Science.gov

Sample records for crystal structure

  1. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

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

  2. Photonic Crystal Laser Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M

    2003-05-21

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

  3. Demonstration of Crystal Structure.

    ERIC Educational Resources Information Center

    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)

  4. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Needle-shaped single crystals of the title compound, C14H9ClF3NO2, 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.

  5. Generation of crystal structures using known crystal structures as analogues

    PubMed Central

    Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

    2016-01-01

    This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

  6. Concerning inorganic crystal structure types.

    PubMed

    Bergerhoff; Berndt; Brandenburg; Degen

    1999-04-01

    All representatives of an inorganic crystal structure type can be found systematically in the new database SICS (Standardized Inorganic Crystal Structures). It is derived from the Inorganic Crystal Structure Database (ICSD) by selecting the best determination of each phase. In addition, each entry is given in a standardized description and complemented by searchable descriptors Delta, which give the difference between all structures of an isopointal set. Because of the large number of structures the full information on relationships present can only be found by means of the new database itself. Some examples are given here in printed form. The limitations and the possibilities of expansion of SICS in terms of the concept of 'structure types' are demonstrated. PMID:10927350

  7. Crystal structure of triclopyr

    PubMed Central

    Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2014-01-01

    In the title compound {systematic name: 2-[(3,5,6-tri­chloro­pyridin-2-yl)­oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the mean plane of the carb­oxy­lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter­molecular O—H⋯O hydrogen bonds form dimers through an R 2 2(8) ring motif and are extended into chains along [100] by weak π–π inter­actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter­molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4). PMID:25309266

  8. Crystal structure of triclopyr.

    PubMed

    Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2014-09-01

    In the title compound {systematic name: 2-[(3,5,6-tri-chloro-pyridin-2-yl)-oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol-ecules in which the dihedral angles between the mean plane of the carb-oxy-lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter-molecular O-H⋯O hydrogen bonds form dimers through an R 2 (2)(8) ring motif and are extended into chains along [100] by weak π-π inter-actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter-molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4). PMID:25309266

  9. Crystal structure determination of Efavirenz

    SciTech Connect

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

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 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.

  10. Crystal structure refinement with SHELXL

    PubMed Central

    Sheldrick, George M.

    2015-01-01

    The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors. PMID:25567568

  11. Crystal structure refinement with SHELXL

    SciTech Connect

    Sheldrick, George M.

    2015-01-01

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

  12. Crystal structure of pyrazoxyfen

    PubMed Central

    Kwon, Eunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-01-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di­chloro­benzo­yl)-1,3-di­methyl­pyrazol-5-yl}­oxy}-1-phenyl­ethan-1-one), is the benzoyl­pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol­ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the di­chloro­phenyl and phenyl rings. In the crystal, C—H⋯O and C—H⋯N hydrogen bonds, and C—H⋯π and π–π [3.646 (2) Å] inter­actions link adjacent mol­ecules, forming a two-dimensional network parellel to (011). In addition, the networks are linked by weak inter­molecular C—Cl⋯π [3.356 (2), 3.950 (2), 3.250 (2) and 3.575 (2) Å] inter­actions, resulting in a three-dimensional architecture. PMID:26870483

  13. Crystal structure of pyrazoxyfen.

    PubMed

    Kwon, Eunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-12-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di-chloro-benzo-yl)-1,3-di-methyl-pyrazol-5-yl}-oxy}-1-phenyl-ethan-1-one), is the benzoyl-pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol-ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the di-chloro-phenyl and phenyl rings. In the crystal, C-H⋯O and C-H⋯N hydrogen bonds, and C-H⋯π and π-π [3.646 (2) Å] inter-actions link adjacent mol-ecules, forming a two-dimensional network parellel to (011). In addition, the networks are linked by weak inter-molecular C-Cl⋯π [3.356 (2), 3.950 (2), 3.250 (2) and 3.575 (2) Å] inter-actions, resulting in a three-dimensional architecture. PMID:26870483

  14. Crystal structure of guggulsterone Z

    SciTech Connect

    Gupta, V. K. Bandhoria, P.; Gupta, B. D.; Gupta, K. K.

    2006-03-15

    The crystal structure of the title compound (4,17(20)-trans-pregnadiene-3,16-dione, C{sub 21}H{sub 28}O{sub 2}) has been determined by direct methods using single-crystal X-ray diffraction data. The compound crystallizes into the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with the unit cell parameters a = 7.908(2) A, b = 13.611(3) A, c = 16.309(4) A, and Z = 4. The structure has been refined to R = 0.058 for 3667 observed reflections. The bond distances and angles are in good agreement with guggulsterone E and other related steroid molecules. Ring A exists in the distorted sofa conformation, while rings B and C adopt the distorted chair conformation. Five-membered ring D is intermediate between the half-chair and envelope conformations. The A/B ring junction is quasi-trans, while ring systems B/C and C/D are trans fused about the C(8)-C(9) and C(13)-C(14) bonds, respectively. The steroid nucleus has a small twist, as shown by the C(19)-C(10)...C(13)-C(18) pseudo-torsion angle of 7.2{sup o}. The crystal structure is stabilized by intra-and intermolecular C-H...O hydrogen bonds.

  15. Crystal structure of prethrombin-1

    SciTech Connect

    Chen, Zhiwei; Pelc, Leslie A.; Di Cera, Enrico

    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.

  16. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, B.; /SLAC

    2005-09-19

    We discuss simulated photonic crystal structure designs for laser-driven particle acceleration, focusing on three-dimensional planar structures based on the so-called ''woodpile'' lattice. We demonstrate guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice and discuss the properties of this mode. We also discuss particle beam dynamics in the structure, presenting a novel method for focusing the beam. In addition we describe some potential coupling methods for the structure.

  17. Crystal structure of benzimidazolium salicylate

    PubMed Central

    Amudha, M.; Kumar, P. Praveen; Chakkaravarthi, G.

    2015-01-01

    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 R 4 4(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. PMID:26594483

  18. Crystal structure of a perfect carbyne

    SciTech Connect

    Belenkov, E. A. Mavrinsky, V. V.

    2008-01-15

    The crystal structure of a perfect carbyne is calculated by the molecular mechanics methods. It is established that the carbyne crystals should consist of polycumulene chains arranged in hexagonal bundles. The unit cell of the perfect carbyne crystal is trigonal and contains one carbon atom. The unit cell parameters are as follows: a = b = c = 0.3580 nm, {alpha} = {beta} = {gamma} = 118.5{sup o}, and space group P3m1. The perfect carbyne single crystals have a stable structure at room temperature if the length of their constituent chains is larger than 500 nm.

  19. Crystal structures of MBP fusion proteins.

    PubMed

    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. PMID:26682969

  20. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

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

  1. Crystal structure prediction of rigid molecules.

    PubMed

    Elking, Dennis M; Fusti-Molnar, Laszlo; Nichols, Anthony

    2016-08-01

    A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r(6) dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups. PMID:27484371

  2. Structures of cyano-biphenyl liquid crystals

    NASA Technical Reports Server (NTRS)

    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.

  3. Liquid crystal light valve structures

    NASA Technical Reports Server (NTRS)

    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.

  4. Pholcodine monohydrate: Crystal structure and polymorphism

    NASA Astrophysics Data System (ADS)

    Petruševski, Gjorgji; Zbačnik, Marija; Kajdžanoska, Marina; Ugarkovic, Sonja; Trimčeski, Vase; Kaitner, Branko; Jovanovski, Gligor; Makreski, Petre

    2013-07-01

    The first crystal structure elucidation of pholcodine monohydrate, an important antitussive active pharmaceutical ingredient is reported herein. The studied compound crystallizes in the orthorhombic system in the space group P212121. Each H2O molecule is shared by two pholcodine molecules via three strong hydrogen bonds. The detailed crystallization screening from several different organic solvents afforded single crystals with various quality, all exhibiting prism-to-needlelike micro morphology. The investigation of the obtained single crystals by means of several physico-chemical, solid-state instrumental techniques (FT-IR, DSC, TG/DTG and XRPD) proved that pholcodine monohydrate exists in a single crystalline modification, identical to the commercial form of the compound.

  5. Structural complexity and configurational entropy of crystals.

    PubMed

    Krivovichev, Sergey V

    2016-04-01

    Using a statistical approach, it is demonstrated that the complexity of a crystal structure measured as the Shannon information per atom [Krivovichev (2012). Acta Cryst. A68, 393-398] represents a negative contribution to the configurational entropy of a crystalline solid. This conclusion is in full accordance with the general agreement that information and entropy are reciprocal variables. It also agrees well with the understanding that complex structures possess lower entropies relative to their simpler counterparts. The obtained equation is consistent with the Landauer principle and points out that the information encoded in a crystal structure has a physical nature. PMID:27048729

  6. Crystal structure of anagyrine perchlorate.

    PubMed

    Turgunov, Kambarali K; Rakhimov, Shukhrat B; Vinogradova, Valentina I; Tashkhodjaev, Bakhodir

    2015-05-01

    The title mol-ecular salt, C15H21N2O(+)·ClO4 (-), crystallizes with four cations (A, B, C and D) and four anions in the chiral unit cell (space group P21). The alkaloid was isolated from the aerial parts of Genista Hispanica collected in the Samarkand region of Uzbekistan. Each cation is protonated at the N atom that bridges the alkaloid rings C and D. In each cation, ring A is almost planar and ring B adops a sofa conformation with the methyl-ene group bridging to the C ring as the flap. Rings C and D adopt chair conformations with a cis ring junction in all four cations. In the crystal, A+B and C+D dimeric pairs linked by pairs of N-H⋯O hydrogen bonds are observed, which generate R 2 (2)(16) loops in each case. The dimers are consolidated by weak aromatic π-π stacking inter-actions between the A rings [centroid-centroid distances = 3.913 (3) and 3.915 (3) Å]. PMID:25995939

  7. Crystal structure of levomepromazine maleate.

    PubMed

    Gál, Gyula Tamás; May, Nóra Veronika; Bombicz, Petra

    2016-05-01

    The asymmetric unit of the title salt, C19H25N2OS(+)·C4H3O4 (-) [systematic name: (S)-3-(2-meth-oxy-pheno-thia-zin-10-yl)-N,N,2-tri-methyl-propanaminium 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 meth-oxy substituent at the pheno-thia-zine ring system. The crystal components form a three-dimensional supra-molecular network via N-H⋯O, C-H⋯O and C-H⋯π inter-actions. A comparison of the conformations of the levomepromazine cations with those of the neutral mol-ecule and similar protonated mol-ecules reveals significant conformational flexibility of the pheno-thia-zine ring system and the substituent at the pheno-thia-zine N atom. PMID:27308001

  8. Nucleation and structural growth of cluster crystals.

    PubMed

    Leitold, Christian; Dellago, Christoph

    2016-08-21

    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. PMID:27544116

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

    USGS Publications Warehouse

    Evans, H.T., Jr.; 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

  10. Crystal structure of potassium sodium tartrate trihydrate

    SciTech Connect

    Egorova, A. E. Ivanov, V. A.; Somov, N. V.; Portnov, V. N.; Chuprunov, E. V.

    2011-11-15

    Crystals of potassium sodium tartrate trihydrate (dl-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 3H{sub 2}O) were obtained from an aqueous solution. The crystal shape was described. The atomic structure of the compound was determined and compared with the known structures of dl-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 4H{sub 2}O and l-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 4H{sub 2}O.

  11. Crystal structure of canagliflozin hemihydrate.

    PubMed

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

    2016-05-01

    There are two canagliflozin mol-ecules (A and B) and one water mol-ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro-phen-yl)thio-phen-2-yl]meth-yl}-4-methylphen-yl)-6-(hy-droxy-meth-yl)-3,4,5,6-tetra-hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl-benzene and thio-phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro-benzene and thio-phene rings are 24.2 (6) and 20.5 (9)° in mol-ecules A and B, respectively. The hydro-pyran ring exhibits a chair conformation in both canagliflozin mol-ecules. In the crystal, the canagliflozin mol-ecules and lattice water mol-ecules are connected via O-H⋯O hydrogen bonds into a three-dimensional supra-molecular architecture. PMID:27308030

  12. Crystal structure of canagliflozin hemihydrate

    PubMed Central

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

    2016-01-01

    There are two canagliflozin mol­ecules (A and B) and one water mol­ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro­phen­yl)thio­phen-2-yl]meth­yl}-4-methylphen­yl)-6-(hy­droxy­meth­yl)-3,4,5,6-tetra­hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl­benzene and thio­phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro­benzene and thio­phene rings are 24.2 (6) and 20.5 (9)° in mol­ecules A and B, respectively. The hydro­pyran ring exhibits a chair conformation in both canagliflozin mol­ecules. In the crystal, the canagliflozin mol­ecules and lattice water mol­ecules are connected via O—H⋯O hydrogen bonds into a three-dimensional supra­molecular architecture. PMID:27308030

  13. Crystal structure of levomepromazine maleate

    PubMed Central

    Gál, Gyula Tamás; May, Nóra Veronika; Bombicz, Petra

    2016-01-01

    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. PMID:27308001

  14. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  15. Structure-property evolution during polymer crystallization

    NASA Astrophysics Data System (ADS)

    Arora, Deepak

    The main theme of this research is to understand the structure-property evolution during crystallization of a semicrystalline thermoplastic polymer. A combination of techniques including rheology, small angle light scattering, differential scanning calorimetry and optical microscopy are applied to follow the mechanical and optical properties along with crystallinity and the morphology. Isothermal crystallization experiments on isotactic poly-1-butene at early stages of spherulite growth provide quantitative information about nucleation density, volume fraction of spherulites and their crystallinity, and the mechanism of connecting into a sample spanning structure. Optical microscopy near the fluid-to-solid transition suggests that the transition, as determined by time-resolved mechanical spectroscopy, is not caused by packing/jamming of spherulites but by the formation of a percolating network structure. The effect of strain, Weissenberg number (We ) and specific mechanical work (w) on rate of crystallization (nucleation followed by growth) and on growth of anisotropy was studied for shear-induced crystallization of isotactic poly-1-butene. The samples were sheared for a finite strain at the beginning of the experiment and then crystallized without further flow (Janeschitz-Kriegl protocol). Strain requirements to attain steady state/leveling off of the rate of crystallization were found to be much larger than the strain needed to achieve steady state of flow. The large strain and We>1 criteria were also observed for morphological transition from spherulitic growth to oriented growth. An apparatus for small angle light scattering (SALS) and light transmission measurements under shear was built and tested at the University of Massachusetts Amherst. As a new development, the polarization direction can be rotated by a liquid crystal polarization rotator (LCPR) with a short response time of 20 ms. The experiments were controlled and analyzed with a LabVIEW(TM) based

  16. Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Bitto, Eduard; Aceti, David J.; Phillips, Jr., George N.

