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Sample records for crystal structure polymorphism

  1. Polymorphism in phenobarbital: discovery of a new polymorph and crystal structure of elusive form V.

    Science.gov (United States)

    Roy, Saikat; Goud, N Rajesh; Matzger, Adam J

    2016-03-21

    This report highlights the discovery of a new polymorph of the anticonvulsant drug phenobarbital (PB) using polymer-induced heteronucleation (PIHn) and unravelling the crystal structure of the elusive form V. Both forms are characterized by structural, thermal and VT-Raman spectroscopy methods to elucidate phase transformation behavior and shed light on stability relationships.

  2. Orthorhombic polymorph of ErP{sub 5}O{sub 14}, crystal structure and characterization

    Energy Technology Data Exchange (ETDEWEB)

    Katrusiak, A. [Uniwersytet Adama Mickiewicza, Poznan (Poland); Kaczmarek, F. [Uniwersytet Adama Mickiewicza, Poznan (Poland)

    1995-08-01

    Erbium pentaphosphate crystals have been characterized and the structure of the orthorhombic polymorph (type III) determined by X-rays. It has been found that the orthorhombic samples of ErP{sub 5}O{sub 14}, space group Pnma, crystallize mainly at higher temperatures and usually are much larger than monoclinic crystals, space group C2/c, obtained from lower-temperature crystallizations. Differences in fluorescence and upconversion properties between orthorhombic and monoclinic polymorphs have been detected. (orig.)

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

    Science.gov (United States)

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

    2015-03-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination...

  5. Crystal Structures of Polymorphic Prion Protein β1 Peptides Reveal Variable Steric Zipper Conformations.

    Science.gov (United States)

    Yu, Lu; Lee, Seung-Joo; Yee, Vivien C

    2015-06-16

    The pathogenesis of prion diseases is associated with the conformational conversion of normal, predominantly α-helical prion protein (PrP(C)) into a pathogenic form that is enriched with β-sheets (PrP(Sc)). Several PrP(C) crystal structures have revealed β1-mediated intermolecular sheets, suggesting that the β1 strand may contribute to a possible initiation site for β-sheet-mediated PrP(Sc) propagation. This β1 strand contains the polymorphic residue 129 that influences disease susceptibility and phenotype. To investigate the effect of the residue 129 polymorphism on the conformation of amyloid-like continuous β-sheets formed by β1, crystal structures of β1 peptides containing each of the polymorphic residues were determined. To probe the conformational influence of the peptide construct design, four different lengths of β1 peptides were studied. From the 12 peptides studied, 11 yielded crystal structures ranging in resolution from 0.9 to 1.4 Å. This ensemble of β1 crystal structures reveals conformational differences that are influenced by both the nature of the polymorphic residue and the extent of the peptide construct, indicating that comprehensive studies in which peptide constructs vary are a more rigorous approach to surveying conformational possibilities.

  6. Crystal and molecular structure of a second, high-density polymorph of silver malonate

    Science.gov (United States)

    Prakasha Reddy, J.; Foxman, Bruce M.

    2008-11-01

    A new orthorhombic polymorph of silver malonate ( II) has been synthesized and structurally characterized. Compound II crystallizes in space group Pnma, with a = 12.8180(11), b = 9.2479(8), c = 4.0219(3) Å; V = 476.75(7) Å 3; Z = 4; ρcalc = 4.427 g cm -3. Full-matrix least-squares refinement converged to R1 = 0.0099 ( I > 2 σ( I), 765 data) and w R2 = 0.0264 ( F2, 785 data, 51 parameters). The familiar eight-membered Ag 2(RCO 2) 2 ring, characteristic of most silver(I) carboxylate complexes, has a Ag-Ag distance of 2.977(1) Å. Puckered sheets in the crystal ab plane are connected along c to form a three-dimensional coordination polymer. The density of II is >30% higher than that of the monoclinic polymorph ( I), first characterized in 1981. A survey of the density ratios of polymorphs in the Cambridge Structural Database indicates that virtually all of the pairs of entries having a density ratio >1.2 involve at least one form with significant void volume, as estimated using PLATON. However, neither I nor II have significant void volume, which suggests that the silver malonate polymorphs represent one of the largest density differences observed to date for a polymorphic pair. To date, it has not been possible to prepare I in our laboratories.

  7. A New, More Stable Polymorphic Form of Otilonium Bromide: Solubility, Crystal Structure, and Phase Transformation.

    Science.gov (United States)

    Vega, Daniel R; Halac, Emilia; Segovia, Luciano; Baggio, Ricardo

    2016-10-01

    A new polymorphic form of otilonium bromide is presented (Form I), and a thorough analysis of its crystal and molecular structure is performed. The compound suffers a temperature-driven first-order phase transition at about 396 K, which transforms it into the polymorph reported by Dapporto P and Sega A (Acta Cryst. 1986;C42:474-478) (Form II). Through thermal analysis and solubility experiments the relative stability of both crystal modifications were determined, confirming that at room temperature this new Form I is the more stable one, Form II existing just in a metastable state. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  8. About the polymorphism of [Li(C4H8O3]I: crystal structures of trigonal and tetragonal polymorphs

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    Stefanie Gärtner

    2014-12-01

    Full Text Available Two new trigonal and tetragonal polymorphs of the title compound, iodidotris(tetrahydrofuran-κOlithium, are presented, which both include the isolated ion pair Li(THF3+·I−. One Li—I ion contact and three tetrahydrofuran (THF molecules complete the tetrahedral coordination of the lithium cation. The three-dimensional arrangement in the two polymorphs differs notably. In the trigonal structure, the ion pair is located on a threefold rotation axis of space group P-3 and only one THF molecule is present in the asymmetric unit. In the crystal, strands of ion pairs parallel to [001] are observed with an eclipsed conformation of the THF molecules relative to the Li...I axis of two adjacent ion pairs. In contrast, the tetragonal polymorph shows a much larger unit cell in which all atoms are located on general positions of the space group I41cd. The resulting three-dimensional arrangement shows helical chains of ion pairs parallel to [001]. Apart from van der Waals contacts, no remarkable intermolecular forces are present between the isolated ion pairs in both structures.

  9. Crystal structure of a second triclinic polymorph of 2-methylpyridinium picrate

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    Jeganathan Gomathi

    2015-11-01

    Full Text Available The title molecular salt, C6H8N+·C6H2N3O7− (systematic name: 2-methylpyridinium 2,4,6-trinitrophenolate, crystallizes with two cations and two anions in the asymmetric unit. In the crystal, the cations are linked to the anions via bifurcated N—H...(O,O hydrogen bonds, generating R12(6 graph-set motifs. Numerous C—H...O hydrogen bonds are observed between these cation–anion pairs, which result in a three-dimensional network. In addition, weak aromatic π–π stacking between the 2-methylpyridinium rings [inter-centroid distance = 3.8334 (19 Å] and very weak stacking [inter-centroid distance = 4.0281 (16 Å] between inversion-related pairs of picrate anions is observed. The title salt is a second triclinic polymorph of the structure (also with Z′ = 2 reported earlier [Anita et al. (2006. Acta Cryst. C62, o567–o570; Chan et al. (2014. CrystEngComm, 16, 4508–4538]. In the title compound, the cations and anions display a chequerboard arrangement when viewed down [100], whereas in the first polymorph, (010 layers of alternating cations and anions are apparent in a [100] view. It is interesting that the unit-cell lengths are almost identical for the two polymorphs, although the inter-axial angles are quite different.

  10. THE CRYSTAL STRUCTURE OF THE NEW SILICON CARBIDE POLYMORPH 69R,

    Science.gov (United States)

    The 69R polymorph is one of the 32 silicon carbide polymorphs recently discovered by us. The space group is R3m and the unit cell is hexagonal with...and in two industrial silicon carbide crystal plates. They all pair with the fundamental type 6H. The five ways of pairing are: 6H + 69R + 87R, 6H

  11. Influence of melt structure on the crystallization behavior and polymorphic composition of polypropylene random copolymer

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bin [State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute of Sichuan University, Chengdu 610065 (China); Ecole Normale Supérieure, CNRS-ENS-UPMC UMR 8640, 24 Rue Lhomond, Paris 75005 (France); Chen, Zhengfang [State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute of Sichuan University, Chengdu 610065 (China); Kang, Jian, E-mail: jiankang@scu.edu.cn [State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute of Sichuan University, Chengdu 610065 (China); Yang, Feng; Chen, Jinyao; Cao, Ya; Xiang, Ming [State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute of Sichuan University, Chengdu 610065 (China)

    2015-03-20

    Highlights: • We prepared β-PPR and studied its crystallization behavior with different melt structures. • We observed surprising synergetic effect between β-NA and the ordered structures. • We explored the nature of ordered structures by calculating the equilibrium temperature. - Abstract: Polypropylene random copolymer (PPR) is one of important polypropylene types for the application fields. However, due to the random copolymer chain configuration, it is difficult to obtain high proportion of β-phase even under the influence of β-nucleating agent (β-NA). In this study, the melt structure (namely, the content of ordered structures in the melt) of β-nucleated ethylene-copolymerized PPR (β-PPR) was controlled by tuning the fusion temperature (T{sub f}), and its impact on the crystallization and polymorphic behavior of β-PPR was investigated by differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), polarized optical microscopy (PLM) and scanning electronic microscopy (SEM). The result revealed that compared with the β-nucleated iPP homo-polymer, it is more difficult for β-PPR to form β-crystals; interestingly, when T{sub f} is in the temperature range of 162–173 °C, the ordered structures survived in melt exhibit high β-nucleation efficiency under the influence of β-NA, resulting in significant increase of β-phase proportion and evident variation of crystalline morphology, which is called the Ordered Structure Effect (OSE). Moreover, through investigating the self-nucleation behavior and equilibrium melting temperature of pure PPR (non-nucleated PPR), the physical nature of the lower and upper limiting T{sub f} temperatures for the occurrence of OSE in β-PPR was explored; the role of ethylene co-monomer in the occurrence of OSE was discussed.

  12. Study of the crystallization and polymorphic structures formed in oleogels from avocado oil

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    Ezequiel Pérez-Monterroza

    2016-07-01

    Full Text Available The effect of the concentration of monodiglycerides, beeswax and sorbitan monostearate (SMS on the thermal behavior of oleogels prepared from avocado oil, as well as the effect of the cooling rate on the onset temperature (Tonset and the crystallization temperature (Tc, were evaluated by DSC and X-ray diffraction. The results showed that the structuring agents have a significant effect (P<0.05 on the Tc and Tonset, which demonstrated their ability to form solid lipids. Moreover, it was found that the presence of SMS decreased the Tc and Tonset, possibly due to their cocrystallization process. It was found only in the presence of the polymorphic form β’ in the oleogels prepared. The Tc varied between 1.6 and 51.4 °C and Tonset between 3.9 and 53.8 °C.

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

    Science.gov (United States)

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

    2013-06-10

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

  14. Polymorphism of Alprazolam (Xanax): a review of its crystalline phases and identification, crystallographic characterization, and crystal structure of a new polymorph (form III).

    Science.gov (United States)

    de Armas, Héctor Novoa; Peeters, Oswald M; Van den Mooter, Guy; Blaton, Norbert

    2007-05-01

    A new polymorphic form of Alprazolam (Xanax), 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo-[4,3-alpha][1,4]benzodiazepine, C(17)H(13)ClN(4), has been investigated by means of X-ray powder diffraction (XRPD), single crystal X-ray diffraction, and differential scanning calorimetry (DSC). This polymorphic form (form III) was obtained during DSC experiments after the exothermic recrystallization of the melt of form I. The crystal unit cell dimensions for form III were determined from diffractometer methods. The monoclinic unit cell found for this polymorph using XRPD after indexing the powder diffractogram was confirmed by the cell parameters obtained from single crystal X-ray diffractometry on a crystal isolated from the DSC pans. The single crystal unit cell parameters are: a = 28.929(9), b = 13.844(8), c = 7.361(3) angstroms, beta = 92.82(3) degrees , V = 2944(2) angstroms(3), Z = 8, space group P2(1) (No.4), Dx = 1.393 Mg/m(3). The structure obtained from single crystal X-ray diffraction was used as initial model for Rietveld refinement on the powder diffraction data of form III. The temperature phase transformations of alprazolam were also studied using high temperature XRPD. A review of the different phases available in the Powder Diffraction File (PDF) database for this drug is described bringing some clarification and corrections.

  15. Crystal structure of a new monoclinic polymorph of N-(4-methylphenyl-3-nitropyridin-2-amine

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    Aina Mardia Akhmad Aznan

    2014-08-01

    Full Text Available The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z′ = 4 of the previously reported monoclinic (P21/c, with Z′ = 2 form [Akhmad Aznan et al. (2010. Acta Cryst. E66, o2400]. Four independent molecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intramolecular amine–nitro N—H...O hydrogen bond. The differences between molecules relate to the dihedral angles between the rings which range from 2.92 (19 to 26.24 (19°. The geometry-optimized structure [B3LYP level of theory and 6–311 g+(d,p basis set] has the same features except that the entire molecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C—H...O, C—H...π, nitro-N—O...π and π–π interactions [inter-centroid distances = 3.649 (2–3.916 (2 Å].

  16. Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

    Science.gov (United States)

    de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

    2009-01-01

    Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs.

  17. Crystal structure and prediction.

    Science.gov (United States)

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

    2015-04-01

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

  18. Correction to Revision of the Crystal Structure of the First Molecular Polymorph in History

    DEFF Research Database (Denmark)

    Johansson, Kristoffer E.; van de Streek, Jacco

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Johansson, Kristoffer E.; Van De Streek, Jacco

    2016-01-01

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

  20. Discovery of Black Dye Crystal Structure Polymorphs: Implications for Dye Conformational Variation in Dye-Sensitized Solar Cells.

    Science.gov (United States)

    Cole, Jacqueline M; Low, Kian Sing; Gong, Yun

    2015-12-23

    We present the discovery of a new crystal structure polymorph (1) and pseudopolymorph (2) of the Black Dye, one of the world's leading dyes for dye-sensitized solar cells, DSSCs (10.4% device performance efficiency). This reveals that Black Dye molecules can adopt multiple low-energy conformers. This is significant since it challenges existing models of the Black Dye···TiO2 adsorption process that renders a DSSC working electrode; these have assumed a single molecular conformation that refers to the previously reported Black Dye crystal structure (3). The marked structural differences observed between 1, 2, and 3 make the need for modeling multiple conformations more acute. Additionally, the ordered form of the Black Dye (1) provides a more appropriate depiction of its anionic structure, especially regarding its anchoring group and NCS bonding descriptions. The tendency toward NCS ligand isomerism, evidenced via the disordered form 2, has consequences for electron injection and electron recombination in Black Dye embedded DSSC devices. Dyes 2 and 3 differ primarily by the absence or presence of a solvent of crystallization, respectively; solvent environment effects on the dye are thereby elucidated. This discovery of multiple Black Dye conformers from diffraction, with atomic-level definition, complements recently reported nanoscopic evidence for multiple dye conformations existing at a dye···TiO2 interface, for a chemically similar DSSC dye; those results emanated from imaging and spectroscopy, but were unresolved at the submolecular level. Taken together, these findings lead to the general notion that multiple dye conformations should be explicitly considered when modeling dye···TiO2 interfaces in DSSCs, at least for ruthenium-based dye complexes.

  1. Polymorphism in Spin Transition Systems. Crystal Structure, Magnetic Properties, and Mössbauer Spectroscopy of Three Polymorphic Modifications of [Fe(DPPA)(NCS)(2)] [DPPA = (3-Aminopropyl)bis(2-pyridylmethyl)amine].

    Science.gov (United States)

    Matouzenko, Galina S.; Bousseksou, Azzedine; Lecocq, Sylvain; van Koningsbruggen, Petra J.; Perrin, Monique; Kahn, Olivier; Collet, André

    1997-12-03

    Three polymorphic modifications A-C of [Fe(II)(DPPA)(NCS)(2)], where DPPA = (3-aminopropyl)bis(2-pyridylmethyl)amine is a new tetradentate ligand, have been synthesized, and their structures, magnetic properties, and Mössbauer spectra have been investigated. For polymorph A, variable-temperature magnetic susceptibility measurements as well as Mössbauer spectroscopy have revealed the occurrence of a rather gradual HS if LS transition without hysteresis, centered at about 176 K. The same methods have shown that polymorph B is paramagnetic over the temperature range 4.5-295 K, whereas polymorph C exhibits a very abrupt S = 2 if S = 0 transition with a hysteresis. The hysteresis width is 8 K, the transitions being centered at T(c) downward arrow = 112 K for decreasing and T(c) upward arrow = 120 K for increasing temperatures. The crystal structures of the three polymorphs have been solved by X-ray diffraction at 298 K. Polymorph A is triclinic, space group P&onemacr; with Z = 2, a = 8.710(2) Å, b = 15.645(2) Å, c = 7.985(1) Å, alpha = 101.57(1) degrees, beta = 112.59(2) degrees, and gamma = 82.68(2) degrees. Polymorph B is monoclinic, space group P2(1)/c with Z = 4, a = 8.936(2) Å, b = 16.855(4) Å, c = 13.645(3) Å, and beta = 97.78(2) degrees. Polymorph C is orthorhombic, space group Pbca with Z = 8, a = 8.449(2) Å, b = 14.239(2) Å, and c = 33.463(5) Å. In the three polymorphs, the asymmetric units are almost identical and consist of one chiral complex molecule with the same configuration and conformation. The distorted [FeN(6)] octahedron is formed by four nitrogen atoms belonging to DPPA and two provided by the cis thiocyanate groups. The two pyridine rings of DPPA are in fac positions. The main differences between the structures of the three polymorphs are found in their crystal packing. The stabilization of the high-spin ground state of polymorph B is tentatively explained by the presence of two centers of steric strain in the crystal lattice resulting

  2. Crystallization and Polymorphism of Felodipine

    DEFF Research Database (Denmark)

    Surov, A. O.; Solanko, K. A.; Bond, A. D.

    2012-01-01

    . The crystal structures of the new forms III and IV were determined using single-crystal X-ray diffraction. Forms I, II, and III were obtained in bulk form and characterized by a variety of analytical methods, including thermal analysis, solution calorimetry, intrinsic dissolution rate measurement......, and solubility measurement. Form IV could be obtained only as a few isolated single crystals, and its crystallization could not be reproduced. On the basis of the measured thermochemical data and solubility studies, form I appears to be the thermodynamically most stable phase at ambient conditions, although...

  3. Crystal Structure and Ionic Conductivity of Three Polymorphic Phases of Rubidium Trefluoromethyl Sulfonate, RbSO3CF3

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrandt,L.; Dinnebier, R.; Jansen, M.

    2006-01-01

    The crystal structures of three polymorphic phases of rubidium trifluoromethyl sulfonate (RbSO{sub 3}CF{sub 3}, rubidium 'triflate') were solved from X-ray powder diffraction data. At room temperature, rubidium triflate crystallizes in the monoclinic space group Cm with lattice parameters of a = 19.9611(5) Angstroms, b = 23.4913(7) Angstroms, c = 5.1514(2) Angstroms, = 102.758(2); Z = 16. At T = 321 K, a first-order phase transition occurs toward a monoclinic phase in space group P2{sub 1} with lattice parameters at T = 344 K of a = 10.3434(5) Angstroms, b = 5.8283(3) Angstroms, c = 5.1982(3) Angstroms, = 104.278(6); Z = (2). At T = 461 K, another phase transition, this time of second order, occurs toward an orthorhombic phase in space group Cmcm with lattice parameters at T = 510 K of a = 5.3069(2) Angstroms, b = 20.2423(10) Angstroms, c = 5.9479(2) Angstroms; Z = 4. As a common feature within all three crystal structures of rubidium triflate, the triflate anions are arranged in double layers with the lipophilic CF{sub 3} groups facing each other. The rubidium ions are located between the SO{sub 3} groups. The general packing is similar to the packing in cesium triflate. Rubidium triflate can be classified as a solid electrolyte with a specific ionic conductivity of = 9.89 x 10{sup -9} S/cm at T = 384 K and = 3.84 x 10{sup -6} S/cm at T = 481 K.

