science.gov (United States)

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

    2007-05-01

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

  19. New halides of neodymium and their crystal structures

    International Nuclear Information System (INIS)

    Loechner, U.

    1980-01-01

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

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

    Science.gov (United States)

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

    2015-07-15

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

  1. Crystal structure of the Al2CuIr phase

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  2. 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 Mn 4 CaO 5 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.

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

    Science.gov (United States)

    Deller, Marc C.; Rupp, Bernhard

    2015-09-01

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

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

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-12-01

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

  5. Crystallization and preliminary structural analyses of glutamate dehydrogenase from Peptoniphilus asaccharolyticus

    OpenAIRE

    Oliveira, Tania F.; Carrigan, John B.; Hamza, Muaawia A.; Sharkey, Michael A.; Engel, Paul C.; Khan, Amir R.

    2010-01-01

    Selenomethionine-derivatized glutamate dehydrogenase from P. asaccharolyticus has been crystallized. Diffraction data were collected to 3.5 Å resolution from crystals belonging to the rhombohedral space group H32 and structure determination is in progress.

  6. Structure and Dynamics of Freely Suspended Liquid Crystals

    Science.gov (United States)

    Clark, Noel A.

    2004-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase

  7. Correlation between crystal structure and mobility in organic field-effect transistors based on single crystals of tetrathiafulvalene derivatives.

    Science.gov (United States)

    Mas-Torrent, Marta; Hadley, Peter; Bromley, Stefan T; Ribas, Xavi; Tarrés, Judit; Mas, Montserrat; Molins, Elies; Veciana, Jaume; Rovira, Concepció

    2004-07-14

    Recently, it was reported that crystals of the organic material dithiophene-tetrathiafulvalene (DT-TTF) have a high field-effect charge carrier mobility of 1.4 cm(2)/(V x s). These crystals were formed by a simple drop-casting method, making this material interesting to investigate for possible applications in low-cost electronics. Here, organic single-crystal field-effect transistors based on materials related to DT-TTF are presented and a clear correlation between the crystal structure and the electrical characteristics is observed. The observed relationship between the mobilities in the different crystal structures is strongly corroborated by calculations of both the molecular reorganization energies and the maximum intermolecular transfer integrals. The most suitable materials described here exhibit mobilities that are among the highest reported for organic field-effect transistors and that are the highest reported for solution-processed materials.

  8. Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase

    International Nuclear Information System (INIS)

    Zhang, R.; Evans, G.; Rotella, F.J.; Westbrook, E.M.; Beno, D.; Huberman, E.; Joachimiak, A.; Collart, F.R.

    1999-01-01

    IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K m for NAD (1180 μM) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 (angstrom) with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione β-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors

  9. Crystal structure of La2Mo2O9 single crystals doped with bismuth

    International Nuclear Information System (INIS)

    Alekseeva, O. A.; Verin, I. A.; Sorokina, N. I.; Krasil'nikova, A. E.; Voronkova, V. I.

    2010-01-01

    Precision X-ray diffraction studies of La 2-x Bi x Mo 2 O 9 (x = 0.04, 0.06, and 0.18) single crystals are performed. It is found that in the compounds doped with bismuth, analogously with the structure of the metastable β ms phase of pure La 2 Mo 2 O 9 (LM), the La, Mo1, and O1 atoms deviate from the threefold axis on which they are located in the high-temperature β phase. It is shown that bismuth atoms substitute for part of lanthanum atoms and occupy a position at the threefold axis in the neighborhood of the split lanthanum position. The implantation of bismuth atoms in the LM structure results in the return of a part of the molybdenum atoms to the position at the threefold axis. The occupancy of this position is equal to the occupancy of the bismuth atomic position.

  10. Crystal Structures of Human GlyRα3 Bound to Ivermectin

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Xin; Chen, Hao; Shaffer, Paul L.

    2017-06-01

    Ivermectin acts as a positive allosteric modulator of several Cys-loop receptors including the glutamate-gated chloride channels (GluCls), γ-aminobutyric acid receptors (GABAARs), glycine receptors (GlyRs), and neuronal α7-nicotinic receptors (α7 nAChRs). The crystal structure of Caenorhabditis elegans GluCl complexed with ivermectin revealed the details of its ivermectin binding site. Although the electron microscopy structure of zebrafish GlyRα1 complexed with ivermectin demonstrated a similar binding orientation, detailed structural information on the ivermectin binding and pore opening for Cys-loop receptors in vertebrates has been elusive. Here we present the crystal structures of human GlyRα3 in complex with ivermectin at 2.85 and 3.08 Å resolution. Our structures allow us to explore in detail the molecular recognition of ivermectin by GlyRs, GABAARs, and α7 nAChRs. Comparisons with previous structures reveal how the ivermectin binding expands the ion channel pore. Our results hold promise in structure-based design of GlyR modulators for the treatment of neuropathic pain.

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

    Indian Academy of Sciences (India)

    Wintec

    tion for the growth of these crystals is given. The stoichiometry of the grown crystals ... 646. Table 1. Growth parameters of zirconium sulphoselenide single crystal grown using chemical vapour transport technique. Physical .... The needle shaped, black or radish shining layered single crystals of zirconium sulphoselenide ...

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2010-09-01

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

  14. Crystal structure and Hirshfeld surface analysis of pulcherrin J

    Directory of Open Access Journals (Sweden)

    K. Osahon Ogbeide

    2017-10-01

    Full Text Available The title compound, C29H36O4 [systematic name (4aR,5R,6aS,7R,11aS,11bR-4a-hydroxy-4,4,7,11b-tetramethyl-1,2,3,4,4a,5,6,6a,7,11,11a,11b-dodecahydrophenanthro[3,2-b]furan-5-yl cinnamate], a natural diterpene known as pulcherrin J, was isolated from stem barks of medicinally important Caesalpinia pulcherrima (L.. The crystal structure of pulcherrin J shows it to be composed of a central core of three trans-fused cyclohexane rings and a near planar five-membered furan ring, along with an axially oriented cinnamate moiety and an hydroxy substituent attached at positions 4a and 5 of the steroid ring system, respectively. The absolute structure was established with the use of Cu Kα radiation. In the crystal, molecules are linked by O—H...O hydrogen bonds to generate [100] C(8 chains. Hirshfeld surface analysis indicates that the most significant contacts in packing are H...H (67.5%, followed by C...H (19.6% and H...O (12.9%.

  15. Structure and properties of some directionally crystallized nickel base eutectiecs

    International Nuclear Information System (INIS)

    Nesterovich, L.N.; Kupchenko, G.V.; Ivanov, N.P.; Budnikov, V.T.

    1976-01-01

    A microstructure of eutectic alloys has been studied depending on the rate of crystallization. The Chokhralsky-Bridgeman methods have been employed to obtain the eutectic composite structures in γ Ni/W/-W, γ Ni/Mo/-MoNi, γ NiNi/W/-W, γ Ni/Al, Mo/-Mo show a high short-term strength at 900 to 1100 deg C and, inspite of their fairly high melting temperatures (1500 and 1300 deg C), the long-term strength of these alloys corresponds to tast of commercial casting heat-resistant products. The derected crystallized eutectic Ni 3 Al-Ni 3 Nb with a melting temperature of 1280 deg C exhibits far better long-term strength characteristics sigma sup(1000)sub(100) and sigma sup(1000)sub(1000) both as compared with the other eutectics under study and with the best commercial casting heat-resistant alloys. The eutectics under study differ not only in their melting temperature, structure and volumetric phase relation, but also in the nature of hardening phases

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  17. Structure of cleaved (001) USb2 single crystal

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  18. Enabling structure-based drug design of Tyk2 through co-crystallization with a stabilizing aminoindazole inhibitor

    Science.gov (United States)

    2012-01-01

    Background Structure-based drug design (SBDD) can accelerate inhibitor lead design and optimization, and efficient methods including protein purification, characterization, crystallization, and high-resolution diffraction are all needed for rapid, iterative structure determination. Janus kinases are important targets that are amenable to structure-based drug design. Here we present the first mouse Tyk2 crystal structures, which are complexed to 3-aminoindazole compounds. Results A comprehensive construct design effort included N- and C-terminal variations, kinase-inactive mutations, and multiple species orthologs. High-throughput cloning and expression methods were coupled with an abbreviated purification protocol to optimize protein solubility and stability. In total, 50 Tyk2 constructs were generated. Many displayed poor expression, inadequate solubility, or incomplete affinity tag processing. One kinase-inactive murine Tyk2 construct, complexed with an ATP-competitive 3-aminoindazole inhibitor, provided crystals that diffracted to 2.5–2.6 Å resolution. This structure revealed initial “hot-spot” regions for SBDD, and provided a robust platform for ligand soaking experiments. Compared to previously reported human Tyk2 inhibitor crystal structures (Chrencik et al. (2010) J Mol Biol 400:413), our structures revealed a key difference in the glycine-rich loop conformation that is induced by the inhibitor. Ligand binding also conferred resistance to proteolytic degradation by thermolysin. As crystals could not be obtained with the unliganded enzyme, this enhanced stability is likely important for successful crystallization and inhibitor soaking methods. Conclusions Practical criteria for construct performance and prioritization, the optimization of purification protocols to enhance protein yields and stability, and use of high-throughput construct exploration enable structure determination methods early in the drug discovery process. Additionally, specific

  19. 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.

  20. Silicon crystals: Process for manufacturing wafer-like silicon crystals with a columnar structure

    Science.gov (United States)

    Authier, B.

    1978-01-01

    Wafer-like crystals suitable for making solar cells are formed by pouring molten Si containing suitable dopants into a mold of the desired shape and allowing it to solidify in a temperature gradient, whereby the large surface of the melt in contact with the mold is kept at less than 200 D and the free surface is kept at a temperature of 200-1000 D higher, but below the melting point of Si. The mold can also be made in the form of a slit, whereby the 2 sides of the mold are kept at different temperatures. A mold was milled in the surface of a cylindrical graphite block 200 mm in diameter. The granite block was induction heated and the bottom of the mold was cooled by means of a water-cooled Cu plate, so that the surface of the mold in contact with one of the largest surfaces of the melt was held at approximately 800 D. The free surface of the melt was subjected to thermal radiation from a graphite plate located 2 mm from the surface and heated to 1500 D. The Si crystal formed after slow cooling to room temperature had a columnar structure and was cut with a diamond saw into wafers approximately 500 mm thick. Solar cells prepared from these wafers had efficiencies of 10 to 11%.

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

    Science.gov (United States)

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

    2009-10-01

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

  2. Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

    Science.gov (United States)

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

    The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

  3. Investigation into the crystal structure of the perovskite lead hafnate, PbHfO3

    International Nuclear Information System (INIS)

    Corker, D.L.; Glazer, A.M.; Kaminsky, W.; Whatmore, R.W.; Dec, J.; Roleder, K.