    2008-08-13

    Since first discovered in Zea mays, cytokinin dehydrogenase (CKX) genes have been identified in many plants including rice and Arabidopsis thaliana, which possesses CKX homologues (AtCKX1-AtCKX7). So far, the three-dimensional structure of only Z. mays CKX (ZmCKX1) has been determined. The crystal structures of ZmCKX1 have been solved in the native state and in complex with reaction products and a slowly reacting substrate. The structures revealed four glycosylated asparagine residues and a histidine residue covalently linked to FAD. Combined with the structural information, recent biochemical analyses of ZmCKX1 concluded that the final products of the reaction, adenine and a side chain aldehyde, are formed by nonenzymatic hydrolytic cleavage of cytokinin imine products resulting directly from CKX catalysis. Here, we report the crystal structure of AtCKX7 (gene locus At5g21482.1, UniProt code Q9FUJ1).

  17. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

    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.

  18. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  19. Crystal structure of monobasic sodium tartrate monohydrate

    SciTech Connect

    Titaeva, E. K. Somov, N. V.; Portnov, V. N.; Titaev, D. N.

    2015-01-15

    Crystals of a new polymorphic modification of monobasic sodium tartrate monohydrate NaHC{sub 4}H{sub 4}O{sub 6} · H{sub 2}O have been grown in a metasilicate gel. Their atomic structure is solved by X-ray diffraction.

  20. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

    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.

  1. Crystal structure of a plectonemic RNA supercoil

    SciTech Connect

    Stagno, Jason R.; Ma, Buyong; Li, Jess; Altieri, Amanda S.; Byrd, R. Andrew; Ji, Xinhua

    2012-12-14

    Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.

  2. Crystal structure of zwitterionic bisimidazolium sulfonates

    NASA Astrophysics Data System (ADS)

    Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

    2012-05-01

    Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

  3. Crystal Structure of Human Enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    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.

  4. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    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.

  5. Crystal structure of riboflavin synthase

    SciTech Connect

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

    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.

  6. Absorption enhancement in graphene photonic crystal structures.

    PubMed

    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. PMID:27139857

  7. Crystal structure of low-symmetry rondorfite

    SciTech Connect

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

    2008-03-15

    The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca{sub 16}[Mg{sub 2}(Si{sub 7}Al)(O{sub 31}OH)]Cl{sub 4} from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) A, b = 15.110(2) A, c = 15.092(2) A, {alpha} = 90.06(1) deg., {beta} = 90.01(1) deg., {gamma} = 89.93(1) deg., Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3{sigma}(F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group (a = 15.105 A, sp. gr. Fd-bar 3, seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3{sigma}(F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

  8. Crystal structure of low-symmetry rondorfite

    SciTech Connect

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

    2008-03-15

    The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca{sub 16}[Mg{sub 2}(Si{sub 7}Al)(O{sub 31}OH)]Cl{sub 4} from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Angstrom-Sign , b = 15.110(2) Angstrom-Sign , c = 15.092(2) Angstrom-Sign , {alpha} = 90.06(1) Degree-Sign , {beta} = 90.01(1) Degree-Sign , {gamma} = 89.93(1) Degree-Sign , Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3{sigma}(F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group (a = 15.105 Angstrom-Sign , sp. gr. Fd 3 bar , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3{sigma}(F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

  9. The Surface Structure of Ground Metal Crystals

    NASA Technical Reports Server (NTRS)

    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).

  10. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2009-02-01

    The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability. PMID:19155561

  11. Synthesis and Crystal Structure of Gold Nanobelts

    PubMed Central

    2015-01-01

    Gold nanobelts were synthesized by the reduction of tetrachloroauric acid with ascorbic acid in the presence of the surfactants cetyltrimethylammonium bromide and sodium dodecylsulfate. The resulting structures have rectangular cross sectional dimensions that are tens of nanometers and lengths that are tens to hundreds of micrometers. We find that the nanobelt yield and resulting structures are very sensitive to temperature which is likely due to the transition of the surfactant solution from wormlike micelles to spherical micelles. The nanobelt crystal structure contains a mixture of face centered cubic and hexagonally close packed lattice phases that can be isolated and examined individually due to the unique nanobelt size and shape. PMID:24803725

  12. Coagulation factor XII protease domain crystal structure

    PubMed Central

    Pathak, M; Wilmann, P; Awford, J; Li, C; Hamad, BK; Fischer, PM; Dreveny, I; Dekker, LV; Emsley, J

    2015-01-01

    Background Coagulation factor XII is a serine protease that is important for kinin generation and blood coagulation, cleaving the substrates plasma kallikrein and FXI. Objective To investigate FXII zymogen activation and substrate recognition by determining the crystal structure of the FXII protease domain. Methods and results A series of recombinant FXII protease constructs were characterized by measurement of cleavage of chromogenic peptide and plasma kallikrein protein substrates. This revealed that the FXII protease construct spanning the light chain has unexpectedly weak proteolytic activity compared to β-FXIIa, which has an additional nine amino acid remnant of the heavy chain present. Consistent with these data, the crystal structure of the light chain protease reveals a zymogen conformation for active site residues Gly193 and Ser195, where the oxyanion hole is absent. The Asp194 side chain salt bridge to Arg73 constitutes an atypical conformation of the 70-loop. In one crystal form, the S1 pocket loops are partially flexible, which is typical of a zymogen. In a second crystal form of the deglycosylated light chain, the S1 pocket loops are ordered, and a short α-helix in the 180-loop of the structure results in an enlarged and distorted S1 pocket with a buried conformation of Asp189, which is critical for P1 Arg substrate recognition. The FXII structures define patches of negative charge surrounding the active site cleft that may be critical for interactions with inhibitors and substrates. Conclusions These data provide the first structural basis for understanding FXII substrate recognition and zymogen activation. PMID:25604127

  13. Photonic crystal and photonic wire device structures

    NASA Astrophysics Data System (ADS)

    De La Rue, Richard; Sorel, Marc; Johnson, Nigel; Rahman, Faiz; Ironside, Charles; Cronin, Lee; Watson, Ian; Martin, Robert; Jin, Chongjun; Pottier, Pierre; Chong, Harold; Gnan, Marco; Jugessur, Aju; Camargo, Edilson; Erwin, Grant; Md Zain, Ahmad; Ntakis, Iraklis; Hobbs, Lois; Zhang, Hua; Armenise, Mario; Ciminelli, Caterina; Coquillat, Dominique

    2005-09-01

    Photonic devices that exploit photonic crystal (PhC) principles in a planar environment continue to provide a fertile field of research. 2D PhC based channel waveguides can provide both strong confinement and controlled dispersion behaviour. In conjunction with, for instance, various electro-optic, thermo-optic and other effects, a range of device functionality is accessible in very compact PhC channel-guide devices that offer the potential for high-density integration. Low enough propagation losses are now being obtained with photonic crystal channel-guide structures that their use in real applications has become plausible. Photonic wires (PhWs) can also provide strong confinement and low propagation losses. Bragg-gratings imposed on photonic wires can provide dispersion and frequency selection in device structures that are intrinsically simpler than 2D PhC channel guides--and can compete with them under realistic conditions.

  14. Observations on the crystal structures of lueshite

    NASA Astrophysics Data System (ADS)

    Mitchell, Roger H.; Burns, Peter C.; Knight, Kevin S.; Howard, Christopher J.; Chakhmouradian, Anton R.

    2014-06-01

    Laboratory powder XRD patterns of the perovskite-group mineral lueshite from the type locality (Lueshe, Kivu, DRC) and pure NaNbO3 demonstrate that lueshite does not adopt the same space group ( Pbma; #57) as the synthetic compound. The crystal structures of lueshite (2 samples) from Lueshe, Mont Saint-Hilaire (Quebec, Canada) and Sallanlatvi (Kola, Russia) have been determined by single-crystal CCD X-ray diffraction. These room temperature X-ray data for all single-crystal samples can be satisfactorily refined in the orthorhombic space group Pbnm (#62). Cell dimensions, atomic coordinates of the atoms, bond lengths and octahedron tilt angles are given for four crystals. Conventional neutron diffraction patterns for Lueshe lueshite recorded over the temperature range 11-1,000 K confirm that lueshite does not adopt space group Pbma within these temperatures. Neutron diffraction indicates no phase changes on cooling from room temperature to 11 K. None of these neutron diffraction data give satisfactorily refinements but suggest that this is the space group Pbnm. Time-of-flight neutron diffraction patterns for Lueshe lueshite recorded from room temperature to 700 °C demonstrate phase transitions above 550 °C from Cmcm through P4 /mbm to above 650 °C. Cell dimensions and atomic coordinates of the atoms are given for the three high-temperature phases. The room temperature to 400 °C structures cannot be satisfactorily resolved, and it is suggested that the lueshite at room temperature consists of domains of pinned metastable phases with orthorhombic and/or monoclinic structures. However, the sequence of high-temperature phase transitions observed is similar to those determined for synthetic NaTaO3, suggesting that the equilibrated room temperature structure of lueshite is orthorhombic Pbnm.

  15. Crystal Structures of New Ammonium 5-Aminotetrazolates

    PubMed Central

    Lampl, Martin; Salchner, Robert; Laus, Gerhard; Braun, Doris E.; Kahlenberg, Volker; Wurst, Klaus; Fuhrmann, Gerda; Schottenberger, Herwig; Huppertz, Hubert

    2015-01-01

    The crystal structures of three salts of anionic 5-aminotetrazole are described. The tetramethylammonium salt (P1‒) forms hydrogen-bonded ribbons of anions which accept weak C–H⋯N contacts from the cations. The cystamine salt (C2/c) shows wave-shaped ribbons of anions linked by hydrogen bonds to screw-shaped dications. The tetramethylguanidine salt (P21/c) exhibits layers of anions hydrogen-bonded to the cations. PMID:26753100

  16. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    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.

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

    ERIC Educational Resources Information Center

    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)

  18. Crystal Structure of the Protealysin Precursor

    PubMed Central

    Demidyuk, Ilya V.; Gromova, Tania Yu.; Polyakov, Konstantin M.; Melik-Adamyan, William R.; Kuranova, Inna P.; Kostrov, Sergey V.

    2010-01-01

    Protealysin (PLN) belongs to the M4 family of peptidases that are commonly known as thermolysin-like proteases (TLPs). All TLPs are synthesized as precursors containing N-terminal propeptides. According to the primary structure of the N-terminal propeptides, the family is divided into two distinct groups. Representatives of the first group including thermolysin and all TLPs with known three-dimensional structures have long prosequences (∼200 amino acids). Enzymes of the second group, whose prototype is protealysin, have short (∼50 amino acids) propeptides. Here, we present the 1.8 Å crystal structure of PLN precursor (proPLN), which is the first three-dimensional structure of a TLP precursor. Whereas the structure of the catalytic domain of proPLN is similar overall to previously reported structures of mature TLPs, it has specific features, including the absence of calcium-binding sites, and different structures of the N-terminal region and substrate-binding site. PLN propeptide forms a separate domain in the precursor and likely acts as an inhibitor that blocks the substrate-binding site and fixes the “open” conformation of the active site, which is unfavorable for catalysis. Furthermore the conserved PPL motif identified in our previous studies directly interacts with the S′ subsites of the active center being a critical element of the propeptide-catalytic domain interface. Comparison of the primary structures of TLPs with short propeptides suggests that the specific features revealed in the proPLN crystal structure are typical for all protealysin-like enzymes. Thus, such proteins can be considered as a separate subfamily of TLPs. PMID:19915005

  19. Crystal structure of natural phaeosphaeride A.

    PubMed

    Abzianidze, Victoria V; Poluektova, Ekaterina V; Bolshakova, Ksenia P; Panikorovskii, Taras L; Bogachenkov, Alexander S; Berestetskiy, Alexander O

    2015-08-01

    The asymmetric unit of the title compound, C15H23NO5, contains two independent mol-ecules. 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 mol-ecules form layered structures. Nearly planar sheets, parallel to the (001) plane, form bilayers of two-dimensional hydrogen-bonded networks with the hy-droxy groups located on the inter-ior 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 inter-digitate 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). PMID:26396831

  20. Crystal structures and freezing of dipolar fluids.

    PubMed

    Groh, B; Dietrich, S

    2001-02-01

    We investigate the crystal structure of classical systems of spherical particles with an embedded point dipole at T=0. The ferroelectric ground state energy is calculated using generalizations of the Ewald summation technique. Due to the reduced symmetry compared to the nonpolar case the crystals are never strictly cubic. For the Stockmayer (i.e., Lennard-Jones plus dipolar) interaction three phases are found upon increasing the dipole moment: hexagonal, body-centered orthorhombic, and body-centered tetragonal. An even richer phase diagram arises for dipolar soft spheres with a purely repulsive inverse power law potential approximately r(-n). A crossover between qualitatively different sequences of phases occurs near the exponent n=12. The results are applicable to electro- and magnetorheological fluids. In addition to the exact ground state analysis we study freezing of the Stockmayer fluid by density-functional theory. PMID:11308482

  1. The First Mammalian Aldehyde Oxidase Crystal Structure

    PubMed Central

    Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

    2012-01-01

    Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

  2. Crystal structure of MboIIA methyltransferase.

    SciTech Connect

    Osipiuk, J.; Walsh, M. A.; Joachimiak, A.; Biosciences Division; Univ. of Gdansk; Medical Research Council France

    2003-09-15

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

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

    SciTech Connect

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

    2009-10-07

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

  4. Flowing crystals: nonequilibrium structure of foam.

    PubMed

    Garstecki, Piotr; Whitesides, George M

    2006-07-14

    Bubbles pushed through a quasi-two-dimensional channel self-organize into a variety of periodic lattices. The structures of these lattices correspond to local minima of the interfacial energy. The "flowing crystals" are long-lived metastable states, a small subset of possible local minima of confined quasi-two-dimensional foams [P. Garstecki and G. M. Whitesides, Phys. Rev. E 73, 031603 (2006)10.1103/PhysRevE.73.031603]. Experimental results suggest that the choice of the structures that we observe is dictated by the dynamic stability of the cyclic processes of their formation. Thus, the dynamic system that we report provides a unique example of nonequilibrium self-organization that results in structures that correspond to local minima of the relevant energy functional. PMID:16907453

  5. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

    Ben-Shem, Adam; Frolow, Felix; Nelson, Nathan

    2003-12-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.