  4. Crystal structure and ionic conductivity of three polymorphic phases of rubidium trifluoromethyl sulfonate, RbSO3CF3.

    Science.gov (United States)

    Hildebrandt, Lars; Dinnebier, Robert; Jansen, Martin

    2006-04-17

    The crystal structures of three polymorphic phases of rubidium trifluoromethyl sulfonate (RbSO3CF3, rubidium 'triflate') were solved from X-ray powder diffraction data. At room temperature, rubidium triflate crystallizes in the monoclinic space group Cm with lattice parameters of a = 19.9611(5) A, b = 23.4913(7) A, c = 5.1514(2) A, beta = 102.758(2) degrees; Z = 16. At T = 321 K, a first-order phase transition occurs toward a monoclinic phase in space group P2(1) with lattice parameters at T = 344 K of a = 10.3434(5) A, b = 5.8283(3) A, c = 5.1982(3) A, beta = 104.278(6) degrees; Z = 2). At T = 461 K, another phase transition, this time of second order, occurs toward an orthorhombic phase in space group Cmcm with lattice parameters at T = 510 K of a = 5.3069(2) A, b = 20.2423(10) A, c = 5.9479(2) A; Z = 4. As a common feature within all three crystal structures of rubidium triflate, the triflate anions are arranged in double layers with the lipophilic CF3 groups facing each other. The rubidium ions are located between the SO3 groups. The general packing is similar to the packing in cesium triflate. Rubidium triflate can be classified as a solid electrolyte with a specific ionic conductivity of sigma = 9.89 x 10(-9) S/cm at T = 384 K and sigma = 3.84 x 10(-6) S/cm at T = 481 K.

  5. Crystal structure, polymorphism, and thermal properties of yttrium borohydride Y(BH{sub 4}){sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Frommen, Christoph, E-mail: christoph.frommen@ife.n [Institute for Energy Technology, Physics Department, P.O. Box 40, NO-2027 Kjeller (Norway); Aliouane, Nadir; Deledda, Stefano; Fonnelop, Jon Erling; Grove, Hilde; Lieutenant, Klaus; Llamas-Jansa, Isabel; Sartori, Sabrina; Sorby, Magnus H.; Hauback, Bjorn C. [Institute for Energy Technology, Physics Department, P.O. Box 40, NO-2027 Kjeller (Norway)

    2010-04-30

    Y(BH{sub 4}){sub 3} was synthesized by cryo-milling mixtures of LiBH{sub 4} and YCl{sub 3} and characterized by powder X-ray and neutron diffraction (PXD, PND), differential scanning calorimetry (DSC), and temperature programmed desorption (TPD). The crystal structure was refined in the space group Pa-3 (no. 205) with lattice constant a = 10.8522(7) A from {sup 11}B and D ({sup 2}H) substituted samples using PND. It was found to contain Y{sup 3+} cations in a highly distorted octahedral environment formed by six [BD{sub 4}]{sup -} complex anions. Heat treatment under 10 MPa of deuterium at 475 K led to a phase transformation from the primitive cubic room-temperature phase to a face-centered cubic high-temperature phase with space group Fm-3c (no. 226) and lattice constant a = 11.0086(1) A. This high-temperature phase shows an ideal and undistorted octahedral coordination around the central Y{sup 3+} cation. In situ synchrotron radiation powder X-ray diffraction experiments (SR-PXD) show the presence of an intermediate phase during the thermal decomposition of Y(BH{sub 4}){sub 3} with presumably orthorhombic symmetry, and lattice constants a = 12.170(14) A, b = 7.670(5) A, and c = 7.478 (6) A, in a narrow temperature region between 473 K and 520 K.

  6. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...

  7. Formation of Piroxicam Polymorphism in Solution Crystallization

    DEFF Research Database (Denmark)

    Bruun Hansen, Thomas; Qu, Haiyan

    2015-01-01

    also explored, and new insights into polymorphic control are documented and discussed. The crystal landscape was mapped for cooling crystallization of piroxicam from acetone/water mixtures (0.5 K/min) and for antisolvent crystallization from acetone with water as the antisolvent. Varying cooling rates...

  8. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  9. Exploring polymorphism in molecular crystals with a computational approach

    NARCIS (Netherlands)

    Ende, J.A. van den

    2016-01-01

    Different crystal structures can possess different properties and therefore the control of polymorphism in molecular crystals is a goal in multiple industries, e.g. the pharmaceutical industry. Part I of this thesis is a computational study at the molecular scale of a particular solid-solid polymorp

  10. Exploring polymorphism in molecular crystals with a computational approach

    NARCIS (Netherlands)

    Ende, J.A. van den

    2016-01-01

    Different crystal structures can possess different properties and therefore the control of polymorphism in molecular crystals is a goal in multiple industries, e.g. the pharmaceutical industry. Part I of this thesis is a computational study at the molecular scale of a particular solid-solid

  11. Crystal structures of CaSiO3 polymorphs control growth and osteogenic differentiation of human mesenchymal stem cells on bioceramic surfaces.

    Science.gov (United States)

    Zhang, Nianli; Molenda, James A; Mankoci, Steven; Zhou, Xianfeng; Murphy, William L; Sahai, Nita

    2013-10-01

    The repair and replacement of damaged or diseased human bone tissue requires a stable interface between the orthopedic implant and living tissue. The ideal material should be both osteoconductive (promote bonding to bone) and osteoinductive (induce osteogenic differentiation of cells and generate new bone). Partially resorbable bioceramic materials with both properties are developed by expensive trial-and-error methods. Structure-reactivity relationships for predicting the osteoinductive properties of ceramics would significantly increase the efficiency of developing materials for bone tissue engineering. Here we propose the novel hypothesis that the crystal structure of a bioceramic controls the release rates, subsequent surface modifications due to precipitation of new phases, and thus, the concentrations of soluble factors, and ultimately, the attachment, viability and osteogenic differentiation of human Mesenchymal Stem Cells (hMSCs). To illustrate our hypothesis, we used two CaSiO3 polymorphs, pseudo-wollastonite (psw, β-CaSiO3) and wollastonite (wol, α-CaSiO3) as scaffolds for hMSC culture. Polymorphs are materials which have identical chemical composition and stoichiometry, but different crystal structures. We combined the results of detailed surface characterizations, including environmental Scanning Electron Microscopy (SEM) back-scattered imaging, and spot-analysis and 2D elemental mapping by SEM-Energy Dispersive X-ray (SEM-EDX), High Resolution Transmission Electron Microscopy (HRTEM) and surface roughness analysis; culture medium solution analyses; and molecular/genetic assays from cell culture. Our results confirmed the hypothesis that the psw polymorph, which has a strained silicate ring structure, is more osteoinductive than the wol polymorph, which has a more stable, open silicate chain structure. The observations could be attributed to easier dissolution (resorption) of psw compared to wol, which resulted in concentration profiles that were more

  12. Crystal structures of CaSiO3 polymorphs control growth and osteogenic differentiation of human mesenchymal stem cells on bioceramic surfaces†

    Science.gov (United States)

    Zhang, Nianli; Molenda, James A.; Mankoci, Steven; Zhou, Xianfeng; Murphy, William L.

    2014-01-01

    The repair and replacement of damaged or diseased human bone tissue requires a stable interface between the orthopedic implant and living tissue. The ideal material should be both osteoconductive (promote bonding to bone) and osteoinductive (induce osteogenic differentiation of cells and generate new bone). Partially resorbable bioceramic materials with both properties are developed by expensive trial-and-error methods. Structure–reactivity relationships for predicting the osteoinductive properties of ceramics would significantly increase the efficiency of developing materials for bone tissue engineering. Here we propose the novel hypothesis that the crystal structure of a bioceramic controls the release rates, subsequent surface modifications due to precipitation of new phases, and thus, the concentrations of soluble factors, and ultimately, the attachment, viability and osteogenic differentiation of human Mesenchymal Stem Cells (hMSCs). To illustrate our hypothesis, we used two CaSiO3 polymorphs, pseudo-wollastonite (psw, β-CaSiO3) and wollastonite (wol, α-CaSiO3) as scaffolds for hMSC culture. Polymorphs are materials which have identical chemical composition and stoichiometry, but different crystal structures. We combined the results of detailed surface characterizations, including environmental Scanning Electron Microscopy (SEM) back-scattered imaging, and spot-analysis and 2D elemental mapping by SEM-Energy Dispersive X-ray (SEM-EDX), High Resolution Transmission Electron Microscopy (HRTEM) and surface roughness analysis; culture medium solution analyses; and molecular/genetic assays from cell culture. Our results confirmed the hypothesis that the psw polymorph, which has a strained silicate ring structure, is more osteoinductive than the wol polymorph, which has a more stable, open silicate chain structure. The observations could be attributed to easier dissolution (resorption) of psw compared to wol, which resulted in concentration profiles that were

  13. Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

    KAUST Repository

    Stevens, Loah A.

    2015-01-13

    We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

  14. Contrasting 1D tunnel-structured and 2D layered polymorphs of V2O5: relating crystal structure and bonding to band gaps and electronic structure.

    Science.gov (United States)

    Tolhurst, Thomas M; Leedahl, Brett; Andrews, Justin L; Marley, Peter M; Banerjee, Sarbajit; Moewes, Alexander

    2016-06-21

    New V2O5 polymorphs have risen to prominence as a result of their open framework structures, cation intercalation properties, tunable electronic structures, and wide range of applications. The application of these materials and the design of new, useful polymorphs requires understanding their defining structure-property relationships. We present a characterization of the band gap and electronic structure of nanowires of the novel ζ-phase and the orthorhombic α-phase of V2O5 using X-ray spectroscopy and density functional theory calculations. The band gap is found to decrease from 1.90 ± 0.20 eV in the α-phase to 1.50 ± 0.20 eV in the ζ-phase, accompanied by the loss of the α-phase's characteristic split-off dxy band in the ζ-phase. States of dxy origin continue to dominate the conduction band edge in the new polymorph but the inequivalence of the vanadium atoms and the increased local symmetry of [VO6] octahedra results in these states overlapping with the rest of the V 3d conduction band. ζ-V2O5 exhibits anisotropic conductivity along the b direction, defining a 1D tunnel, in contrast to α-V2O5 where the anisotropic conductivity is along the ab layers. We explain the structural origins of the differences in electronic properties that exist between the α- and ζ-phase.

  15. Vitamin K 3 family members - Part II: Single crystal X-ray structures, temperature-induced packing polymorphism, magneto-structural correlations and probable anti-oncogenic candidature

    Science.gov (United States)

    Rane, Sandhya; Ahmed, Khursheed; Salunke-Gawali, Sunita; Zaware, Santosh B.; Srinivas, D.; Gonnade, Rajesh; Bhadbhade, Mohan

    2008-12-01

    Temperature-induced packing polymorphism is observed for vitamin K 3 (menadione, 3-methyl-1,4-naphthoquinone, 1). Form 1a crystallizes at 300 K and 1b at 277 K both in the same space group P2 1/ c. Form 1b contains one molecule per asymmetric unit, performing anisotropy in g-factor viz. g z = 2.0082, g y = 2.0055 and g x = 2.0025, whereas form 1a contains two molecules in its asymmetric unit. Vitamin K 3 family members 2, [2-hydroxy vitamin K 3] and 3, [2-hydroxy-1-oximino vitamin K 3] also perform intrinsic neutral active naphthosemiquinone valence tautomers even in dark having spin concentrations due to hydrogen bonding and aromatic stacking interactions which are compared to vitamin K 3. The significant lateral C-H⋯O and O-H⋯π bifurcated or π-π ∗ interactions are discussed for molecular associations and radical formations. X-ray structure of 3 revealed π-π ∗ stack dimers as radicals signatured in EPR as triplet with five hyperfine splits [ Ā( 14N) = 11.9 G]. The centrosymmetric biradicals in 3 show diamagnetism at high temperature but below 10 K it shows paramagnetism with μeff as 0.19 B.M. Vitamin K 3 and its family members inhibit biological activities of acid phosphatase ( APase), which are proportional to their spin concentrations. This may relate to their probable anti-oncogenic candidature in future.

  16. Frustrated polymer crystal structures

    Science.gov (United States)

    Lotz, B.; Strasbourg, 67083

    1997-03-01

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

  17. Polymorphic behavior of isonicotinamide in cooling crystallization from various solvents

    Science.gov (United States)

    Hansen, Thomas B.; Taris, Alessandra; Rong, Ben-Guang; Grosso, Massimiliano; Qu, Haiyan

    2016-09-01

    In this work the nucleation of different polymorphs of isonicotinamide (INA) from different solvents has been studied. The metastable zone width of INA in cooling crystallization from five different solvents has been investigated and attempts have been made to reveal the link between the INA molecular self-association to the polymorphism of the nucleated crystals using ATR FT-IR (Attenuated Total Reflectance Fourier Transform Infrared) and Raman spectroscopy. Raman and IR spectra of INA dissolved in different solvents have demonstrated that the INA molecules might associate in different configurations, whereas, the link between the structure of the molecular self-association and the structure of the nucleated polymorph is complicated by the influence of INA concentration. This is consistent with our previous study with piroxicam. The cooling crystallization of INA from five different solvents resulted in two different polymorphs depending on the initial concentration of the solution. The results obtained in the present work showed that information about self-association of an API (Active Pharmaceutical Ingredient) in a given solvent is not sufficient to predict the polymorphic behavior in all scenarios.

  18. Molecular Docking Study of Conformational Polymorph: Building Block of Crystal Chemistry

    Directory of Open Access Journals (Sweden)

    Rashmi Dubey

    2013-01-01

    Full Text Available Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2 receptor than the standard (Nimesulide.

  19. Molecular Docking Study of Conformational Polymorph: Building Block of Crystal Chemistry

    Science.gov (United States)

    Dubey, Rashmi; Tewari, Ashish Kumar; Singh, Ved Prakash; Singh, Praveen; Dangi, Jawahar Singh; Puerta, Carmen; Valerga, Pedro; Kant, Rajni

    2013-01-01

    Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl)-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b) seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2) receptor than the standard (Nimesulide). PMID:24250264

  20. Predicting crystal structures of organic compounds.

    Science.gov (United States)

    Price, Sarah L

    2014-04-07

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

  1. The crystal structure of a new polymorph of hexaaquanickel(II bis(6-oxo-1,6-dihydropyridine-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Rubén Pérez-Aguirre

    2015-12-01

    Full Text Available In a new polymorph of the title salt, [Ni(H2O6](C6H4NO32, the metal atom of the cationic complex lies on a symmetry centre and is coordinated by six water molecules to provide a quite regular octahedral coordination environment. These cations interact with 6-oxo-1,6-dihydropyridine-3-carboxylate anions through electrostatic interactions and by means of O—H...O and N—H...O hydrogen bonds involving the carboxylate, keto and protonated imine groups of the anion, and the coordinating water molecules from the cationic complex entity to generate a supramolecular three-dimensional architecture. The previously reported polymorph of this compound presents a network of hydrogen bonds, in which the organic anions establish mutual hydrogen-bonding interactions involving their keto and protonated imine groups.

  2. Crystallization and disorder of the polytypic α1 and α2 polymorphs of piroxicam

    DEFF Research Database (Denmark)

    Upadhyay, Pratik Pankaj; Bond, Andrew

    2015-01-01

    Polymorphism of the active pharmaceutical ingredient piroxicam, C15H13N3O4S, is investigated with an aim to clarify the identity and crystallization conditions of the α1 and α2 polymorphs. The structures are polytypic, containing identical 2-dimensional layers, with different symmetry relationships...

  3. Studying microstructure in molecular crystals with nanoindentation: intergrowth polymorphism in felodipine.

    Science.gov (United States)

    Mishra, Manish Kumar; Desiraju, Gautam R; Ramamurty, Upadrasta; Bond, Andrew D

    2014-11-24

    Intergrowth polymorphism refers to the existence of distinct structural domains within a single crystal of a compound. The phenomenon is exhibited by form II of the active pharmaceutical ingredient felodipine, and the associated microstructure is a significant feature of the compound's structural identity. Employing the technique of nanoindentation on form II reveals a bimodal mechanical response on specific single-crystal faces, demonstrating distinct properties for two polymorphic forms within the same crystal. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Reconciling thermal and structural data from the polymorphic transitions of malonamide

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, Eugene Y. [TransForm Pharmaceuticals, 29 Hartwell Avenue, Lexington, MA 02421 (United States)], E-mail: echeung@its.jnj.com; Peterson, Matthew L. [TransForm Pharmaceuticals, 29 Hartwell Avenue, Lexington, MA 02421 (United States)

    2009-01-15

    Although screening for organic polymorphs has become a hot topic in recent years, polymorph screens continue to be largely based on solution crystallization. Other routes to different crystal forms, such as grinding, annealing, and melt crystallization can also be used to look for polymorphs when chemical stability allows. Thermal analysis is often the first method for identifying polymorphic transitions in solids. However, reconciling the thermal data with the structural data is rarely straightforward without a single crystal X-ray structure. By using differential scanning calorimetry, infrared spectroscopy, and powder X-ray diffraction, the polymorphic transitions of malonamide have now been studied, and two solid state pathways, solid state grinding and annealing, are verified to independently yield the tetragonal polymorph of malonamide from the monoclinic form. In addition, melt recrystallization yields a third polymorph, which has now been confirmed to be the orthorhombic polymorph.

  5. Crystal Structures of Furazanes

    OpenAIRE

    Klapötke, Thomas; Schmid, Philipp; Stierstorfer, Jörg

    2015-01-01

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

  6. Structures of four polymorphs of the pesticide dithianon solved from X-ray powder diffraction data.

    Science.gov (United States)

    Halasz, Ivan; Dinnebier, Robert; Chiodo, Tiziana; Saxell, Heidi

    2012-12-01

    The crystal structures of four polymorphs of the pesticide dithianon (5,10-dihydro-5,10-dioxonaphtho[2,3-b]-1,4-dithiine-2,3-dicarbonitrile) have been solved from powder diffraction data and refined using the Rietveld method. Three polymorphs crystallize in non-centrosymmetric space groups. Two polymorphs have Z' > 1. The structures are assembled via interactions between carbonyl groups of quinoid fragments into layers which further interact only by weak interactions.

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

    Science.gov (United States)

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

    2015-04-01

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

  8. Tuning the crystal polymorphs of organic semiconductor towards high performance organic transistors (Conference Presentation)

    Science.gov (United States)

    Zhen, Yonggang; He, Ping; Yi, Yuanping; Hu, Wenping

    2016-11-01

    Generally, the differences in crystal polymorph exhibit different narrow band structures, electron-phonon coupling, optoelectronic characteristics and charge transport properties, thus leading to different device performances of organic semiconductors for application in organic field-effect transistors (OFETs). Nowadays it still remains a big challenge to control organic crystal polymorph because the slight non-directional intermolecular interactions lead to the very small differences instructure and energy of cystal phases with several alternative packing arrangements. Therefore, the control of the crystal polymorphism towards high device performance has become a crucial issue in the field of organic semiconductors. Thienoacenes have been intensively investigated as very promising organic semiconductors with high stability and superior mobility for OFETs in the last decade. However, scare studies focused on the crystal polymorph of thienoacenes. Herein, we report the controllable growth of different crystal phases of dihexyl-substituted dibenzo[d,d']thieno[3,2-b;4,5-b']dithiophene (C6-DBTDT), which was synthesized in a new, facile and efficient method. Furthermore, OFETs based on microribbon-shaped β phase crystals showed the hole mobility up to 18.9 cm2 V-1 s-1, which is one of the highest value for p-type organic semiconductors measured under ambient conditions, while platelet-shaped α phase crystals displayed the lower hole mobility of 8.5 cm2 V-1 s-1. We clearly demonstrated that the selective growth of different crystal polymorph for C6-DBTDT can be achieved by using different substrate and solvents. The simple drop-cast fabrication with controllable crystal phase and air operation stability would open the possibility of thienoacene derivatives in the construction of micro- and nanoelectronics.

  9. Crystal Structures of Furazanes

    Directory of Open Access Journals (Sweden)

    Thomas M. Klapötke

    2015-09-01

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

  10. High-performance single crystal organic field-effect transistors based on two dithiophene-tetrathiafulvalene (DT-TTF) polymorphs.

    Science.gov (United States)

    Pfattner, Raphael; Mas-Torrent, Marta; Bilotti, Ivano; Brillante, Aldo; Milita, Silvia; Liscio, Fabiola; Biscarini, Fabio; Marszalek, Tomasz; Ulanski, Jacek; Nosal, Andrzej; Gazicki-Lipman, Maciej; Leufgen, Michael; Schmidt, Georg; Molenkamp, Laurens W; Laukhin, Vladimir; Veciana, Jaume; Rovira, Concepció

    2010-10-01

    Solution prepared single crystal organic field-effect transistors (OFETs) combine low-cost with high performance due to structural ordering of molecules. However, in organic crystals polymorphism is a known phenomenon, which can have a crucial influence on charge transport. Here, the performance of solution-prepared single crystal OFETs based on two different polymorphs of dithiophene-tetrathiafulvalene, which were investigated by confocal Raman spectroscopy and X-ray diffraction, are reported. OFET devices prepared using different configurations show that both polymorphs exhibited excellent device performance, although the -phase revealed charge carrier mobility between two and ten times higher in accordance to the closer stacking of the molecules.