    1998-01-01

    The room-temperature crystal structure of the perovskite lead hafnate PbHfO 3 is investigated using both low-temperature single crystal X-ray diffraction (Mo Kα radiation, λ = 0.71069 A) and polycrystalline neutron diffraction (D1A instrument, ILL, λ = 1.90788 A). Single crystal X-ray data at 100 K: space group Pbam, a = 5.856 (1), b = 11.729 (3), c = 8.212 (2) A, V = 564.04 A 3 with Z = 8, μ = 97.2 mm -1 , F(000) = 1424, final R 0.038, wR = 0.045 over 439 reflections with F > 1.4σ(F). Polycrystalline neutron data at 383 K: a = 5.8582 (3), b = 11.7224 (5), c = 8.2246 (3) A, V 564.80 A 3 with χ 2 = 1.62. Although lead hafnate has been thought to be isostructural with lead zirconate, no complete structure determination has been reported, as crystal structure analysis in both these materials is not straightforward. One of the main difficulties encountered is the determination of the oxygen positions, as necessary information lies in extremely weak l = 2n + 1 X-ray reflections. To maximize the intensity of these reflections the X-ray data are collected at 100 K with unusually long scans, a procedure which had previously been found successful with lead zirconate. In order to establish that no phase transitions exist between room temperature and 100 K, and hence that the collected X-ray data are relevant to the room-temperature structure, birefringence measurements for both PbZrO 3 and PbHfO 3 are also reported. (orig.)

  4. Crystal structure of the adenosine A2Areceptor bound to an antagonist reveals a potential allosteric pocket.

    Science.gov (United States)

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K

    2017-02-21

    The adenosine A 2A receptor (A 2A R) has long been implicated in cardiovascular disorders. As more selective A 2A R ligands are being identified, its roles in other disorders, such as Parkinson's disease, are starting to emerge, and A 2A R antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A 2A receptor bound to compound 1 (Cmpd-1), a novel A 2A R/ N -methyl d-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A 2A receptor with a cytochrome b562-RIL (BRIL) fusion (A 2A R-BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A 2A R-BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1-bound A 2A R-BRIL prevented formation of the lattice observed with the ZM241385-bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A 2A R structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr9 1.35 and Tyr271 7.36 , which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A 2A R structures, highlighting flexibility in the binding pocket that may facilitate the development of A 2A R-selective compounds for the treatment of Parkinson's disease.

  5. The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.

    Directory of Open Access Journals (Sweden)

    Zamia Diaz

    2009-08-01

    Full Text Available Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2. Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (alphabeta(8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.

  6. Crystal structures of the isochorismatase domains from Vibrio anguillarum.

    Science.gov (United States)

    Du, Jiansen; Deng, Tian; Ma, Qingjun

    2017-08-26

    Antibiotic resistance is becoming a global threat and overuse of antibiotics in aquaculture disease control worsens the situation. To reduce the risk of drug resistance developed in aquaculture, safer biocontrol programs are needed. Antivirulence therapy, with less chance for developing drug resistance, is a promising approach. To facilitate antivirulence inhibitor design against Vibrio anguillarum, a serious aquaculture pathogen, we present crystal structures for isochorismatase domains of AngB and VabB, which are required to synthesize siderophore, a critical virulence factor. Both structures are highly similar to known isochorismatases in fold and active site, therefore we conclude inhibitors for isochorismatases can be developed in a common framework. The structural information will improve design of virulence inhibitors against Vibrio anguillarum. We also firstly report that isochorismatase family could bind endogenous metabolite during the hetero-expression process, which is likely nicotinic acid, nicotinamide or pyrazinic acid, based on structural analysis and affinity prediction. Taken together, our results provide precise structural information of isochorismatase domains for antivirulence inhibitor design against Vibrio anguillarum. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. A computational tool to design and generate crystal structures

    Science.gov (United States)

    Ferreira, R. C.; Vieira, M. B.; Dantas, S. O.; Lobosco, M.

    2014-03-01

    The evolution of computers, more specifically regarding the increased storage and data processing capacity, allowed the construction of computational tools for the simulation of physical and chemical phenomena. Thus, practical experiments are being replaced, in some cases, by computational ones. In this context, we can highlight models used to simulate different phenomena on atomic scale. The construction of these simulators requires, by developers, the study and definition of accurate and reliable models. This complexity is often reflected in the construction of complex simulators, which simulate a limited group of structures. Such structures are sometimes expressed in a fixed manner using a limited set of geometric shapes. This work proposes a computational tool that aims to generate a set of crystal structures. The proposed tool consists of a) a programming language, which is used to describe the structures using for this purpose their characteristic functions and CSG (Constructive Solid Geometry) operators, and b) a compiler/interpreter that examines the source code written in the proposed language, and generates the objects accordingly. This tool enables the generation of an unrestricted number of structures, which can be incorporated in simulators such as the Monte Carlo Spin Engine, developed by our group at UFJF.

  8. Crystal Structure of the Human Cytomegalovirus Glycoprotein B.

    Directory of Open Access Journals (Sweden)

    Heidi G Burke

    2015-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-08-09

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  11. Crystal growth, structure, and electronic band structure of tetracene-TCNQ

    NARCIS (Netherlands)

    Buurma, A. J. C.; Jurchescu, O. D.; Shokaryev, I.; Baas, J.; Meetsma, A.; de Wijs, G. A.; de Groot, R. A.; Palstra, T. T. M.

    2007-01-01

    We have grown the charge-transfer salt of the electron acceptor 7,7,8,8-tetracyanoquinodimethane (TCNQ) and the electron donor tetracene using physical vapor transport. The crystal structure was solved by singlecrystal X-ray diffraction and the symmetry was found to be triclinic (space group PT).

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

    African Journals Online (AJOL)

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

  13. VO2 (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    Science.gov (United States)

    Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michaël

    2014-05-01

    Well crystallized VO2 (A) microrods were grown via a single step hydrothermal reaction in the presence of V2O5 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 VO2 (A) micro rods. The structural and electronic transitions in VO2 (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 VO2 (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO2 (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO2 (M1) are described.

  14. Crystal and mol-ecular structure of aflatrem.

    Science.gov (United States)

    Lenta, Bruno N; Ngatchou, Jules; Kenfack, Patrice T; Neumann, Beate; Stammler, Hans-Georg; Sewald, Norbert

    2015-11-01

    The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the mol-ecule. 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-dioxabi-cyclo-[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 dioxabi-cyclo-[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the mol-ecule exhibits a tilt of 2.02 (1)° between its two rings. In the crystal, O-H⋯O hydrogen bonds connect mol-ecules into chains along [010]. Weak N-H⋯π inter-actions connect these chains, forming sheets parallel to (10-1).

  15. Observations of structural features and characteristics of biological apatite crystals. 3. Observation on ultrastructure of human dentin crystals.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-03-01

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

  16. The use of small-molecule structures to complement protein-ligand crystal structures in drug discovery.

    Science.gov (United States)

    Groom, Colin R; Cole, Jason C

    2017-03-01

    Many ligand-discovery stories tell of the use of structures of protein-ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein-ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.

  17. Crystal structure of microbial transglutaminase from Streptoverticillium mobaraense.

    Science.gov (United States)

    Kashiwagi, Tatsuki; Yokoyama, Kei-Ichi; Ishikawa, Kohki; Ono, Kunio; Ejima, Daisuke; Matsui, Hiroshi; Suzuki, Ei-ichiro

    2002-11-15

    The crystal structure of a microbial transglutaminase from Streptoverticillium mobaraense has been determined at 2.4 A resolution. The protein folds into a plate-like shape, and has one deep cleft at the edge of the molecule. Its overall structure is completely different from that of the factor XIII-like transglutaminase, which possesses a cysteine protease-like catalytic triad. The catalytic residue, Cys(64), exists at the bottom of the cleft. Asp(255) resides at the position nearest to Cys(64) and is also adjacent to His(274). Interestingly, Cys(64), Asp(255), and His(274) superimpose well on the catalytic triad "Cys-His-Asp" of the factor XIII-like transglutaminase, in this order. The secondary structure frameworks around these residues are also similar to each other. These results imply that both transglutaminases are related by convergent evolution; however, the microbial transglutaminase has developed a novel catalytic mechanism specialized for the cross-linking reaction. The structure accounts well for the catalytic mechanism, in which Asp(255) is considered to be enzymatically essential, as well as for the causes of the higher reaction rate, the broader substrate specificity, and the lower deamidation activity of this enzyme.

  18. 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.

  19. Crystal Structure of Three Compounds Related to Triphenylene and Tetracyanoquinodimethane

    DEFF Research Database (Denmark)

    Andresen, T.L.; Krebs, Frederik C; Larsen, M.

    1999-01-01

    The crystal structures of a charge-transfer complex of triphenylene with 1,3,5-tris(2,2-dicyanovinyl) benzene (1), a complex of 2,3,6,7,10,11-hexamethoxytriphenylene with 2,5-dichlorotetracyanoquinodimethane (2) and also 2,5-dichlorotetracyanoquinodimethane itself (3) have been determined. Compound...... = 83.73(3), gamma = 66.06(3)degrees. Compound 3 is monoclinic, space group I2/a (C2/c), with a = 13.692(3), b = 7.7183(15), c = 16.391(3) Angstrom, beta = 99.47(3)degrees. The structures of 1 and 2 consist of mixed stacks of donors and accepters. The structures of 2 and 3 both include 1......,2-dichlorobenzene solvent molecules. Weak hydrogen bonds are present in the structures of 1 and 2. Based on comparisons of bond lengths the electronic charge-transfer in 2 has been estimated to be about 0.3 e. The synthesis of 1,3,5-tris(2,2-dicyanovinyl) benzene is also reported....