  6. Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine

    PubMed Central

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

    2015-01-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable. PMID:25843964

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  8. Structural investigation of the potassium vanadomolybdate crystal

    SciTech Connect

    Mucha, D.; Olszewski, P.K.; Napruszewska, B.

    1999-08-01

    Potassium vanadomolybdate KVMoO{sub 6} crystallizes in the orthorhombic system (space group Pnma, a = 10.3478(1) {angstrom}, b = 3.6967(1) {angstrom}, c = 13.3769(2) {angstrom}, Z = 4). With an X-ray powder diffraction technique, its structure was solved and refined by direct and Rietveld methods, respectively (R{sub F} = 3.33, R{sub 1} = 4.70, R{sub wp} = 12.44). The crystals are isostructural with PbV{sub 2}O{sub 6}. Octahedra of two types build chains parallel to the b direction; there is disorder in the octahedra described by different occupation numbers of V and Mo atoms: 0.721(4) and 0.279(4), respectively. Potassium atoms occupy the space between the octahedra chains. They play a decisive role, due to the large ionic radius, in generating both KVMoO{sub 6} and pseudobrannerite, K{sub x}V{sub x}Mo{sub 2{minus}x}O{sub 6} (0.76 {le} x {le} 0.82) structures, contrary to other alkali-metal vanadomolybdates of the brannerite structure type. The melting point of KVMoO{sub 6} was detected at 480 C using the DTA method.

  9. Crystal structure of a DNA catalyst.

    PubMed

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

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms. PMID:26735012

  10. Temperature dependent spin structures in Hexaferrite crystal

    NASA Astrophysics Data System (ADS)

    Chao, Y. C.; Lin, J. G.; Chun, S. H.; Kim, K. H.

    2016-01-01

    In this work, the Hexaferrite Ba0.5Sr1.5Zn2Fe12O22 (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.

  11. Crystal structure of yeast Sco1

    SciTech Connect

    Abajian, Carnie; Rosenzweig, Amy C.

    2010-03-05

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

  12. The Crystal Structure of Human Argonaute2

    SciTech Connect

    Schirle, Nicole T.; MacRae, Ian J.

    2012-07-18

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

  13. Crystal structure of human nicotinamide riboside kinase.

    PubMed

    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. PMID:17698003

  14. Crystal Structure of Human Nicotinamide Riboside Kinase

    SciTech Connect

    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.

  15. The crystal structure of human Argonaute2.

    PubMed

    Schirle, Nicole T; MacRae, Ian J

    2012-05-25

    Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans. PMID:22539551

  16. Crystal structure of mammalian acid sphingomyelinase.

    PubMed

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann-Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  17. Crystal structure of mammalian acid sphingomyelinase

    PubMed Central

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X.; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann–Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann–Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  18. Structure, thermodynamics, and crystallization of amorphous hafnia

    NASA Astrophysics Data System (ADS)

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-01

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO2. The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia.

  19. Structure, thermodynamics, and crystallization of amorphous hafnia

    SciTech Connect

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-28

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

  20. Structural studies of tubular discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Mindyuk, Oksana Yaroslavovna

    1999-11-01

    Discotic liquid crystals based on the rigid ring-shaped phenylacetylene macrocycle molecule (PAM) are of great interest due to their potential organization into supramolecular channels. We have used high resolution X-ray diffraction to study the structure of pure and doped PAM and to demonstrate that PAM forms a tubular columnar liquid crystal with an unexpected distortion and doubling of the underlying hexagonal lattice. We have doped PAM with different percentages of silver ions and determined that doping did not change peak positions on the powder diffraction data but significantly altered the intensity of the peaks. This implies that the silver ions were most likely intercalated within the channels formed by the PAM molecules, thus leaving the lattice parameters unaffected. We have also used grazing incidence X-ray diffraction and X-ray reflectivity to study Langmuir films of PAM. PAM adopts an "edge-on" molecular arrangement at the air-water interface. We will discuss the direct observation of the structural reorganization within macromolecular Langmuir films of disc-shaped ionophoric molecules arising from interactions with potassium and cesium ions in the subphase. The columnar order is disrupted by CsCl in the subphase and strongly enhanced by KCl in the subphase, thus effectively tailoring the structural properties of the Langmuir films for potential applications. We have also used X-ray reflectivity (XR) and grazing incidence x-ray diffraction (GID) to study Langmuir films of another macrocyclic ionophore: torand (tributyldodecahydrohexaazakekulene, "TBDK") molecules. TBDK is a rigid, triangular molecule; it has been investigated as a potential surface-active complexing agent. The system forms a stable monolayer at the air-water interface and exhibits two distinct structural phases at lower and higher pressures.

  1. Prediction of binary hard-sphere crystal structures.

    PubMed

    Filion, Laura; Dijkstra, Marjolein

    2009-04-01

    We present a method based on a combination of a genetic algorithm and Monte Carlo simulations to predict close-packed crystal structures in hard-core systems. We employ this method to predict the binary crystal structures in a mixture of large and small hard spheres with various stoichiometries and diameter ratios between 0.4 and 0.84. In addition to known binary hard-sphere crystal structures similar to NaCl and AlB2, we predict additional crystal structures with the symmetry of CrB, gammaCuTi, alphaIrV, HgBr2, AuTe2, Ag2Se, and various structures for which an atomic analog was not found. In order to determine the crystal structures at infinite pressures, we calculate the maximum packing density as a function of size ratio for the crystal structures predicted by our GA using a simulated annealing approach. PMID:19518387

  2. Crystal structure of bacterioferritin from Rhodobacter sphaeroides

    SciTech Connect

    Nam, Ki Hyun; Xu, Yongbin; Piao, Shunfu; Priyadarshi, Amit; Lee, Eun Hye; Kim, Hye-Yeon; Jeon, Young Ho; Ha, Nam-Chul; Hwang, Kwang Yeon

    2010-01-01

    Iron is essential for the survival of organisms, but either excess or deficient levels of iron induce oxidative stress, thereby causing cell damage. As a result, iron regulation is essential for proper cell growth and proliferation in most organisms. Bacterioferritin is a ferritin-like family protein that contains a heme molecule and a ferroxidase site at the di-iron center. This protein plays a primary role in intracellular iron storage for iron homeostasis, as well as in the maintenance of iron in a soluble and non-toxic form. Although several bacterioferritin structures have been determined, no structural studies have successfully elucidated the molecular function of the heme molecule and the ferroxidase center. Here, we report the crystal structure of bacterioferritin from Rhodobacter sphaeroides. This protein exists in a roughly spherical configuration via the assembly of 24 subunits. We describe the oligomeric arrangement, ferroxidase center and heme-binding site based on this structure. The protein contains a single iron-binding configuration in the ferroxidase center, which allows for the release of iron by His130 when the protein is in the intermediate state. The heme molecule in RsBfr is stabilized by shifting of the van der Waals interaction center between the porphyrin of the heme and Trp26. We anticipate that further structural analysis will provide a more complete understanding of the molecular mechanisms of members of the ferritin-like family.

  3. Structural Transitions in Cholesteric Liquid Crystal Droplets.

    PubMed

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

    2016-07-26

    Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates. PMID:27249186

  4. Crystal structure of strontium dinickel iron orthophosphate

    PubMed Central

    Ouaatta, Said; Assani, Abderrazzak; Saadi, Mohamed; El Ammari, Lahcen

    2015-01-01

    The title compound, SrNi2Fe(PO4)3, 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. PMID:26594419

  5. Crystal structures of five 6-mercaptopurine derivatives.

    PubMed

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

    2016-03-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(3-meth-oxy-phen-yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-meth-oxy-phen-yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-chloro-phen-yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-bromo-phen-yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth-oxy-phen-yl)-2-[(9H-purin-6-yl)sulfan-yl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their mol-ecular and supra-molecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the mol-ecules 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 mol-ecules 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-sulfanyl-ethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles. PMID:27006794

  6. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    PubMed

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  7. Crystal structures of the human adiponectin receptors.

    PubMed

    Tanabe, Hiroaki; Fujii, Yoshifumi; Okada-Iwabu, Miki; Iwabu, Masato; Nakamura, Yoshihiro; Hosaka, Toshiaki; Motoyama, Kanna; Ikeda, Mariko; Wakiyama, Motoaki; Terada, Takaho; Ohsawa, Noboru; Hato, Masakatsu; Ogasawara, Satoshi; Hino, Tomoya; Murata, Takeshi; Iwata, So; Hirata, Kunio; Kawano, Yoshiaki; Yamamoto, Masaki; Kimura-Someya, Tomomi; Shirouzu, Mikako; Yamauchi, Toshimasa; Kadowaki, Takashi; Yokoyama, Shigeyuki

    2015-04-16

    Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases the activities of 5' AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor (PPAR), respectively, thereby contributing to healthy longevity as key anti-diabetic molecules. AdipoR1 and AdipoR2 were predicted to contain seven transmembrane helices with the opposite topology to G-protein-coupled receptors. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9 and 2.4 Å resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of G-protein-coupled receptors, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may have a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the carboxy-terminal tail, of the receptors. The present information will facilitate the understanding of novel structure-function relationships and the development and optimization of AdipoR agonists for the treatment of obesity-related diseases, such as type 2 diabetes. PMID:25855295

  8. Crystal structure of natural phaeosphaeride A

    PubMed Central

    Abzianidze, Victoria V.; Poluektova, Ekaterina V.; Bolshakova, Ksenia P.; Panikorovskii, Taras L.; Bogachenkov, Alexander S.; Berestetskiy, Alexander O.

    2015-01-01

    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). PMID:26396831

  9. Crystal Structures of Respiratory Pathogen Neuraminidases

    SciTech Connect

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

    2009-01-01

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

  10. Crystal Structure of the VS ribozyme

    PubMed Central

    Suslov, Nikolai B.; DasGupta, Saurja; Huang, Hao; Fuller, James R.; Lilley, David M.J.; Rice, Phoebe A.; Piccirilli, Joseph A.

    2015-01-01

    Varkud Satellite (VS) ribozyme mediates rolling circle replication of a plasmid found in the Neurospora mitochondria. We report crystal structures of this ribozyme at 3.1Å resolution, revealing an intertwined dimer formed by an exchange of substrate helices. Within each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional significance of active site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution. PMID:26414446

  11. Crystal structure of oligoacenes under high pressure

    SciTech Connect

    Oehzelt, M.; Aichholzer, A.; Resel, R.; Heimel, G.; Venuti, E.; Della Valle, R. G.

    2006-09-01

    We report crystal structures of anthracene, tetracene, and pentacene under pressure. Energy dispersive x-ray diffraction experiments up to 9 GPa were performed. Quasiharmonic lattice dynamics calculations are compared to the experimental results and show excellent agreement. The results are discussed with particular emphasis on the pressure dependence of the unit cell dimensions and the rearrangement of the molecules. The high pressure data also allow an analysis of the equation of state of these substances as a function of molecular length. We report the bulk modulus of tetracene and pentacene (B{sub 0}=9.0 and 9.6 GPa, respectively) and its pressure derivative (B{sub 0}{sup '}=7.9 and 6.4, respectively). We find that the unit-cell volume and bulk modulus at ambient pressure follow a linear relationship with the molecular length.

  12. Exploring structural phase transitions of ion crystals

    PubMed Central

    Yan, L. L.; Wan, W.; Chen, L.; Zhou, F.; Gong, S. J.; Tong, X.; Feng, M.

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled 40Ca+ ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

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

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

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

  14. Crystal structure of human GDF11.

    PubMed

    Padyana, Anil K; Vaidialingam, Bhamini; Hayes, David B; Gupta, Priyanka; Franti, Michael; Farrow, Neil A

    2016-03-01

    Members of the TGF-β family of proteins are believed to play critical roles in cellular signaling processes such as those involved in muscle differentiation. The extent to which individual family members have been characterized and linked to biological function varies greatly. The role of myostatin, also known as growth differentiation factor 8 (GDF8), as an inhibitor of muscle differentiation is well understood through genetic linkages. In contrast, the role of growth differentiation factor 11 (GDF11) is much less well understood. In humans, the mature forms of GDF11 and myostatin are over 94% identical. In order to understand the role that the small differences in sequence may play in the differential signaling of these molecules, the crystal structure of GDF11 was determined to a resolution of 1.50 Å. A comparison of the GDF11 structure with those of other family members reveals that the canonical TGF-β domain fold is conserved. A detailed structural comparison of GDF11 and myostatin shows that several of the differences between these proteins are likely to be localized at interfaces that are critical for the interaction with downstream receptors and inhibitors. PMID:26919518

  15. Crystal Structure of Amylomaltase from Corynebacterium glutamicum.

    PubMed

    Joo, Seongjoon; Kim, Sangwoo; Seo, Hogyun; Kim, Kyung-Jin

    2016-07-20

    Amylomaltase is an essential enzyme in maltose utilization and maltodextrin metabolism, and it has been industrially used for the production of cyclodextrin and modification of starch. We determined the crystal structure of amylomaltase from Corynebacterium glutamicum (CgAM) at a resolution of 1.7 Å. Although CgAM forms a dimer without NaCl, it exists as a monomer in physiological concentration of NaCl. CgAM is composed of N- and C-terminal domains, which can be further divided into two and four subdomains, respectively. It exhibits a unique structural feature at the functionally unknown N-domain and also shows two striking differences at the C-domain compared to other amylomaltases. These differences at extended edge of the substrate-binding site might affect substrate specificity for large cyclodextrin formation. The bis-tris methane and sulfate molecules bound at the substrate-binding site of our current structure mimic the binding of the hydroxyl groups of glucose bound at subsites -1 and -2, respectively. PMID:27366969

  16. The Crystal Structure of Triuranyl Diphosphate Tetrahydrate

    NASA Astrophysics Data System (ADS)

    Locock, Andrew J.; Burns, Peter C.

    2002-01-01

    The hydrated neutral uranyl phosphate, (UO2)3(PO4)2(H2O)4, was synthesized by hydrothermal methods. Intensity data were collected using MoKα radiation and a CCD-based area detector. The crystal structure was solved by direct methods and refined by full-matrix least-squares techniques to agreement indices wR2=0.116 for all data, and R1=0.040, calculated for the 2764 unique observed reflections (∣Fo∣≥4σF). The compound is orthorhombic, space group Pnma, Z=4, a=7.063(1) Å, b=17.022(3) Å, c=13.172(3) Å, V=1583.5(5) Å3. The structure consists of sheets of phosphate tetrahedra and uranyl pentagonal bipyramids, with composition [(UO2)(PO4)]- and the uranophane sheet anion topology. The sheets are connected by a uranyl pentagonal bipyramid in the interlayer that shares corners with a phosphate tetrahedron on each of two adjacent sheets, resulting in an open framework with isolated H2O groups in the larger cavities of the structure.