  11. The effect of surfactants on the crystallization and polymorphic transformation of glutamic acid

    Science.gov (United States)

    Garti, Nissim; Zour, Hadassa

    1997-03-01

    Glutamic acid can crystallize in two polymorphic structures depending on the crystallization regime. The study demonstrates an efficient method to preferentially crystallize the non-stable polymorphic structure (the α-form) in the presence of surface active agents. The rate of transformation was found to depend on the rate of growth of β and not on the rate of dissolution of α. The growth rate of β was a function of the supersaturation of the solute in solution. It was shown that the transformation could be inhibited by the addition of surfactants. The surfactants are capable of adsorbing preferentially to the α-growing crystals and solution mediating (retarding) the transformation of the α- to the β-form. It was suggested that the surfactant nature and steric considerations were important for the inhibition of both nucleation and growth of the β-polymorph. A Langmuir approach indicated that the kinetic parameter was related to the volume of surfactant adsorbed at the crystal surface. No changes in crystal morphology were observed, indicating that adsorption was not specific to any crystal face. Different mechanisms of surfactant adsorption were suggested: adsorption of single molecules at low concentrations of surfactant and formation of hemimicelles at higher concentrations.

  12. Nucleation control and separation of paracetamol polymorphs through swift cooling crystallization process

    Science.gov (United States)

    Sudha, C.; Srinivasan, K.

    2014-09-01

    Polymorphic nucleation behavior of pharmaceutical solid paracetamol has been investigated by performing swift cooling crystallization process. Saturated aqueous solution prepared at 318 K was swiftly cooled to 274 K in steps of every 1 K in the temperature range from 274 K to 313 K with uniform stirring of 100 rpm. The resultant supersaturation generated in the mother solution favours the nucleation of three different polymorphs of paracetamol. Lower supersaturation region σ=0.10-0.83 favours stable mono form I; the intermediate supersaturation region σ=0.92-1.28 favours metastable ortho form II and the higher supersaturation region σ=1.33-1.58 favours unstable form III polymorphic nucleation. Depending upon the level of supersaturation generated during swift cooling process and the corresponding solubility limit and metastable zone width (MSZW) of each polymorph, the nucleation of a particular polymorph occurs in the system. The type of polymorphs was identified by in-situ optical microscopy and the internal structure was confirmed by Powder X-ray diffraction (PXRD) study. By this novel approach, the preferred nucleation regions of all the three polymorphs of paracetamol are optimized in terms of different cooling ranges employed during the swift cooling process. Also solution mediated polymorphic transformations from unstable to mono and ortho to mono polymorphs have been studied by in-situ.

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

    NARCIS (Netherlands)

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

    2006-01-01

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

  14. A monoclinic polymorph of [(Z-N-(3-chlorophenyl-O-methylthiocarbamato-κS](triphenylphosphane-κPgold(I: crystal structure and Hirshfeld surface analysis

    Directory of Open Access Journals (Sweden)

    Chien Ing Yeo

    2016-08-01

    Full Text Available The title compound, [Au(C8H7ClNOS(C18H15P], is a monoclinic (P21/n, Z′ = 1; form β polymorph of the previously reported triclinic form (P-1, Z′ = 1; form α [Tadbuppa & Tiekink (2010. Acta Cryst. E66, m664]. The molecular structures of both forms feature an almost linear gold(I coordination geometry [P—Au—S = 175.62 (5° in the title polymorph], being coordinated by thiolate S and phosphane P atoms, a Z conformation about the C=N bond and an intramolecular Au...O contact. The major conformational difference relates to the relative orientations of the residues about the Au—S bond: the P—Au—S—C torsion angles are −8.4 (7 and 106.2 (7° in forms α and β, respectively. The molecular packing of form β features centrosymmetric aggregates sustained by aryl-C—H...O interactions, which are connected into a three-dimensional network by aryl-C—H...π contacts. The Hirshfeld analysis of forms α and β shows many similarities with the notable exception of the influence of C—H...O interactions in form β.

  15. Influence of amorphous structure on polymorphism in vanadia

    Science.gov (United States)

    Stone, Kevin H.; Schelhas, Laura T.; Garten, Lauren M.; Shyam, Badri; Mehta, Apurva; Ndione, Paul F.; Ginley, David S.; Toney, Michael F.

    2016-07-01

    Normally we think of the glassy state as a single phase and therefore crystallization from chemically identical amorphous precursors should be identical. Here we show that the local structure of an amorphous precursor is distinct depending on the initial deposition conditions, resulting in significant differences in the final state material. Using grazing incidence total x-ray scattering, we have determined the local structure in amorphous thin films of vanadium oxide grown under different conditions using pulsed laser deposition (PLD). Here we show that the subsequent crystallization of films deposited using different initial PLD conditions result in the formation of different polymorphs of VO2. This suggests the possibility of controlling the formation of metastable polymorphs by tuning the initial amorphous structure to different formation pathways.

  16. The Role of Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

    Science.gov (United States)

    Leiserowitz, Leslie; Marom, Noa; Distasio, Robert A., Jr.; Atalla, Viktor; Levchenko, Sergey; Kapishnikov, Sergey; Chelikowsky, James R.; Tkatchenko, Alexandre

    2012-02-01

    Molecular crystals often have several polymorphs that are close in energy (few meV per molecule), but possess very different physical and chemical properties. Treating polymorphism from first principles has been a long standing problem because conventional density-functional theory (DFT) lacks a proper description of long-range dispersion interactions that govern the structure and energetics of molecular crystals. Here we assess the effect of the many-body dispersion (MBD) energy on the structure and relative energies of the polymorphs of benchmark molecular crystals: glycine, alanine, and para-diiodobenzene. This is accomplished by using the recently developed first-principles DFT+MBD method [A. Tkatchenko, R.A. DiStasio Jr., R. Car, M. Scheffler, submitted], based on the earlier Tkatchenko-Scheffler (TS) dispersion correction [PRL 102, 073005 (2009)]. We show that the non-additive MBD energy plays a crucial role in making qualitatively and quantitatively accurate predictions for the structure and relative energies of polymorphs.

  17. Inorganic Crystal Structure Database (ICSD)

    Science.gov (United States)

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

  18. Crystal structure of ruthenocenecarbonitrile

    Directory of Open Access Journals (Sweden)

    Frank Strehler

    2015-04-01

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

  19. Crystal structure of propaquizafop

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2014-12-01

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

  20. Photonic Crystal Laser Accelerator Structures

    Energy Technology Data Exchange (ETDEWEB)

    Cowan, Benjamin M

    2003-05-21

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

  1. Crystal structure of fipronil

    Directory of Open Access Journals (Sweden)

    Hyunjin Park

    2017-10-01

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

  2. Polymorphism of felodipine co-crystals with 4,4'-bipyridine

    DEFF Research Database (Denmark)

    Surov, Artem Olegovich; Solanko, Katarzyna A.; Bond, Andrew;

    2014-01-01

    The calcium-channel blocking agent felodipine (Fel) forms co-crystals with 4,4′-bipyridine (BP) with 1:1 and 2:1 molar ratios. The [Fel + BP] (1:1) co-crystal exists in two polymorphic forms. Differential scanning calorimetry and solution calorimetry show that form I of the [Fel + BP] (1:1) co......-crystal is the most thermodynamically stable phase. The difference in the crystal lattice energies between different polymorphs of the co-crystal is found to be comparable with that between the polymorphic forms of pure felodipine. The enthalpies of formation of the co-crystals are small, which indicates...

  3. THE CRYSTAL STRUCTURE OF DIPHENYLTELLURIUM DIBROMIDE,

    Science.gov (United States)

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

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

    Science.gov (United States)

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

  5. Comparative analysis of lipid composition and thermal, polymorphic, and crystallization behaviors of granular crystals formed in beef tallow and palm oil.

    Science.gov (United States)

    Meng, Zong; Liu, Yuan-Fa; Jin, Qing-Zhe; Huang, Jian-Hua; Song, Zhi-Hua; Wang, Feng-Yan; Wang, Xing-Guo

    2011-02-23

    Six rectangular block all beef tallow (BT)-based and all palm oil (PO)-based model shortenings prepared on a laboratory scale, respectively denoted BTMS and POMS, were stored under temperature fluctuation cycles of 5-20 °C until granular crystals were observed. The lipid composition and thermal, polymorphic, and isothermal crystallization behaviors of the granular crystals and their surrounding materials separated from BTMS and POMS, respectively, were evaluated. The changes of nanostructure including the aggregation of high-melting triacylglycerols (TAGs) and polymorphic transformation from β' form of double chain length structures to complicated crystal structures, in which the β and β' form crystals of triple and double chain length structures simultaneously coexist, had occurred in granular crystals compared with surrounding materials, whether in BTMS or in POMS. Consequently, a slower crystallization rate appeared in granular crystal parts of both model shortenings noted above, which would yield larger and fewer crystals indicated by the Avrami model analysis that would further aggregate to form large granular crystals.

  6. Shear induced structures in crystallizing cocoa butter

    Science.gov (United States)

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

    2004-03-01

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

  7. Demonstration of Crystal Structure.

    Science.gov (United States)

    Neville, Joseph P.

    1985-01-01

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

  8. Crystal structure of oxamyl

    Directory of Open Access Journals (Sweden)

    Eunjin Kwon

    2016-12-01

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

  9. NQR investigation and characterization of cocrystals and crystal polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Seliger, Janez, E-mail: janez.seliger@fmf.uni-lj.si; Zagar, Veselko [Jozef Stefan Institute (Slovenia); Asaji, Tetsuo [Nihon University, Department of Chemistry, College of Humanities and Sciences (Japan)

    2013-05-15

    The application of {sup 14}N NQR to the study of cocrystals and crystal polymorphs is reviewed. In ferroelectric and antiferroelectric organic cocrystals {sup 14}N NQR is used to determine proton position in an N-H...O hydrogen bond and proton displacement below T{sub C}. In cocrystal isonicitinamide - oxalic acid (2:1) {sup 14}N NQR is used to distinguish between two polymorphs and to determine the type of the hydrogen bond (N{sup -}...H-O). The difference in the {sup 14}N NQR spectra of cocrystal formers and cocrystal is investigated in case of carbamazepine, saccharin and carbamazepine - saccharin (1:1). The experimental resolution allows an unambiguous distinction between the {sup 14}N NQR spectrum of the cocrystal and the {sup 14}N NQR spectra of the cocrystal formers. The possibility of application of NQR and double resonance for the determination of the inhomogeneity of the sample and for the study of the life time of an unstable polymorph is discussed.

  10. Crystallization and polymorphism of triacylglycerols contribute to the rheological properties of processed cheese.

    Science.gov (United States)

    Gliguem, Hela; Ghorbel, Dorra; Lopez, Christelle; Michon, Camille; Ollivon, Michel; Lesieur, Pierre

    2009-04-22

    The thermal, rheological, and structural behaviors of a spreadable processed cheese were studied by complementary techniques including differential scanning calorimetry (DSC), rheology, and X-ray diffraction as a function of temperature. In this product, fat is present as a dispersed phase. Thermal and rheological properties were studied at different cooling rates between 0.5 and 10 degrees C min(-1) from 60 to 3 degrees C. Crystallization properties of fat were monitored at a cooling rate of -2 degrees C min(-1) from 60 to -10 degrees C. Fat triacylglycerols (TGs) crystallized at 15 degrees C in a triple-chain length 3Lalpha (72 A) structure correlated to exothermic events and to the sudden increase in the rheological moduli G' and G''. Upon heating at 2 degrees C min(-1), the polymorphic transition of TGs evidence the melting of the 3Lalpha structure and the formation of a 2Lbeta' (36.7-41.5 A) structure. Melting of the latter follows. These transformations coincide with thermal events observed by DSC and the decrease in two steps of the rheological moduli. The influence of fat crystallization, melting, and polymorphism upon the viscoelastic properties is clearly demonstrated upon both heating and cooling.

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

    Science.gov (United States)

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

    2017-07-26

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

  12. A flow-free droplet-based device for high throughput polymorphic crystallization.

    Science.gov (United States)

    Yang, Shih-Mo; Zhang, Dapeng; Chen, Wang; Chen, Shih-Chi

    2015-06-21

    Crystallization is one of the most crucial steps in the process of pharmaceutical formulation. In recent years, emulsion-based platforms have been developed and broadly adopted to generate high quality products. However, these conventional approaches such as stirring are still limited in several aspects, e.g., unstable crystallization conditions and broad size distribution; besides, only simple crystal forms can be produced. In this paper, we present a new flow-free droplet-based formation process for producing highly controlled crystallization with two examples: (1) NaCl crystallization reveals the ability to package saturated solution into nanoliter droplets, and (2) glycine crystallization demonstrates the ability to produce polymorphic crystallization forms by controlling the droplet size and temperature. In our process, the saturated solution automatically fills the microwell array powered by degassed bulk PDMS. A critical oil covering step is then introduced to isolate the saturated solution and control the water dissolution rate. Utilizing surface tension, the solution is uniformly packaged in the form of thousands of isolating droplets at the bottom of each microwell of 50-300 μm diameter. After water dissolution, individual crystal structures are automatically formed inside the microwell array. This approach facilitates the study of different glycine growth processes: α-form generated inside the droplets and γ-form generated at the edge of the droplets. With precise temperature control over nanoliter-sized droplets, the growth of ellipsoidal crystalline agglomerates of glycine was achieved for the first time. Optical and SEM images illustrate that the ellipsoidal agglomerates consist of 2-5 μm glycine clusters with inner spiral structures of ~35 μm screw pitch. Lastly, the size distribution of spherical crystalline agglomerates (SAs) produced from microwells of different sizes was measured to have a coefficient variation (CV) of less than 5%, showing

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

    Science.gov (United States)

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

    2009-12-24

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

  14. Single crystal growth in spin-coated films of polymorphic phthalocyanine derivative under solvent vapor

    Energy Technology Data Exchange (ETDEWEB)

    Higashi, T.; Ohmori, M.; Ramananarivo, M. F.; Fujii, A., E-mail: afujii@opal.eei.eng.osaka-u.ac.jp; Ozaki, M. [Division of Electrical, Electronic, and Information Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan)

    2015-12-01

    The effects of solvent vapor on spin-coated films of a polymorphic phthalocyanine derivative were investigated. Growth of single crystal films via redissolving organic films under solvent vapor was revealed by in situ microscopic observations of the films. X-ray diffraction measurement of the films after exposing to solvent vapor revealed the phase transition of polymorphs under solvent vapor. The direction of crystal growth was clarified by measuring the crystal orientation in a grown monodomain film. The mechanism of crystal growth based on redissolving organic films under solvent vapor was discussed in terms of the different solubilities of the polymorphs.

  15. Single crystal growth in spin-coated films of polymorphic phthalocyanine derivative under solvent vapor

    Directory of Open Access Journals (Sweden)

    T. Higashi

    2015-12-01

    Full Text Available The effects of solvent vapor on spin-coated films of a polymorphic phthalocyanine derivative were investigated. Growth of single crystal films via redissolving organic films under solvent vapor was revealed by in situ microscopic observations of the films. X-ray diffraction measurement of the films after exposing to solvent vapor revealed the phase transition of polymorphs under solvent vapor. The direction of crystal growth was clarified by measuring the crystal orientation in a grown monodomain film. The mechanism of crystal growth based on redissolving organic films under solvent vapor was discussed in terms of the different solubilities of the polymorphs.

  16. Crystal structure of cafenstrole

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

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

  17. Crystal structure of pseudoguainolide

    Directory of Open Access Journals (Sweden)

    Noureddine Beghidja

    2015-03-01

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

  18. Ab initio prediction of the polymorphic structures of pyrazinamide: A validation study

    Directory of Open Access Journals (Sweden)

    David Stephen Arputhara

    2016-01-01

    Full Text Available A validation study to predict the possible stable polymorphs of Pyrazinamide within a low energy conformational region of the flexible torsion angle was made through a potential energy surface (PES scan by gas phase optimisation using the MP2/6-31G(d,p method. Hypothetical crystal structures with favourable packing density for each of the stable conformers generated from the PES scan were generated using a global search with a repulsion only potential field. The densest crystal structures with stable energy were analyzed with more accurate lattice energy minimisation via distributed multipole analysis using a repulsion-dispersion potential. The stability of the predicted crystal structures with similar close packing to the known experimental polymorphs of Pyrazinamide molecule was analyzed by inspecting their intermolecular short contacts. Studies to analyze the second derivative mechanical properties from the hessian matrix were carried out to emphasise the thermodynamic stability of predicted polymorphs of Pyrazinamide.

  19. Characterization of crystal polymorphs of the organic semiconductor non-peripheral octa-hexyl phthalocyanine

    Science.gov (United States)

    Yoneya, Makoto; Miyamoto, Ayano; Shimizu, Yo; Ohmori, Masashi; Fujii, Akihiko; Ozaki, Masanori

    2017-08-01

    The carrier-transport and thermodynamic properties of two crystal polymorphs, i.e., bulk and needle polymorphs, of non-peripheral octa-hexyl substituted phthalocyanine were investigated using density functional theory calculations and molecular dynamics simulations. The calculated results show that the bulk and needle polymorphs have hole mobilities of the same order of magnitude and that the hole mobility of the bulk polymorph was approximately twice that of the needle polymorph. For ideal one-dimensional transport along π stacking columns, the difference in mobility between the two polymorphs was larger by a factor of approximately 8. Therefore, we can expect the bulk polymorph to have 2 (or 8) times higher mobility than the values for the needle polymorph. These results predict that the bulk polymorph has the potential to show higher device performance than the needle polymorph. We also obtained the results that imply that a needle-polymorph-like phase with uniform (monoclinic) phthalocyanine-core tilting (instead of the alternative tilting of the needle polymorph) could be a new polymorph in this crystal system.

  20. Crystal structure of nuarimol

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

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

  1. Crystal structure of the cis and trans polymorphs of bis­[μ-2-(1,3-benzo­thia­zol-2-yl)phenolato]-κ3 N,O:O;κ3 O:N,O-bis­[fac-tri­carbonyl­rhenium(I)]1

    Science.gov (United States)

    Priyatharsini, Maruthupandiyan; Shankar, Bhaskaran; Sathiyendiran, Malaichamy; Srinivasan, Navaneethakrishnan

    2017-01-01

    The title dinuclear complex, [Re2(C13H8NOS)2(CO)6], crystallizes in two polymorphs where the 2-(1,3-benzo­thia­zol-2-yl)phenolate ligands and two carbonyl groups are trans- (I) or cis-arranged (II) with respect to the [Re2O2(CO)4] core. Polymorphs I and II exhibit a crystallographically imposed centre of symmetry and a twofold rotation axis, respectively. The structures may be described as being formed by two octa­hedrally distorted metal-coordinating units fused through μ-oxido bridges, leading to edge-sharing dimers. The crystal packing is governed by C—H⋯O hydrogen-bonding inter­actions, forming chains parallel to the c axis in I and a three-dimensional network in II.

  2. Polymorphs of 4-isopropylbenzylidine thiophene-2-carbohydrazide: Crystal growth and density functional theory computations

    Science.gov (United States)

    Rajavel, A.; Aditya Prasad, A.; Jeyakumar, T.

    2017-02-01

    The structural features of conformational isomerism in 4-isopropylbenzylidine thiophene-2-carbohydrazide (ITC) polymorphs have been investigated to conquer distinguishable strong Nsbnd H⋯O and weak Csbnd H⋯S hydrogen bond interactions. The single crystals were grown at constant temperature and have characterized by density functional theory computations using B3LYP method by 3-21G basis set. The conformational isomers of ITC were compared and spectroscopically characterized by FT-IR and Raman spectroscopy. The bulk phases were studied by the powder X-ray diffraction patterns. External morphology of ITC was discussed using scanning electron microscopic and transmission electron microscopic studies. Comparisons between various types of intermolecular interactions in the two polymorphic forms have been quantified via Fingerprint and Hirshfeld surface analysis. DFT computations were used to illustrate molecular electrostatic potential, HOMO-LUMO, mulliken atomic charges and electron density of states.