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

    International Nuclear Information System (INIS)

    Dreveny, Ingrid

    2001-09-01

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

  1. Refinement of crystal structures by the Rietveld method

    International Nuclear Information System (INIS)

    Izumi, Fujio

    1990-01-01

    The Rietveld method which makes structures fine by one step, by applying the method of least squares to X-ray powder diffraction and neutron powder diffraction data, is rooting as the powerful research means for studying the structures of polycrystalline bodies also in Japan. By measuring the data of high resolution utilizing a radiant light source or a powerful neutron source, as for the compounds having relatively simple structures, the results of analysis with the accuracy comparable with single crystal process can be obtained. In order to take further more information in, it is better to add restraining condition to the distance between atoms and coupling angle, or to analyze by combining plural sets of intensity data. These techniques were applied to the analysis of modulated structures, and contributed to the determination of oxygen configuration, and to the elucidation of the cause of doping positive holes into CuO 2 sheets. The more exact description of theoretical diffraction intensity remains as an important subject hereafter. The significance of existence of Rietveld method, the course of its development, model function, the comparison with other powder data analysis method, the method of collecting intensity data, profile function, analysis software and others are reported. (K.I.) 61 refs

  2. Crystal structure of substrate free form of glycerol dehydratase

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Der-Ing; Dotson, Garry; Turner, Jr., Ivan; Reiss, Lisa; Emptage, Mark (Du Pont)

    2010-03-08

    Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B{sub 12}-dependent radical mechanism. The crystal structure of substrate free form of GDH in complex with cobalamin and K{sup +} has been determined at 2.5 {angstrom} resolution. Its overall fold and the subunit assembly closely resemble those of DDH. Comparison of this structure and the DDH structure, available only in substrate bound form, shows the expected change of the coordination of the essential K{sup +} from hexacoordinate to heptacoordinate with the displacement of a single coordinated water by the substrate diol. In addition, there appears to be an increase in the rigidity of the K{sup +} coordination (as measured by lower B values) upon the binding of the substrate. Structural analysis of the locations of conserved residues among various GDH and DDH sequences has aided in identification of residues potentially important for substrate preference or specificity of protein-protein interactions.

  3. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-09

    ABSTRACT

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

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

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

    Directory of Open Access Journals (Sweden)

    Gerd Meyer

    2010-12-01

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

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

    Science.gov (United States)

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

    2014-08-01

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  7. Similarity of the crystal and solution structure of yeast tRNAPhe

    NARCIS (Netherlands)

    Robillard, G.T.; Tarr, C.E.; Vosman, F.; Berendsen, H.J.C.

    1976-01-01

    A comparison of the crystal and the solution structure of yeast tRNAPhe has been carried out by calculating the low field NMR spectrum from refined X-ray structure coordinates. The similarity between the computed and observed spectra show that the crystal and solution structure are virtually

  8. Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism.

    Science.gov (United States)

    O'Neal, Claire J; Amaya, Edward I; Jobling, Michael G; Holmes, Randall K; Hol, Wim G J

    2004-04-06

    Cholera toxin (CT) is a heterohexameric bacterial protein toxin belonging to a larger family of A/B ADP-ribosylating toxins. Each of these toxins undergoes limited proteolysis and/or disulfide bond reduction to form the enzymatically active toxic fragment. Nicking and reduction render both CT and the closely related heat-labile enterotoxin from Escherichia coli (LT) unstable in solution, thus far preventing a full structural understanding of the conformational changes resulting from toxin activation. We present the first structural glimpse of an active CT in structures from three crystal forms of a single-site A-subunit CT variant, Y30S, which requires no activational modifications for full activity. We also redetermined the structure of the wild-type, proenzyme CT from two crystal forms, both of which exhibit (i) better geometry and (ii) a different A2 "tail" conformation than the previously determined structure [Zhang et al. (1995) J. Mol. Biol. 251, 563-573]. Differences between wild-type CT and active CTY30S are observed in A-subunit loop regions that had been previously implicated in activation by analysis of the structure of an LT A-subunit R7K variant [van den Akker et al. (1995) Biochemistry 34, 10996-11004]. The 25-36 activation loop is disordered in CTY30S, while the 47-56 active site loop displays varying degrees of order in the three CTY30S structures, suggesting that disorder in the activation loop predisposes the active site loop to a greater degree of flexibility than that found in unactivated wild-type CT. On the basis of these six new views of the CT holotoxin, we propose a model for how the activational modifications experienced by wild-type CT are communicated to the active site.

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

    International Nuclear Information System (INIS)

    Serna, Pedro Vera; Campos, Cecilio Garcia; De Jesus, Felix Sanchez; Miro, Ana Maria Bolarin; Loran, Jose Antonio Juanico; Longwell, Jeffrey

    2016-01-01

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

  10. Crystal structure of 6-deoxy-α-l-psicofuranose

    Directory of Open Access Journals (Sweden)

    Akihide Yoshihara

    2015-12-01

    Full Text Available The title compound, C6H12O5, was crystallized from an aqueous solution of 6-deoxy-l-psicose (6-deoxy-l-allulose, (3S,4S,5S-1,3,4,5-tetrahydroxyhexan-2-one, and the molecule was confirmed as α-furanose with a 3T4 (or E4 conformation, which is a predominant tautomer in solution. This five-membered furanose ring structure is the second example in the field of the 6-deoxy-ketohexose family. The cell volume of the title compound [742.67 (7 Å3, Z = 4 at room temperature] is only 1.4% smaller than that of β-d-psicopyranose, C6H12O6 (753.056 Å3, Z = 4 at room temperature.

  11. Interfacial structure in epitaxial perovskite oxides on (001) Ge crystal

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Xuan [National Laboratory of Solid State Microstructures and Department of Materials Science and Engineering, College of Engineering and Applied Science, Collaborative Innovation Center of Advanced Materials, Nanjing University, Nanjing 210093 (China); Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973 (United States); Ahmadi-Majlan, K.; Ngai, Joseph H. [Department of Physics, University of Texas at Arlington, 502 Yates Street, Arlington, Texas 76019 (United States); Wu, Di [National Laboratory of Solid State Microstructures and Department of Materials Science and Engineering, College of Engineering and Applied Science, Collaborative Innovation Center of Advanced Materials, Nanjing University, Nanjing 210093 (China); Su, Dong, E-mail: dsu@bnl.gov [Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973 (United States)

    2015-01-19

    We investigated the interfacial structure of hetero-epitaxial SrZr{sub 0.68}Ti{sub 0.32}O{sub 3} thin film deposited on (001) Ge single crystal via transmission electron microscopy (TEM). The results from high-resolution scanning TEM and electron energy-loss spectroscopy show an atomically abrupt interface without secondary phase. We found misfit dislocations with Burgers vector of 1/2a 〈111〉 and threading dislocations with Burgers vector of a 〈100〉. Furthermore, we observed the coupling between dislocation half-loop and anti-phase boundary induced by the lattice terrace of Ge along 〈100〉 direction and their decoupling after annealing. We proposed models based on half-loop theory to interpret the coupling and the dislocation reactions.

  12. Crystal structure of 2,5-dimethylanilinium salicylate

    Directory of Open Access Journals (Sweden)

    A. Mani

    2015-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Khairi Suhud

    2017-10-01

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

  14. The crystal structure of γ-AlD3

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-15

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

  16. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  17. Electronic structure of a perfect BeO crystal

    International Nuclear Information System (INIS)

    Lobach, V.A.; Rubin, I.R.; Kruzhalov, A.V.; Sul'gin, B.V.; Ivanov, V.Yu.

    1987-01-01

    The BeO electronic structure is calculated by the crystal cluster method. The calculated value E g is in good agreement with the experiment. The valence band width is slightly underrated (2.3 eV). The calculated electron density distribution reveals considerable delocalization of oxygen 2p-functions in BeO, that is in good agreemet with the well-known results for cubic rare earth oxides. The calculated partial composition of the valence band ceiling and conduction band bottom suggests that a free and autolocalized exciton states can coexist in BeO. As a consequence, there can be two types of intrinsic luminescence with different Stokes shift

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

    Indian Academy of Sciences (India)

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

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

    Science.gov (United States)

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

    2017-12-01

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

  20. Crystal Structure of Human Plasma Platelet-Activating Factor Acetylhydrolase

    Energy Technology Data Exchange (ETDEWEB)

    Samanta, U.; Bahnson, B

    2008-01-01

    Human plasma platelet-activating factor (PAF) acetylhydrolase functions by reducing PAF levels as a general anti-inflammatory scavenger and is linked to anaphylactic shock, asthma, and allergic reactions. The enzyme has also been implicated in hydrolytic activities of other pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids. This plasma enzyme is tightly bound to low and high density lipoprotein particles and is also referred to as lipoprotein-associated phospholipase A{sub 2}. The crystal structure of this enzyme has been solved from x-ray diffraction data collected to a resolution of 1.5{angstrom}. It has a classic lipase {alpha}/{beta}-hydrolase fold, and it contains a catalytic triad of Ser{sup 273}, His{sup 351}, and Asp{sup 296}. Two clusters of hydrophobic residues define the probable interface-binding region, and a prediction is given of how the enzyme is bound to lipoproteins. Additionally, an acidic patch of 10 carboxylate residues and a neighboring basic patch of three residues are suggested to play a role in high density lipoprotein/low density lipoprotein partitioning. A crystal structure is also presented of PAF acetylhydrolase reacted with the organophosphate compound paraoxon via its active site Ser{sup 273}. The resulting diethyl phosphoryl complex was used to model the tetrahedral intermediate of the substrate PAF to the active site. The model of interface binding begins to explain the known specificity of lipoprotein-bound substrates and how the active site can be both close to the hydrophobic-hydrophilic interface and at the same time be accessible to the aqueous phase.

  1. Structure of sodium above 100 GPa by single-crystal x-ray diffraction.

    Science.gov (United States)

    McMahon, M I; Gregoryanz, E; Lundegaard, L F; Loa, I; Guillaume, C; Nelmes, R J; Kleppe, A K; Amboage, M; Wilhelm, H; Jephcoat, A P

    2007-10-30

    At pressures above a megabar (100 GPa), sodium crystallizes in a number of complex crystal structures with unusually low melting temperatures, reaching as low as 300 K at 118 GPa. We have utilized this unique behavior at extreme pressures to grow a single crystal of sodium at 108 GPa, and have investigated the complex crystal structure at this pressure using high-intensity x-rays from the new Diamond synchrotron source, in combination with a pressure cell with wide angular apertures. We confirm that, at 108 GPa, sodium is isostructural with the cI16 phase of lithium, and we have refined the full crystal structure of this phase. The results demonstrate the extension of single-crystal structure refinement beyond 100 GPa and raise the prospect of successfully determining the structures of yet more complex phases reported in sodium and other elements at extreme pressures.

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

    Science.gov (United States)

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

    2014-06-16

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2014-08-01

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

  5. Crystal and magnetic structures of hexagonal YMnO3.

    Science.gov (United States)

    Howard, Christopher J; Campbell, Branton J; Stokes, Harold T; Carpenter, Michael A; Thomson, Richard I

    2013-12-01

    The available data on the structural and magnetic transitions in multiferroic hexagonal YMnO3 have been reviewed, first making use of the computer programs from the group theoretical ISOTROPY software suite to list possible crystal and magnetic structures, then taking into account the capability of neutron diffraction and other physical methods to distinguish them. This leads to a clear view of the transformation sequence, as follows. Hexagonal YMnO3 is paraelectric in P63/mmc at elevated temperatures, and undergoes a single structural transition on cooling through 1250 K to a ferrielectric phase in P63cm that is retained through room temperature. At a much lower temperature, 70 K, there is a magnetic transition from paramagnetic to a triangular antiferromagnetic arrangement, most likely with symmetry P63'cm'. Comment is made on the unusual coupling of ferroelectric and magnetic domains reported to occur in this material, as well as on the so-called `giant magneto-elastic' effect.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  8. 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.