  17. Crystal structure of human nicotinic acid phosphoribosyltransferase.

    PubMed

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss-Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

  18. Crystal structure of human nicotinic acid phosphoribosyltransferase

    PubMed Central

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss–Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

  19. Crystal Structure of Homo Sapiens Kynureninase†

    PubMed Central

    Lima, Santiago; Kristoforov, Roman; Momany, Cory; Phillips, Robert S.

    2008-01-01

    Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal-5′-phosphate dependent enzymes known as the aspartate aminotransferase superfamily or α-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-L-kynurenine to produce 3-hydroxyanthranilate and L-alanine, while L-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni-metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km= 28.3 ± 1.9 μM, and a specific activity of 1.75 μmol min-1 mg-1 for 3-hydroxy-DL-kynurenine. Crystals of recombinant kynureninase were obtained that diffracted to 2.0 Å, and the atomic structure of the PLP-bound holoenzyme was solved by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB accession 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the “open” and “closed” conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins’ small domains and reveals a role for Arg-434 similar to that in other AAT α-family members. Docking of 3-hydroxy-L-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates. PMID:17300176

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

    PubMed

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

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  1. Structure dependent hydrogen induced etching features of graphene crystals

    NASA Astrophysics Data System (ADS)

    Thangaraja, Amutha; Shinde, Sachin M.; Kalita, Golap; Papon, Remi; Sharma, Subash; Vishwakarma, Riteshkumar; Sharma, Kamal P.; Tanemura, Masaki

    2015-06-01

    H2 induced etching of graphene is of significant interest to understand graphene growth process as well as to fabricate nanoribbons and various other structures. Here, we demonstrate the structure dependent H2 induced etching behavior of graphene crystals. We synthesized graphene crystals on electro-polished Cu foil by an atmospheric pressure chemical vapor deposition process, where some of the crystals showed hexagonal shaped snowflake-dendritic morphology. Significant differences in H2 induced etching behavior were observed for the snowflake-dendritic and regular graphene crystals by annealing in a gas mixture of H2 and Ar. The regular graphene crystals were etched anisotropically creating hexagonal holes with pronounced edges, while etching of all the dendritic crystals occurred from the branches of lobs creating symmetrical fractal structures. The etching behavior provides important clue of graphene nucleation and growth as well as their selective etching to fabricate well-defined structures for nanoelectronics.

  2. Crystal structures of five 6-mercaptopurine derivatives

    PubMed Central

    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

  3. Crystal Structure of Human Kynurenine Aminotransferase ll*

    SciTech Connect

    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.

  4. Crystal structure of a Trypanosoma brucei metacaspase

    PubMed Central

    McLuskey, Karen; Rudolf, Jana; Proto, William R.; Isaacs, Neil W.; Coombs, Graham H.; Moss, Catherine X.; Mottram, Jeremy C.

    2012-01-01

    Metacaspases are distantly related caspase-family cysteine peptidases implicated in programmed cell death in plants and lower eukaryotes. They differ significantly from caspases because they are calcium-activated, arginine-specific peptidases that do not require processing or dimerization for activity. To elucidate the basis of these differences and to determine the impact they might have on the control of cell death pathways in lower eukaryotes, the previously undescribed crystal structure of a metacaspase, an inactive mutant of metacaspase 2 (MCA2) from Trypanosoma brucei, has been determined to a resolution of 1.4 Å. The structure comprises a core caspase fold, but with an unusual eight-stranded β-sheet that stabilizes the protein as a monomer. Essential aspartic acid residues, in the predicted S1 binding pocket, delineate the arginine-specific substrate specificity. In addition, MCA2 possesses an unusual N terminus, which encircles the protein and traverses the catalytic dyad, with Y31 acting as a gatekeeper residue. The calcium-binding site is defined by samarium coordinated by four aspartic acid residues, whereas calcium binding itself induces an allosteric conformational change that could stabilize the active site in a fashion analogous to subunit processing in caspases. Collectively, these data give insights into the mechanistic basis of substrate specificity and mode of activation of MCA2 and provide a detailed framework for understanding the role of metacaspases in cell death pathways of lower eukaryotes. PMID:22529389

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

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination. PMID:26676036

  6. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    ERIC Educational Resources Information Center

    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…

  7. Three-Dimensional Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, B.; /SLAC

    2006-09-07

    We discuss simulated photonic crystal structure designs for laser-driven particle acceleration, focusing on three-dimensional planar structures based on the so-called ''woodpile'' lattice. We describe guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice and discuss the properties of this mode, including particle beam dynamics and potential coupling methods for the structure. We also discuss possible materials and power sources for this structure and their effects on performance parameters, as well as possible manufacturing techniques and the required tolerances. In addition we describe the computational technique and possible improvements in numerical modeling that would aid development of photonic crystal structures.

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

    ERIC Educational Resources Information Center

    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)

  9. Crystal structure of tolyl­fluanid

    PubMed Central

    Cho, Seonghwa; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2014-01-01

    The title compound, C10H13Cl2FN2O2S2 {systematic name: N-[(di­chloro­fluoro­methyl)­sulfanyl]-N′,N′-dimethyl-N-p-tolyl­sulfamide}, is a well known fungicide. The dihedral angle between the mean plane of the di­methyl­amino group and that of the benzene ring is 32.3 (3)°. One Cl atom and one F atom of the di­chloro­fluoro­methyl­thio group are disordered over two sets of sites with an occupancy ratio of 0.605 (9):0.395 (9). In the crystal structure, two C—H⋯Cl hydrogen bonds link adjacent mol­ecules, forming dimers with R 2 2(14) loops. C—H⋯O hydrogen bonds link pairs of dimers into chains along the b-axis direction. These chains are joined by an additional C—H⋯O contact, generating a sheet in the ab plane. PMID:25484703

  10. Crystal structure of Clostridium difficile toxin A.

    PubMed

    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

    2016-01-01

    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(1,2). The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host(3,4). 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. PMID:27571750

  11. Microstructure and Crystal Structure in TAGS Compositions

    SciTech Connect

    Thompson, A. J.; Sharp, J; Rawn, Claudia J

    2009-01-01

    GeTe, a small bandgap semiconductor that has native p-type defects due to Ge vacancies, is an important constituent in the thermoelectric material known as TAGS. TAGS is an acronym for alloys of GeTe with AgSbTe{sub 2}, and compositions are normally designated as TAGS-x, where x is the fraction of GeTe. TAGS-85 is the most important with regard to applications, and there is also commercial interest in TAGS-80. The crystal structure of GeTe{sub 1+{delta}} has a composition-dependent phase transformation at a temperature ranging from 430 C ({delta} = 0) to {approx}400 C ({delta} = 0.02). The high-temperature form is cubic. The low-temperature form is rhombohedral for {delta} < 0.01, as is the case for good thermoelectric performance. Addition of AgSbTe{sub 2} shifts the phase transformation to lower temperatures, and one of the goals of this work is a systematic study of the dependence of transformation temperature on the parameter x. We present results on phase transformations and associated instabilities in TAGS compositions in the range of 70 at.% to 85 at.% GeTe.

  12. Crystal structure of Clostridium difficile toxin A

    PubMed Central

    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

    2016-01-01

    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 colon1,2. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host3,4. 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. PMID:27512603

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

    SciTech Connect

    Thomas, J. Lincy, A. Mahalakshmi, V.; Saban, K. V.

    2013-01-15

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

  14. Novel photonic crystal cavities and related structures.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

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

  15. A Dominant Factor for Structural Classification of Protein Crystals.

    PubMed

    Qi, Fei; Fudo, Satoshi; Neya, Saburo; Hoshino, Tyuji

    2015-08-24

    With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (n = 284), HEWL (n = 336), HSA (n = 63), and HIV-1 PR (n = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures. PMID:26230289

  16. Photonic crystal structures with tunable structure color as colorimetric sensors.

    PubMed

    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

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

    PubMed Central

    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

  18. In vivo protein crystallization opens new routes in structural biology

    PubMed Central

    Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; DePonte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael

    2012-01-01

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology. PMID:22286384

  19. Structural and Thermoelectric Properties of Tungsten Diselenide Crystals

    NASA Astrophysics Data System (ADS)

    Patel, K. K.; Patel, K. D.; Patel, Mayur; Patel, C. A.; Pathak, V. M.; Srivastava, R.

    2011-12-01

    Crystals of Tungsten diselenide (WSe2) have been grown by direct vapour transport (DVT) technique using micro processor controlled dual zone horizontal furnace. The chemical composition and structure of grown crystals were confirmed using energy dispersive analysis of X-ray (EDAX) and X-ray diffraction (XRD). In the present investigation thermoelectric power measurements (TEP) have been carried out on the grown crystals. Different electrical transport parameters of semiconductors have been determined and discussed in the paper.

  20. Optical phonon modes and crystal structure of NaLaF4 single crystals

    NASA Astrophysics Data System (ADS)

    Lage, Márcio Martins; Matinaga, Franklin Massami; Gesland, Jean-Yves; Moreira, Roberto Luiz

    2006-03-01

    Polarized Raman scattering and infrared reflectivity measurements have been used to investigate the crystal structure of Czochralski-grown NaLaF4 single crystals. The phonon symmetries, the simultaneous presence of polar modes in the infrared and Raman spectra, as well as the observation of piezoelectric resonance, helped us to identify the P6 group as the correct one for this crystal. This material belongs to a family of sodium lanthanide tetrafluorides (NaLnF4) crystals, whose photoluminescence efficiency is comparable to LiYF4. Therefore, NaLaF4 crystals may be important in the development of diode pumped up-conversion solid-state lasers. The number and behavior of the observed optical phonon modes were analyzed in terms of group theory predictions for the group symmetry found. A few anomalies in the phonon characteristics are discussed in terms of cationic disorder in the crystal lattice.

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

    NASA Astrophysics Data System (ADS)

    Manikandan, M.; Vijaya Prasath, G.; Bhagavannarayan, G.; Vijayan, N.; Mahalingam, T.; Ravi, G.

    2012-09-01

    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.

  2. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  3. Hydroflux synthesis and crystal structure of new lanthanide tungstate oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Latshaw, Allison M.; Smith, Mark D.; Chance, W. Michael; zur Loye, Hans-Conrad

    2015-04-01

    Single crystals of Na5Ln(OH)6WO4 where Ln = Er, Tm, and Yb were grown out of a NaOH hydroflux. The crystals were characterized by single crystal X-ray diffraction and were found to crystallize in the monoclinic space group I2/a. The lattice parameter ranges for the three structures are a = 11.2024(7) Å-11.2412(6) Å, b = 16.1850(10) Å-16.2220(10) Å, and c = 11.9913(7) Å-12.0323(7) Å while the β angle range is 101.999(2)°-102.025(2)°.

  4. Errors in Crystal structure of HINT from Helicobacter pylori

    PubMed Central

    Maize, Kimberly M.

    2016-01-01

    Inaccuracies in the article, Crystal structure of HINT from Helicobacter pylori by Tarique et al. [(2016) Acta Cryst. F72, 42–48] are presented, and a brief history of HINT nomenclature is discussed. PMID:27050269

  5. Determination of channeling perspectives for complex crystal structures

    SciTech Connect

    Allen, W.R.

    1993-03-01

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

  6. Crystal Structure and Crystal Chemistry of Some Common REE Minerals and Nanpingite

    NASA Astrophysics Data System (ADS)

    Ni, Yunxiang

    1995-01-01

    Part I. Crystal structure and crystal chemistry of fluorocarbonate minerals. The crystal structure of bastnasite-(Ce) have been solved in P-62c and refined to R = 0.018. The structure is composed of (001) (CeF) layers interspersed with (CO_3) layers in a 1:1 ratio. The Ce atom is coordinated in rm CeO_6F_3 polyhedra. The atomic arrangement of synchysite-(Ce) has been solved and refined to R = 0.036 with a monoclinic space group C2/c. It possesses a (001) layer structure, with layers of (Ca) and (CeF) separated by layers of carbonate groups. The layers stack in a manner analogous to C2/c muscovite. Polytypism similar to the micas may exist in synchysite. The crystal structures of cordylite-(Ce) have been solved in P6 _3/mmc and refined to R = 0.023. The structure and chemical formula are different from those deduced by Oftedal. The formula is rm MBaCe_2(CO _3)_4F, where M is rm Na^+, Ca^{2+}_{1/2 }+ O_{1/2}, or any solution. The presence of (NaF) layer in the structure is the key difference from the Oftedal's structure. This redefinition of the chemical formula and crystal structure of cordylite will be proposed to IMA-CNMMN. Part II. Crystal structure and crystal chemistry of monazite-xenotime series. Monazite is monoclinic, P2 _1/n, and xenotime is isostructural with zircon (I4_1/amd). Both atomic arrangements are based on (001) chains of intervening phosphate tetrahedra and RE polyhedra, with a REO_8 polyhedron in xenotime that accommodates HRE (Tb - Lu) and a REO_9 polyhedron in monazite that preferentially incorporates LRE (La - Gd). As the structure "transforms" from xenotime to monazite, the crystallographic properties are comparable along the (001) chains, with structural adjustments of 2.2 A along (010) to accommodate the different size RE atoms. Part III. Crystal structure of nanpingite-2M _2, the Cs end-member of muscovite. The crystal structure of nanpingite has been refined to R = 0.058. Compared to K^+ in muscovite, the largest interlayer Cs^+ in

  7. Crystal structure of a methimazole-based ionic liquid.

    PubMed

    Gaitor, Jamie C; Zayas, Manuel Sanchez; Myrthil, Darrel J; White, Frankie; Hendrich, Jeffrey M; Sykora, Richard E; O'Brien, Richard A; Reilly, John T; Mirjafari, Arsalan

    2015-12-01

    The structure of 1-methyl-2-(prop-2-en-1-ylsulfan-yl)-1H-imidazol-3-ium bromide, C7H11N2S(+)·Br(-), has monoclinic (P21/c) symmetry. In the crystal, the components are linked by N-H⋯Br and C-H⋯Br hydrogen bonds. The crystal structure of the title compound undeniably proves that methimazole reacts through the thione tautomer, rather than the thiol tautomer in this system. PMID:26870468

  8. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

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

    PubMed

    Marx, Ailie; Adir, Noam

    2013-03-01

    X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed. PMID:23201474

  10. Quantitative crystal structure descriptors from multiplicative congruential generators.

    PubMed

    Hornfeck, Wolfgang

    2012-03-01

    Special types of number-theoretic relations, termed multiplicative congruential generators (MCGs), exhibit an intrinsic sublattice structure. This has considerable implications within the crystallographic realm, namely for the coordinate description of crystal structures for which MCGs allow for a concise way of encoding the numerical structural information. Thus, a conceptual framework is established, with some focus on layered superstructures, which proposes the use of MCGs as a tool for the quantitative description of crystal structures. The multiplicative congruential method eventually affords an algorithmic generation of three-dimensional crystal structures with a near-uniform distribution of atoms, whereas a linearization procedure facilitates their combinatorial enumeration and classification. The outlook for homometric structures and dual-space crystallography is given. Some generalizations and extensions are formulated in addition, revealing the connections of MCGs with geometric algebra, discrete dynamical systems (iterative maps), as well as certain quasicrystal approximants. PMID:22338652

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

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463

  12. Predicting inclusion behaviour and framework structures in organic crystals.

    PubMed

    Cruz-Cabeza, Aurora J; Day, Graeme M; Jones, William

    2009-12-01

    We have used well-established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well-known inclusion behaviour. Using these methods, we are able to generate both close-packed crystal structures and high-energy open frameworks containing voids of molecular dimensions. Some of these high-energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent-accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules. PMID:19876969

  13. Crystal structure of the co-crystal butyl­paraben–isonicotinamide (1/1)

    PubMed Central

    Bhardwaj, Rajni M.; Yang, Huaiyu; Florence, Alastair J.