  3. Crystal structure refinement with SHELXL.

    Science.gov (United States)

    Sheldrick, George M

    2015-01-01

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

  4. Crystal structure refinement with SHELXL

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-01

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

  5. Crystal structure of pymetrozine

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

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

  6. Polymorphism control of p-aminobenzoic acid by isothermal anti-solvent crystallization

    Science.gov (United States)

    Garg, Rakesh Kumar; Sarkar, Debasis

    2016-11-01

    We report, for the first time, the control of polymorphism of p-aminobenzoic acid by isothermal anti-solvent crystallization using ethanol as solvent and water as anti-solvent. p-aminobenzoic (p-ABA) acid crystallizes in two distinct polymorphic forms: the α-polymorph, which is commercially available form and appears as long fibrous needles; and the β-polymorph, which appears in the form of prisms. The solubility of p-ABA was determined gravimetrically for various water/ethanol mixtures at 15 °C and isothermal anti-solvent crystallization experiments were conducted at 15 °C over a range of supersaturation ratio from 1.01 to 1.30 and at different anti-solvent addition rates of 4, 6, 8, and10 ml/h. The needle-type α-polymorph was always obtained at higher supersaturation ratio and higher flow-rates of anti-solvent addition. The prismatic β-polymorph was obtained at lower supersaturation range of 1.01-1.06 when anti-solvent was added at 4 and 6 ml/h. The obtained polymorphs were characterized using scanning electron microscopy, powder x-ray diffraction, and differential scanning calorimetry. The region of occurrence of each polymorph with respect to supersaturation ratio and anti-solvent wt% is presented for these addition rates. The careful selection of supersaturation ratio and anti-solvent addition rate can produce desired polymorph of p-ABA by anti-solvent crystallization.

  7. Structural colours through photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-10-01

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

  8. Crystal chemistry of trialkylsilyl-capped (3Z)-4-(methylthio)-3-penten-1-yne: polymorphism, twinning and ambiguity of order-disorder descriptions.

    Science.gov (United States)

    Lumpi, Daniel; Kautny, Paul; Stöger, Berthold; Fröhlich, Johannes

    2016-10-01

    The crystallization behavior of trimethylsilyl-capped (3Z)-4-(methylthio)-3-penten-1-yne (1-TMS) and the triisopropylsilyl and tert-butyldimethylsilyl analogues (1-TIPS) and (1-TBDMS) was investigated. (1-TMS) crystallizes in the Sohncke space group P212121 with Z' = 1. (1-TIPS) exists as two polymorphs, both crystallizing in P\\overline 1 with Z' = 2 independent molecules. Polymorph (I) is an order-disorder (OD) twin. Two interpretations in terms of M = 1 or M = 2 kinds of OD layers are possible, with different degrees of idealization. Polymorph (II) is fully ordered (non-twinned). Its structure can be derived from polymorph (I) by inverting the orientation of every second molecule. (1-TBDMS) (P\\overline1, Z' = 2) is an OD twin, where the OD description is unambiguously in M = 1 kinds of layers.

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

    Science.gov (United States)

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

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

    Science.gov (United States)

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

    2015-09-02

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

  11. Pattern information extraction from crystal structures

    OpenAIRE

    Okuyan, Erhan

    2005-01-01

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

  12. Crystal structure of gold hydride

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-05

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

  13. Structural study of piracetam polymorphs and cocrystals: crystallography redetermination and quantum mechanics calculations.

    Science.gov (United States)

    Tilborg, Anaëlle; Jacquemin, Denis; Norberg, Bernadette; Perpète, Eric; Michaux, Catherine; Wouters, Johan

    2011-12-01

    Pharmaceutical compounds are mostly developed as solid dosage forms containing a single-crystal form. It means that the selection of a particular crystal state for a given molecule is an important step for further clinical outlooks. In this context, piracetam, a pharmaceutical molecule known since the sixties for its nootropic properties, is considered in the present work. This molecule is analyzed using several experimental and theoretical approaches. First, the conformational space of the molecule has been systematically explored by performing a quantum mechanics scan of the two most relevant dihedral angles of the lateral chain. The predicted stable conformations have been compared to all the reported experimental geometries retrieved from the Cambridge Structural Database (CSD) covering polymorphs and cocrystals structures. In parallel, different batches of powders have been recrystallized. Under specific conditions, single crystals of polymorph (III) of piracetam have been obtained, an outcome confirmed by crystallographic analysis. © 2011 International Union of Crystallography. Printed in Singapore – all rights reserved.

  14. Redetermined structure of gossypol (P3 polymorph

    Directory of Open Access Journals (Sweden)

    Muhabbat Honkeldieva

    2015-07-01

    Full Text Available An improved crystal structure of the title compound, C30H30O8 (systematic name: 1,1′,6,6′,7,7′-hexahydroxy-5,5′-diisopropyl-3,3′-dimethyl[2,2′-binaphthalene]-8,8′-dicarbaldehyde, was determined based on modern CCD data. Compared to the previous structure [Talipov et al. (1985. Khim. Prirod. Soedin. (Chem. Nat. Prod., 6, 20–24], geometrical precision has been improved (typical C—C bond-distance s.u. = 0.002 Å in the present structure compared to 0.005 Å in the previous structure and the locations of several H atoms have been corrected. The gossypol molecules are in the aldehyde tautomeric form and the dihedral angle between the naphthyl fragments is 80.42 (4°. Four intramolecular O—H...O hydrogen bonds are formed. In the crystal, inversion dimers with graph-set motif R22(20 are formed by pairs of O—H...O hydrogen bonds; another pair of O—H...O hydrogen bonds with the same graph-set motif links the dimers into [001] chains. The packing of such chains in the crystal leads to the formation of channels (diameter = 5–8 Å propagating in the [101] direction. The channels presumably contain highly disordered solvent molecules; their contribution to the scattering was removed with the SQUEEZE [Spek (2015. Acta Cryst. C71, 9–18] routine in PLATON and the stated molecular mass, density etc., do not take them into account.

  15. Crystal structure of 6-(p-tolylbenzo[b]naphtho[2,3-d]thiophene and of an orthorhombic polymorph of 7-phenylanthra[2,3-b]benzo[d]thiophene

    Directory of Open Access Journals (Sweden)

    S. Gopinath

    2016-09-01

    Full Text Available The title compounds, C23H16S, (I, and C26H16S, (II, are benzothiophene derivatives in which the benzothiophene moiety is fused with a naphthalene ring system in (I, and with an anthracene ring system in (II. In (I, the mean plane of the benzothiophene ring system makes a dihedral angle of 2.28 (6° with the naphthalene ring system, and a dihedral angle of 1.28 (6° with the anthracene ring system in (II, showing that the fused units are essentially planar. In (I, the 4-methylbenzene ring substituent makes a dihedral angle of 71.40 (9° with the naphthalene ring system, while the phenyl ring substituent in (II makes a dihedral angle of 67.08 (12° with the anthracene ring system. In the crystals of both compounds, molecules are linked by C—H...π interactions, leading to the formation of slabs parallel to (001 in (I and to zigzag chains along [001] in (II. There are also offset π–π interactions present within the slabs in (I. In the crystal of (II, they link the chains, forming sheets parallel to (010. The triclinic polymorph of compound (II has been reported [Sivasakthikumaran et al., (2012. J. Org. Chem. 77, 9053–9071].

  16. Structural, mechanical and thermodynamic properties of ZrO2 polymorphs by first-principles calculation

    Science.gov (United States)

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

    2017-04-01

    The structural, mechanical and thermodynamic properties of ZrO2 polymorphs (namely, monoclinic (P21/c), tetragonal (P42/nmc), cubic (Fm 3 bar m), and orthorhombic (Pbca and Pnma)) are investigated systematically by employing DFT functionals (LDA, PBE and PW91). It is found that the structural parameters of ZrO2 polymorphs calculated by PBE and PW91 functionals are highly consistent with previous experiments with low absolute relative error (ARE). Moreover, all considered structures are mechanically stable according to the Born-Huang criterion and the PBE and PW91 functionals are more accurate than the LDA functional in predicting mechanical and thermodynamic properties. Significantly, we described mechanical and thermodynamic properties of ZrO2 polymorphs by introducing the charge density difference of related surfaces, which provides a better understanding of different behaviors of elastic constants (Cij) in various crystal structures of ZrO2.

  17. Crystal structure of fiber structured pentacene thin films

    OpenAIRE

    2007-01-01

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

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

    Indian Academy of Sciences (India)

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

    2008-08-01

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

  19. Influence of microgravity on protein crystal structures

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

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

  20. Crystal landscape in the orcinol:4,4′-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

    Directory of Open Access Journals (Sweden)

    Ritesh Dubey

    2014-01-01

    Full Text Available Polymorphism in the orcinol:4,4′-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O—H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O—H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

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

    Science.gov (United States)

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

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

  2. Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs.

    Science.gov (United States)

    Quarti, Claudio; Milani, Alberto; Civalleri, Bartolomeo; Orlando, Roberto; Castiglioni, Chiara

    2012-07-19

    State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.

  3. Fat crystal migration and aggregation and polymorphism evolution during the formation of granular crystals in beef tallow and palm oil.

    Science.gov (United States)

    Meng, Zong; Geng, Wenxin; Wang, Xingguo; Liu, Yuanfa

    2013-12-26

    Six rectangular block all beef tallow (BT)-based and all palm oil (PO)-based model shortenings prepared on a laboratory scale, denoted BTMS and POMS, respectively, were stored under two storage conditions, (1) constant temperatures (5 and 20 °C, respectively and (2) temperature fluctuations (5 °C for 12 h and 20 °C for 12 h for a cycle), to induce granular crystals. The fat crystal migration and aggregation, sensory evaluations, and polymorphism evolutions during the formation of granular crystals in the above samples were investigated systematically. In comparison to the constant temperature storage, the crystal growth and hierarchical aggregation process were more quick and the conversion rate of the β-form crystal was also faster in both BTMS and POMS under temperature cycling storage and, concomitantly, easier to induce the formation of granular crystals. From the comprehensive analysis of crystal sizes and the sensory evaluation results, it can be concluded that the detection threshold for graininess ranged from 40 to 90 μm, with the smaller size being perceived only at higher crystal concentrations. The possible formation mechanism and the realistic control approaches for granular crystals in plastic fats also are clarified in the present study.

  4. The polymorphic weddellite crystals in three species of Cephalocereus (Cactaceae).

    Science.gov (United States)

    Bárcenas-Argüello, María-Luisa; Gutiérrez-Castorena, Ma C-del-Carmen; Terrazas, Teresa

    2015-10-01

    Mineral inclusions in plant cells are genetically regulated, have an ecological function and are used as taxonomic characters. In Cactaceae, crystals in epidermal and cortical tissues have been reported; however, few studies have conducted chemical and morphological analyses on these crystals, and even fewer have reported non-mineral calcium to determine its systematic value. Cephalocereus apicicephalium, C. totolapensis and C. nizandensis are Cactaceae species endemic to the Isthmus of Tehuantepec, Mexico with abundant epidermal prismatic crystals. In the present study, we characterize the mineral cell inclusions, including their chemical composition and their morphology, for three species of Cephalocereus. Crystals of healthy branches of the three species were isolated and studied. The crystals were identified by X-ray diffraction (XRD), their morphology was described using a petrographic and scanning electron microscope (SEM), and their elemental composition was measured with Energy Dispersive X-ray (EDXAR). The three species synthesized weddellite with different degrees of hydration depending on the species. The optical properties of calcium oxalate crystals were different from the core, which was calcium carbonate. We observed a large diversity of predominantly spherical forms with SEM. EDXAR analysis detected different concentrations of Ca and significant amounts of elements, such as Si, Mg, Na, K, Cl, and Fe, which may be related to the edaphic environment of these cacti. The occurrence of weddellite is novel for the genus according to previous reports. The morphological diversity of the crystals may be related to their elemental composition and may be a source of phylogenetic characters.

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

    Science.gov (United States)

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

    2010-10-01

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

  6. Crystal structure analysis of intermetallic compounds

    Science.gov (United States)

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

    1968-01-01

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

  7. Shear and Rapeseed Oil Addition Affect the Crystal Polymorphic Behavior of Milk Fat

    DEFF Research Database (Denmark)

    Kaufmann, Niels; Kirkensgaard, Jacob Judas Kain; Andersen, Ulf;

    2013-01-01

    The effect of shear on the crystallization kinetics of anhydrous milk fat (AMF) and blends with 20 and 30 % w/w added rapeseed oil (RO) was studied. Pulse 1H NMR was used to follow the a to b0 polymorphic transition. The NMR method was confirmed and supported by SAXS/WAXS experiments. Samples wer...

  8. Solid solution hardening of molecular crystals: tautomeric polymorphs of omeprazole.

    Science.gov (United States)

    Mishra, Manish Kumar; Ramamurty, Upadrasta; Desiraju, Gautam R

    2015-02-11

    In the context of processing of molecular solids, especially pharmaceuticals, hardness is an important property that often determines the manufacturing steps employed. Through nanoindentation studies on a series of omeprazole polymorphs, in which the proportions of the 5- and 6-methoxy tautomers vary systematically, we demonstrate that solid-solution strengthening can be effectively employed to engineer the hardness of organic solids. High hardness can be attained by increasing lattice resistance to shear sliding of molecular layers during plastic deformation.

  9. THE CRYSTAL STRUCTURE OF ALPHA-DIMETHYLTELLURIUM DICHLORIDE,

    Science.gov (United States)

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

  10. Crystal Structure of Isoquinoline Derivatives

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  11. Crystal structure of 2-pentyloxybenzamide

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2014-10-01

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

  12. Method of fabricating patterned crystal structures

    KAUST Repository

    Yu, Liyang

    2016-12-15

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

  13. Influence of solvent polarity and supersaturation on template-induced nucleation of carbamazepine crystal polymorphs

    Science.gov (United States)

    Parambil, Jose V.; Poornachary, Sendhil K.; Tan, Reginald B. H.; Heng, Jerry Y. Y.

    2017-07-01

    Studies on the use of template surfaces to induce heterogeneous crystal nucleation have gained momentum in recent years-with potential applications in selective crystallisation of polymorphs and in the generation of seed crystals in a continuous crystallisation process. In developing a template-assisted solution crystallisation process, the kinetics of homogeneous versus heterogeneous crystal nucleation could be influenced by solute-solvent, solute-template, and solvent-template interactions. In this study, we report the effect of solvents of varying polarity on the nucleation of carbamazepine (CBZ) crystal polymorphs, a model active pharmaceutical ingredient. The experimental results demonstrate that functionalised template surfaces are effective in promoting crystallisation of either the metastable (form II) or stable (form III) polymorphs of CBZ only in moderately (methanol, ethanol, isopropanol) and low polar (toluene) solvents. A solvent with high polarity (acetonitrile) is thought to mask the template effect on heterogeneous nucleation due to strong solute-solvent and solvent-template interactions. The current study highlights that a quality-by-design (QbD) approach-considering the synergistic effects of solute concentration, solvent type, solution temperature, and template surface chemistry on crystal nucleation-is critical to the development of a template-induced crystallisation process.

  14. In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

    Science.gov (United States)

    Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

    2016-04-01

    Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods.

  15. Novel polymorphic form of adefovir dipivoxil derived from polymer-directed crystallization.

    Science.gov (United States)

    Lee, Min Kyung; Lee, Hyeseung; Kim, Il Won; Lee, Jonghwi

    2011-10-01

    Crystallization is an essential step in pharmaceutical processing. The discovery of a non-classical crystallization pathway would be a promising strategy to engineer the properties of drug crystalline particles for specific delivery conditions. Herein, polymer-directed crystallization was successfully employed to modify the characteristics of a model drug, adefovir dipivoxil (AD). Polyacrylic acid (PAA), ethyl cellulose (EC), and hydroxypropyl cellulose were added as active polymers to control the crystallization pathway of AD. Changes in crystal habit were observed in all cases. A novel polymorph was found after the addition of PAA and EC, and was confirmed by XRD and DSC results. In FTIR investigations, the crystals derived from PAA-directed crystallization showed strong interactions between PAA and AD. The polymer content in polymer-directed crystallization-derived powders varied from 7 to 24 wt%, and the presence of polymers lead to sustained release of AD. These results make polymer-directed crystallization a simple and efficient technique to engineer the physical and chemical properties of drug crystals.

  16. Studying the Crystallization of Various Polymorphic Forms of Nifedipine from Binary Mixtures with the Use of Different Experimental Techniques.

    Science.gov (United States)

    Madejczyk, O; Kaminska, E; Tarnacka, M; Dulski, M; Jurkiewicz, K; Kaminski, K; Paluch, M

    2017-06-05

    In this paper the crystal growth of nifedipine from pure system and from binary mixtures composed of active substance (API) and two acetylated disaccharides, maltose and sucrose (NIF-acMAL, NIF-acSUC, 5:1 weight ratio), was investigated. Optical snapshots supported by X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) measurements showed that mainly β and α forms of nifedipine grow up in all investigated samples. They also revealed that the morphology of growing crystals strongly depends on the presence of modified carbohydrates and temperature conditions. Interestingly, it was found that the activation barrier for the crystal growth of the β polymorph is not affected by acetylated saccharides while the one estimated for the α form changes significantly from 48.5 kJ/mol (pure API) up to 122 kJ/mol (NIF-acMAL system). Moreover, the relationship between the crystal growth rate and structural relaxation times for pure NIF and solid dispersions were analyzed. It turned out that there is a clear decoupling between the crystal growth rate and structural dynamics in both NIF-acMAL and NIF-acSUC binary mixtures. This is in line with recent reports indicating the decoupling phenomenon to be a universal feature of soft matter in the close vicinity of the glass transition temperature.

  17. Crystal structure and Hirshfeld surface analysis of 1-carboxy-2-(3,4-dihydroxyphenylethan-1-aminium chloride 2-ammonio-3-(3,4-dihydroxyphenylpropanoate: a new polymorph of l-dopa HCl and isotypic with its bromide counterpart

    Directory of Open Access Journals (Sweden)

    Perumal Kathiravan

    2016-11-01

    Full Text Available The title molecular salt, C9H12NO4+·Cl−·C9H11NO4, is isotypic with that of the bromide counterpart [Kathiravan et al. (2016. Acta Cryst. E72, 1544–1548]. The title salt is a second monoclinic polymorph of the l-dopa HCl structure reported earlier in the monoclinic space group P21 [Jandacek & Earle (1971. Acta Cryst. B27, 841–845; Mostad & Rømming (1974. Acta Chemica Scand. B28, 1161–1168]. In the title compound, monoclinic space group I2, one of the dopa molecules has a positive charge with a protonated α-amino group and the α-carboxylic acid group uncharged, while the second dopa molecule has a neutral charge, the α-amino group is protonated and the α-carboxylic acid is deprotonated. In the previously reported form, a single dopa molecule is observed in which the α-amino group is protonated and the α-carboxylic acid group is uncharged. The invariant and variations of various types of intermolecular interactions present in these two forms of dopa HCl structures are discussed with the aid of two-dimensional fingerprint plots.

  18. Electronic Structure of High-Pressure Alumina Polymorphs

    Institute of Scientific and Technical Information of China (English)

    LIU Xiao-Lei; DUAN Wen-Hui; GU Bing-Lin

    2000-01-01

    Electronic properties are investigated for three alumina polymorphs (corundum, Rb2 O3 (Ⅱ) and Pbnm perovskite),which are predicted as the stable structures under different pressure range, by means of the first-principles molecular dynamics method within local density functional framework. The similarity in electronic properties of the polymorphs of alumina is observed. The effect of possible phase transitions on ruby (Cr+3-doped Al2 O3)fluorescences is discussed.

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

    African Journals Online (AJOL)

    Preferred Customer

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

  20. Pattern information extraction from crystal structures

    Science.gov (United States)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-01

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

  2. Photonic-crystal fibre: Mapping the structure

    DEFF Research Database (Denmark)

    Markos, Christos

    2015-01-01

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

  3. Single Crystal Structure Determination of Alumina to 1 Mbar

    Science.gov (United States)

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

    2014-12-01

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

  4. Aligning the Band Structures of Polymorphic Molybdenum Oxides and Organic Emitters in Light-Emitting Diodes

    Science.gov (United States)

    Yun, Jongmin; Jang, Woosun; Lee, Taehun; Lee, Yonghyuk; Soon, Aloysius

    2017-02-01

    Heavy transition-metal oxides are widely studied for key applications in electronics and energy technologies. In cutting-edge organic-light-emitting-diode (OLED) devices, there remain scientific challenges to achieve an efficient transfer of charges between electrodes and the organic layer. Recently, polymorphic MoO3 has been actively investigated to exploit its unique high work-function values, especially for its use in the electrode buffer layer to effectively transfer the charges in OLED devices. However, no systematic fundamental studies of its electronic structure are available. Thus, in this study, we use first-principles density-functional theory to investigate both the crystal structure and the electronic structure of the MoO3 polymorphs, and we conclude with a simple perspective to screen the best candidate for OLED applications via a hole transport-barrier descriptor.