  9. Crystal structure of LeuD from Methanococcus jannaschii.

    Science.gov (United States)

    Lee, Eun Hye; Cho, Yong Wook; Hwang, Kwang Yeon

    2012-03-09

    3-Isopropylmalate/citramalate (IPM) isomerase catalyzes the second step in the leucine biosynthesis pathway. IPM isomerase from Methanococcus jannaschii is a complex protein consisting of a large (MjLeuC) and a small subunit (MjLeuD). It has broad substrate specificity, unlike other bacterial IPM isomerases. In order to understand the reasons for this broad substrate specificity, we determined the crystal structure of MjLeuD at a resolution of 2.0 Å. The asymmetric unit contained 6 molecules of LeuD, including three homodimers. The overall structure had a β/β/α sandwich-fold consisting of 8 α-helices and 7 β-strands. The C-terminal helix, which is important in homodimer formation, showed conformational differences between two homodimer forms of MjLeuD. In addition, we identified a hydrophobic residue (Val28) near the substrate recognition region that may explain the broad substrate specificity of IPM isomerase. Therefore, we suggest that LeuD proteins can be divided into 2 subfamilies, LeuD subfamilies 1 and 2, which show differences in overall structure and in the substrate recognition region. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Crystal structure of an HIV assembly and maturation switch

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-14

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

  11. Crystal structure of an HIV assembly and maturation switch.

    Science.gov (United States)

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

    2016-07-14

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

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

    Directory of Open Access Journals (Sweden)

    Manickam Thairiyaraja

    2015-12-01

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

  13. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains.

    Science.gov (United States)

    Lewis, H A; Chen, H; Edo, C; Buckanovich, R J; Yang, Y Y; Musunuru, K; Zhong, R; Darnell, R B; Burley, S K

    1999-02-15

    Nova-1 and Nova-2 are related neuronal proteins that were initially cloned using antisera obtained from patients with the autoimmune neurological disease paraneoplastic opsoclonus-myoclonus ataxia (POMA). Both of these disease gene products contain three RNA-binding motifs known as K-homology or KH domains, and their RNA ligands have been identified via binding-site selection experiments. The KH motif structure has been determined previously using NMR spectroscopy, but not using X-ray crystallography. Many proteins contain more than one KH domain, yet there is no published structural information regarding the behavior of such multimers. We have obtained the first X-ray crystallographic structures of KH-domain-containing proteins. Structures of the third KH domains (KH3) of Nova-1 and Nova-2 were determined by multiple isomorphous replacement and molecular replacement at 2.6 A and 2.0 A, respectively. These highly similar RNA-binding motifs form a compact protease-resistant domain resembling an open-faced sandwich, consisting of a three-stranded antiparallel beta sheet topped by three alpha helices. In both Nova crystals, the lattice is composed of symmetric tetramers of KH3 domains that are created by two dimer interfaces. The crystal structures of both Nova KH3 domains are similar to the previously determined NMR structures. The most significant differences among the KH domains involve changes in the positioning of one or more of the alpha helices with respect to the betasheet, particularly in the NMR structure of the KH1 domain of the Fragile X disease protein FMR-1. Loop regions in the KH domains are clearly visible in the crystal structure, unlike the NMR structures, revealing the conformation of the invariant Gly-X-X-Gly segment that is thought to participate in RNA-binding and of the variable region. The tetrameric arrangements of the Nova KH3 domains provide insights into how KH domains may interact with each other in proteins containing multiple KH motifs.

  14. Correlation of crystal structures, electronic structures and photocatalytic properties in W-based oxides

    International Nuclear Information System (INIS)

    Shi Haifeng; Huang Xianli; Tian Hanmin; Lv Jun; Li Zhaosheng; Zou Zhigang; Ye Jinhua

    2009-01-01

    We reported a novel W-based oxide NaBi(WO 4 ) 2 with WO 4 tetrahedral crystal structure as a photocatalyst for decomposition of 2-propanol. The physical characteristics of the sample were examined by XRD, BET measurement and SEM, respectively. The band gap of NaBi(WO 4 ) 2 was determined to be 3.6 eV according to the diffuse reflectance spectra of the sample. The photocatalytic activity of NaBi(WO 4 ) 2 was confirmed by decomposing 2-propanol into acetone and CO 2 . It showed a higher acetone generation rate (211 ppm h -1 ) in contrast to that of WO 3 (120 ppm h -1 ), which consisted of WO 6 octahedra. Their electronic structures were further investigated by the plane-wave based density function theory. The results suggested that the crystal field (WO 6 and WO 4 ) significantly influenced the electronic structures and hence affected the photocatalytic activity.

  15. Crystal structure and inhibition studies of transglutaminase from Streptomyces mobaraense.

    Science.gov (United States)

    Yang, Ming-Te; Chang, Cheng-Hsiang; Wang, Jiou Ming; Wu, Tung Kung; Wang, Yu-Kuo; Chang, Chin-Yuan; Li, TienHsiung Thomas

    2011-03-04

    The crystal structure of the microbial transglutaminase (MTGase) zymogen from Streptomyces mobaraense has been determined at 1.9-Å resolution using the molecular replacement method based on the crystal structure of the mature MTGase. The overall structure of this zymogen is similar to that of the mature form, consisting of a single disk-like domain with a deep active cleft at the edge of the molecule. A major portion of the prosequence (45 additional amino acid residues at the N terminus of the mature transglutaminase) folds into an L-shaped structure, consisting of an extended N-terminal segment linked with a one-turn short helix and a long α-helix. Two key residues in the short helix of the prosequence, Tyr-12 and Tyr-16, are located on top of the catalytic triad (Cys-110, Asp-301, and His-320) to block access of the substrate acyl donors and acceptors. Biochemical characterization of the mature MTGase, using N-α-benzyloxycarbonyl-L-glutaminylglycine as a substrate, revealed apparent K(m) and k(cat)/K(m) values of 52.66 mM and 40.42 mM(-1) min(-1), respectively. Inhibition studies using the partial prosequence SYAETYR and homologous sequence SQAETYR showed a noncompetitive inhibition mechanism with IC(50) values of 0.75 and 0.65 mM, respectively, but no cross-linking product formation. Nevertheless, the prosequence homologous oligopeptide SQAETQR, with Tyr-12 and Tyr-16 each replaced with Gln, exhibited inhibitory activity with the formation of the SQAETQR-monodansylcadaverine fluorophore cross-linking product (SQAETQR-C-DNS). MALDI-TOF tandem MS analysis of SQAETQR-C-DNS revealed molecular masses corresponding to those of (N)SQAETQ(C)-C-DNS and C-DNS-(N)QR(C) sequences, suggesting the incorporation of C-DNS onto the C-terminal Gln residue of the prosequence homologous oligopeptide. These results support the putative functional roles of both Tyr residues in substrate binding and inhibition.

  16. High resolution crystal structures of the receptor-binding domain of Clostridium botulinum neurotoxin serotypes A and FA

    Directory of Open Access Journals (Sweden)

    Jonathan R. Davies

    2018-03-01

    Full Text Available The binding specificity of botulinum neurotoxins (BoNTs is primarily a consequence of their ability to bind to multiple receptors at the same time. BoNTs consist of three distinct domains, a metalloprotease light chain (LC, a translocation domain (HN and a receptor-binding domain (HC. Here we report the crystal structure of HC/FA, complementing an existing structure through the modelling of a previously unresolved loop which is important for receptor-binding. Our HC/FA structure also contains a previously unidentified disulphide bond, which we have also observed in one of two crystal forms of HC/A1. This may have implications for receptor-binding and future recombinant toxin production.

  17. Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-18

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

  18. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins.

    Science.gov (United States)

    Harrison, Oliver J; Jin, Xiangshu; Hong, Soonjin; Bahna, Fabiana; Ahlsen, Goran; Brasch, Julia; Wu, Yinghao; Vendome, Jeremie; Felsovalyi, Klara; Hampton, Cheri M; Troyanovsky, Regina B; Ben-Shaul, Avinoam; Frank, Joachim; Troyanovsky, Sergey M; Shapiro, Lawrence; Honig, Barry

    2011-02-09

    Adherens junctions, which play a central role in intercellular adhesion, comprise clusters of type I classical cadherins that bind via extracellular domains extended from opposing cell surfaces. We show that a molecular layer seen in crystal structures of E- and N-cadherin ectodomains reported here and in a previous C-cadherin structure corresponds to the extracellular architecture of adherens junctions. In all three ectodomain crystals, cadherins dimerize through a trans adhesive interface and are connected by a second, cis, interface. Assemblies formed by E-cadherin ectodomains coated on liposomes also appear to adopt this structure. Fluorescent imaging of junctions formed from wild-type and mutant E-cadherins in cultured cells confirm conclusions derived from structural evidence. Mutations that interfere with the trans interface ablate adhesion, whereas cis interface mutations disrupt stable junction formation. Our observations are consistent with a model for junction assembly involving strong trans and weak cis interactions localized in the ectodomain. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Growth, crystal structure and characterization of a nonlinear optical crystal: Deuterated L-arginine trifluoroacetate

    Energy Technology Data Exchange (ETDEWEB)

    Sun, G.H., E-mail: sgh2@mail.sdu.edu.cn [State Key Lab of Crystal Materials and Institute of Crystal Materials, Shandong, University, Jinan, 250100 (China); Zhang, G.H.; Sun, Z.H.; Wang, X.Q. [State Key Lab of Crystal Materials and Institute of Crystal Materials, Shandong, University, Jinan, 250100 (China); Xu, D., E-mail: xdoffice@sdu.edu.cn [State Key Lab of Crystal Materials and Institute of Crystal Materials, Shandong, University, Jinan, 250100 (China)

    2011-05-16

    Research highlights: {yields} Bulk crystals of deuterated L-arginine trifluoroacetate (DLATF) have been grown successfully. {yields} The distances between the N-D covalent bonds in DLATF crystal is about 0.4% shorter than N-H bonds in LATF crystal, which agrees with other reports. {yields} Due to deuterating, the degree of transmission and the transparent region of the crystal have been improved observably. {yields} Furthermore, the crystal possesses relatively large specific heat and higher laser damage threshold. - Abstract: In order to reduce the absorption of L-arginine trifluoroacetate (LATF) in near-infrared region, deuterated LATF (DLATF) crystals have been synthesized and grown successfully. The grown crystals were characterized by the single crystal and powder X-ray diffraction methods, Fourier transform infrared and Raman spectra. DLATF belongs to monoclinic space system, space group P2{sub 1}, with unit cell parameters: a = 10.547(6), b = 5.696(3), c = 10.825(6) A, {beta} = 106.747(10){sup o}, V = 622.8(6) A{sup 3} and Z = 2. Thermogravimetric (TG) and differential thermal analysis (DTA) studies were carried out to characterize its thermal behaviors. The specific heat has been investigated in the temperature range of 293-453 K. Optical transmission spectrum and second harmonic generation were investigated to study its optical properties. The laser-induced damage threshold measurement revealed that the crystal has a higher damage threshold than that of LATF.