    2016-01-01

    The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hy­droxy­benzoate–isonicotinamide (1/1)], crystallizes with one mol­ecule of butyl­paraben (BPN) and one mol­ecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN mol­ecules form hydrogen-bonded (O—H⋯N and N—H⋯O) dimers of paired BPN and ISN mol­ecules. These dimers are further connected to each other via N—H⋯O=C hydrogen bonds, creating ribbons in [011] which further stack along the a axis to form a layered structure with short C⋯C contacts of 3.285 (3) Å. Packing inter­actions within the crystal structure were assessed using PIXEL calculations. PMID:26870584

  14. Growth, characterization, and crystal structure of a new chalcone derivative single crystal

    NASA Astrophysics Data System (ADS)

    Shettigar, Venkataraya; Dharmaprakash, S. M.

    2006-09-01

    A new organic nonlinear optical (NLO) chalcone derivative viz.1- ( 4- methoxyphenyl )-3- (3,4 - dimethoxy phenyl ) - 2 - propene-1-one, has been synthesized by Claisen-Schmidt condensation method. The synthesized compound was purified by repeated recrystallization process. To confirm the identity of the synthesized compound, FTIR spectra was recorded and various functional groups present were identified. NMR spectra were recorded for structural identity and purity confirmation of the synthesized compound. Good quality single crystals were grown by solvent evaporation and slow cooling technique using acetone as solvent. The grown crystals were characterized by UV-Visible , differential thermal analysis and linear refractive index measurement. The hardness of the crystal was determined using Vicker's indentation method. The single crystal structure analysis of the crystal was performed and it is found that the crystal belongs to monoclinic system with space group P2 I. The powder second harmonic generation(SHG)frequency conversion efficiency of the crystal was determined using Nd: YAG laser(λ = 1064nm)and it is 15 times that of Urea.

  15. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

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

    PubMed

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

    2002-12-01

    A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%. PMID:12594078

  17. Crystal structure of benzobi-cyclon.

    PubMed

    Kang, Gihaeng; Kim, Jineun; Lim, Hansu; Kim, Tae Ho

    2015-12-01

    In the title compound, C22H19ClO4S2 [systematic name: 3-(2-chloro-4-mesylbenzo-yl)-4-(phenyl-sulfan-yl)bi-cyclo-[3.2.1]oct-3-en-2-one], which is an unclassified herbicide, the dihedral angle between the plane of the phenyl and chloro-benzene rings is 19.9 (2)°. In the crystal, C-H⋯O hydrogen bonds link adjacent mol-ecules, generating two-dimensional networks extending parellel to (011). PMID:26870484

  18. Optical and structural properties of chalcone NLO single crystals

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Manjunath, H. R.; Karegouda, Prakash; Crasta, Vincent; Sridhar, M. A.

    2011-11-01

    Organic compound (E)-1-(4-methoxyphenyl)-3-(2,3,5-trichlorophenyl)prop-2-en-1-one [MPTCPP] with molecular formula C 16H 11Cl 3O 2 was synthesized using Claisen-Schmidt condensation reaction method. 1H NMR spectra was recorded to identify the various functional groups present in the compound and confirm the chemical structure. The single crystals were grown using slow evaporation solution growth technique. The UV-Visible spectrum study reveals that the crystal is transparent in the entire visible region and the absorption is observed at 364 nm. The Kurtz powder second harmonic generation (SHG) test shows that the MPTCPP is NLO active and its SHG efficiency is three times that of urea. Single crystal XRD study shows that the compound crystallizes in the monoclinic system with a space group Cc. The corresponding lattice parameters of the crystal are a = 28.215(5) Å, b = 3.9740(4) Å, c = 16.178(3) Å and V = 1503.0(4) Å 3. The micro hardness test was carried out and the work hardening coefficient value ( n) of the crystal was found to be 1.48. This indicates that the crystal is hard and is suitable for device application. The thermal study reveals that the thermal stability of the crystal is good.

  19. Single-Crystal Structure of a Covalent Organic Framework

    SciTech Connect

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

    2013-11-06

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

  20. The different conformations and crystal structures of dihydroergocristine

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  1. Crystal Structure of L-Histidinium 2-Nitrobenzoate

    PubMed Central

    Natarajan, Subramanian; Moovendaran, Kalimuthu; Kalyana Sundar, Jeyaperumal; Ravikumar, Krishnan

    2012-01-01

    A new nonlinear optical organic compound, namely, L-histidinium 2-nitrobenzoate (abbreviated as LH2NB (I); ([C6H10N3O2]+ [C7H4NO4]−)), was synthesized. The molecular structure of LH2NB (I) was elucidated using single crystal X-ray diffraction technique. The second harmonic generation (SHG) efficiency of this compound is about two times that of the standard potassium dihydrogen phosphate crystals. PMID:22536482

  2. Boron-oxygen polyanion in the crystal structure of tunellite

    USGS Publications Warehouse

    Clark, J.R.

    1963-01-01

    The crystal structure of tunellite, SrO??3B2O 3??4H2O, with infinite sheets of composition n[B6O9(OH)2]2-, has cations and water molecules in the spaces within the sheets. Adjacent sheets are held together by hydrogen bonding through the water molecules. The boron-oxygen polyanions provide the first example in hydrated borate crystals of one oxygen linked to three borons.

  3. Structure of ice crystallized from supercooled water

    PubMed Central

    Malkin, Tamsin L.; Murray, Benjamin J.; Brukhno, Andrey V.; Anwar, Jamshed; Salzmann, Christoph G.

    2012-01-01

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652

  4. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds

    PubMed Central

    2016-01-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  5. Crystal engineering with thioureas: A structure-based inquiry

    NASA Astrophysics Data System (ADS)

    Paisner, Kathryn A.

    2011-12-01

    Structural trends applicable to crystal engineering were studied in three classes of thiourea-based compounds. The aim of the study was to identify, predict, and ultimately design reliable single-molecule structural features, which could then be used to engineer crystals with desirable properties. In one class of compounds, this goal was achieved: N-alkyl and N-aryl derivatives of N,N'-bis(3-thioureidopropyl)piperazine adopted an identical conformation in the solid state, which resulted in near-identical crystal packing. A second class of closely related compounds, N-substituted tris(2-thioureidoethyl)amines, showed no such reliability in the solid state, likely because the parent structure lacked hydrogen-bonding functionalities sufficient to control intramolecular structure. In the third class of compounds that we studied, 1-benzoyl-3-(2-pyridyl)thioureas, substitution patterns were often predictive of molecular conformation; however, these intramolecular trends did not lead to recognizable crystal packing motifs. Nevertheless, certain physical properties observed in this last class of compounds---color, solubility, and often crystallinity---were conformer-specific, interestingly without any apparent relevance to crystal lattice structure. Solution-state and solid-state conformational trends in these 1-benzoyl-3-(2-pyridyl)thioureas have been documented, and speculations as to the source of color in one of the two observed conformations have been noted.

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

    PubMed

    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. PMID:27050261

  7. Crystal structure of ammonia dihydrate II.

    PubMed

    Griffiths, Gareth I G; Fortes, A Dominic; Pickard, Chris J; Needs, R J

    2012-05-01

    We have used density-functional-theory (DFT) methods together with a structure searching algorithm to make an experimentally constrained prediction of the structure of ammonia dihydrate II (ADH-II). The DFT structure is in good agreement with neutron diffraction data and verifies the prediction. The structure consists of the same basic structural elements as ADH-I, with a modest alteration to the packing, but a considerable reduction in volume. The phase diagram of the known ADH and ammonia monohydrate + water-ice structures is calculated with the Perdew-Burke-Ernzerhof density functional, and the effects of a semi-empirical dispersion corrected functional are investigated. The results of our DFT calculations of the finite-pressure elastic constants of ADH-II are compared with the available experimental data for the elastic strain coefficients. PMID:22583254

  8. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-07-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.

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

    DOEpatents

    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.

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

    DOEpatents

    Payne, S.A.; Kway, W.L.; DeLoach, L.D.; Krupke, W.F.; Chai, B.H.T.

    1994-08-23

    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 [minus

  11. Photonic crystal structures for efficent localization or extraction of light

    NASA Astrophysics Data System (ADS)

    Vuckovic, Jelena

    Three-dimensional (3D) photonic crystals offer the opportunity of light manipulation in all directions in space, but they are very difficult to fabricate. On the other hand, planar photonic crystals are much simpler to make, but they exhibit only a "quasi-3D" confinement, resulting from the combined action of 2D photonic crystal and internal reflection. The imperfect confinement in the third dimension produces some unwanted out-of-plane loss, which is usually a limiting factor in performance of these structures. This thesis proposes how to fully take advantage of the relatively simple fabrication of planar photonic crystals, by addressing a problem of loss-reduction. One of the greatest challenges in photonics is a construction of optical microcavities with small mode volumes and large quality factors, for efficient localization of light. Beside standard applications of these structures (such as lasers or filters), they can potentially be used for cavity QED experiments, or as building blocks for quantum networks. This work also presents the design and fabrication of optical microcavities based on planar photonic crystals, with mode volumes of the order of one half of cubic wavelength of light (measured in material) and with Q factors predicted to be even larger than 10 4. In addition to photonic crystals fabricated in semiconductors, we also address interesting properties of metallic photonic crystals and present our theoretical and experimental work on using them to improve the output of light emissive devices. Feature sizes of structures presented here are below those achievable by photolithography. Therefore, a high resolution lithography is necessary for their fabrication. The presently used e-beam writing techniques suffer from limitations in speed and wafer throughput, and they represent a huge obstacle to commercialization of photonic crystals. Our preliminary work on electron beam projection lithography, the technique that could provide us with the speed

  12. The high-resolution crystal structure of human LCAT.

    PubMed

    Piper, Derek E; Romanow, William G; Gunawardane, Ruwanthi N; Fordstrom, Preston; Masterman, Stephanie; Pan, Oscar; Thibault, Stephen T; Zhang, Richard; Meininger, David; Schwarz, Margrit; Wang, Zhulun; King, Chadwick; Zhou, Mingyue; Walker, Nigel P C

    2015-09-01

    LCAT is intimately involved in HDL maturation and is a key component of the reverse cholesterol transport (RCT) pathway which removes excess cholesterol molecules from the peripheral tissues to the liver for excretion. Patients with loss-of-function LCAT mutations exhibit low levels of HDL cholesterol and corneal opacity. Here we report the 2.65 Å crystal structure of the human LCAT protein. Crystallization required enzymatic removal of N-linked glycans and complex formation with a Fab fragment from a tool antibody. The crystal structure reveals that LCAT has an α/β hydrolase core with two additional subdomains that play important roles in LCAT function. Subdomain 1 contains the region of LCAT shown to be required for interfacial activation, while subdomain 2 contains the lid and amino acids that shape the substrate binding pocket. Mapping the naturally occurring mutations onto the structure provides insight into how they may affect LCAT enzymatic activity. PMID:26195816

  13. Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin; Lin, M.C.; Schwartz, Brian; Byer, Robert; McGuinness, Christopher; Colby, Eric; England, Robert; Noble, Robert; Spencer, James; /SLAC

    2012-07-02

    Photonic crystal waveguides are promising candidates for laser-driven accelerator structures because of their ability to confine a speed-of-light mode in an all-dielectric structure. Because of the difference between the group velocity of the waveguide mode and the particle bunch velocity, fields must be coupled into the accelerating waveguide at frequent intervals. Therefore efficient, compact couplers are critical to overall accelerator efficiency. We present designs and simulations of high-efficiency coupling to the accelerating mode in a three-dimensional photonic crystal waveguide from a waveguide adjoining it at 90{sup o}. We discuss details of the computation and the resulting transmission. We include some background on the accelerator structure and photonic crystal-based optical acceleration in general.

  14. Free-Standing Photonic Crystal Films with Gradient Structural Colors.

    PubMed

    Ding, Haibo; Liu, Cihui; Ye, Baofen; Fu, Fanfan; Wang, Huan; Zhao, Yuanjin; Gu, Zhongze

    2016-03-23

    Hydrogel colloidal crystal composite materials have a demonstrated value in responsive photonic crystals (PhCs) via controllable stimuli. Although they have been successfully exploited to generate a gradient of color distribution, the soft hydrogels have limitations in terms of stability and storage caused by dependence on environment. Here, we present a practical strategy to fabricate free-standing PhC films with a stable gradient of structural colors using binary polymer networks. A colloidal crystal hydrogel film was prepared for this purpose, with continuously varying photonic band gaps corresponding to the gradient of the press. Then, a second polymer network was used to lock the inside non-close-packed PhC structures and color distribution of the hydrogel film. It was demonstrated that our strategy could bring about a solution to the angle-dependent structural colors of the PhC films by coating the surface with special microstructures. PMID:26962967

  15. Modulated crystal structure of InMo4O6.

    PubMed

    Schultz, Peter; Simon, Arndt; Oeckler, Oliver

    2016-08-01

    The (3 + 1)-dimensional modulated crystal structure of the metal-rich cluster compound InMo4O6 was solved and refined from single-crystal data in the superspace group P4/mbm(00γ)00ss [q = 0, 0, 0.1536 (4); a = 9.6664 (9), c = 2.8645 (3) Å; R1(all) = 0.046, wR(all) = 0.076]. The crystal structure is closely related to the NaMo4O6 structure type. It is built from rods of Mo6 clusters condensed via trans edges. These form channels parallel to [001], in which In6 and In7 oligomers alternate. Weak diffuse planes parallel to (001)* interconnect the satellite reflections; they occur due to two-dimensional rod disorder of the In oligomer chains. PMID:27484384

  16. The Crystal Structure of GXGD Membrane Protease FlaK

    SciTech Connect

    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.