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

    Science.gov (United States)

    Skála, Roman; Císařová, Ivana

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

  6. Cross-nucleation between clathrate hydrate polymorphs: assessing the role of stability, growth rate, and structure matching.

    Science.gov (United States)

    Nguyen, Andrew H; Molinero, Valeria

    2014-02-28

    Cross-nucleation is a phenomenon where a new crystal nucleates and grows upon the surface of a different polymorph. Previous studies indicate that faster growth rate of the new crystal is a necessary but not sufficient condition for cross-nucleation. The thermodynamic stability of the different polymorphs can also affect cross-nucleation by modulating the rates of crystal growth. The interplay between thermodynamic stability of the polymorphs involved, the growth rate of the crystals, and the need for creation of an interfacial transition layer that seamlessly connects the two structures has not yet been fully elucidated. Predicting cross-nucleation is particularly challenging for clathrate hydrates, for which there are sometimes several polymorphs with similar stability and for which growth rates are not known. In this work, we use molecular dynamics simulations to investigate which factor (stability, growth rate, or formation of interfacial transition layer) controls cross-nucleation between the four known Frank-Kasper clathrate hydrate polymorphs: sI, sII, TS, and HS-I. We investigate the growth and cross-nucleation of these four hydrates filled with a set of guest molecules that produce different order of stabilities for the four crystal structures. We determine that the growth rate of sII clathrate is the fastest, followed by TS, HS-I, and sI. We find that cross-nucleation into or from sII clathrates is preceded by the formation of an interfacial transition layer at the seed crystal/liquid interface because sII does not share a crystal plane with sI, HS-I, or TS. Cross-nucleation between the latter three can occur seamlessly and is determined only by their growth rates. Our results indicate that nucleation of an interfacial transition layer between non-matching polymorphs can control cross-nucleation or lack thereof under conditions of small driving force. Under conditions of sufficient supercooling clathrate hydrate polymorphs cross-nucleate into the fastest

  7. Development of simultaneous control of polymorphism and morphology in indomethacin crystallization

    Science.gov (United States)

    Wada, Shuichi; Kudo, Shoji; Takiyama, Hiroshi

    2016-02-01

    In order to improve the bioavailability, it is desired to obtain the polymorph which has the higher solubility of indomethacin (IMC α-form). However, when α-form crystals were obtained by conventional anti-solvent crystallization, the stirring operation could not be continued because cotton agglomerates were formed in the solution. In order to simultaneously satisfy the bioavailability of IMC and the operability of IMC production, the modification of the morphology (external shape) of α-form agglomerates is important. So, the purpose of this present study is the development of the crystallization method. In order to modify the cotton agglomerates, the anti-solvent crystallization was carried out by using electrolyte aqueous solution (NaCl aq. solution) as the anti-solvent. By using the electrolyte aqueous solution, the liquid-liquid phase separation (LLPS) was observed depending on the solution composition. From the experimental results, under the condition both of high electrolyte concentration and of high stirring speed, dispersion of droplets was obtained, and spherical agglomerates of α-form were formed in the slurry. The stirring operation could be continued in the slurry because the modification of α-form cotton agglomerates was achieved. So, the simultaneous control method of the polymorphism and the morphology in IMC crystallization was realized.

  8. Structures of cyano-biphenyl liquid crystals

    Science.gov (United States)

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

    1989-01-01

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

  9. Nucleation and structural growth of cluster crystals

    CERN Document Server

    Leitold, Christian

    2016-01-01

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

  10. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

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

  11. Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing.

    Science.gov (United States)

    Panini, Piyush; Venugopala, K N; Odhav, Bharti; Chopra, Deepak

    2014-08-01

    A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (A and B) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N-H](+)···Cl(-) and [C-H](+)···Cl(-) hydrogen bonds mainly stabilizes the crystal packing in both forms A and B, while in the case of B·H2O [N-H](+)···O(water) and O(water)-H···Cl(-) hydrogen bonds along with [N-H](+)···Cl(-) and [C-H](+)···Cl(-) provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case of A, form (I) (monoclinic) is more stable whereas for B it is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms of A and B and its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. The R/E (distance-energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organic R(+) and Cl(-)) or highly

  12. Polymorph control of luminescence properties in molecular crystals of a platinum and organoarsenic complex and formation of stable one-dimensional nanochannel.

    Science.gov (United States)

    Unesaki, Hikaru; Kato, Takuji; Watase, Seiji; Matsukawa, Kimihiro; Naka, Kensuke

    2014-08-18

    The mononuclear diiodoplatinum(II) complex (trans-PtI2(cis-DHDAMe)2), where cis-DHDAMe = cis-1,4-dihydro-1,4-dimethyl-2,3,5,6-tetrakis(methoxycarbonyl)-1,4-diarsinine, forms three different crystalline polymorphs that can be either concomitantly or separately obtained on varying the recrystallization conditions. Cubic red crystals (α-phase) and red-orange needles (β-phase) exhibit solid-state red emissions at room temperature. Cubic red crystals of the γ-phase show no solid-state emission at room temperature. All crystalline structures were confirmed by X-ray crystallography. Room-temperature strongly luminescent crystals (α-phase) (λem = 657 nm, Φ = 0.52) have a triclinic P1 (No. 2) structure and no voids in the crystal structure. Red-orange needle-shaped crystals of the β-phase exhibit moderate red luminescence (λem = 695 nm, Φ = 0.09) at room temperature and have a trigonal, R3 (No. 148), structure. In the needlelike crystals of the β-phase, stable hexagonal arrays of nanoporous channels, 5.0 Å in diameter, are formed. Room-temperature nonluminescent crystals (γ-phase) have an orthorhombic, Pbca (No. 61), structure with a void volume that is 4.9% of the total crystal volume. After heating the α-phase crystals at 150 °C for 2 min, a powder XRD pattern different from the original crystal is obtained, and its solid-state emission at room temperature decreased. After heating the β-phase crystals at 150 °C for 2 min, the emission wavelength and the quantum yield of the solid-state emission at room temperature and the powder XRD pattern are the same as those of the α-phase after heating at 150 °C. A crystal-to-crystal transition triggered by the thermal stimulus produces a different stable polymorph of the mononuclear diiodoplatinum(II) complex. The one-dimensional nanoporous crystals encapsulated iodine without distorting the crystal packing.

  13. Control of structure and growth of polymorphic crystalline thin films of amphiphilic molecules on liquid surfaces

    DEFF Research Database (Denmark)

    Weinbach, S.P.; Kjær, K.; Bouwman, W.G.;

    1994-01-01

    The spontaneous formation and coexistence of crystalline polymorphic trilayer domains in amphiphilic films at air-liquid interfaces is demonstrated by grazing incidence synchrotron x-ray diffraction. These polymorphic crystallites may serve as models for the early stages of crystal nucleation...... and growth, helping to elucidate the manner in which additives influence the progress of crystal nucleation, growth, and polymorphism and suggesting ways of selectively generating and controlling multilayers on liquid surfaces. Auxiliary molecules have been designed to selectively inhibit development...

  14. Structure of crystals of hard colloidal spheres

    Energy Technology Data Exchange (ETDEWEB)

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

    1989-12-18

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

  15. Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Tang-Qing, E-mail: tangqing.yu@nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@cims.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States); Chen, Pei-Yang; Chen, Ming [Department of Chemistry, New York University, New York, New York 10003 (United States); Samanta, Amit [Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA and Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Tuckerman, Mark, E-mail: mark.tuckerman@nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States); Department of Chemistry, New York University, New York, New York 10003 (United States); NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 (China)

    2014-06-07

    The problem of predicting polymorphism in atomic and molecular crystals constitutes a significant challenge both experimentally and theoretically. From the theoretical viewpoint, polymorphism prediction falls into the general class of problems characterized by an underlying rough energy landscape, and consequently, free energy based enhanced sampling approaches can be brought to bear on the problem. In this paper, we build on a scheme previously introduced by two of the authors in which the lengths and angles of the supercell are targeted for enhanced sampling via temperature accelerated adiabatic free energy dynamics [T. Q. Yu and M. E. Tuckerman, Phys. Rev. Lett. 107, 015701 (2011)]. Here, that framework is expanded to include general order parameters that distinguish different crystalline arrangements as target collective variables for enhanced sampling. The resulting free energy surface, being of quite high dimension, is nontrivial to reconstruct, and we discuss one particular strategy for performing the free energy analysis. The method is applied to the study of polymorphism in xenon crystals at high pressure and temperature using the Steinhardt order parameters without and with the supercell included in the set of collective variables. The expected fcc and bcc structures are obtained, and when the supercell parameters are included as collective variables, we also find several new structures, including fcc states with hcp stacking faults. We also apply the new method to the solid-liquid phase transition in copper at 1300 K using the same Steinhardt order parameters. Our method is able to melt and refreeze the system repeatedly, and the free energy profile can be obtained with high efficiency.

  16. Crystal Structure of Macrocalyxin J

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  17. Intergrown new zeolite beta polymorphs with interconnected 12-ring channels solved by combining electron crystallography and single-crystal X-ray diffraction

    KAUST Repository

    Yu, Zhengbao

    2012-10-09

    Two new polymorphs of zeolite beta, denoted as SU-78A and SU-78B, were synthesized by employing dicyclohexylammonium hydroxides as organic structure-directing agents. The structure was solved by combining transmission electron microscopy and single-crystal X-ray diffraction. SU-78 is an intergrowth of SU-78A and SU-78B and contains interconnected 12-ring channels in three directions. The two polymorphs are built from the same building layer, similar to that for the zeolite beta family. The layer stacking in SU-78, however, is different from those in zeolite beta polymorph A, B, and C, showing new zeolite framework topologies. SU-78 is thermally stable up to 600 °C. © 2012 American Chemical Society.

  18. Structure-Dependent Spin Polarization in Polymorphic CdS:Y Semiconductor Nanocrystals.

    Science.gov (United States)

    Wang, Pan; Xiao, Bingxin; Zhao, Rui; Ma, Yanzhang; Zhang, Mingzhe

    2016-03-01

    Searching for the polymorphic semiconductor nanocrystals would provide precise and insightful structure-spin polarization correlations and meaningful guidance for designing and synthesizing high spin-polarized spintronic materials. Herein, the high spin polarization is achieved in polymorphic CdS:Y semiconductor nanocrystals. The high-pressure polymorph of rock-salt CdS:Y nanocrystals has been recovered at ambient conditions synthesized by the wurtzite CdS:Y nanocrystals as starting material under 5.2 GPa and 300 °C conditions. The rock-salt CdS:Y polymorph displays more robust room-temperature ferromagnetism than wurtzite sample, which can reach the ferromagnetic level of conventional semiconductors doped with magnetic transition-metal ions, mainly due to the significantly enhanced spin configuration and defect states. Therefore, crystal structure directly governs the spin configuration, which determines the degree of spin polarization. This work can provide experimental and theoretical methods for designing the high spin-polarized semiconductor nanocrystals, which is important for applications in semiconductor spintronics.

  19. Crystal structure of levomepromazine maleate

    Directory of Open Access Journals (Sweden)

    Gyula Tamás Gál

    2016-05-01

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

  20. Crystal structure of 3-(hydroxymethylchromone

    Directory of Open Access Journals (Sweden)

    Yoshinobu Ishikawa

    2015-07-01

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

  1. Crystal structure of 9-methacryloylanthracene

    Directory of Open Access Journals (Sweden)

    Aditya Agrahari

    2015-04-01

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

  2. Surface induces different crystal structures in a room temperature switchable spin crossover compound.

    Science.gov (United States)

    Gentili, Denis; Liscio, Fabiola; Demitri, Nicola; Schäfer, Bernhard; Borgatti, Francesco; Torelli, Piero; Gobaut, Benoit; Panaccione, Giancarlo; Rossi, Giorgio; Degli Esposti, Alessandra; Gazzano, Massimo; Milita, Silvia; Bergenti, Ilaria; Ruani, Giampiero; Šalitroš, Ivan; Ruben, Mario; Cavallini, Massimiliano

    2016-01-01

    We investigated the influence of surfaces in the formation of different crystal structures of a spin crossover compound, namely [Fe(L)2] (LH: (2-(pyrazol-1-yl)-6-(1H-tetrazol-5-yl)pyridine), which is a neutral compound thermally switchable around room temperature. We observed that the surface induces the formation of two different crystal structures, which exhibit opposite spin transitions, i.e. on heating them up to the transition temperature, one polymorph switches from high spin to low spin and the second polymorph switches irreversibly from low spin to high spin. We attributed this inversion to the presence of water molecules H-bonded to the complex tetrazolyl moieties in the crystals. Thin deposits were investigated by means of polarized optical microscopy, atomic force microscopy, X-ray diffraction, X-ray absorption spectroscopy and micro Raman spectroscopy; moreover the analysis of the Raman spectra and the interpretation of spin inversion were supported by DFT calculations.

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

    Science.gov (United States)

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

    1994-01-01

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

  4. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

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

    2017-01-01

    structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full......-length structure has been determined of GluK2 by cryo electron microscopy to 7.6 Å resolution as well as 84 high-resolution crystal structures of N-terminal domains and ligand-binding domains, including agonist and antagonist bound structures, modulatory ions and mutations. However, there are still many unanswered...

  5. Crystal structure of putrescine aspartic acid complex

    OpenAIRE

    Ramaswamy, S.; Murthy, MRN

    1990-01-01

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

  6. Crystal structure of canagliflozin hemihydrate

    Directory of Open Access Journals (Sweden)

    Kai-Hang Liu

    2016-05-01

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

  7. Crystal structure of canagliflozin hemihydrate.

    Science.gov (United States)

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

    2016-05-01

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

  8. Crystal Structure of 8-Demethoxyrunanine

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Ling

    2008-01-01

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

  9. Identification and physicochemical characterization of caffeine-citric acid co-crystal polymorphs.

    Science.gov (United States)

    Mukaida, Makoto; Watanabe, Yuka; Sugano, Kiyohiko; Terada, Katsuhide

    2015-11-15

    The purpose of the present study was to identify a new caffeine-citric acid co-crystal (CA-CI) polymorph and characterize three CA-CI polymorphs. The stability order among the three CA-CI polymorphs was also determined. One new and two known CA-CI polymorphs were prepared by the liquid-assisted grinding method or the slurry methods. The three CA-CIs were then identified and characterized by powder X-ray diffraction (PXRD), thermal analysis, IR spectroscopy, Raman spectroscopy, and dynamic vapor sorption (DVS). The stability order of the CA-CIs was determined by the slurry conversion method. Each CA-CI showed distinct PXRD, IR, Raman, and DVS data. The melting points of CA-CIs were 131°C (a new form, Form III), 141°C (Form I), and 160°C (Form II). The order of thermodynamic stability was CA-CI Form II>CA-CI Form I>CA-CI Form III. CA-CI Forms I and II were relatively stable against humidity compared to CA, CI and CA-CI Form III.

  10. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Piero Morales

    2010-05-01

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

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

    Science.gov (United States)

    Thomas, Noel W

    2015-08-01

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

  13. Structural characterization of ice polymorphs from self-avoiding walks

    CERN Document Server

    Herrero, Carlos P

    2014-01-01

    Topological properties of crystalline ice structures are studied by means of self-avoiding walks on their H-bond networks. The number of self-avoiding walks, C_n, for eight ice polymorphs has been obtained by direct enumeration up to walk length n = 27. This has allowed us to determine the `connective constant' or effective coordination number `mu' of these structures as the limit of the ratio C_n/C_{n-1} for large n. This structure-dependent parameter `mu' is related with other topological characteristics of ice polymorphs, such as the mean and minimum ring size, or the topological density of network sites. A correlation between the connective constant and the configurational entropy of hydrogen-disordered ice structures is discussed.

  14. Structural and electronic properties of BeH2 polymorphs: a study by density functional theory

    Science.gov (United States)

    Trivedi, D. K.; Galav, K. L.; Jaaffrey, S. N. A.; Joshi, K. B.

    2016-11-01

    Structural and electronic properties of α, β, δ and ɛ polymorphs of BeH2 are studied. The effect of pressure on these properties is also seen. Investigations are carried out using the linear combination of atomic orbitals method. The lattice parameters, computed by coupling total energy calculations with the Murnaghan equation of state for the four crystals, are overall in agreement with the experimental data and other calculations. Enthalpy-pressure diagram indicates structural phase transitions α → β, α → δ, α → ɛ, β → δ, β → ɛ, and δ → ɛ to occur at 8.75, 12.75, 18.34, 39.53, 55.57 and 76.60 GPa respectively. Electronic band structure and density of states from PBE-GGA show that all polymorphs have wide bandgap. However, quantitative and qualitative agreement of the bandgap from hybrid calculations is observed with available GW data in α-BeH2. Therefore bandgaps from hybrid calculations are also proposed. In the three polymorphs the bandgap decreases slowly with pressure. Beyond 100 GPa, the β structure exhibits overlap of bands at the Γ point.

  15. [Crystallography of drug polymorphism: emergence of new resolution methods and prediction of crystalline structures].

    Science.gov (United States)

    Perrin, M A

    2002-05-01

    For the pharmaceutical and agrochemical industries, reducing development time is currently a primary objective to accelerate the marketing of new products. In-depth solid-state characterization is an essential element in achieving this performance. For this purpose, it is now recognized that, in a department of solid-state physical characterization, theoretical approaches have to be integrated with experimental tools. Benefiting from the constant improvement in computer hardware and software in terms of computing powers and algorithm development, these approaches appear to be a complementary method that can help explain and rationalize experimental data. In recent years, with the help of both molecular modeling tools and crystallographic databases, original methods have been developed and successfully applied to systems of variable complexity. The X-ray diffraction crystal structure determination makes it possible to calibrate the force field and to adapt it more precisely to the compound studied, thereby reducing one of the sources of uncertainty. Although crystal structures are preferentially determined from single crystal data, it has been recently shown that powder diffraction data can also be used when single crystals are missing. Therefore, the different benefits of such an approach are the following: ab initio predictive study of crystalline polymorphism, molecular packing analysis and detection of cleavage planes, prediction of morphology in vacuum. In conjunction with crystallite preferred orientation observed in powder patterns, grinding effects on the crystal habit and solvent effects in modifying growth can be clearly understood. Selected industrial cases exemplify the operational application of this methodology.

  16. Crystal structure of the eukaryotic ribosome.

    Science.gov (United States)

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

    2010-11-26

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

  17. Modular crystals as modulated structures

    DEFF Research Database (Denmark)

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

    2008-01-01

    The use of the superspace formalism is extended to the description and refinement of the homologous series of modular structures with two symmetry-related modules with different orientations. The lillianite homologous series has been taken as a study case. Starting from a commensurate modulated c...

  18. An Optical and Structural Study of Pentacene Thin-film Polymorphs

    Directory of Open Access Journals (Sweden)

    Franklin Wong

    2006-01-01

    Full Text Available Because of its high conductivity, pentacene is an attractive organic material for electronic applications, but the understanding of its thin-film polymporphism is still lacking. In this work, two pentacene films, 70nm and 2.5μm thick, were evaporated onto silicon dioxide substrates. X-ray Diffraction identified two different phases in the 70nm film and four in the 2.5μm film. Oxygen and fluorine impurities were detected by X-ray Photoelectron Spectroscopy, suggesting that some of the phases in the films may be impurity-based mixed crystals of pentacene. With improved sensitivity from the resonance Raman effect, low-energy intermolecular phonons were studied and assigned as signature modes to the different polymorphs identified in the films. The 39cm-1 mode is characteristic of the 14.3Å pure pentacene polymorph, and the 45 and 50cm-1 modes are signatures of the 15.3Å pure polymorph. This is the first time that the intermolecular modes of pentacene thin films has been studied, and a more thorough analysis can further elucidate the structures of the different thin-film polymorphs.

  19. Predicted and experimental crystal structures of ethyl-tert-butyl ether.

    Science.gov (United States)

    Hammer, Sonja M; Alig, Edith; Fink, Lothar; Schmidt, Martin U

    2011-04-01

    Possible crystal structures of ethyl-tert-butyl ether (ETBE) were predicted by global lattice-energy minimizations using the force-field approach. 33 structures were found within an energy range of 2 kJmol(-1) above the global minimum. Low-temperature crystallization experiments were carried out at 80-160 K. The crystal structure was determined from X-ray powder data. ETBE crystallizes in C2/m, Z = 4, with molecules on mirror planes. The ETBE molecule adopts a trans conformation with a (CH(3))(3)C-O-C-C torsion angle of 180°. The experimental structure corresponds with high accuracy to the predicted structure with energy rank 2, which has an energy of 0.54 kJmol(-1) above the global minimum and is the most dense low-energy structure. In some crystallization experiments a second polymorph was observed, but the quality of the powder data did not allow the determination of the crystal structure. Possibilities and limitations are discussed for solving crystal structures from powder diffraction data by real-space methods and lattice-energy minimizations.