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

    Science.gov (United States)

    Karthigha, S.; Krishnamoorthi, C.

    2018-03-01

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

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

    Science.gov (United States)

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

    2009-08-01

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

  2. Single crystal growth, crystal structure and characterization of a novel crystal: L-arginine 4-nitrophenolate 4-nitrophenol dehydrate (LAPP)

    Science.gov (United States)

    Wang, L. N.; Wang, X. Q.; Zhang, G. H.; Liu, X. T.; Sun, Z. H.; Sun, G. H.; Wang, L.; Yu, W. T.; Xu, D.

    2011-07-01

    A novel organic crystal, L-arginine 4-nitrophenolate 4-nitrophenol dehydrate (LAPP), synthesized and grown from aqueous solution, is presented. X-ray single diffraction shows that LAPP belongs to the monoclinic crystallographic system with space group P2 1. FT-IR and UV/vis/NIR transmission spectra have been employed to characterize the crystal. The computational calculation based on the density functional theory at the B3LYP/6-31G (d, p) level has been used to compute the first-order hyperpolarizability of LAPP relating to different molecular models. The morphology, nonlinear characteristic and thermal stability of the crystal have also been investigated.

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

    Science.gov (United States)

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

    2017-06-17

    Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum - Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-06-01

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

  5. Comparison of Cyclooxygenase-1 Crystal Structures: Cross-Talk between Monomers Comprising Cyclooxygenase-1 Homodimers

    Energy Technology Data Exchange (ETDEWEB)

    Sidhu, Ranjinder S.; Lee, Jullia Y.; Yuan, Chong; Smith, William L. (Michigan)

    2010-11-01

    Prostaglandin endoperoxide H synthases (PGHSs)-1 and -2 (also called cyclooxygenases (COXs)-1 and -2) catalyze the committed step in prostaglandin biosynthesis. Both isoforms are targets of nonsteroidal antiinflammatory drugs (NSAIDs). PGHSs are homodimers that exhibit half-of-sites COX activity; moreover, some NSAIDs cause enzyme inhibition by binding only one monomer. To learn more about the cross-talk that must be occurring between the monomers comprising each PGHS-1 dimer, we analyzed structures of PGHS-1 crystallized under five different conditions including in the absence of any tightly binding ligand and in the presence of nonspecific NSAIDs and of a COX-2 inhibitor. When crystallized with substoichiometric amounts of an NSAID, both monomers are often fully occupied with inhibitor; thus, the enzyme prefers to crystallize in a fully occupied form. In comparing the five structures, we only observe changes in the positions of residues 123-129 and residues 510-515. In cases where one monomer is fully occupied with an NSAID and the partner monomer is incompletely occupied, an alternate conformation of the loop involving residues 123-129 is seen in the partially occupied monomer. We propose, on the basis of this observation and previous cross-linking studies, that cross-talk between monomers involves this mobile 123-129 loop, which is located at the dimer interface. In ovine PGHS-1 crystallized in the absence of an NSAID, there is an alternative route for substrate entry into the COX site different than the well-known route through the membrane binding domain.

  6. Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

    Science.gov (United States)

    Egli, M.; Usman, N.; Rich, A.

    1993-01-01

    We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

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

    Science.gov (United States)

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

    2016-08-01

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

  8. Crystal structure of a new polymorph of di(thiophen-3-yl ketone

    Directory of Open Access Journals (Sweden)

    Jörg Hübscher

    2017-10-01

    Full Text Available The crystal structure of the title compound, C9H6OS2, represents a new polymorph. The crystal structure was solved in the orthorhombic space group Pbcn with one half of the molecule in the asymmetric unit. The thiophene rings are perfectly planar and twisted with respect to each other, showing the molecule to be in an S,O-trans/S,O-trans conformation. In the crystal, C—H...O hydrogen bonds connect the molecules into layers extending parallel to the ab plane. The crystal structure also features π–π interactions.

  9. Crystal structure of a new polymorph of di(thio-phen-3-yl) ketone.

    Science.gov (United States)

    Hübscher, Jörg; Augustin, André U; Seichter, Wilhelm; Weber, Edwin

    2017-10-01

    The crystal structure of the title compound, C 9 H 6 OS 2 , represents a new polymorph. The crystal structure was solved in the ortho-rhom-bic space group Pbcn with one half of the mol-ecule in the asymmetric unit. The thio-phene rings are perfectly planar and twisted with respect to each other, showing the mol-ecule to be in an S,O- trans /S,O- trans conformation. In the crystal, C-H⋯O hydrogen bonds connect the mol-ecules into layers extending parallel to the ab plane. The crystal structure also features π-π inter-actions.

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

    Science.gov (United States)

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

    2016-07-01

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

  11. Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport

    Energy Technology Data Exchange (ETDEWEB)

    Long, Feng; Su, Chih-Chia; Zimmermann, Michael T.; Boyken, Scott E.; Rajashankar, Kanagalaghatta R.; Jernigan, Robert L.; Yu, Edward W. (Cornell); (Iowa State)

    2010-09-23

    Gram-negative bacteria, such as Escherichia coli, frequently use tripartite efflux complexes in the resistance-nodulation-cell division (RND) family to expel various toxic compounds from the cell. The efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions. No previous structural information was available for the heavy-metal efflux (HME) subfamily of the RND efflux pumps. Here we describe the crystal structures of the inner-membrane transporter CusA in the absence and presence of bound Cu(I) or Ag(I). These CusA structures provide new structural information about the HME subfamily of RND efflux pumps. The structures suggest that the metal-binding sites, formed by a three-methionine cluster, are located within the cleft region of the periplasmic domain. This cleft is closed in the apo-CusA form but open in the CusA-Cu(I) and CusA-Ag(I) structures, which directly suggests a plausible pathway for ion export. Binding of Cu(I) and Ag(I) triggers significant conformational changes in both the periplasmic and transmembrane domains. The crystal structure indicates that CusA has, in addition to the three-methionine metal-binding site, four methionine pairs - three located in the transmembrane region and one in the periplasmic domain. Genetic analysis and transport assays suggest that CusA is capable of actively picking up metal ions from the cytosol, using these methionine pairs or clusters to bind and export metal ions. These structures suggest a stepwise shuttle mechanism for transport between these sites.

  12. Crystal structure of a chimaeric bacterial glutamate dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-23

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-01

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

  14. Crystal structure of a chimaeric bacterial glutamate dehydrogenase.

    Science.gov (United States)

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

    2016-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Manickam Thairiyaraja

    2015-12-01

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

  16. Synthesis and Crystal Structures of N-Substituted Pyrazolines

    Directory of Open Access Journals (Sweden)

    Balladka Kunhanna Sarojini

    2013-02-01

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

  17. Large scale structures in liquid crystal/clay colloids

    International Nuclear Information System (INIS)

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

    2005-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  19. Crystal structures and atomic model of NADPH oxidase.

    Science.gov (United States)

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

    2017-06-27

    NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.

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

    Science.gov (United States)

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

    2017-01-26

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-01

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

  2. Likelihood-based modification of experimental crystal structure electron density maps

    Science.gov (United States)

    Terwilliger, Thomas C [Sante Fe, NM

    2005-04-16

    A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

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

    Science.gov (United States)

    Zhang, Shuo

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

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

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

    KAUST Repository

    Reiner, T.

    2011-01-01

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

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

    KAUST Repository

    Haque, M.A.

    2016-01-01

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

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

    KAUST Repository

    Al-Masri, H.T.

    2012-01-01

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

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

    KAUST Repository

    Reiner, Thomas

    2013-01-01

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

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

    KAUST Repository

    Queval, Pierre

    2014-01-01

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

  10. CCDC 1419754: Experimental Crystal Structure Determination : octakis(mu2-2-phenylethanethiolato)-tetra-nickel

    KAUST Repository

    Joya, Khurram S.

    2016-01-01

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

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

    KAUST Repository

    Joya, Khurram S.

    2016-01-01

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

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

    KAUST Repository

    Wu, Melissa M.

    2017-01-01

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

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

    KAUST Repository

    Wu, Melissa M.

    2017-01-01

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

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

    KAUST Repository

    Vummaleti, Sai V. C.

    2015-01-01

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

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

    KAUST Repository

    El-Assaad, Tarek H.

    2015-01-01

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

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

    KAUST Repository

    El-Assaad, Tarek H.

    2015-01-01

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

  17. CCDC 1436716: Experimental Crystal Structure Determination : 5-fluoro-4-iodo-2,1,3-benzothiadiazole

    KAUST Repository

    Shi, Qinqin

    2016-01-01

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

  18. CCDC 1436717: Experimental Crystal Structure Determination : 2-bromo-4,5-diiodo-1,3-thiazole

    KAUST Repository

    Shi, Qinqin

    2016-01-01

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

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

    KAUST Repository

    Roesle, Philipp

    2015-01-01

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

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

    KAUST Repository

    Chen, Jiawei

    2016-01-01

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

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

    KAUST Repository

    Reiner, T.

    2011-01-01

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

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

    KAUST Repository

    Reiner, Thomas

    2013-01-01

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

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

    KAUST Repository

    Al-Masri, H.T.

    2012-01-01

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

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

    KAUST Repository

    Dang, Yangyang

    2016-01-01

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

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

    KAUST Repository

    Dang, Yangyang

    2016-01-01

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

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

    KAUST Repository

    Urbina-Blanco, C.A.

    2014-01-01

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

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

    KAUST Repository

    Queval, Pierre

    2014-01-01

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

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

    KAUST Repository

    Shi, Xueliang

    2015-01-01

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

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

    KAUST Repository

    Kuhn, Paul-Steffen

    2015-01-01

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

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

    African Journals Online (AJOL)

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

  11. CCDC 1427126: Experimental Crystal Structure Determination : bis(1,10-Phenanthroline)-copper pentafluoropropanoate

    KAUST Repository

    Huang, Yangjie

    2016-01-01

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

  12. CCDC 1446069: Experimental Crystal Structure Determination : tris(Pentafluorophenyl)-(triethylsilyl formate)-aluminium

    KAUST Repository

    Chen, Jiawei

    2016-01-01

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

  13. CCDC 1420582: Experimental Crystal Structure Determination : catena-[(mu-4,4'-sulfonyldibenzoato)-calcium ethane

    KAUST Repository

    Plonka, Anna M.