  17. The crystal structure of GXGD membrane protease FlaK

    SciTech Connect

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya

    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.

  18. Constraints and restraints in crystal structure analysis

    PubMed Central

    Immirzi, Attilio

    2009-01-01

    The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed. PMID:22477768

  19. Ab initio modelling: Genesis of crystal structures

    NASA Astrophysics Data System (ADS)

    van de Walle, Axel

    2005-05-01

    Genetic algorithms prove useful to distil a complex quantum mechanical calculation of interatomic interactions down to its simplest mathematical expression. This makes it possible to predict the structure of new compounds from first principles.

  20. Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

    PubMed Central

    Bruhn, Jessica F.; Barnett, Katherine C.; Bibby, Jaclyn; Thomas, Jens M. H.; Keegan, Ronan M.; Rigden, Daniel J.; Bornholdt, Zachary A.

    2014-01-01

    The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle. PMID:24155387

  1. Electronic structure of the CuBS2 crystal

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Gordienko, A. B.; Filippov, S. I.

    2012-09-01

    The band structure and spectra of the total and projected densities of states of a new crystal of the chalcopyrite family, namely, CuBS2, have been calculated in terms of the density functional theory. It has been found that the crystal is a pseudo-direct-band-gap semiconductor, and the best theoretical estimate of the optical band gap is 3.44 eV. The upper valence band of the CuBS2 crystal basically consists of the contributions from the p states of S atoms and the d states of Cu atoms. The crystal splitting is 0.2 eV. The bottom of the conduction band is basically formed by the sp states of boron and sulfur atoms with an admixture of the s states of copper atoms.

  2. Utilization of Protein Crystal Structures in Industry

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kohki

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

  3. Crystal Structure Effect on Electrical Properties of Ysz Ceramics

    NASA Astrophysics Data System (ADS)

    Zhang, Chunxia; Gong, Shengkai; Zhou, Chungen; Xu, Huibin

    YSZ samples were prepared by Plasma Spray (PS) and Electron Beam Physical Vapor Deposition (EB-PVD) respectively. Microstructure and morphology were observed by SEM and XRD. Grain size of PS-YSZ was non-uniform caused by the inclusion of nano particle by molten particle and column crystal structure was observed for EB-PVD-YSZ. The Arrhenius plots of two samples were graphed by analysis of the measurement results of AC impedance spectra. The conductive mechanisms for EB-PVD and PS YSZ were different due to the crystal structure.

  4. Crystal chemistry and structure refinement of five hydrated calcium borates

    USGS Publications Warehouse

    Clark, J.R.; Appleman, D.E.; Christ, C.L.

    1964-01-01

    The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. Photonics of liquid-crystal structures: A review

    SciTech Connect

    Palto, S. P. Blinov, L. M.; Barnik, M. I.; Lazarev, V. V.; Umanskii, B. A.; Shtykov, N. M.

    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.

  7. Structure of self - assembled two-dimensional spherical crystals

    NASA Astrophysics Data System (ADS)

    Bausch, Andreas R.

    2004-03-01

    Dense spherical particles on a flat surface usually pack into a simple triangular lattice, similar to billiard balls at the start of a game. The minimum energy configuration for interacting particles on the curved surface of a sphere, however, presents special difficulties, as recognized already by J.J. Thomson. We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries or "scars" not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. First experiments where the melting of the crystal structure was observable will be discussed. Dynamic triangulation methods allow the analysis of the dynamics of the defects. Possible modifications towards mechanically stabilized self assembly structures result in so called Colloidosomes, which are promising for many different encapsulation purposes.

  8. Crystal structures of two engineered thiol trypsins.

    PubMed

    McGrath, M E; Wilke, M E; Higaki, J N; Craik, C S; Fletterick, R J

    1989-11-28

    We have determined the three-dimensional structures of engineered rat trypsins which mimic the active sites of two classes of cysteine proteases. The catalytic serine was replaced with cysteine (S195C) to test the ability of sulfur to function as a nucleophile in a serine protease environment. This variant mimics the cysteine trypsin class of thiol proteases. An additional mutation of the active site aspartate to an asparagine (D102N) created the catalytic triad of the papain-type cysteine proteases. Rat trypsins S195C and D102N,S195C were solved to 2.5 and 2.0 A, respectively. The refined structures were analyzed to determine the structural basis for the 10(6)-fold loss of activity of trypsin S195C and the 10(8)-fold loss of activity of trypsin D102N,S195C, relative to rat trypsin. The active site thiols were found in a reduced state in contrast to the oxidized thiols found in previous thiol protease structures. These are the first reported structures of serine proteases with the catalytic centers of sulfhydryl proteases. Structure analysis revealed only subtle global changes in enzyme conformation. The substrate binding pocket is unaltered, and active site amino acid 102 forms hydrogen bonds to H57 and S214 as well as to the backbone amides of A56 and H57. In trypsin S195C, D102 is a hydrogen-bond acceptor for H57 which allows the other imidazole nitrogen to function as a base during catalysis. In trypsin D102N,S195C, the asparagine at position 102 is a hydrogen-bond donor to H57 which places a proton on the imidazole nitrogen proximal to the nucleophile. This tautomer of H57 is unable to act as a base in catalysis.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2611228

  9. Formation of the structure of gold nanoclusters during crystallization

    SciTech Connect

    Gafner, Yu. Ya. Goloven'ko, Zh. V.; Gafner, S. L.

    2013-02-15

    The structure formation in gold nanoparticles 1.6-5.0 nm in diameter is studied by molecular dynamics simulation using a tight-binding potential. The simulation shows that the initial fcc phase in small Au clusters transforms into other structural modifications as temperature changes. As the cluster size increases, the transition temperature shifts toward the melting temperature of the cluster. The effect of various crystallization conditions on the formation of the internal structure of gold nanoclusters is studied in terms of microcanonical and canonical ensembles. The stability boundaries of various crystalline isomers are analyzed. The obtained dependences are compared with the corresponding data obtained for copper and nickel nanoparticles. The structure formation during crystallization is found to be characterized by a clear effect of the particle size on the stability of a certain isomer modification. Nickel and copper clusters are shown to exhibit common features in the formation of their structural properties, whereas gold clusters demonstrate much more complex behavior.

  10. The crystal structure of aluminum doped β-rhombohedral boron

    NASA Astrophysics Data System (ADS)

    Bykova, Elena; Parakhonskiy, Gleb; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-01

    A crystal structure of aluminum doped β-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B12 icosahedra with voids occupied by the B28-B-B28 units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) Å lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the β-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB44.8(5) and AlB37.8(5), which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB44.8(5) is described in detail.

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

    SciTech Connect

    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.

  12. Crystal structure of HINT from Helicobacter pylori.

    PubMed

    Tarique, K F; Devi, S; Abdul Rehman, S A; Gourinath, S

    2016-01-01

    Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT from Helicobacter pylori (HpHINT) in complex with AMP is reported at a resolution of 3 Å. The final model has R and Rfree values of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis shows H. pylori HINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom. PMID:26750483

  13. Determining complex crystal structures from high pressure single-crystal diffraction data collected on synchrotron sources

    NASA Astrophysics Data System (ADS)

    McMahon, M. I.; Loa, I.; Stinton, G. W.; Lundegaard, L. F.

    2013-08-01

    As part of a Long Term Project, single-crystal diffraction techniques have been developed for use at the high pressure beamlines ID09 and ID27 at the European Synchrotron Radiation Facility, and have been utilised to determine the crystal structures of various high pressure phases, including those with incommensurate structures, at both high and low temperatures. The same techniques have also been used to determine the structures of high pressure phases at the SRS, Diamond and Petra-III synchrotron sources. In this paper, we describe technical details of the methods developed, and describe some of the considerations necessary for planning experiments and collecting and processing the data. We then illustrate the quality of data that can be obtained, and the complexity of the structures that can be refined, using recent results obtained from complex high pressure phases of N2 and Ba.

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

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  15. Crystallization of interleukin-18 for structure-based inhibitor design

    PubMed Central

    Krumm, Brian; Meng, Xiangzhi; Xiang, Yan; Deng, Junpeng

    2015-01-01

    Interleukin-18 (IL-18) is a pleiotropic pro-inflammatory cytokine belonging to the IL-1 superfamily. IL-18 plays an important role in host innate and acquired immune defense, with its activity being modulated in vivo by its naturally occurring antagonist IL-18 binding protein (IL-18BP). Recent crystal structures of human IL-18 (hIL-18) in complex with its antagonist or cognate receptor(s) have revealed a conserved binding interface on hIL-18 representing a promising drug target. An important step in this process is obtaining crystals of apo hIL-18 or hIL-18 in complex with small-molecule inhibitors, preferably under low ionic strength conditions. In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design. PMID:26057800

  16. Can antimonide-based nanowires form wurtzite crystal structure?

    NASA Astrophysics Data System (ADS)

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A.

    2016-01-01

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires.The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents

  17. A unified picture of the crystal structures of metals

    NASA Astrophysics Data System (ADS)

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

    1995-04-01

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

  18. Structural and optical properties of a new chalcone single crystal

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Poojary, Boja

    2012-09-01

    A new nonlinear optical material 1-(4-methylthiophenyl)-3-(4-methoxyphenyl)prop-2-en-1-one with molecular formula C17H16O2S was synthesized by using the Claisen-Schmidt condensation reaction method. The Various functional groups present in the compound were identified using recorded FT-IR spectrum. The crystal growth parameters have been studied using solubility test and acetone is found to be a very good solvent for the crystal growth at an ambient temperature. The transparent high quality single crystals up to a size of 26×2×2 mm3 were grown using the slow evaporation solution growth technique. UV-visible study was carried out and the spectrum reveals that the crystal is transparent in the entire visible region and absorptive in the UV region. The refractive index is determined using Brewster's angle method. The optical energy band gap of the material is measured using Tauc's plot and the direct method. The single crystal XRD of MMPP crystal shows the following cell parameters: a=5.9626(2) Å, b=15.3022(6) Å, c=16.0385(7) Å, α=β=γ=90°, volume=1463.37(10) Å3 with a space group of Pna21. The compound MMPP exhibits optical nonlinearity (NLO) and its second order NLO efficiency is 3.15 times to that of urea. The effect of functional groups OCH3 and SCH3 on the non-linearity as well as the structural property of the compound has been discussed. The crystal is thermally stable. High NLO efficiency, good thermal stability, good transparency and ability to grow as a high quality single crystal make this material very attractive for opto-electronic applications.

  19. Crystal structures of fusion proteins with large-affinity tags.

    PubMed

    Smyth, Douglas R; Mrozkiewicz, Marek K; McGrath, William J; Listwan, Pawel; Kobe, Bostjan

    2003-07-01

    The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. PMID:12824478

  20. Redetermination of the crystal structure of NbF4.

    PubMed

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-08-01

    Single crystals of NbF4, niobium(IV) tetra-fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182-186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95-104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa-hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  1. Redetermination of the crystal structure of NbF4

    PubMed Central

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-01-01

    Single crystals of NbF4, niobium(IV) tetra­fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182–186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95–104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa­hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

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

    ERIC Educational Resources Information Center

    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.…

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

    NASA Technical Reports Server (NTRS)

    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.

  4. The diammoniate of diborane: Crystal structure and hydrogen release

    SciTech Connect

    Bowden, Mark E.; Heldebrant, David J.; Karkamkar, Abhijeet J.; Proffen, Thomas E.; Schenter, Gregory K.; Autrey, Thomas

    2010-10-12

    [(NH3)2BH2]+[BH4]- is formed from the room temperature decomposition of NH4+BH4-, via a NH3BH3 intermediate. Its crystal structure has been determined and contains disordered BH4- ions in 2 distinct sites. Hydrogen release is similar to that from NH3BH3 but with faster kinetics.

  5. Co-crystal formation based on structural matching.

    PubMed

    Zhou, Liping; Dodd, Stephanie; Capacci-Daniel, Christina; Garad, Sudhakar; Panicucci, Riccardo; Sethuraman, Vijay

    2016-06-10

    A co-crystal is defined as a single crystalline structure composed of two or more components with no proton transfer which are solid at room temperature. Our group has come up with the following rationale selection of co-formers for initial co-crystal screening: 1) selection of co-formers with the highest potential for hydrogen bonding with the API and 2) selection of co-formers with diversity of secondary structural characteristics. We demonstrate the feasibility of this technique with a Novartis drug candidate A. In the first tier, 20 co-formers were screened and two hits were identified. By examining the two co-formers, which worked from the first round, a second round of screening was undertaken with more focused chemical matter. Nineteen co-crystal formers closely related to the two hits in the first screen were screened in the second tier. From this screen five hits were identified. All the hits were compared for their physical and chemical stability and dissolution profile. Based on the comparison 4-aminobenzoic co-crystal was chosen for in-vivo comparison with the free form. The co-crystal had 12 times higher exposure than the free form thus overcoming the solubility limited exposure. PMID:26948852

  6. Analysis of voids in crystal structures: the methods of 'dual' crystal chemistry.

    PubMed

    Blatov, V A; Shevchenko, A P

    2003-01-01

    The theoretical basics of the analysis of voids in crystal structures by means of Voronoi-Dirichlet polyhedra (VDP) and of the graph theory are stated. Topological relations are considered between VDPs and atomic domains in a crystal field. These relations allow the separation of two non-intersecting topological subspaces in a crystal structure, whose connectednesses are defined by two finite 'reduced' graphs. The first, 'direct', subspace includes the atoms (VDP centres) and the network of interatomic bonds (VDP faces), the second, 'dual', one comprises the void centres (VDP vertices) and the system of channels (VDP edges) between them. Computer methods of geometrical-topological analysis of the 'dual' subspace are developed and implemented within the program package TOPOS. They are designed for automatically restoring the system of channels, visualizing and sizing voids and void conglomerates, dimensional analysis of continuous void systems, and comparative topological analysis of 'dual' subspaces for various substances. The methods of analysis of 'dual' and 'direct' subspaces are noted to differ from each other only in some details that allows the term 'dual' crystal chemistry to be introduced. The efficiency of the methods is shown with the analysis of compounds of different chemical nature: simple substances, ionic structures, superionic conductors, zeolites, clathrates, organic supramolecular complexes. PMID:12496460

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

    SciTech Connect

    Sankari, R. Siva; Perumal, Rajesh Narayana

    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.