  20. Relationship between crystal structure and solid-state properties of pharmaceuticals

    Science.gov (United States)

    Sheth, Agam R.

    This thesis strives to understand the structure-property relationships of some pharmaceutical crystals at the molecular level with emphasis on the effect of secondary processing on the solid phase. Using single crystal X-ray diffractometry (SCXRD), the structure of warfarin sodium 2-propanol adduct (W) was established to be a true solvate, contrary to previous reports. Using dynamic water vapor sorption, optical and environmental scanning electron microscopy, SCXRD, powder X-ray diffractometry (PXRD), volume computations and molecular modeling, the effect of relative humidity and temperature on the crystal structure of W was investigated. Ab initio calculations on piroxicam showed that the difference in energy between the two polymorphs, I and II, arises predominantly from the difference between their lattice energies. The detailed hydrogen bonding networks of the two polymorphs are described and compared using graph sets. Despite stabilization of the polymorphs by hydrogen bonds, pair-wise distribution function transforms show a loss of polymorphic memory upon cryogrinding the two polymorphs, leading to a difference in recrystallization behavior between amorphous piroxicam prepared from polymorphs I and II. Structural and solid-state changes of piroxicam polymorphs under mechanical stress were investigated using cryogenic grinding, PXRD, diffuse-reflectance solid-state ultraviolet-visible spectroscopy, 13C solid-state nuclear magnetic resonance spectroscopy, and diffuse-reflectance solid-state Fourier-transform infrared spectroscopy. Intermolecular proton transfer was found to accompany changes in phase and color observed upon cryogrinding the two polymorphs. Model-free and model-fitting studies of the dehydration kinetics of piroxicam monohydrate (PM) showed the dependence of activation energy ( Ea) on both isothermal and non-isothermal heating conditions, and on the fraction of conversion. In the constant-E a region, isothermal dehydration follows the two

  1. A novel analytical method for pharmaceutical polymorphs by terahertz spectroscopy and the optimization of crystal form at the discovery stage.

    Science.gov (United States)

    Ikeda, Yukihiro; Ishihara, Yoko; Moriwaki, Toshiya; Kato, Eiji; Terada, Katsuhide

    2010-01-01

    A novel analytical method for the determination of pharmaceutical polymorphs was developed using terahertz spectroscopy. It was found out that each polymorph of a substance showed a specific terahertz absorption spectrum. In particular, analysis of the second derivative spectrum was enormously beneficial in the discrimination of closely related polymorphs that were difficult to discern by powder X-ray diffractometry. Crystal forms that were obtained by crystallization from various solvents and stored under various conditions were specifically characterized by the second derivative of each terahertz spectrum. Fractional polymorphic transformation for substances stored under stressed conditions was also identified by terahertz spectroscopy during solid-state stability test, but could not be detected by powder X-ray diffractometry. Since polymorphs could be characterized clearly by terahertz spectroscopy, further physicochemical studies could be conducted in a timely manner. The development form of compound examined was determined by the results of comprehensive physicochemical studies that included thermodynamic relationships, as well as chemical and physicochemical stability. In conclusion, terahertz spectroscopy, which has unique power in the elucidation of molecular interaction within a crystal lattice, can play more important role in physicochemical research. Terahertz spectroscopy has a great potential as a tool for polymorphic determination, particularly since the second derivative of the terahertz spectrum possesses high sensitivity for pharmaceutical polymorphs.

  2. Structure analysis on synthetic emerald crystals

    Science.gov (United States)

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

    2013-05-01

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

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

    Science.gov (United States)

    Harlow, Richard L

    1996-01-01

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

  4. Determining crystal structures through crowdsourcing and coursework

    OpenAIRE

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit pla...

  5. Determining crystal structures through crowdsourcing and coursework

    OpenAIRE

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

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit pla...

  6. Crystal Structure of Human Enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-04-08

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

  7. Single crystal structures of thallium (I) thorium fluorides and crystal chemistry of monovalent tetravalent cation pentafluorides

    Science.gov (United States)

    Oudahmane, Abdelghani; El-Ghozzi, Malika; Jouffret, Laurent; Avignant, Daniel

    2015-12-01

    Two thallium (I) thorium (IV) fluorides, TlTh3F13 and TlThF5 were obtained by solid state synthesis and their crystal structures determined from single crystal X-ray diffraction data recorded at room temperature with an APEX-II CCD diffractometer. TlTh3F13 is orthorhombic, space group Pmc21, with a=8.1801(2) Å, b=7.4479(2) Å, c=8.6375(2) Å, V=526.24(2) Å3, Z=2 and TlThF5 is monoclinic, space group P21/n, with a=8.1128(5) Å, b=7.2250(4) Å, c=8.8493(6) Å, β=116.683(3)°, V=463.46(5) Å3, Z=4. The structure of TlTh3F13 comprises layers of corner and edge-sharing ThF9 polyhedra further linked by chains of trans connected tricapped trigonal prisms ThF9 through corners and edges. The three dimensional thorium frameworks delimits channels parallel to [0 0 1] where the 11-coordinated Tl+ ions are arranged into double columns located in mirror planes of the structure. TlTh3F13 is isotypic with RbTh3F13, RbU3F13 and with one of the two polymorphs of CsTh3F13. The structure of TlThF5 may be regarded as a layer structure built up from the regular succession of 2∞[ M ‧F5 ] - corrugated layers further held by the Tl+ ions along the [1 0 1 ̅] direction. The layers are built up from edge and corner-sharing thorium polyhedra where each (ThF9)5- monocapped square antiprism is connected to five others by sharing three edges and two corners. TlThF5 is isostructural with β-NH4UF5 and with one of the polymorphs of CsThF5. A comparison of the different structural types of MM‧F5 pentafluorides is presented and a diagram of repartition of their structures is given. From the comparison of the Tl structures with their Rb or Cs homologs, where very similar monovalent cation environments are observed it should be concluded to a stereochemically inactivity of the 6s2 lone pair of Tl(I) in both TlTh3F13 and TlThF5, contrary to what is observed in richer Tl(I) content Tl3ThF7 fluorothorate.

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

    Science.gov (United States)

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

  9. Photonic Crystal Laser-Driven Accelerator Structures

    Energy Technology Data Exchange (ETDEWEB)

    Cowan, Benjamin M.

    2007-08-22

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

  10. Synthesis and Crystal Structure of Dehydroandrographolide Dipolycyclophosphate

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Saray Argibay-Otero

    2017-09-01

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

  12. Crystal structure of low-symmetry rondorfite

    Science.gov (United States)

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

    2008-03-01

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

  13. Vapor diffusion method: Dependence of polymorphs and morphologies of calcium carbonate crystals on the depth of an aqueous solution

    Science.gov (United States)

    Liu, Qing; Wang, Hai-Shui; Zeng, Qiang

    2016-09-01

    The polymorph control of calcium carbonate by the vapor diffusion method is still a challenging issue because the resultant crystal polymorphs and morphologies highly depend on the experimental setup. In this communication, we demonstrated that the concentration gradients accompanied by the vapor diffusion method (ammonia concentration, pH and the ratio of CO32- to Ca2+ are changed with the solution depth and with time) are probably the main reasons to significantly affect the formation of crystal polymorphs. Raman, SEM and XRD data showed that calcite and vaterite crystals were preferred to nucleate and grow in the upper or the lower areas of aqueous solution respectively. The above results can be explained by the gradient effect.

  14. Polymorphism and tautomeric preference in fenobam and the utility of NLO response to detect polymorphic impurities.

    Science.gov (United States)

    Thomas, Sajesh P; Nagarajan, K; Row, T N Guru

    2012-11-04

    Crystal structures of polymorphs and solvatomorphs of the potential anxiolytic drug fenobam exhibit an exclusive preference for one of the two possible tautomeric structures. A novel methodology based on nonlinear optical response has been successfully employed to detect the presence of a polymorphic impurity in a mixture of polymorphs.

  15. Structure sensitive properties of KTP-type crystals

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  16. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  17. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

    Science.gov (United States)

    Price, Sarah L; Leslie, Maurice; Welch, Gareth W A; Habgood, Matthew; Price, Louise S; Karamertzanis, Panagiotis G; Day, Graeme M

    2010-08-14

    Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the

  18. Crystal structure of tris(hydroxylammonium orthophosphate

    Directory of Open Access Journals (Sweden)

    Malte Leinemann

    2015-11-01

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

  19. Crystal Structures of New Ammonium 5-Aminotetrazolates

    Directory of Open Access Journals (Sweden)

    Martin Lampl

    2014-11-01

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

  20. Crystal Structure of a New Cembranolide Diterpene

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  1. Crystal structure of an archaeal actin homolog.

    Science.gov (United States)

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

    2006-04-21

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

  2. Crystal Structure Refinement of Synthetic Pure Gyrolite

    Directory of Open Access Journals (Sweden)

    Arūnas Baltušnikas

    2015-03-01

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

  3. Lessons from crystal structures of kainate receptors.

    Science.gov (United States)

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

    2017-01-01

    Kainate receptors belong to the family of ionotropic glutamate receptors. These receptors assemble from five subunits (GluK1-5) into tetrameric ion channels. Kainate receptors are located at both pre- and postsynaptic membranes in the central nervous system where they contribute to excitatory synaptic transmission and modulate network excitability by regulating neurotransmitter release. Dysfunction of kainate receptors has been implicated in several neurological disorders such as epilepsy, schizophrenia and depression. Here we provide a review on the current understanding of kainate receptor structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full-length structure has been determined of GluK2 by cryo electron microscopy to 7.6 Å resolution as well as 84 high-resolution crystal structures of N-terminal domains and ligand-binding domains, including agonist and antagonist bound structures, modulatory ions and mutations. However, there are still many unanswered questions and challenges in front of us. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'.

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

    Science.gov (United States)

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

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

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

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

  6. Influence of Teflon substrate on crystallization and enzymatic degradation of polymorphic poly(butylene adipate)

    DEFF Research Database (Denmark)

    Ning, Zhenbo; Nielsen, Ronnie Bo Højstrup; Zhao, Lifen;

    2014-01-01

    Oriented and non-oriented Teflon films, which were found to have the same crystalline structure, but different surface morphologies, were used to sandwich poly(butylene adipate) (PBA) films during isothermal crystallization. It was found that both the Teflon surface structure and the PBA...

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

    Science.gov (United States)

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

  8. Crystal structure of natural phaeosphaeride A

    Directory of Open Access Journals (Sweden)

    Victoria V. Abzianidze

    2015-08-01

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

  9. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2014-01-28

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

  11. Crystal structure of Cryptosporidium parvum pyruvate kinase.

    Directory of Open Access Journals (Sweden)

    William J Cook

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

  12. Comparative Analysis of Thermal Behavior, Isothermal Crystallization Kinetics and Polymorphism of Palm Oil Fractions

    Directory of Open Access Journals (Sweden)

    Bing Li

    2013-01-01

    Full Text Available Thermal behavior of palm stearin (PS and palm olein (PO was explored by monitoring peak temperature transitions by differential scanning calorimetry (DSC. The fatty acid composition (FAC, isothermal crystallization kinetics studied by pulsed Nuclear Magnetic Resonance (pNMR and isothermal microstructure were also compared. The results indicated that the fatty acid composition had an important influence on the crystallization process. PS and PO both exhibited more multiple endotherms than exotherms which showed irregular peak shapes. An increasing in cooling rate, generally, was associated with an increase in peak size. Application of the Avaimi equation to isothermal crystallization of PS and PO revealed different nucleation and growth mechanisms based on the Avrami exponents. PS quickly reached the end of crystallization because of more saturated triacylglycerol (TAG. The Avrami index of PS were the same as PO under the same isothermal condition at lower temperatrue, indicating that the crystallization mechanism of the two samples based on super-cooling state were the same. According to the polarized light microscope (PLM images, crystal morphology of PS and PO was different. With the temperature increased, the structure of crystal network of both PS and PO gradually loosened.

  13. Diterbium heptanickel: a crystal structure redetermination

    Directory of Open Access Journals (Sweden)

    Volodymyr Levytskyy

    2014-08-01

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

  14. A polymorph structure of copper(II hydrogenphosphite dihydrate

    Directory of Open Access Journals (Sweden)

    Lei Yang

    2009-04-01

    Full Text Available The title compound, poly[[diaquacopper(II]-μ3-hydrogenphosphito], [Cu(HPO3(H2O2]n, (I, has been prepared by hydrothermal synthesis at 393 K. Its non-centrosymmetric polymorph structure, (II, was known previously and has been redetermined at 193 (2 K [El Bali & Massa (2002. Acta Cryst. E58, i29–i31]. The Cu atoms in (I and (II are square-pyramidal coordinated. A distorted octahedral geometry around the Cu atoms is considered by including the strongly elongated apical distances of 2.8716 (15 Å in (I and 3.000 (1 Å in (II. The Cu...Cu separation of the dimeric unit is 3.1074 (3 Å. The secondary building units (SBU (the Cu2O2 dimer and two HPO3 units in (I are inversion related and form a two-dimensional layered structure, with sheets parallel to the bc plane, whereas in the structure of (II, the chain elements are connected via screw-axis symmetry to form a three-dimensional microporous framework. In both polymorph structures, strong O—H...O hydrogen bonds are observed.

  15. Tailoring quantum structures for active photonic crystals

    DEFF Research Database (Denmark)

    Kuznetsova, Nadezda

    This work is dedicated to the tailoring of quantum structures, with particular attention to the integration of selective area grown (SAG) active material into photonic crystal (PhC) slabs. The platform based on active PhC is vital to the realization of highly efficient elements with low energy...... consumption for on-chip and chip-to-chip optical communication. In order to develop metal-organic vapor phase epitaxial selective area etching and growth, a mask was fabricated in the HSQ e-beam resist including optimization of exposure and development conditions. By use of CBr4 as an etchant, in situ etching...... area and between the structures oriented along the [0-1-1] and [0-11] directions. Strong wavelength dependence with variations of the mask width of a few μm and opening sizes of hundreds of nanometers was observed. Incorporation of an active medium into PhC structures has showed promising results...

  16. Isolation and Crystal Structure of Horminone

    Institute of Scientific and Technical Information of China (English)

    陈晓; 廖仁安; 翁林红; 谢庆兰; 邓锋杰

    2000-01-01

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

  17. Crystal structure of (ferrocenylmethyldimethylammonium hydrogen oxalate

    Directory of Open Access Journals (Sweden)

    Mamadou Ndiaye

    2015-08-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  19. Crystal structure of hexaaquadichloridoytterbium(III chloride

    Directory of Open Access Journals (Sweden)

    Kevin M. Knopf

    2015-06-01

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

  20. Crystal Structure of Marburg Virus VP24

    OpenAIRE

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

    2014-01-01

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

  1. Crystal structure of Marburg virus VP24.

    Science.gov (United States)

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

    2014-05-01

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

  2. Elasticity of some mantle crystal structures. II.

    Science.gov (United States)

    Wang, H.; Simmons, G.

    1973-01-01

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

  3. Crystal structure of a DNA catalyst.

    Science.gov (United States)

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

    2016-01-14

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

  4. Syntheses and Crystal Structures of Pyrazoline Derivants

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  5. A study on the effect of the polymeric additive HPMC on morphology and polymorphism of ortho-aminobenzoic acid crystals

    Science.gov (United States)

    Simone, E.; Cenzato, M. V.; Nagy, Z. K.

    2016-07-01

    In the present study, the effect of Hydroxy Propyl Methyl Cellulose (HPMC) on the crystallization of ortho-aminobenzoic acid (OABA) was investigated by seeded and unseeded cooling crystallization experiments. The influence of HPMC on the induction time, crystal shape of Forms I and II of OABA and the polymorphic transformation time was studied. Furthermore, the capability of HPMC to inhibit growth of Form I was evaluated quantitatively and modeled using population balance equations (PBE) solved with the method of moments. The additive was found to strongly inhibit nucleation and growth of Form I as well as to increase the time for the polymorphic transformation from Form II to I. Solvent was also found to influence the shape of Form I crystals at equal concentrations of HPMC. In situ process analytical technology (PAT) tools, including Raman spectroscopy, focused beam reflectance measurement (FBRM) and attenuated total reflectance (ATR) UV-vis spectroscopy were used in combination with off-line techniques, such as optical microscopy, scanning electron microscopy (SEM), Raman spectroscopy, Malvern Mastersizer and differential scanning calorimetry (DSC) to study the crystals produced. The results illustrate how shape, size and stability of the two polymorphs of OABA can be controlled and tailored using a polymeric additive.

  6. Diffusion-controlled anisotropic growth of stable and metastable crystal polymorphs in the phase-field crystal model.

    Science.gov (United States)

    Tegze, G; Gránásy, L; Tóth, G I; Podmaniczky, F; Jaatinen, A; Ala-Nissila, T; Pusztai, T

    2009-07-17

    We use a simple density functional approach on a diffusional time scale, to address freezing to the body-centered cubic (bcc), hexagonal close-packed (hcp), and face-centered cubic (fcc) structures. We observe faceted equilibrium shapes and diffusion-controlled layerwise crystal growth consistent with two-dimensional nucleation. The predicted growth anisotropies are discussed in relation with results from experiment and atomistic simulations. We also demonstrate that varying the lattice constant of a simple cubic substrate, one can tune the epitaxially growing body-centered tetragonal structure between bcc and fcc, and observe a Mullins-Sekerka-Asaro-Tiller-Grinfeld-type instability.

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

    Institute of Scientific and Technical Information of China (English)

    Liu Xiao-Jian; Fan You-Hua

    2013-01-01

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

  8. Crystal structure of yeast Sco1

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-05

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

  9. Modeling of photonic crystal waveguide structures

    Science.gov (United States)

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

    2007-05-01

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

  10. Temperature dependent spin structures in Hexaferrite crystal

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-01

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

  11. Syntheses and Crystal Structures of Ferrocenoindenes

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2013-02-01

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

  12. Crystal structure of human nicotinamide riboside kinase.

    Science.gov (United States)

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

    2007-08-01

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

  13. Crystal Structure of Human Nicotinamide Riboside Kinase

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-01

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

  14. The Crystal Structure of Human Argonaute2

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-07-18

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

  15. The crystal structures of three pyrazine-2,5-dicarboxamides: three-dimensional supramolecular structures

    Directory of Open Access Journals (Sweden)

    Dilovan S. Cati

    2017-05-01

    Full Text Available The complete molecules of the title compounds, N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (I, 3,6-dimethyl-N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C20H20N6O2 (II, and N2,N5-bis(pyridin-4-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (III, are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each molecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7° in (I, 75.83 (8° in (II and by 82.71 (6° in (III. In the crystal of (I, molecules are linked by N—H...N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (II, molecules are also linked by N—H...N hydrogen bonds, forming layers lying parallel to the (10-1 plane. As in (I, the layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (III, molecules are again linked by N—H...N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π–π interactions [intercentroid distance = 3.739 (1 Å]. The sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. Compound (I crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008, 11, 1–4]. The molecular structures of the two polymorphs are compared.

  16. Crystal polymorphism: dependence of oxygen diffusion through 2D ordered Co nanocrystals.

    Science.gov (United States)

    Yang, Zhijie; Yang, Jianhui; Bergström, Johanna; Khazen, Khashayar; Pileni, Marie-Paule

    2014-06-07

    8 nm Co nanoparticles with various crystalline structures called polymorphs were produced using different synthetic procedures, such as using reverse micelles, the thermal decomposition of organometallics approach or the hot injection process. These 8 nm Co nanoparticles differing by their crystalline structures are exposed to oxygen at elevated temperature. The fcc Co polycrystalline nanoparticles produce either Co-CoO yolk-shell or CoO hollow structures whereas amorphous Co nanoparticles produce Co-CoO core-shell nanoparticles. Furthermore, single domains with either hcp or ε crystalline structure behave differently upon oxygen diffusion. Co-CoO nanoparticles were produced from the hcp phase while CoO hollow nanoparticles were the product for ε-phase Co nanocrystals.