    2016-01-01

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

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

    KAUST Repository

    Plonka, Anna M.

    2016-01-01

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

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

    KAUST Repository

    Xu, Jun

    2016-01-01

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

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

    KAUST Repository

    Dang, Yangyang

    2016-01-01

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

  17. CCDC 1420580: Experimental Crystal Structure Determination : catena-[(mu-4,4'-sulfonyldibenzoato)-calcium acetylene

    KAUST Repository

    Plonka, Anna M.

    2016-01-01

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

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

    KAUST Repository

    Dang, Yangyang

    2016-01-01

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

  19. CCDC 1427127: Experimental Crystal Structure Determination : bis(1,10-Phenanthroline)-copper heptafluorobutanoate benzene solvate

    KAUST Repository

    Huang, Yangjie

    2016-01-01

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

  20. CCDC 1048729: Experimental Crystal Structure Determination : bis(2-(hydroxyimino)-3-phenylpropanoato)-tin(ii)

    KAUST Repository

    Khanderi, Jayaprakash

    2015-01-01

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

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

    KAUST Repository

    Khanderi, Jayaprakash

    2015-01-01

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

  2. CCDC 1048728: Experimental Crystal Structure Determination : ammonium tris(2-(methoxyimino)propanoato)-tin(ii) dihydrate

    KAUST Repository

    Khanderi, Jayaprakash

    2015-01-01

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

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

    KAUST Repository

    Chen, Yin

    2013-01-01

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

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

    KAUST Repository

    Shekhah, Osama

    2014-01-01

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

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

    Science.gov (United States)

    Pankove, Jacques I.; Wu, Chung P.

    1983-01-01

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

  6. Crystal Structures, Thermal Analysis, and Dissolution Behavior of New Solid Forms of the Antiviral Drug Arbidol with Dicarboxylic Acids

    Directory of Open Access Journals (Sweden)

    Alex N. Manin

    2015-12-01

    Full Text Available Salts of the antiviral drug arbidol (umifenovir (Arb with maleate (Mlc and fumarate (Fum anions have been obtained, and their crystal structures have been described. The crystal structure of arbidol maleate has been redetermined by single crystal X-ray diffraction at 180K. A new arbidol cocrystal in zwitterion form with succinic acid (Suc has also been found and characterized. The arbidol zwitterion was not previously seen in any of the drug crystal forms, and the [Arb + Suc] cocrystal seems to be the first found instance. Analysis of the conformational preferences of the arbidol molecule in the crystal structures has shown that it adopts two types of conformations, namely “open” and “closed” ones. Thermal stability of the arbidol salts and cocrystal have been analyzed by means of differential scanning calorimetry, thermogravimetric, and mass-spectrometry analysis. The dissolution study of the arbidol salts and cocrystal performed in aqueous buffer solutions with pH 1.2 and 6.8 has shown that both the salts and the cocrystal dissolve incongruently to form an arbidol hydrochloride monohydrate at pH 1.2 and an arbidol base at pH 6.8, respectively. The cocrystal reaches the highest solubility level in both pH 1.2 and pH 6.8 solutions.

  7. Synthesis, crystal structure, spectral and thermal properties of 4-dimethylaminopyridinium salicylate monohydrate

    Science.gov (United States)

    Arunkumar, A.; Ramasamy, P.

    2013-06-01

    4-dimethylaminopyridinium salicylate monohydrate (DMAPSA) was synthesized and its crystal structure was determined using single crystal X-ray diffraction analysis. From the crystal structure analysis it can be inferred that the crystal belongs to monoclinic system with space group of P21/n. Investigation has been carried out to assign the vibrational frequencies of the grown crystals by FTIR spectral studies. 1H and 13C FT-NMR has been recorded to elucidate the molecular structure. The molecular mass of DMAPSA has been measured using mass spectroscopic analysis. The thermal stability and thermal decomposition of DMAPSA have been investigated by means of thermogravimetric analysis and differential thermal analysis. The melting point of crystal was observed as 172 °C by melting point apparatus. Fluorescence spectra were taken for the excitation wavelength of 240 nm.

  8. The Crystal Structure of Toxoplasma gondii Pyruvate Kinase 1

    Energy Technology Data Exchange (ETDEWEB)

    Bakszt, R.; Wernimont, A; Allali-Hassani, A; Mok, M; Hills, T; Hui, R; Pizarro, J

    2010-01-01

    Pyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population. We have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers. We hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two {alpha}-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.

  9. Crystal Structure of the Capsid Protein from Zika Virus.

    Science.gov (United States)

    Shang, Zifang; Song, Hao; Shi, Yi; Qi, Jianxun; Gao, George F

    2018-03-30

    Recently, Zika virus (ZIKV) emerged as a global public health concern and is distinct from other flaviviruses in many aspects, for example, causing transplacental infection, fetal abnormalities and vector-independent transmission through body fluids in humans. The capsid (C) protein is a multifunctional protein, since it binds to viral RNA in the process of nucleocapsid assembly and plays important roles in virus infection processes by interacting with cellular proteins, modulating cellular metabolism, apoptosis and immune response. Here we solved the crystal structure of ZIKV C protein at a resolution of 1.9Å. The ZIKV C protein structure contains four α helices with a long pre-α1 loop and forms dimers. The unique long pre-α1 loop in ZIKV C contributes to the tighter association of dimeric assembly and renders a divergent hydrophobic feature at the lipid bilayer interface in comparison with the known C structures of West Nile and dengue viruses. We reported the interaction between the ZIKV C protein and lipid droplets through confocal microscopy analysis. Substitutions of key amino acids in the pre-α1 loop of ZIKV C disrupted the interaction with lipid droplets, indicating that the loop is critical for membrane association. We also recognized that ZIKV C protein possesses broad binding capability to different nucleotide types, including single-stranded and double-stranded RNAs or DNAs. Furthermore, the highly positively charged interface, mainly formed by α4 helix, is proposed to be responsible for nucleotide binding. These findings will greatly enhance our understanding of ZIKV C protein, providing information for anti-ZIKV drug design targeting the C protein. Copyright © 2018. Published by Elsevier Ltd.

  10. Crystal structures of expressed non-polymerizable monomeric actin in the ADP and ATP states.

    Science.gov (United States)

    Rould, Mark A; Wan, Qun; Joel, Peteranne B; Lowey, Susan; Trybus, Kathleen M

    2006-10-20

    Actin filament growth and disassembly, as well as affinity for actin-binding proteins, is mediated by the nucleotide-bound state of the component actin monomers. The structural differences between ATP-actin and ADP-actin, however, remain controversial. We expressed a cytoplasmic actin in Sf9 cells, which was rendered non-polymerizable by virtue of two point mutations in subdomain 4 (A204E/P243K). This homogeneous monomer, called AP-actin, was crystallized in the absence of toxins, binding proteins, or chemical modification, with ATP or ADP at the active site. The two surface mutations do not perturb the structure. Significant differences between the two states are confined to the active site region and sensor loop. The active site cleft remains closed in both states. Minor structural shifts propagate from the active site toward subdomain 2, but dissipate before reaching the DNase binding loop (D-loop), which remains disordered in both the ADP and ATP states. This result contrasts with previous structures of actin made monomeric by modification with tetramethylrhodamine, which show formation of an alpha-helix at the distal end of the D-loop in the ADP-bound but not the ATP-bound form (Otterbein, L. R., Graceffa, P., and Dominguez, R. (2001) Science 293, 708-711). Our reanalysis of the TMR-modified actin structures suggests that the nucleotide-dependent formation of the D-loop helix may result from signal propagation through crystal packing interactions. Whereas the observed nucleotide-dependent changes in the structure present significantly different surfaces on the exterior of the actin monomer, current models of the actin filament lack any actin-actin interactions that involve the region of these key structural changes.

  11. Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development.

    Science.gov (United States)

    Kim, In Jung; Kim, Sangsoo; Park, Jeahyun; Eom, Intae; Kim, Sunam; Kim, Jin-Hong; Ha, Sung Chul; Kim, Yeon Gil; Hwang, Kwang Yeon; Nam, Ki Hyun

    2016-09-01

    Many fluorescent proteins (FPs) show fluorescence quenching by specific metal ions, which can be applied towards metal biosensor development. In this study, we investigated the significant fluorescence quenching of Dronpa by Co(2+) and Cu(2+) ions. Crystal structures of Co(2+) -, Ni(2+) - and Cu(2+) -bound Dronpa revealed previously unseen, unique, metal-binding sites for fluorescence quenching. These metal ions commonly interact with surface-exposed histidine residues (His194-His210 and His210-His212), and interact indirectly with chromophores. Structural analysis of the Co(2+) - and Cu(2+) - binding sites of Dronpa provides insight into FP-based metal biosensor engineering. © 2016 Federation of European Biochemical Societies.

  12. Crystal Structures of Human and Staphylococcus aureus Pyruvate Carboxylase and Molecular Insights into the Carboxyltransfer Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Xiang,S.; Tong, L.

    2008-01-01

    Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-Angstroms resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in the active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.

  13. Boron Arsenide and Boron Phosphide for High Temperature and Luminescent Devices. [semiconductor devices - crystal growth/crystal structure

    Science.gov (United States)

    Chu, T. L.

    1975-01-01

    The crystal growth of boron arsenide and boron phosphide in the form of bulk crystals and epitaxial layers on suitable substrates is discussed. The physical, chemical, and electrical properties of the crystals and epitaxial layers are examined. Bulk crystals of boron arsenide were prepared by the chemical transport technique, and their carrier concentration and Hall mobility were measured. The growth of boron arsenide crystals from high temperature solutions was attempted without success. Bulk crystals of boron phosphide were also prepared by chemical transport and solution growth techniques. Techniques required for the fabrication of boron phosphide devices such as junction shaping, diffusion, and contact formation were investigated. Alloying techniques were developed for the formation of low-resistance ohmic contacts to boron phosphide. Four types of boron phosphide devices were fabricated: (1) metal-insulator-boron phosphide structures, (2) Schottky barriers; (3) boron phosphide-silicon carbide heterojunctions; and (4) p-n homojunctions. Easily visible red electroluminescence was observed from both epitaxial and solution grown p-n junctions.