  8. Crystal Structure of the Bacillus subtilis Superoxide Dismutase

    SciTech Connect

    Liu, Ping; Ewis, H.E.; Huang, Y.-J; Lu, C.-D.; Tai, P.C.; Weber, Irene T.

    2008-06-01

    The sodA gene of Bacillus subtilis was expressed in Escherichia coli, purified and crystallized. The crystal structure of MnSOD was solved by molecular replacement with four dimers per asymmetric unit and refined to an R factor of 21.1% at 1.8 {angstrom} resolution. The dimer structure is very similar to that of the related enzyme from B. anthracis. Larger structural differences were observed with the human MnSOD, which has one less helix in the helical domain and a longer loop between two -strands and also showed differences in three amino acids at the intersubunit interface in the dimer compared with the two bacterial MnSODs. These structural differences can be exploited in the design of drugs that selectively target the Bacillus enzymes.

  9. Crystal structure of SiB/sub 6/

    SciTech Connect

    Vlasse, M.; Slack, G.A.; Garbauskas, M.; Kasper, J.S.; Viala, J.C.

    1986-06-01

    The accurate and detailed structure of the compound SiB/sub 6/ has been determined by single-crystal X-ray diffraction. The final R value was 6.1% for 4225 reflections. The cell is orthorhombic with space group Pnnm and a = 14.397(7) A, b = 18.318(9) A, c = 9.911(7) A, and from the electron density appears to contain 43 silicon atoms and 238 boron atoms. The structure contains many features found in other structures of boron-rich phases, and obeys the crystal chemistry rules established for them. It contains interconnected icosahedra, icosihexahedra, as well as several isolated boron and silicon atoms. An unusual feature of this structure is the presence of icosihexahedra containing silicon atoms similar to those found previously in BeB/sub 3/.

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

    PubMed Central

    Parshin, Alexander M.; Gunyakov, Vladimir A.; Zyryanov, Victor Y.; Shabanov, Vasily F.

    2013-01-01

    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. PMID:23965955

  11. Domain structures in nematic liquid crystals on a polycarbonate surface.

    PubMed

    Parshin, Alexander M; Gunyakov, Vladimir A; Zyryanov, Victor Y; Shabanov, Vasily F

    2013-01-01

    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. PMID:23965955

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

    SciTech Connect

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

    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.

  13. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. Crystal structure of new AsS2 compound

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    AsS2 single crystals have been obtained for the first time from an As2S3 melt at pressures above 6 GPa and temperatures above 800 K in the As2S3 → AsS + AsS2 reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

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

    SciTech Connect

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

    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.

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

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom. PMID:18642947

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

    NASA Astrophysics Data System (ADS)

    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.

  18. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  19. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  20. Solvent-controlled assembly of crystal structures: From centrosymmetric structure to noncentrosymmetric structure

    NASA Astrophysics Data System (ADS)

    Zhang, Le; Dang, Lilong; Luo, Feng; Feng, Xuefeng

    2016-02-01

    Reported here are two isomeric organic crystals and two HgI2-based coordination compounds by solvo(hydro)thermal method: [(TPTA)·H2O]n (1, Cc), [(TPTA)·H2O]n (2, Pbca), [Hg1.5I3(TPTA)0.5(CH3CN)·(H2O)0.5]n (3, P21) and [HgI2(TPTA)·H2O]n (4, P21/c) (TPTA = N,N‧,N″-tris(3-pyridyl)trimesic amide). Single crystal X-ray diffraction show that they afford noncentrosymmetric and centrosymmetric structures, respectively. Note that this kind of formations can be precisely controlled by changing the reaction solvent, thus indicating a facile method towards generating noncentrosymmetric structure.

  1. Can antimonide-based nanowires form wurtzite crystal structure?

    PubMed

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A

    2016-02-01

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires. PMID:26763161

  2. Projection structure of frog rhodopsin in two crystal forms.

    PubMed Central

    Schertler, G F; Hargrave, P A

    1995-01-01

    Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved. Images Fig. 1 Fig. 2 Fig. 6 PMID:8524807

  3. Structure and melting behavior of classical bilayer crystals of dipoles

    SciTech Connect

    Lu Xin; Wu Changqin; Micheli, Andrea; Pupillo, Guido

    2008-07-01

    We study the structure and melting of a classical bilayer system of dipoles in a setup where the dipoles are oriented perpendicular to the planes of the layers and the density of dipoles is the same in each layer. Due to the anisotropic character of the dipole-dipole interactions, we find that the ground-state configuration is given by two hexagonal crystals positioned on top of each other, independent of the interlayer spacing and dipolar density. For large interlayer distances these crystals are independent, while in the opposite limit of small interlayer distances the system behaves as a two-dimensional crystal of paired dipoles. Within the harmonic approximation for the phonon excitations, the melting temperature of these crystalline configurations displays a nonmonotonic dependence on the interlayer distance, which is associated with a re-entrant melting behavior in the form of solid-liquid-solid-liquid transitions at fixed temperature.

  4. Crystal structure and density of helium to 232 kbar

    NASA Technical Reports Server (NTRS)

    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.

  5. Crystal structure and density of helium to 232 kbar

    NASA Astrophysics Data System (ADS)

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

    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.

  6. Use of Pom Pons To Illustrate Cubic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Cady, Susan G.

    1997-07-01

    In general chemistry classes, students are introduced to the ways in which atoms are arranged in cubic crystal structures. Transposing the textbook illustrations into three dimensional structures is difficult for some students. This transitions is easier if a three dimensional model is available for examination. Several 3D models are cited. A quick to assemble, inexpensive, colorful, and durable alternative to these models and styrofoam balls is the use of olefin pom pons. Different sized pom pons can be used to demonstrate how the atomic radius will vary when comparing the different types of cubic crystal unit cells. Being made of a coarse material, pom pons can be stacked to illustrate different packing arrangements such as hexagonal close-packed and cubic close-packed structures. Pom pons make great atoms.

  7. Crystal structure of Brinzolamide: a carbonic anhydrase inhibitor.

    PubMed

    Zheng, Huirong; Lou, Benyong

    2016-05-01

    In crystal structure of the title compound, C12H21N3O5S3 [systematic name: (R)-4-ethyl-amino-2-(3-meth-oxy-prop-yl)-3,4-di-hydro-2H-thieno[3,2-e][1,2]thia-zine-6-sulfonamide 1,1-dioxide], there exist three kinds of hydrogen-bonding inter-actions. The sulfonamide group is involved in hydrogen bonding with the secondary amine and the meth-oxy O atom, resulting in the formation of layers parallel to the bc plane. The layers are linked by an N-H⋯O hydrogen bond involving a sulfonamide O atom as acceptor and the secondary amine H atom as donor, which gives rise to the formation of a unique bilayer structure. The absolute structure of the mol-ecule in the crystal was determined by resonant scattering [Flack parameter = 0.01 (4)]. PMID:27308020

  8. Crystal structure and spectroscopic elucidation of 3-phenylpyridinium hydrogensquarate.

    PubMed

    Koleva, Bojidarka B; Kolev, Tsonko; Tsanev, Tsanko; Kotov, Stefan; Mayer-Figge, Heike; Spiteller, Michael; Sheldrick, William S

    2010-01-01

    The novel 3-phenylpyridinium hydrogensquarate (1) has been synthesized and its structure and properties are elucidated spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy, TGA, DSC, DTA and ESI MS. Quantum chemical calculations were used to obtain the electronic structure, vibrational data and electronic spectrum. 3-Phenylpyridinium hydrogensquarate, crystallizes in the space group P-1 and the ions in the unit cell are joined into layers by intermolecular NH...O=C((Sq)) bonds with bond lengths of 2.625 and 2.626 A, respectively. Hydrogentartarates form dimers by strong O=COH...OCO interactions (2.499 A). PMID:19931483

  9. Crystal structure of a symbiosis-related lectin from octocoral.

    PubMed

    Kita, Akiko; Jimbo, Mitsuru; Sakai, Ryuichi; Morimoto, Yukio; Miki, Kunio

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide. PMID:26022515

  10. Lattice dynamics of crystals having R2MX6 structure

    NASA Astrophysics Data System (ADS)

    Torres, D. I.; Freire, J. D.; Katiyar, R. S.

    1997-10-01

    The theory of lattice dynamics in the harmonic approximation using a rigid-ion model due to Born and Huang [Dynamical Theory of Crystal Lattices (Oxford University Press, New York, 1954)], is applied to ionic crystals of the R2MX6 type with antifluorite structure namely, K2SnCl6, K2PtBr6, Cs2SnBr6, and Rb2SnBr6 in the cubic phase. The model expresses the potential energy as the sum of long-range Coulomb interactions and repulsive short-range interactions between ions in the primitive cell. A function of axially symmetric type is used to approximate the short-range part, and the number of force constant parameters were reduced utilizing stability conditions in the manner described by Katiyar [J. Phys. C 3, 1087 (1970)]. The remaining constants were determined by a nonlinear least-squares analysis of some experimental frequencies at the critical point Γ. The long-range contributions were calculated using the Ewald transformation as described by Cowley [Acta Crystallogr. 15, 687 (1962)]. Phonon frequencies and the normal modes of vibrations at the zone center were obtained; of particular interest is the resulting lowest librational frequency for each crystal. We obtained excellent agreement between the calculated and the observed frequencies. The resulting effective charge parameters indicated that these crystals are partially ionic. In general, the results offered a better vision of the structural phase transition mechanism involving the rotational mode T1g.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  12. Structural engineering of three-dimensional phononic crystals

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  13. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

    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.

  14. Revisiting the crystal structure of rhombohedral lead metaniobate.

    PubMed

    Olsen, Gerhard Henning; Sørby, Magnus Helgerud; Hauback, Bjørn Christian; Selbach, Sverre Magnus; Grande, Tor

    2014-09-15

    Lead metaniobate (PbNb2O6) can exist both as a stable rhombohedral and a metastable orthorhombic tungsten-bronze-type polymorph. Although the orthorhombic is a well-known ferroelectric material, the rhombohedral polymorph has been far less studied. The crystal structure and energetic stability of the stable rhombohedral polymorph of lead metaniobate is re-examined by powder X-ray diffraction and powder neutron diffraction in combination with ab initio calculations. We show that this structure is described by the polar space group R3, in contradiction to the previously reported space group R3m. The crystal structure is unusual, consisting of edge-sharing dimers of NbO(6/2) octahedra forming layers with 6- and 3-fold rings of octahedra and lead ions in channels formed by these rings. The layers are connected by corner-sharing between octahedra. Finally, the crystal structure is discussed in relation to other AB2O6 compounds with B = Nb, Ta. PMID:25167129

  15. Crystal structure optimisation using an auxiliary equation of state.

    PubMed

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

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1. PMID:26567640

  16. Crystal structure optimisation using an auxiliary equation of state

    SciTech Connect

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

    2015-11-14

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

  17. Tunable photonic structures based on silicon and liquid crystals

    NASA Astrophysics Data System (ADS)

    Perova, Tatiana S.; Tolmachev, Vladimir A.; Astrova, Ekaterina V.

    2008-01-01

    This paper is focused on the design, fabrication and characterization of the conventional and tunable photonic devices based on grooved silicon, serving as one-dimensional (1D) photonic crystal. The advantages of these photonic structures are as follows: the large refractive index contrast, in-plane moulding of the light flow, the possibility to fabricate a composite photonic structures by filling the grooves with a different compounds and compatibility with current semiconductor processing techniques. The optical properties of grooved Si structures were simulated using a transfer matrix method and gap map method and have been verified experimentally using FTIR microscopy. The air spaces in the basic silicon-air matrices were infiltrated with nematic liquid crystal E7. It is shown that the optical properties of the obtained composite 1D photonic crystals can be tuned by means of electro- and thermo-optical effects. Such a structures suit well for the various elements of the integrated optics and can serve as a building blocks for optical interconnects.

  18. Crystal structure optimisation using an auxiliary equation of state

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  19. EVO—Evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    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

  20. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening.

    PubMed

    Neumann, M A; van de Streek, J; Fabbiani, F P A; Hidber, P; Grassmann, O

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

  1. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    PubMed Central

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

  2. Micro-spectroscopic mapping: revealing internal structures of zircon crystals

    NASA Astrophysics Data System (ADS)

    Nasdala, L.; Reiners, P. W.; Hanchar, J. M.

    2003-04-01

    Natural zircon crystals typically deviate from perfect crystallinity and ideal chemical composition. If non-ideality features are not homogeneously distributed within a crystal but show a heterogeneity pattern, this is referred to as its "internal structure". Internal structures of zircon are mostly first caused by the heterogeneous incorporation of trace elements during crystal growth. Over time, these primary patterns may become more complex after being overprinted by radioactive self-irradiation and heterogeneous alteration or recrystallization. Internal structures may provide valuable information about the origin and post-growth history of zircon crystals. Further, they need to be recognized for sound microprobe dating, for instance to avoid biased results when straddling zones of different age. Revealing internal structures has thus become an important tool in zircon research. It is mostly done by means of backscattered electrons or cathodoluminescence imaging. These two techniques are advantageous over optical microscopy in the cross-polarized mode as the volume resolution is better and simple polished mounts instead of doubly-sided sections are needed. A disadvantage, however, is that the impact of electron beam during analysis causes local structural changes. Quantitative studies of the real structure of zircon samples, such as determination of the degree of the radiation damage, is therefore tainted with potential uncertainty when being done after electron probe analysis. As an alternative, we present images of internal zircon structures generated through visible laser excitation and mapping of the Raman and photoluminescence light. Due to the time-consuming mapping procedure, such images will perhaps not be routinely used. For detailed studies, however, they may provide most valuable information. Photoluminescence maps provide, for instance, information on both the distribution of rare earth elements (band integrals) and the short-range order (band

  3. Crystal structure of tris­(hydroxyl­ammonium) orthophosphate

    PubMed Central

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

    2015-01-01

    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. PMID:26594525

  4. The crystal structure of ice under mesospheric conditions

    NASA Astrophysics Data System (ADS)

    Murray, Benjamin J.; Malkin, Tamsin L.; Salzmann, Christoph G.

    2015-05-01

    Ice clouds form in the summer high latitude mesopause region, which is the coldest part of the Earth's atmosphere. At these very low temperatures (<150 K) ice can exist in metastable forms, but the nature of these ices remains poorly understood. In this paper we show that ice which is grown at mesospherically relevant temperatures does not have a structure corresponding to the well-known hexagonal form or the metastable cubic form. Instead, the ice which forms under mesospheric conditions is a material in which cubic and hexagonal sequences of ice are randomly arranged to produce stacking disordered ice (ice Isd). The structure of this ice is in the trigonal crystal system, rather than the cubic or hexagonal systems, and is expected to produce crystals with aspect ratios consistent with lidar observations.