  17. Structural Transitions in Cholesteric Liquid Crystal Droplets

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-01

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

  18. Polymorphic structures of Alzheimer's β-amyloid globulomers.

    Directory of Open Access Journals (Sweden)

    Xiang Yu

    Full Text Available BACKGROUND: Misfolding and self-assembly of Amyloid-β (Aβ peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphicstructures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation. METHODS AND FINDINGS: Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR. CONCLUSIONS: Our computationally modeled Aβ globulomers provide useful

  19. Crystal structure of strontium dinickel iron orthophosphate

    Directory of Open Access Journals (Sweden)

    Said Ouaatta

    2015-10-01

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

  20. Crystal structures of five 6-mercaptopurine derivatives

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    Lígia R. Gomes

    2016-03-01

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

  1. Crystal Structures of Respiratory Pathogen Neuraminidases

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  2. Extraction and Crystal Structure of Karounidiol

    Institute of Scientific and Technical Information of China (English)

    巢志茂; 王诚

    2003-01-01

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

  3. Crystal and molecular structure of aflatrem

    Directory of Open Access Journals (Sweden)

    Bruno N. Lenta

    2015-11-01

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

  4. The crystal structure Escherichia coli Spy.

    Science.gov (United States)

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

    2010-11-01

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

  5. Crystal structure of zirconia by Rietveld refinement

    Institute of Scientific and Technical Information of China (English)

    王大宁; 郭永权; 梁开明; 陶琨

    1999-01-01

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

  6. Evolution by structural polymorphism in a Miocene neogastropod

    Energy Technology Data Exchange (ETDEWEB)

    Allmon, W.D.

    1985-01-01

    Morphological change in the shallow marine species Bullia (Bulliopsis) quadrata (Nassariidae) from the middle to late Miocene of Maryland and Virginia seems to have been by anagenesis within a single lineage rather than by cladogenesis, or associated with a speciation event. The mechanism for this change seems to have been a shift in frequency of a shell form polymorphism. When B.quadrata first appears in the lower St. Mary's Fm., all individuals show a similar smooth shell form. In the middle St. Mary's a distinct carinate morphotype appears, represented by only a few individuals. In the upper St. Mary's a higher proportion of these more ornate forms occurs. Finally in the upper member of the overlying Eastover Fm. the ornate morphology becomes dominant. Specimens from the Eastover Fm. are not only mostly of the more ornate type, but maximum size has increased and the ornate morphology has become more pronounced. This occurs in an area geographically and ecologically marginal to the previous main species range and so may represent an ecophenotypic effect. The genetics of gastropod shell form are very poorly understood. This study represents one of the few documented examples of the role of structural polymorphism in gastropod evolution.

  7. From Trioleoyl glycerol to extra virgin olive oil through multicomponent triacylglycerol mixtures: Crystallization and polymorphic transformation examined with differential scanning calorimetry and X-ray diffration techniques.

    Science.gov (United States)

    Bayés-García, L; Calvet, T; Cuevas-Diarte, M A; Ueno, S

    2017-09-01

    The polymorphic crystallization and transformation behavior of extra virgin olive oil (EVOO) was examined by using differential scanning calorimetry (DSC) and X-ray diffraction with both laboratory-scale (XRD) and synchrotron radiation source (SR-XRD). The complex behavior observed was studied by previously analyzing mixtures composed by its main 2 to 6 triacylglycerol (TAG) components. Thus, component TAGs were successively added to simulate EVOO composition, until reaching a 6 TAGs mixture, composed by trioleoyl glycerol (OOO), 1-palmitoyl-2,3-dioleoyl glycerol (POO), 1,2-dioleoyl-3-linoleoyl glycerol (OOL), 1-palmitoyl-2-oleoyl-3-linoleoyl glycerol (POL), 1,2-dipalmitoyl-3-oleoyl glycerol (PPO) and 1-stearoyl-2,3-dioleoyl glycerol (SOO). Molten samples were cooled from 25°C to -80°C at a controlled rate of 2°C/min and subsequently heated at the same rate. The polymorphic behavior observed in multicomponent TAG mixtures was interpreted by considering three main groups of TAGs with different molecular structures: triunsaturated OOO and OOL, saturated-unsaturated-unsaturated POO, POL and SOO, and saturated-saturated-unsaturated PPO. As confirmed by our previous work, TAGs belonging to the same structural group displayed a highly similar polymorphic behavior. EVOO exhibited two different β'-2L polymorphic forms (β'2-2L and β'1-2L), which transformed into β'-3L when heated. Equivalent polymorphic pathways were detected when the same experimental conditions were applied to the 6 TAG components mixture. Hence, minor components may not exert a strong influence in this case. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Y. AaminaNaaz

    2015-12-01

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

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

    Science.gov (United States)

    Marechal, Matthieu; Dijkstra, Marjolein

    2008-06-01

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

  10. Affine structures and a tableau model for E_6 crystals

    CERN Document Server

    Jones, Brant

    2009-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Olfa Mtioui-Sghaier

    2015-07-01

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

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

    Science.gov (United States)

    Hong, Y. S.; And Others

    1980-01-01

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

  15. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination......-based cluster analysis. The tree resulting from the subgroup analysis clearly separated all subgroups with high bootstrap values with the species S. bongori being the most distantly related of the subgroups. The tree resulting from the analysis of the SARB collection showed that some serotypes are very clonal...... whereas others are highly divergent. Conclusions: AFLP clearly clustered strains representing the subgroups of Salmonella together with high bootstrap values and the serotypes of subspecies enterica were divided into polyphyletic or monophyletic types corresponding well with multilocus enzyme...

  16. Electronic structure and insulating gap in epitaxial VO2 polymorphs

    Directory of Open Access Journals (Sweden)

    Shinbuhm Lee

    2015-12-01

    Full Text Available Determining the origin of the insulating gap in the monoclinic V O2(M1 is a long-standing issue. The difficulty of this study arises from the simultaneous occurrence of structural and electronic transitions upon thermal cycling. Here, we compare the electronic structure of the M1 phase with that of single crystalline insulating V O2(A and V O2(B thin films to better understand the insulating phase of VO2. As these A and B phases do not undergo a structural transition upon thermal cycling, we comparatively study the origin of the gap opening in the insulating VO2 phases. By x-ray absorption and optical spectroscopy, we find that the shift of unoccupied t2g orbitals away from the Fermi level is a common feature, which plays an important role for the insulating behavior in VO2 polymorphs. The distinct splitting of the half-filled t2g orbital is observed only in the M1 phase, widening the bandgap up to ∼0.6 eV. Our approach of comparing all three insulating VO2 phases provides insight into a better understanding of the electronic structure and the origin of the insulating gap in VO2.

  17. Crystal structures of cristobalite-type and coesite-type PON redetermined on the basis of single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Maxim Bykov

    2015-11-01

    Full Text Available Hitherto, phosphorus oxonitride (PON could not be obtained in the form of single crystals and only powder diffraction experiments were feasible for structure studies. In the present work we have synthesized two polymorphs of phosphorus oxonitride, cristobalite-type (cri-PON and coesite-type (coe-PON, in the form of single crystals and reinvestigated their crystal structures by means of in house and synchrotron single-crystal X-ray diffraction. The crystal structures of cri-PON and coe-PON are built from PO2N2 tetrahedral units, each with a statistical distribution of oxygen and nitrogen atoms. The crystal structure of the coe-PON phase has the space group C2/c with seven atomic sites in the asymmetric unit [two P and three (N,O sites on general positions, one (N,O site on an inversion centre and one (N,O site on a twofold rotation axis], while the cri-PON phase possesses tetragonal I-42d symmetry with two independent atoms in the asymmetric unit [the P atom on a fourfold inversion axis and the (N,O site on a twofold rotation axis]. In comparison with previous structure determinations from powder data, all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles.

  18. Crystal structures of cristobalite-type and coesite-type PON redetermined on the basis of single-crystal X-ray diffraction data.

    Science.gov (United States)

    Bykov, Maxim; Bykova, Elena; Dyadkin, Vadim; Baumann, Dominik; Schnick, Wolfgang; Dubrovinsky, Leonid; Dubrovinskaia, Natalia

    2015-11-01

    Hitherto, phospho-rus oxonitride (PON) could not be obtained in the form of single crystals and only powder diffraction experiments were feasible for structure studies. In the present work we have synthesized two polymorphs of phospho-rus oxonitride, cristobalite-type (cri-PON) and coesite-type (coe-PON), in the form of single crystals and reinvestigated their crystal structures by means of in house and synchrotron single-crystal X-ray diffraction. The crystal structures of cri-PON and coe-PON are built from PO2N2 tetra-hedral units, each with a statistical distribution of oxygen and nitro-gen atoms. The crystal structure of the coe-PON phase has the space group C2/c with seven atomic sites in the asymmetric unit [two P and three (N,O) sites on general positions, one (N,O) site on an inversion centre and one (N,O) site on a twofold rotation axis], while the cri-PON phase possesses tetra-gonal I-42d symmetry with two independent atoms in the asymmetric unit [the P atom on a fourfold inversion axis and the (N,O) site on a twofold rotation axis]. In comparison with previous structure determinations from powder data, all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles.

  19. A shock-induced polymorph of anatase and rutile from the Chesapeake Bay impact structure, Virginia, U.S.A

    Science.gov (United States)

    Jackson, J.C.; Horton, J.W.; Chou, I.-Ming; Belkin, H.E.

    2006-01-01

    A shock-induced polymorph (TiO2II) of anatase and rutile has been identified in breccias from the late Eocene Chesapeake Bay impact structure. The breccia samples are from a recent, partially cored test hole in the central uplift at Cape Charles, Virginia. The drill cores from 744 to 823 m depth consist of suevitic crystalline-clast breccia and brecciated cataclastic gneiss in which the TiO2 phases anatase and rutile are common accessory minerals. Electron-microprobe imaging and laser Raman spectroscopy of TiO2 crystals, and powder X-ray diffraction (XRD) of mineral concentrates, confirm that a high-pressure, ??-PbO2 structured polymorph of TiO2 (TiO2II) coexists with anatase and rutile in matrix-hosted crystals and in inclusions within chlorite. Raman spectra of this polymorph include strong bands at wavenumbers (cm-1) 175, 281, 315, 342, 356, 425, 531, 571, and 604; they appear with anatase bands at 397, 515, and 634 cm-1, and rutile bands at 441 and 608 cm-1. XRD patterns reveal 12 lines from the polymorph that do not significantly interfere with those of anatase or rutile, and are consistent with the TiO2II that was first reported to occur naturally as a shock-induced phase in rutile from the Ries crater in Germany. The recognition here of a second natural shock-induced occurrence of TiO2II suggests that its presence in rocks that have not been subjected to ultrahigh-pressure regional metamorphism can be a diagnostic indicator for confirmation of suspected impact structures.

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

    Science.gov (United States)

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

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

  1. Protective colloids and polylactic acid co-affecting the polymorphic crystal forms and crystallinity of indomethacin encapsulated in microspheres.

    Science.gov (United States)

    Lin, S Y; Chen, K S; Teng, H H

    1999-01-01

    The co-effect of protective colloids and polylactic acid (PLA) on the polymorphic crystal forms and crystallinity of indomethacin (IMC) in IMC-loaded PLA microspheres was investigated with differential scanning calorimetry, infrared spectroscopy and x-ray diffractometry, to evaluate the polymorphic crystal forms and crystallinity of IMC encapsulated in PLA microspheres. The surfactant, sodium dodecyl sulphate (SDS), was also used as a dispersing agent. The results indicate that the polymorphism and crystallinity of IMC encapsulated in IMC-loaded PLA microspheres was dependent on the type of protective colloid and PLA used. The amorphous state and alpha-form of IMC were found in the IMC-loaded PLA microspheres prepared using polysaccharide (pectin or beta-cyclodextrin) as a protective colloid or SDS as a dispersing agent. However, the amorphous and methylene chloride solvate of IMC seemed to exist in the IMC-loaded PLA microspheres prepared with the proteins (gelatin or albumin), synthetic cellulose derivative (methyl cellulose or hydroxylpropyl methylcellulose) or the synthetic nonionic polymer (polyvinyl alcohol, polyvinyl pyrrolidone or biosoluble polymer) as a protective colloid. PLA was found to express a certain crystallinity in microspheres and not be affected by the protective colloids, but it played a more important role in influencing the crystallization of IMC during microencapsulation than the protective colloids. No interaction occurred in the physical mixture of IMC and PLA, nor in the IMC-loaded PLA microspheres.

  2. Polymorphic phases of galactocerebrosides: spectroscopic evidence of lamellar crystalline structures.

    Science.gov (United States)

    Bou Khalil, M; Carrier, D; Wong, P T; Tanphaichitr, N

    2001-06-06

    Fourier transform infrared spectroscopy was applied to study the structural and thermal properties of bovine brain galactocerebroside (GalCer) containing amide linked non-hydroxylated or alpha-hydroxy fatty acids (NFA- and HFA-GalCer, respectively). Over the temperature range 0-90 degrees C, both GalCer displayed complex thermal transitions, characteristic of polymorphic phase behavior. Upon heating, aqueous dispersions of NFA- and HFA-GalCer exhibited high order-disorder transition temperatures near 80 and 72 degrees C, respectively. En route to the chain melting transition, the patterns of the amide I band of NFA-GalCer were indicative of two different lamellar crystalline phases, whereas those of HFA-GalCer were suggestive of lamellar gel and crystalline bilayers. Cooling from the liquid-crystalline phase resulted in the formation of another crystalline phase of NFA-GalCer and a gel phase of HFA-GalCer, with a phase transition near 62 and 66 degrees C, respectively. Prolonged incubation of GalCer bilayers at 38 degrees C revealed conversions among lamellar crystalline phases (NFA-GalCer) or between lamellar gel and crystalline bilayer structures (HFA-GalCer). Spectral changes indicated that the temperature and/or time induced formation of the lamellar crystalline structures of NFA- and HFA-GalCer was accompanied by partial dehydration and by rearrangements of the hydrogen bonding network and bilayer packing mode of GalCer.

  3. Crystal structure refinement a crystallographers guide to SHELXL

    CERN Document Server

    2006-01-01

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

  4. The Crystal Structure of Cu4Bi4Se9

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  5. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    Science.gov (United States)

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

    2014-01-01

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

  6. The Crystal Structure of Cu4Bi4Se9

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    KAUST Repository

    Bernatowicz, Piotr

    2015-01-01

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

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

    Science.gov (United States)

    Cady, Susan G.

    1997-01-01

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

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

    Science.gov (United States)

    Obata, Shigeaki; Goto, Hitoshi

    2015-02-01

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

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

    Science.gov (United States)

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

    2016-04-14

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    OpenAIRE

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

    2010-01-01

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

  13. Structural characterization of three crystalline modifications of telmisartan by single crystal and high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Dinnebier, R E; Sieger, P; Nar, H; Shankland, K; David, W I

    2000-11-01

    Three crystalline modifications (A, B, and C) of 4'-[[2-n-propyl-4-methyl-6-(1-methyl-benzimidazol-2-yl)benzi midazol-1-yl]methyl]biphenyl-2-carboxylic acid (INN name, telmisartan) have been detected and their crystal structures have been determined by single-crystal X-ray diffraction (pseudopolymorph C) and the method of simulated annealing from high-resolution X-ray powder diffraction data (polymorphs A and B). The compound is of interest because of its use as an angiotensin II receptor antagonist. Polymorph A crystallizes in space group P2(I)/c, Z = 4, with unit cell parameters a = 18.7798(3), b = 18.1043(2), and c = 8.00578(7) A, beta = 97.066(1) degrees, and V = 2701.31 A(3). Polymorph B crystallizes in space group P2(I)/a, Z = 4, with unit cell parameters a = 16.0646(5), b = 13.0909(3), and c = 13.3231(3) A, beta = 99.402(1) degrees, and V = 2764.2(1) A(3). The solvated form C crystallizes in space group C2/c, Z = 8, with unit cell parameters a = 30.990(5), b = 13.130(3), and c = 16.381(3) A, beta = 95.02(2) degrees, and V = 6639(2) A(3). For the structure solutions of polymorphs A and B, 13 degrees of freedom (3 translational, 3 orientational, 7 torsion angles) were determined in approximately 2 h of computer time, demonstrating that the crystal packing and the molecular conformation of medium-sized (MW approximately 500) pharmaceutical compounds can now be solved quickly and routinely from high-resolution X-ray powder diffraction data.

  14. PLANAR OPTICAL WAVEGUIDES WITH PHOTONIC CRYSTAL STRUCTURE

    DEFF Research Database (Denmark)

    2003-01-01

    Planar optical waveguide comprising a core region and a cladding region comprising a photonic crystal material, said photonic crystal material having a lattice of column elements, wherein at least a number of said column elements are elongated substantially in an axial direction for said core reg...

  15. DFT study of the molecular and crystal structure and vibrational analysis of cisplatin

    Science.gov (United States)

    Georgieva, I.; Trendafilova, N.; Dodoff, N.; Kovacheva, D.

    2017-04-01

    DFT and periodic-DFT (PAW-PBE method, code VASP) calculations have been performed to study the structural and vibrational characteristics of cis-diamminedichloroplatinum(II) (cisplatin) at molecular and outside molecular level. To estimate the effect of the intermolecular interactions in crystal on the structural and vibrational properties of cisplatin, three theoretical models are considered in the present study: monomer (isolated molecule), hydrogen bonded dimer and periodic solid state structures. The work focused on the role of the theoretical models for correct modeling and prediction of geometrical and vibrational parameters of cisplatin. It has been found that the elaborate three-dimensional intermolecular hydrogen bonding network in the crystalline cisplatin significantly influences the structural and vibrational pattern of cisplatin and therefore the isolated cisplatin molecule is not the correct computational model regardless of the theoretical level used. To account for the whole intermolecular hydrogen bonding network in direction of both a and c axis and for more reliable calculations of structural and vibrational parameters periodic DFT calculations were carried out in the full crystalline periodic environment with the known lattice parameters for each cisplatin polymorph phase. The model calculations performed both at molecular level and for the periodic structures of alpha and beta cisplatin polymorph forms revealed the decisive role of the extended theoretical model for reliable prediction of the structural and vibrational characteristics of cisplatin. The powder diffraction pattern and the calculated IR and Raman spectra predicted beta polymorph form of our cisplatin sample freshly synthesized for the purposes of the present study using the Dhara's method. The various rotamers realized in the polymorph forms of cisplatin were explained by the low population of the large number of rotamers in solution as well as with the high rotamer

  16. Crystal structure of Clostridium difficile toxin A

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-11

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

  17. Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.

    Science.gov (United States)

    Moonens, Kristof; Gideonsson, Pär; Subedi, Suresh; Bugaytsova, Jeanna; Romaõ, Ema; Mendez, Melissa; Nordén, Jenny; Fallah, Mahsa; Rakhimova, Lena; Shevtsova, Anna; Lahmann, Martina; Castaldo, Gaetano; Brännström, Kristoffer; Coppens, Fanny; Lo, Alvin W; Ny, Tor; Solnick, Jay V; Vandenbussche, Guy; Oscarson, Stefan; Hammarström, Lennart; Arnqvist, Anna; Berg, Douglas E; Muyldermans, Serge; Borén, Thomas; Remaut, Han

    2016-01-13

    The Helicobacter pylori adhesin BabA binds mucosal ABO/Le(b) blood group (bg) carbohydrates. BabA facilitates bacterial attachment to gastric surfaces, increasing strain virulence and forming a recognized risk factor for peptic ulcers and gastric cancer. High sequence variation causes BabA functional diversity, but the underlying structural-molecular determinants are unknown. We generated X-ray structures of representative BabA isoforms that reveal a polymorphic, three-pronged Le(b) binding site. Two diversity loops, DL1 and DL2, provide adaptive control to binding affinity, notably ABO versus O bg preference. H. pylori strains can switch bg preference with single DL1 amino acid substitutions, and can coexpress functionally divergent BabA isoforms. The anchor point for receptor binding is the embrace of an ABO fucose residue by a disulfide-clasped loop, which is inactivated by reduction. Treatment with the redox-active pharmaceutic N-acetylcysteine lowers gastric mucosal neutrophil infiltration in H. pylori-infected Le(b)-expressing mice, providing perspectives on possible H. pylori eradication therapies.