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

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1992-12-01

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

  15. crystal

    Science.gov (United States)

    Yu, Yi; Huang, Yisheng; Zhang, Lizhen; Lin, Zhoubin; Sun, Shijia; Wang, Guofu

    2014-07-01

    A Nd3+:Na2La4(WO4)7 crystal with dimensions of ϕ 17 × 30 mm3 was grown by the Czochralski method. The thermal expansion coefficients of Nd3+:Na2La4(WO4)7 crystal are 1.32 × 10-5 K-1 along c-axis and 1.23 × 10-5 K-1 along a-axis, respectively. The spectroscopic characteristics of Nd3+:Na2La4(WO4)7 crystal were investigated. The Judd-Ofelt theory was applied to calculate the spectral parameters. The absorption cross sections at 805 nm are 2.17 × 10-20 cm2 with a full width at half maximum (FWHM) of 15 nm for π-polarization, and 2.29 × 10-20 cm2 with a FWHM of 14 nm for σ-polarization. The emission cross sections are 3.19 × 10-20 cm2 for σ-polarization and 2.67 × 10-20 cm2 for π-polarization at 1,064 nm. The fluorescence quantum efficiency is 67 %. The quasi-cw laser of Nd3+:Na2La4(WO4)7 crystal was performed. The maximum output power is 80 mW. The slope efficiency is 7.12 %. The results suggest Nd3+:Na2La4(WO4)7 crystal as a promising laser crystal fit for laser diode pumping.

  16. Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

    Science.gov (United States)

    Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

    1996-04-01

    The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

  17. Topology optimization and fabrication of photonic crystal structures

    DEFF Research Database (Denmark)

    Borel, Peter Ingo; Harpøth, Anders; Frandsen, Lars Hagedorn

    2004-01-01

    Topology optimization is used to design a planar photonic crystal waveguide component resulting in significantly enhanced functionality. Exceptional transmission through a photonic crystal waveguide Z-bend is obtained using this inverse design strategy. The design has been realized in a silicon-on-insulator...

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

    Indian Academy of Sciences (India)

    Wintec

    The effect of sulphur propor- tion on the lattice parameter, unit cell ... Hall effect measure- ments were carried out on grown crystals at room temperature. The negative value of Hall coefficient implies that these crystals are n-type in nature. The conductivity is found to ... Resistivity, Hall coefficient and thermo electric power ...

  19. Topotactic decomposition and crystal structure of white molybdenum trioxide--monohydrate: prediction of structure by topotaxy

    International Nuclear Information System (INIS)

    Oswald, H.R.; Guenter, J.R.; Dubler, E.

    1975-01-01

    Single crystals of the white MoO 3 . H 2 O modification (''α-molybdic acid'') were transformed by heating to 160 0 C into perfect pseudomorphs built up from oriented MoO 3 crystallites of known structure. From the mutual orientation relationship of the unit cells of both phases involved in this topotactic reaction, as determined by X-ray photographs, a model for the so far unknown crystal structure of white MoO 3 . H 2 O could be deduced. Independently, this structure was determined by X-ray diffractometer data then: space group P anti 1, a = 7.388, b = 3.700, c = 6.673 A, α = 107.8, β = 113.6, γ = 91.2 0 , Z = 2. The structure was solved from the Patterson function and refined until R = 0.088. It is built up from isolated double chains of strongly distorted [MoO 5 (H 2 O)]-octahedra sharing two common edges with each other. This result agrees well with the model derived from topotaxy, and it becomes evident how the MoO 3 lattice is formed through corner linking of the isolated double chains after the water molecules are removed. The study of topotactic phenomena seems rather generally applicable to deduce the main features of structures involved and for better understanding of structural relationships. (U.S.)

  20. 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.

  1. Anomalous Ambipolar Transport of Organic Semiconducting Crystals via Control of Molecular Packing Structures.

    Science.gov (United States)

    Park, Beomjin; Kim, Kyunghun; Park, Jaesung; Lim, Heeseon; Lanh, Phung Thi; Jang, A-Rang; Hyun, Chohee; Myung, Chang Woo; Park, Seungkyoo; Kim, Jeong Won; Kim, Kwang S; Shin, Hyeon Suk; Lee, Geunsik; Kim, Se Hyun; Park, Chan Eon; Kim, Jin Kon

    2017-08-23

    Organic crystals deposited on 2-dimensional (2D) van der Waals substrates have been widely investigated due to their unprecedented crystal structures and electrical properties. van der Waals interaction between organic molecules and the substrate induces epitaxial growth of high quality organic crystals and their anomalous crystal morphologies. Here, we report on unique ambipolar charge transport of a "lying-down" pentacene crystal grown on a 2D hexagonal boron nitride van der Waals substrate. From in-depth analysis on crystal growth behavior and ultraviolet photoemission spectroscopy measurement, it is revealed that the pentacene crystal at the initial growth stage have a lattice-strained packing structure and unique energy band structure with a deep highest occupied molecular orbital level compared to conventional "standing-up" crystals. The lattice-strained pentacene few layers enable ambipolar charge transport in field-effect transistors with balanced hole and electron field-effect mobilities. Complementary logic circuits composed of the two identical transistors show clear inverting functionality with a high gain up to 15. The interesting crystal morphology of organic crystals on van der Waals substrates is expected to attract broad attentions on organic/2D interfaces for their electronic applications.

  2. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    International Nuclear Information System (INIS)

    Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

    2010-01-01

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used

  3. Synthesis, crystal structure and applications of palladium thiosalicylate complexes

    Directory of Open Access Journals (Sweden)

    S.B. Moosun

    2017-05-01

    Full Text Available Three palladium thiosalicylate complexes [Pd(tb(bipy]·3H2O (1, [Pd2(tb2(bipy2]·(dtdb2 (2 and [Pd2(tb2(phen2]·dtdb·H2O (3 (bipy = bipyridine; phen = phenanthroline were prepared from the reaction of PdCl2(CH3CN2 with dithiosalicylic acid (dtdb which underwent cleavage to form thiobenzoate anion (tb in DMF/MeOH. Square planar geometries of the complexes with a N2SO coordination type were proposed on the basis of single crystal X-ray structural study. The presence of trapped and uncoordinated dtdb was observed in complexes 2 and 3. Complexes 1–3 were evaluated as catalysts for Heck coupling reactions of methyl acrylate with iodobenzene, and showed moderate activities at a very low catalyst loading. Complex 1 was found to inhibit the growth of bacteria and scavenge free radicals efficiently.

  4. Two Voriconazole salts: Syntheses, crystal structures, solubility and bioactivities

    Science.gov (United States)

    Tang, Gui-Mei; Wang, Yong-Tao

    2018-01-01

    Two Voriconazole salts, namely, (H2FZ)2+·2(Cl-) (1) and (HFZ)+·NO3- (2) (FZ = (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoro-4-pyrimidiny)-1-(1H-1,2,4-triazol-1-yl)-2-butanol) have been obtained through the reaction of Voriconazole, hydrochloric acid and nitrate acid, respectively. They were structurally characterized by FT-IR, elemental analyses (EA), single crystal X-ray diffraction, and thermogravimetric analysis (TGA). A variety of hydrogen bonds (Osbnd H⋯N, Nsbnd H⋯Cl/O, Csbnd H⋯N/OF/Cl) were observed in the compounds 1 and 2, through which a 3D supramolecular architecture is generated. Both two salts 1 and 2 show the promising bioactivities against Aspergillus species (Aspergillus niger, Aspergillus terreus, Aspergillus fumigatus and Aspergillus flavus) and Candida ones (Candida albicans, Candida krusei, Candida glabrata and Cryptococcus neoformans), which is obviously more excellent than that of FZ. Additionally, the solubility of two salts is considerably higher than that of the drug Voriconazole.

  5. Crystal structure of Methanococcus jannaschii TATA box-binding protein.

    Science.gov (United States)

    Adachi, Naruhiko; Senda, Miki; Natsume, Ryo; Senda, Toshiya; Horikoshi, Masami

    2008-11-01

    As the archaeal transcription system consists of a eukaryotic-type transcription apparatus and bacterial-type regulatory transcription factors, analyses of the molecular interface between the transcription apparatus and regulatory transcription factors are critical to reveal the evolutionary change of the transcription system. TATA box-binding protein (TBP), the central components of the transcription apparatus are classified into three groups: eukaryotic, archaeal-I and archaeal-II TBPs. Thus, comparative functional analysis of these three groups of TBP is important for the study of the evolution of the transcription system. Here, we present the first crystal structure of an archaeal-II TBP from Methanococcus jannaschii. The highly conserved and group-specific conserved surfaces of TBP bind to DNA and TFIIB/TFB, respectively. The phylogenetic trees of TBP and TFIIB/TFB revealed that they evolved in a coupled manner. The diversified surface of TBP is negatively charged in the archaeal-II TBP, which is completely different from the case of eukaryotic and archaeal-I TBPs, which are positively charged and biphasic, respectively. This difference is responsible for the diversification of the regulatory functions of TBP during evolution.

  6. Deformation of periodic nanovoid structures in Mg single crystals

    Science.gov (United States)

    Xu, Shuozhi; Su, Yanqing; Zare Chavoshi, Saeed

    2018-01-01

    Large scale molecular dynamics (MD) simulations in Mg single crystal containing periodic cylindrical voids subject to uniaxial tension along the z direction are carried out. Models with different initial void sizes and crystallographic orientations are explored using two interatomic potentials. It is found that (i) a larger initial void always leads to a lower yield stress, in agreement with an analytic prediction; (ii) in the model with x[\\bar{1}100]–y[0001]–z[11\\bar{2}0] orientations, the two potentials predict different types of tension twins and phase transformation; (iii) in the model with x[0001]–y[11\\bar{2}0]–z[\\bar{1}100] orientations, the two potentials identically predict the nucleation of edge dislocations on the prismatic plane, which then glide away from the void, resulting in extrusions at the void surface; in the case of the smallest initial void, these surface extrusions pinch the void into two voids. Besides bringing new physical understanding of the nanovoid structures, our work highlights the variability and uncertainty in MD simulations arising from the interatomic potential, an issue relatively lightly addressed in the literature to date.

  7. Hydrothermal Synthesis and Crystal Structure of Ionic Conductive Metal Tungstates

    Energy Technology Data Exchange (ETDEWEB)

    Shimanouchi, R F; Tsuji, T; Yagi, R; Matsumoto, Y; Nishizawa, H, E-mail: rshima@kochi-u.ac.jp [Department of Natural Science, Faculty of Science, Kochi University, 2-5-1, Akebono-cho, Kochi city, KOCHI 780 (Japan)

    2011-10-29

    Trivalent ion conducting materials with the Sc{sub 2}(WO{sub 4}){sub 3}-type crystal structure, A{sub 2}(WO{sub 4}){sub 3} (A = Sc, In, Y) and solid solutions, (Sc,In){sub 2}(WO{sub 4}){sub 3} were synthesized via an autogenous hydrothermal reaction of aqueous solutions of ScCl{sub 3}, InCl{sub 3}, Y(CH{sub 3}COO){sub 3}, and H{sub 2}WO{sub 4} in a Teflon-lined mini-autoclave for 5 h at a temperature of 523 K. Fine powder samples were pressed into discs under 50 MPa and sintered at 1273 K for 10 h. The impedance measurements of sintered materials showed the dependence of electric conductivity on the size of the conducting cation. From the precise crystallographic data obtained by Rietveld refinements of solid solutions, it was considered that the change of volume of Sc(In)O{sub 6}-octahedra and WO{sub 4}-tetrahedra.