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

    PubMed

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

    2015-11-01

    The crystal structure of the title salt, ([H3NOH](+))3·[PO4](3-), consists of discrete hydroxyl-ammonium cations and ortho-phos-phate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phospho-rus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by inter-molecular O-H⋯O and N-H⋯O hydrogen bonds into a three-dimensional network. Altogether, one very strong O-H⋯O, two N-H⋯O hydrogen bonds of medium strength and two weaker bifurcated N-H⋯O inter-actions are observed. PMID:26594525

  6. Structure development in silicon sheet by shaped crystallization

    NASA Technical Reports Server (NTRS)

    Leipold, M. H.; De Angelis, R. J.

    1978-01-01

    Models are presented for the development of a parallel twinned structure of the 110 plane type and the 112 line type in silicon ribbons. The models are believed to be mutually compatible and operable. The first model relates the requirements for super-cooling during crystallization. The existence of reentrant angles associated with the twin structure is proposed to provide a rough interface to reduce super-cooling. The spacing of the twins is proposed to be limited by the geometrical relationship between the thermal gradient in the liquid and the dimensions of the twinned crystallization front. The second model relates the thermal stress configuration to detail dislocation reactions which would be expected to develop twins. While a specific dislocation mechanism cannot yet be defined, a number of alternatives are presented. All of these various dislocation mechanisms would result in the observed crystalline configuration and the choice among them is not critical.

  7. Crystal structures and properties of nylon polymers from theory

    SciTech Connect

    Dasgupta, S.; Goddard, W.A. III; Hammond, W.B.

    1996-12-11

    A complete force field (MSXX) for simulation of all nylon polymers is derived from ab initio quantum calculations. Special emphasis is given to the accuracy of the hydrogen bond potential for the amide unit and the torsional potential between the peptide and alkane fragments. The MSXX force field was used to predict the structures, moduli, and detailed geometries of all nine nylons for which there are experimental crystal data plus one other. For nylon-(2n) with 2n = 6, the {alpha} crystal structure (with all-trans CH{sub 2} chains nearly coplanar with the hydrogen bonding plane) is more stable, while for 2n > 6, {gamma} (with the alkane plane twisted by 70{degree}) is more stable. This change results from the increased importance of methylene packing interactions over H bonds for larger 2n. We find the highest Young`s modulus for nylon-7. 51 refs., 6 figs., 7 tabs.

  8. Crystal structure of laser-induced subsurface modifications in Si

    SciTech Connect

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in ’t Veld, A. J.

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.

  9. Crystal structure of the human mitochondrial chaperonin symmetrical football complex.

    PubMed

    Nisemblat, Shahar; Yaniv, Oren; Parnas, Avital; Frolow, Felix; Azem, Abdussalam

    2015-05-12

    Human mitochondria harbor a single type I chaperonin system that is generally thought to function via a unique single-ring intermediate. To date, no crystal structure has been published for any mammalian type I chaperonin complex. In this study, we describe the crystal structure of a football-shaped, double-ring human mitochondrial chaperonin complex at 3.15 Å, which is a novel intermediate, likely representing the complex in an early stage of dissociation. Interestingly, the mitochondrial chaperonin was captured in a state that exhibits subunit asymmetry within the rings and nucleotide symmetry between the rings. Moreover, the chaperonin tetradecamers show a different interring subunit arrangement when compared to GroEL. Our findings suggest that the mitochondrial chaperonins use a mechanism that is distinct from the mechanism of the well-studied Escherichia coli system. PMID:25918392

  10. Crystal structure of the human mitochondrial chaperonin symmetrical football complex

    PubMed Central

    Nisemblat, Shahar; Yaniv, Oren; Parnas, Avital; Frolow, Felix; Azem, Abdussalam

    2015-01-01

    Human mitochondria harbor a single type I chaperonin system that is generally thought to function via a unique single-ring intermediate. To date, no crystal structure has been published for any mammalian type I chaperonin complex. In this study, we describe the crystal structure of a football-shaped, double-ring human mitochondrial chaperonin complex at 3.15 Å, which is a novel intermediate, likely representing the complex in an early stage of dissociation. Interestingly, the mitochondrial chaperonin was captured in a state that exhibits subunit asymmetry within the rings and nucleotide symmetry between the rings. Moreover, the chaperonin tetradecamers show a different interring subunit arrangement when compared to GroEL. Our findings suggest that the mitochondrial chaperonins use a mechanism that is distinct from the mechanism of the well-studied Escherichia coli system. PMID:25918392

  11. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    SciTech Connect

    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. Crystal architecture of R(2)SnS(5) (R = Pr, Nd, Gd and Tb): crystal structure relationships in chalcogenides.

    PubMed

    Daszkiewicz, Marek; Gulay, Lubomir D; Shemet, Vasylyna Ya

    2008-04-01

    The crystal structure of the R(2)SnS(5) (R = Pr, Nd, Gd and Tb) compounds has been investigated using X-ray single-crystal diffraction. Crystal architecture and structural relationships among U(3)S(5), Y(2)HfS(5), R(2)SnS(5) compounds are discussed and a structural origin is determined. It is shown that the complex architecture of the crystal structure of Eu(5)Sn(3)S(12) is a result of interweaving of the simple crystal structures. The location of the copper ions in the non-stoichiometric compound Y(2)Cu(0.20)Sn(0.95)S(5) is proposed on the basis of comparative analysis of the R-S interatomic distances in the R(2)SnS(5) series of compounds. PMID:18369288

  13. Crystal Structures of Cisplatin Bound to a Human Copper Chaperone

    SciTech Connect

    Boal, Amie K.; Rosenzweig, Amy C.

    2010-08-16

    Copper trafficking proteins, including the chaperone Atox1 and the P{sub 1B}-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.

  14. Crystal Structure of the Human Laminin Receptor Precursor

    SciTech Connect

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  16. Crystal Structures of the β2-Adrenergic Receptor

    NASA Astrophysics Data System (ADS)

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

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

  17. Structural contribution to the roughness of supersmooth crystal surface

    SciTech Connect

    Butashin, A. V.; Muslimov, A. E. Kanevsky, V. M.; Deryabin, A. N.; Pavlov, V. A.; Asadchikov, V. E.

    2013-05-15

    Technological advances in processing crystals (Si, sapphire {alpha}-Al{sub 2}O{sub 3}, SiC, GaN, LiNbO{sub 3}, SrTiO{sub 3}, etc.) of substrate materials and X-ray optics elements make it possible to obtain supersmooth surfaces with a periodicity characteristic of the crystal structure. These periodic structures are formed by atomically smooth terraces and steps of nano- and subnanometer sizes, respectively. A model surface with such nanostructures is proposed, and the relations between its roughness parameters and the height of atomic steps are determined. The roughness parameters calculated from these relations almost coincide with the experimental atomic force microscopy (AFM) data obtained from 1 Multiplication-Sign 1 and 10 Multiplication-Sign 10 {mu}m areas on the surface of sapphire plates with steps. The minimum roughness parameters for vicinal crystal surfaces, which are due to the structural contribution, are calculated based on the approach proposed. A comparative analysis of the relief and roughness parameters of sapphire plate surfaces with different degrees of polishing is performed. A size effect is established: the relief height distribution changes from stochastic to regular with a decrease in the surface roughness.

  18. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    PubMed Central

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

    2013-01-01

    We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase. PMID:23989605

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

    PubMed

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

    2014-09-16

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

  20. The crystal structure of aluminum doped {beta}-rhombohedral boron

    SciTech Connect

    Bykova, Elena; Materialphysik und Technologie, Lehrstuhl fuer Kristallographie, Physikalisches Institut, Universitaet Bayreuth, Universitaetsstrasse 30, D-95440 Bayreuth ; Parakhonskiy, Gleb; Materialphysik und Technologie, Lehrstuhl fuer Kristallographie, Physikalisches Institut, Universitaet Bayreuth, Universitaetsstrasse 30, D-95440 Bayreuth ; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-15

    A crystal structure of aluminum doped {beta}-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B{sub 12} icosahedra with voids occupied by the B{sub 28}-B-B{sub 28} units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) A lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the {beta}-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB{sub 44.8(5)} and AlB{sub 37.8(5)}, which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB{sub 44.8(5)} is described in detail. - Graphical abstract: The atomic distribution near the B(15) atom (non-labeled atom in the center of the picture) shown along the c axis. Anisotropic displacement ellipses for Al(2) (D-site) and B(15) are shown with 50 % probability level. The mirror plane with Miller indices (1 1 0) and related to it (-1 2 0) and (-2 1 0) generated by the 3-fold rotation-inversion axis parallel to the c axis splits the position of B(16) over two sites. Highlights: Black-Right-Pointing-Pointer The crystal structure of the AlB{sub 44.8(5)} has been refined. Black-Right-Pointing-Pointer Aluminum atoms partially fill certain types of voids (the A1- and D-sites). Black-Right-Pointing-Pointer We have got two possible models of atomic distribution near the D-site.

  1. Crystal structure of a COG4313 outer membrane channel

    PubMed Central

    Berg, Bert van den; Bhamidimarri, Satya Prathyusha; Winterhalter, Mathias

    2015-01-01

    COG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function studies of this protein family have so far been hampered by a lack of structural information. Here we present the X-ray crystal structure of Pput2725 from the biodegrader Pseudomonas putida F1, a COG4313 channel of unknown function, using data to 2.3 Å resolution. The structure shows a 12-stranded barrel with an N-terminal segment preceding the first β-strand occluding the lumen of the barrel. Single channel electrophysiology and liposome swelling experiments suggest that while the narrow channel visible in the crystal structure does allow passage of ions and certain small molecules in vitro, Pput2725 is unlikely to function as a channel for hydrophilic molecules. Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules. Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell. Our results provide the basis for structure-function studies of COG4313 family members with known function, such as the SphA sphingosine uptake channel of Pseudomonas aeruginosa. PMID:26149193

  2. Bio-Inspired Approaches to Crystals with Composite Structures

    NASA Astrophysics Data System (ADS)

    Meldrum, Fiona

    2013-03-01

    Advances in technology demand an ever-increasing degree of control over material structure, properties and function. As the properties of monolithic materials are necessary limited, one route to extending them is to create a composite by combining contrasting materials. The potential of this approach is beautifully illustrated by the formation of biominerals where organic macromolecules are combined with brittle minerals such as calcite to create crystals with considerable fracture toughness. This talk will discuss how bio-inspired approaches can be used to generate single crystals with composite crystals through a simple one-pot method. By precipitating calcite crystals in the presence of ``occlusion species'' ranging from latex particles, to organic and inorganic nanoparticles and finally small molecules we demonstrate that high amounts of foreign species can be incorporated through control over the additive surface chemistry, and that this can lead to an enhancement of the mechanical properties of the calcite. Occlusion of 20 nm anionic diblock copolymer micelles was achieved at levels of over 13 wt%, and the properties of the resuktant composite calcite crystals were measured using a range of techniques including IR spectroscopy, high resolution powder XRD and high resolution TEM. Incorporation of these macromolecules leads to crystals with structures and mechanical properties similar to those of biominerals. With sizes in the range of some intracrystalline proteins, the micelles act as ``pseudo-proteins'', thereby providing an excellent model system for investigation of the mechanism of macromolecule insertion within biominerals. Extension of these studies to the incorporation of small molecules (amino acids) again demonstrated high levels of incorporation without any change in the crystal morphology. Further, occlusion of these small molecules within the calcite lattice again resulted in a significant increase in the hardness of the calcite, a result which

  3. Crystal structure of inactive form of Rab3B

    SciTech Connect

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

    2012-02-24

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

  4. Crystal structure of a soluble cleaved HIV-1 envelope trimer.

    PubMed

    Julien, Jean-Philippe; Cupo, Albert; Sok, Devin; Stanfield, Robyn L; Lyumkis, Dmitry; Deller, Marc C; Klasse, Per-Johan; Burton, Dennis R; Sanders, Rogier W; Moore, John P; Ward, Andrew B; Wilson, Ian A

    2013-12-20

    HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design. PMID:24179159

  5. Molecular-Level Understanding of Structural Changes of Organic Crystals Induced by Macroscopic Mechanical Stimulation.

    PubMed

    Seki, Tomohiro; Ito, Hajime

    2016-03-18

    Structural changes to molecular crystals upon mechanical stimulation have attracted attention for sensing, recording, and microactuation. Comprehensive structure information is required to understand relationships between the mechanical force applied, the crystal structure, and the bulk property changes in order to develop general design concepts for mechanoresponsive compounds. Unfortunately, mechanical stimulation of organic crystals typically deteriorates their integrity, preventing detailed structure analyses by single-crystal X-ray diffraction (XRD) methods. However, in the past three years, several interesting studies have been reported in which molecular crystals retain their integrity even after a mechanically induced crystalline structure change. These materials have allowed us to investigate how macroscopic mechanical forces affect the microscopic structures of molecular crystals by single-crystal XRD analyses. This Minireview summarizes current knowledge of mechanically induced structure changes in molecular crystals, which will facilitate research in this field. PMID:26748640

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

    PubMed

    Smirnov, M; Saint-Grégoire, P

    2014-05-01

    Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the rigid unit modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the TTB-like niobates lends credence to the obtained theoretical predictions. PMID:24815976

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

    NASA Technical Reports Server (NTRS)

    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.

  8. Crystal structure of new AsS{sub 2} compound

    SciTech Connect

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

    2013-01-15

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

  9. Defect structure around two colloids in a liquid crystal.

    PubMed

    Guzmán, O; Kim, E B; Grollau, S; Abbott, N L; de Pablo, J J

    2003-12-01

    This Letter investigates the defect structures that arise between two colloidal spheres immersed in a nematic liquid crystal. Molecular simulations and a dynamic field theory are employed to arrive at molecular-level and mesoscopic descriptions of the systems of interest. At large separations, each sphere is surrounded by a Saturn ring defect. However, at short separations both theory and simulation predict that a third disclination ring appears in between the spheres, in a plane normal to the Saturn rings. This feature gives rise to an effective binding of the particles. The structures predicted by field theory and molecular simulations are consistent with each other. PMID:14683198

  10. Surface-induced structures in nematic liquid crystal colloids.

    PubMed

    Chernyshuk, S B; Tovkach, O M; Lev, B I

    2014-08-01

    We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyamide surfaces using micron sized masks in front of the cell). These bulk structures arise from nonuniform boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configurations) form a square lattice inside a planar NLC cell, which has checkerboard patterns on both its plates. PMID:25215675