  8. Optics of anisotropic metamaterial based structurally chiral photonic crystals

    International Nuclear Information System (INIS)

    Gevorgyan, A H; Rafayelyan, M S

    2013-01-01

    Light transmission through and reflection from a medium layer with dielectric and magnetic helicities are discussed. The axes of the dielectric permittivity tensor, ε-hat , and the magnetic permeability tensor, μ-hat , as well as the medium helix axis are all parallel to each other and they are perpendicular to the boundary surfaces. The possibilities of formation of some new types of photonic bandgaps (PBGs) are presented for large anisotropies of the medium—namely, direct and indirect nonselective PBGs (with respect to the incident light polarization, in contrast to the usual direct PBGs, which are selective with respect to the polarization of the incident light). It is shown that a transmission region can arise among the three types of PBGs, in certain conditions, of course. In this paper we generalize the concept of nihility for structurally chiral media, such as cholesteric liquid crystals (CLCs) and we identify two types of CLC nihilities. It is shown that, for certain characteristic parameters of the medium, superluminal light propagation is possible in the transmission band. The influence of the anisotropy of the medium on the reflection spectra is considered and it is shown that one can tune the width, number and frequency range of PBGs of this layer, at essentially large limits, tuning the parameters of the layer. The case of oblique light incidence on the CLC layer is also discussed. (paper)

  9. Polarization properties and crystal structures of ferroelectric (Ba,CaTiO3 single crystals

    Directory of Open Access Journals (Sweden)

    Ryota Imura

    2014-01-01

    Full Text Available We have investigated the spontaneous polarization (Ps of Ba1-xCaxTiO3 (BCT by polarization hysteresis measurements using single crystals and by density functional theory (DFT calculations. Single crystals of BCT (x = 0.07 were grown by a top-seeded solution growth (TSSG method. The polarization measurements show that the crystals (x = 0.07 have a Ps of 26.0 μC/cm2, which is slightly small compared with BaTiO3 (27.3 μC/cm2. Our DFT calculations based on a supercell approach show that Ca atoms are markedly displaced cooperatively with the adjacent Ti atoms along the Ps direction. It is suggested that the CaTiO3-like octahedral rotation is constructed in the BCT supercell around the Ca atoms, which is the origin of the smaller Ps observed for the BCT crystals.

  10. Annealing effect of H+ -implanted single crystal silicon on strain and crystal structure

    International Nuclear Information System (INIS)

    Duo Xinzhong; Liu Weili; Zhang Miao; Gao Jianxia; Fu Xiaorong; Lin Chenglu

    2000-01-01

    The work focuses on the rocking curves of H + -implanted single silicon crystal detected by Four-Crystal X-ray diffractometer. The samples were annealed under different temperatures. Lattice defect in H + -implanted silicon crystals was detected by Rutherford Backscattering Spectrometry. It appeared that H-related complex did not crush until annealing temperature reached about 400 degree C. At that temperature H 2 was formed, deflated in silicon lattice and strained the lattice. But defects did not come into being in large quantity. The lattice was undamaged. When annealing temperature reached 500 degree C, strain induced by H 2 deflation crashed the silicon lattice. A large number of defects were formed. At the same time bubbles in the crystal and blister/flaking on the surface could be observed

  11. Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog.

    Science.gov (United States)

    Jaehme, Michael; Guskov, Albert; Slotboom, Dirk Jan

    2014-11-01

    PnuC transporters catalyze cellular uptake of the NAD+ precursor nicotinamide riboside (NR) and belong to a large superfamily that includes the SWEET sugar transporters. We present a crystal structure of Neisseria mucosa PnuC, which adopts a highly symmetrical fold with 3+1+3 membrane topology not previously observed in any protein. The high symmetry of PnuC with a single NR bound in the center suggests a simple alternating-access translocation mechanism.

  12. Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

    Science.gov (United States)

    Qiu, Wei; Dong, Aiping; Pizarro, Juan C; Botchkarsev, Alexei; Min, Jinrong; Wernimont, Amy K; Hills, Tanya; Hui, Raymond; Artz, Jennifer D

    2012-03-19

    Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control. To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed PvTrx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of PyTrx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of PyPrx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding. The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group

  13. High-resolution crystal structures of Colocasia esculenta tarin lectin.

    Science.gov (United States)

    Pereira, Patricia R; Meagher, Jennifer L; Winter, Harry C; Goldstein, Irwin J; Paschoalin, Vânia M F; Silva, Joab T; Stuckey, Jeanne A

    2017-01-01

    Tarin, the Colocasia esculenta lectin from the superfamily of α-d-mannose-specific plant bulb lectins, is a tetramer of 47 kDa composed of two heterodimers. Each heterodimer possesses homologous monomers of ~11.9 (A chain) and ~12.7 (B chain) kDa. The structures of apo and carbohydrate-bound tarin were solved to 1.7 Å and 1.91 Å, respectively. Each tarin monomer forms a canonical β-prism II fold, common to all members of Galanthus nivalis agglutinin (GNA) family, which is partially stabilized by a disulfide bond and a conserved hydrophobic core. The heterodimer is formed through domain swapping involving the C-terminal β-strand and the β-sheet on face I of the prism. The tetramer is assembled through the dimerization of the B chains from heterodimers involving face II of each prism. The 1.91 Å crystal structure of tarin bound to Manα(1,3)Manα(1,6)Man reveals an expanded carbohydrate-binding sequence (QxDxNxVxYx 4/6 WX) on face III of the β-prism. Both monomers possess a similar fold, except for the length of the loop, which begins after the conserved tyrosine and creates the binding pocket for the α(1,6)-terminal mannose. This loop differs in size and amino-acid composition from 10 other β-prism II domain proteins, and may confer carbohydrate-binding specificity among members of the GNA-related lectin family. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Synthesis and Crystal Structures of Two New Oxaspirocyclic Compounds

    Directory of Open Access Journals (Sweden)

    Jinhe Jiang

    2016-10-01

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

  15. 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.

  16. Crystal structures of orthorhombic, hexagonal, and cubic compounds of the Sm(x)Yb(2−x)TiO5 series

    International Nuclear Information System (INIS)

    Aughterson, Robert D.; Lumpkin, Gregory R.; Reyes, Massey de los; Sharma, Neeraj; Ling, Christopher D.; Gault, Baptiste; Smith, Katherine L.; Avdeev, Maxim; Cairney, Julie M.

    2014-01-01

    A series of single phase compounds with nominal stoichiometry Sm (x) Yb (2−x) TiO 5 (x=2, 1.4, 1, 0.6, and 0) have been successfully fabricated to generate a range of crystal structures covering the most common polymorphs previously discovered in the Ln 2 TiO 5 series (Ln=lanthanides and yttrium). Four of the five samples have not been previously fabricated in bulk, single phase form so their crystal structures are refined and detailed using powder synchrotron and single crystal x-ray diffraction, neutron diffraction and transmission electron microscopy. Based on the phase information from diffraction data, there are four crystal structure types in this series; orthorhombic Pnma, hexagonal P6 3 /mmc, cubic (pyrochlore-like) Fd-3m and cubic (fluorite-like) Fm-3m. The cubic materials show modulated structures with variation between long and short range ordering and the variety of diffraction techniques were used to describe these complex crystal structure types. - Graphical abstract: A high resolution image of the compound Sm 0.6 Yb 1.4 TiO 5 showing contrast from lattice fringes and the corresponding fast Fourier transform (FFT) of the HREM image with pyrochlore related diffraction spots marked “P” and fluorite marked “F”. The crystal is oriented down the [1 1 0] zone axis based on the Fd-3m structure. The ideal crystal structure (no vacancies) of the cubic, pyrochlore-like (Sm 0.6 Yb 1.4 TiO 5 ). - Highlights: • First fabrication of bulk single-phase material with stoichiometry Sm 2 TiO 5 . • Systematic study of crystal structure types within Ln 2 TiO 5 series (Ln=lanthanides). • A novel technique using IFFT of HREM images to study cubic structures

  17. Structure of the Catalytic Trimer of Methanococcus jannaschii Aspartate Transcarbamoylase in an Orthorhombic Crystal Form

    Energy Technology Data Exchange (ETDEWEB)

    Vitali,J.; Colaneri, M.

    2008-01-01

    Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallographically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4 between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4 between crystal forms.

  18. Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form.

    Science.gov (United States)

    Vitali, Jacqueline; Colaneri, Michael J

    2008-09-01

    Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallographically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4 degrees between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4 degrees between crystal forms.

  19. Local layer structure of smectic liquid crystals by X-ray micro-diffraction

    CERN Document Server

    Takanishi, Y

    2003-01-01

    The local layer structure of smectic liquid crystal has been measured using time-resolved synchrotron X-ray micro-diffraction. Typical layer disorders observed in surface stabilized (anti-) ferroelectric liquid crystals, i.e. a stripe texture, a needed-like defect and a zigzag defect, are directly analyzed. The detailed analysis slows that the surface anchoring force due to the interaction between the liquid crystal molecule and the alignment thin film plays an important role to realize both the static and dynamic local layer structures. The layer structure of the circular domain observed in the liquid crystal of bent-shaped molecules found to depend on the applied electric field though the optical micrograph shows little difference. The frustrated, double and single layer structures of the bent-shaped molecule liquid crystal are determined depending on the terminal alkyl chain length. (author)

  20. Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein

    International Nuclear Information System (INIS)

    Schiffer, M.; Ainsworth, C.; Xu, Z.B.; Carperos, W.; Olsen, K.; Solomon, A.; Stevens, F.J.; Chang, C.H.

    1989-01-01

    The authors have determined the structure of the immunoglobulin light-chain dimer Loc in a second crystal form that was grown from distilled water. The crystal structure was determined to 2.8-angstrom resolution; the R factor is 0.22. The two variable domains are related by local 2-fold axes and form an antigen binding pocket. The variable domain-variable domain interaction observed in this crystal form differs from the one exhibited by the protein when crystallized from ammonium sulfate in which the two variable domains formed a protrusion. The structure attained in the distilled water crystals is similar to, but not identical with, the one observed for the Mcg light-chain dimer in crystals grown from ammonium sulfate. Thus, two strikingly different structures were attained by this multisubunit protein in crystals grown under two different, commonly used, crystallization techniques. The quaternary interactions exhibited by the protein in the two crystal forms are sufficiently different to suggest fundamentally different interpretations of the structural basis for the function of this protein. This observation may have general implications regarding the use of single crystallographic determinations for detailed identification of structural and functional relationships. On the other hand, proteins whose structures can be altered by manipulation of crystallization conditions may provide useful systems for study of fundamental structural chemistry