  18. Anisotropic domain structure of KTiOPO4 crystals

    Science.gov (United States)

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

    2001-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-01-15

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

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

    Science.gov (United States)

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

    2009-06-01

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

  1. SiBr4 - Prediction and Determination of Crystal Structures

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  2. Crystal chemistry of layered structures formed by linear rigid silyl-capped molecules

    Directory of Open Access Journals (Sweden)

    Daniel Lumpi

    2015-09-01

    Full Text Available The crystallization behavior of methylthio- or methylsulfonyl-containing spacer extended Z,Z-bis-ene–yne molecules capped with trimethylsilyl groups obtained by (tandem thiophene ring fragmentation and of two non-spacer extended analogs were investigated. The rigid and linear molecules generally crystallized in layers whereby the flexibility of the layer interfaces formed by the silyl groups leads to a remarkably rich crystal chemistry. The molecules with benzene and thiophene spacers both crystallized with C2/c symmetry and can be considered as merotypes. Increasing the steric bulk of the core by introduction of ethylenedioxythiophene (EDOT gave a structure incommensurately modulated in the [010] direction. Further increase of steric demand in the case of a dimethoxythiophene restored periodicity along [010] but resulted in a doubling of the c vector. Two different polytypes were observed, which feature geometrically different layer interfaces (non-OD, order–disorder, polytypes, one with a high stacking fault probability. Oxidation of the methylthio groups of the benzene-based molecule to methylsulfonyl groups led to three polymorphs (two temperature-dependent, which were analyzed by Hirshfeld surface de/di fingerprint plots. The analogously oxidized EDOT-based molecule crystallized as systematic twins owing to its OD polytypism. Shortening of the backbone by removal of the aryl core resulted in an enantiomorphic structure and a further shortening by removal of a methylthio-ene fragment again in a systematically twinned OD polytype.

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

    Directory of Open Access Journals (Sweden)

    Boguslaw Stec

    2007-10-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

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

    2017-02-09

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

  6. Novel photonic crystal cavities and related structures.

    Energy Technology Data Exchange (ETDEWEB)

    Luk, Ting Shan

    2007-11-01

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

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

    Science.gov (United States)

    Valle, Mario; Oganov, Artem R

    2010-09-01

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

  8. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    OpenAIRE

    2013-01-01

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

  9. Crystal structure and characterization of pyrroloquinoline quinone disodium trihydrate

    Directory of Open Access Journals (Sweden)

    Ikemoto Kazuto

    2012-06-01

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

  10. Structure and Properties of Liquid Crystals

    CERN Document Server

    Blinov, Lev M

    2011-01-01

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

  11. The crystal structure of some rhenium and technetium dichalcogenides

    NARCIS (Netherlands)

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

    1996-01-01

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

  12. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

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

    Directory of Open Access Journals (Sweden)

    Ke-Qin Zhang

    2013-03-01

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

  14. Micromorphology of epicuticular wax structures of the garden strawberry leaves by electron microscopy: syntopism and polymorphism.

    Science.gov (United States)

    Kim, Ki Woo; Ahn, Jeong Joon; Lee, Joon-Ho

    2009-04-01

    Ultrastructural aspects of leaf epicuticular wax structures were investigated in the garden strawberry Fragariaxananassa by scanning and transmission electron microscopy. Both the adaxial and abaxial surfaces of two cultivars (Maehyang and Red Pearl) were collected and subjected to surface observations and ultrathin sections. The most prominent leaf epicuticular wax structures included membraneous platelets and angular rodlets. Most wax platelets were membraneous, and appeared to protrude from the surface at an acute angle. Angular rodlets were usually bent and had rather distinct facets in the abaxial surface of the two cultivars. Membraneous platelets were predominant on the adaxial surface of Maehyang, whereas the adaxial surface of Red Pearl was characterized by angular rodlets. However, both cultivars possessed angular rodlets on the abaxial surface, simultaneously. The combination of air-drying without vacuum and in-lens imaging of secondary electron signals with a field emission gun could impart the superb resolution at low electron dose with minimal specimen shrinkage. In vertical profiles of the leaf epidermis, epicuticular waxes were observed above the cuticle layer, and measured approximately as 50nm in thickness. The natural epicuticular waxes were seemingly mixtures of electron-dense microfibrils, and heterogeneous in shape on ultrathin sections. Distinct crystal-like strata could be hardly discernable in the wax structures. These results suggest that the garden strawberry has the nature of syntopism within one plant and polymorphism within the same species in the formation and occurrence of leaf epicuticular waxes.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-15

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

  16. 热处理对聚己二酸丁二醋多晶结构和降解行为的影响%Polymorphic Crystals from Different Thermal Treatments and Its Effect on Biodegradation Behavior of Poly( butylene adipate)

    Institute of Scientific and Technical Information of China (English)

    赵丽芬; 蒋妮; 甘志华

    2011-01-01

    On the basis of characteristic polymorphic crystals of poly ( butylene adipate) ( PBA), the PBA films with α crystal structure were prepared by melt crystallization and annealing treatment. The polymorphic crystal structure, crystal size and crystalline morphology of PBA α crystals with different thermal history were studied by wide angle X-ray diffraction ( WAXD), atomic force microscope ( AFM ) and differential scanning calorimeter(DSC). The biodegradation behavior of PBA α crystals from different thermal treatments was investigated by following the mass loss with time. The results indicate that the difference of PBA α crystals in spatial orientation of polymer chains in the same crystal lattice due to the different thermal history is the essential reason which results in the different biodegradation rates.%通过熔融结晶并结合退火处理方法得到多晶结构的聚己二酸丁二酯(PBA)及具有不同热历史的热力学稳定的a晶型,采用广角X射线衍射仪(WAXD)、原子力显微镜(AFM)和差示扫描量热仪(DSC)研究了PBA的多晶结构、晶体尺寸和结晶形貌,跟踪了退火处理PBA的生物降解行为.结果表明,分子链在相同晶格排列中围绕c轴空间取向的不同是决定多晶PBA降解速率差别的根本因素.

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

    Institute of Scientific and Technical Information of China (English)

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

    2002-01-01

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

  18. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

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

    2012-01-01

    , such as body-centered cubic and face-centered cubic, can be suppressed by a proper choice of the potential depth and periodicity. Furthermore, by varying the harmonic trap parameters and/or the optical potential in time, controlled transitions between crystal structures can be obtained with close to unit......We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures...

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

    CERN Document Server

    Martirosian, A H; Harurtjunian, V S

    2001-01-01

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

  20. Missing strings of residues in protein crystal structures.

    Science.gov (United States)

    Djinovic-Carugo, Kristina; Carugo, Oliviero

    2015-01-01

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

  1. Growth morphology and structural characteristic of C70single crystals

    Institute of Scientific and Technical Information of China (English)

    周维亚; 解思深; 吴源; 常保和; 王刚; 钱露茜

    1999-01-01

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

  2. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    Science.gov (United States)

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

    2012-06-01

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

  3. Preferential Nucleation during Polymorphic Transformations

    Science.gov (United States)

    Sharma, H.; Sietsma, J.; Offerman, S. E.

    2016-08-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR’s) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR’s with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller - and therefore nucleation more probable - with increasing number of special OR’s. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material.

  4. Crystal structure and Hirshfeld surface analysis of 1-carboxy-2-(3,4-dihydroxyphenyl)ethan-1-aminium chloride 2-ammonio-3-(3,4-dihydroxyphenyl)propanoate: a new polymorph of l-dopa HCl and isotypic with its bromide counterpart

    OpenAIRE

    Perumal Kathiravan; Thangavelu Balakrishnan; Perumal Venkatesan; Kandasamy Ramamurthi; María Judith Percino; Subbiah Thamotharan

    2016-01-01

    The title molecular salt, C9H12NO4+·Cl−·C9H11NO4, is isotypic with that of the bromide counterpart [Kathiravan et al. (2016). Acta Cryst. E72, 1544–1548]. The title salt is a second monoclinic polymorph of the l-dopa HCl structure reported earlier in the monoclinic space group P21 [Jandacek & Earle (1971). Acta Cryst. B27, 841–845; Mostad & Rømming (1974). Acta Chemica Scand. B28, 1161–1168]. In the title compound, monoclinic space group I2, one of the dopa molecules has a positive charge wit...

  5. Crystal structure and Hirshfeld surface analysis of 1-carb­oxy-2-(3,4-di­hydroxy­phen­yl)ethan-1-aminium chloride 2-ammonio-3-(3,4-di­hydroxy­phen­yl)propano­ate: a new polymorph of l-dopa HCl and isotypic with its bromide counterpart

    OpenAIRE

    Kathiravan, Perumal; Balakrishnan, Thangavelu; Venkatesan, Perumal; Ramamurthi, Kandasamy; Percino, María Judith; Thamotharan, Subbiah

    2016-01-01

    The title mol­ecular salt, C9H12NO4 +·Cl−·C9H11NO4, is isotypic with that of the bromide counterpart [Kathiravan et al. (2016 ▸). Acta Cryst. E72, 1544–1548]. The title salt is a second monoclinic polymorph of the l-dopa HCl structure reported earlier in the monoclinic space group P21 [Jandacek & Earle (1971 ▸). Acta Cryst. B27, 841–845; Mostad & Rømming (1974 ▸). Acta Chemica Scand. B28, 1161–1168]. In the title compound, monoclinic space group I2, one of the dopa mol­ecules has a positive c...

  6. Solid state characterization of azelnidipine-oxalic acid co-crystal and co-amorphous complexes: The effect of different azelnidipine polymorphs.

    Science.gov (United States)

    Pan, Yahui; Pang, Wenzhe; Lv, Jie; Wang, Jing; Yang, Caiqin; Guo, Wei

    2017-02-04

    In present study, based on the two polymorphs (α and β form) of azelnidipine (AZE), 12 complexes of AZE and oxalic acid (OXA) were prepared by solvent-assisted grinding (SG) and neat powder grinding (NG) methods at the AZE/OXA molar ratios of 2:1, 1:1, and 1:2. The effect of the different polymorphs of AZE on the micro-structure of the complexes were investigated by powder X-ray diffraction (PXRD), tempreture modulated differential scanning calorimetry and thermogravimetric analysis, cryo-field emission scanning electron microscope system, fourier transform infrared (FTIR), and solid-state nuclear magnetic resonance spectroscopy. β-AZE-OXA co-crystal was produced at β-AZE/OXA molar ratio of 2:1 when SG method was used; while α-AZE was used to produce α-AZE-OXA co-crystal at same condition. However, the other 10 combinations were in co-amorphous forms, including the NG samples with α (or β)-AZE/OXA molar ratios of 2:1, 1:1 (SG and NG), and 1:2 (SG and NG). Although the XRD pattern and IR spectra of the two co-crystals showed no difference, the melting enthalpy and specific heat cp of the β-AZE-OXA co-crystal was higher than that of the α-AZE-OXA co-crystal, indicating that the numbers of solvent molecules which entered the two co-crystal lattices were different. Interestingly, obvious difference occurred in the IR spectra between the α-AZE-OXA and β-AZE-OXA co-amorphous systems. 1745cm(-1) wave-numbers, which were assigned to the free CO groups, appeared in the α-AZE-OXA co-amorphous systems even when just a small amount of OXA was introduced, thereby indicating the presence of different intermolecular forces in the two series of co-amorphous forms. The solubility in different media and the dissolution rate in 0.1molL(-1) HCl of the 12 complexes were determined. The dramatically improved dissolution rates of the α- and β-AZE-OXA 1:2 (NG) combinations in vitro showed potential in improving the physicochemical properties of AZE by co-amorphous complex

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

    Science.gov (United States)

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

    2017-04-26

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

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

    Science.gov (United States)

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

    2017-04-01

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

  9. Molecular and Crystal Structures of Three Berberine Derivatives

    OpenAIRE

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

    2001-01-01

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

  10. Determination of channeling perspectives for complex crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Allen, W.R.

    1993-03-01

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

  11. Stability, structural, elastic and electronic properties of RuN polymorphs from first-principles calculations

    Science.gov (United States)

    Bannikov, V. V.; Shein, I. R.; Ivanovskii, A. L.

    2010-05-01

    First-principles FLAPW-GGA calculations for six possible polymorphs of ruthenium mononitride RuN indicate that the most stable structure is that of zinc blende rather than the rock salt structure recently reported for synthesized RuN samples. The elastic, electronic properties and the features of chemical bonds of zinc-blende RuN polymorph were investigated and discussed in detail.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Z. A. Rahima

    2015-09-01

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

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

    Science.gov (United States)

    Marx, Ailie; Adir, Noam

    2013-03-01

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

  15. Report on the sixth blind test of organic crystal structure prediction methods

    Science.gov (United States)

    Reilly, Anthony M.; Cooper, Richard I.; Adjiman, Claire S.; Bhattacharya, Saswata; Boese, A. Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J.; Bylsma, Rita; Campbell, Josh E.; Car, Roberto; Case, David H.; Chadha, Renu; Cole, Jason C.; Cosburn, Katherine; Cuppen, Herma M.; Curtis, Farren; Day, Graeme M.; DiStasio Jr, Robert A.; Dzyabchenko, Alexander; van Eijck, Bouke P.; Elking, Dennis M.; van den Ende, Joost A.; Facelli, Julio C.; Ferraro, Marta B.; Fusti-Molnar, Laszlo; Gatsiou, Christina-Anna; Gee, Thomas S.; de Gelder, René; Ghiringhelli, Luca M.; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W. M.; Hoja, Johannes; Hylton, Rebecca K.; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T.; Kendrick, John; de Klerk, Niek J. J.; Ko, Hsin-Yu; Kuleshova, Liudmila N.; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J. J.; Lund, Albert M.; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E.; McCabe, Patrick; McMahon, David P.; Meekes, Hugo; Metz, Michael P.; Misquitta, Alston J.; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J.; Neumann, Marcus A.; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R.; Orendt, Anita M.; Pagola, Gabriel I.; Pantelides, Constantinos C.; Pickard, Chris J.; Podeszwa, Rafal; Price, Louise S.; Price, Sarah L.; Pulido, Angeles; Read, Murray G.; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P.; Singh, Pawanpreet; Sugden, Isaac J.; Szalewicz, Krzysztof; Taylor, Christopher R.; Tkatchenko, Alexandre; Tuckerman, Mark E.; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E.; de Wijs, Gilles A.; Yang, Jack; Zhu, Qiang; Groom, Colin R.

    2016-01-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and ‘best practices’ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z′ = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. PMID:27484368

  16. Report on the sixth blind test of organic crystal structure prediction methods.

    Science.gov (United States)

    Reilly, Anthony M; Cooper, Richard I; Adjiman, Claire S; Bhattacharya, Saswata; Boese, A Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J; Bylsma, Rita; Campbell, Josh E; Car, Roberto; Case, David H; Chadha, Renu; Cole, Jason C; Cosburn, Katherine; Cuppen, Herma M; Curtis, Farren; Day, Graeme M; DiStasio, Robert A; Dzyabchenko, Alexander; van Eijck, Bouke P; Elking, Dennis M; van den Ende, Joost A; Facelli, Julio C; Ferraro, Marta B; Fusti-Molnar, Laszlo; Gatsiou, Christina Anna; Gee, Thomas S; de Gelder, René; Ghiringhelli, Luca M; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W M; Hoja, Johannes; Hylton, Rebecca K; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T; Kendrick, John; de Klerk, Niek J J; Ko, Hsin Yu; Kuleshova, Liudmila N; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J J; Lund, Albert M; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E; McCabe, Patrick; McMahon, David P; Meekes, Hugo; Metz, Michael P; Misquitta, Alston J; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J; Neumann, Marcus A; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R; Orendt, Anita M; Pagola, Gabriel I; Pantelides, Constantinos C; Pickard, Chris J; Podeszwa, Rafal; Price, Louise S; Price, Sarah L; Pulido, Angeles; Read, Murray G; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P; Singh, Pawanpreet; Sugden, Isaac J; Szalewicz, Krzysztof; Taylor, Christopher R; Tkatchenko, Alexandre; Tuckerman, Mark E; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E; de Wijs, Gilles A; Yang, Jack; Zhu, Qiang; Groom, Colin R

    2016-08-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

  17. Magnetic properties of geometrically frustrated polymorphic crystals of Cu{sub 4-x}Mg{sub x}(OH){sub 6}Cl{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Chu Shaoyan, E-mail: sc79@mit.edu [Center for Materials Science and Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, MA 02139 (United States)

    2011-01-01

    Geometric frustration can suppress magnetic long-range order (LRO) in either ferromagnetic (FM) [1-3] or antiferromagnetic (AFM) systems with Kagome structure. Crystals of Cu{sub 4-x}Mg{sub x}(OH){sub 6}Cl{sub 2}, magnesium-containing paratacamite and herbertsmithite (x < 1 and x {approx} 1, R3-bar m) and haydeeite (x {approx} 1, P3-bar m1), have been grown by the hydrothermal technique and characterized by single crystal X-ray diffraction. The 2D S =1/2 polymorphs can be classified into the two types of magnets based on the susceptibility at high temperature. Temperature and dc field-dependence of magnetization of the magnesium-containing phase are quite similar to those of isostructural single crystals of Cu{sub 4-x}Zn{sub x}(OH){sub 6}C{sub l2} (R3-bar m), zinc-containing paratacamite (or herbertsmithite). However, for haydeeite, though a ferromagnetic long range ordering at 20.6 K can be predicted by the Curie-Weiss law, the magnetic phase transition is absent until 4.3 K, indicating a high degree of frustration (|{theta}|/T{sub c} {approx} 5). Its ac frequency and dc field-dependence of spin freezing temperature are analogous to those of spin ice and/or spin glass.

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

    DEFF Research Database (Denmark)

    Wolny, Janusz; Lebech, Bente

    1986-01-01

    A crystal structure model of an incommensurately modulated structure is presented. Although six different reciprocal vectors are used to describe the model, all calculations are done in three dimensions making calculation of the real-space structure trivial. Using this model, it is shown that both...

  19. Tuning crystal polymorphs of a Π-extended tetrathiafulvalene-based cruciform molecule towards high-performance organic field-effect transistors

    DEFF Research Database (Denmark)

    Feng, Linlin; Dong, Huanli; Li, Qingyuan

    2017-01-01

    It is a common phenomenon for organic semiconductors to crystallize in two or more polymorphs, leading to various molecular packings and different charge transport properties. Therefore, it is a crucial issue of tuning molecular crystal polymorphs (i.e., adjusting the same molecule with different...... packing arrangements in solid state) towards efficient charge transport and high performance devices. Here, the choice of solvent had a marked effect on controlling the growth of α-phase ribbon and β-phase platelet during crystallization for an indenofluorene (IF) π-extended tetrathiafulvalene (TTF......)-based cruciform molecule, named as IF-TTF. The charge carrier mobility of the α-phase IF-TTF crystals was more than one order of magnitude higher than that of β-phase crystals, suggesting the importance of reasonably tuning molecular packing in solid state for the improvement of charge transport in organic...

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

    Science.gov (United States)

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

    2016-01-18

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

  1. The determination of crystal structures of active pharmaceutical ingredients from X-ray powder diffraction data: a brief, practical introduction, with fexofenadine hydrochloride as example.

    Science.gov (United States)

    Brüning, Jürgen; Schmidt, Martin U

    2015-06-01

    This study describes the general method for the determination of the crystal structures of active pharmaceutical ingredients (API) from powder diffraction data and demonstrates its use to determine the hitherto unknown crystal structure of fexofenadine hydrochloride, a third-generation antihistamine drug. Fexofenadine hydrochloride was subjected to a series of crystallisation experiments using re-crystallisation from solvents, gas diffusion, layering with an antisolvent and gel crystallisation. Powder diffraction patterns of all samples were recorded and inspected for polymorphism and for crystallinity. All samples corresponded to the same polymorph. The crystal structure was determined from an X-ray powder diffraction pattern using a real-space method with subsequent Rietveld refinement. The structure exhibits a two-dimensional hydrogen bond network. Crystal structures of API can be determined from X-ray powder diffraction data with good reliability. Fexofenadine exhibits only one polymorphic form, which is stabilised in the crystal by strong hydrogen bonds of the type (+)N-H···Cl(-), O-H···Cl(-), and between COOH groups. © 2015 Royal Pharmaceutical Society.

  2. Chiral Liquid Crystals: Structures, Phases, Effects

    Directory of Open Access Journals (Sweden)

    Ingo Dierking

    2014-06-01

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

  3. Synthesis and Crystal Structure of a New Manganese Complex

    Institute of Scientific and Technical Information of China (English)

    WANG Jian; LIU Ping; CHEN Yun

    2003-01-01

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

  4. An Investigation into the Polymorphism and Crystallization of Levetiracetam and the Stability of its Solid Form.

    Science.gov (United States)

    Xu, Kailin; Xiong, Xinnuo; Guo, Liuqi; Wang, Lili; Li, Shanshan; Tang, Peixiao; Yan, Jin; Wu, Di; Li, Hui

    2015-12-01

    Levetiracetam (LEV) crystals were prepared using different solvents at different temperatures. The LEV crystals were systematically characterized by X-ray powder diffraction (XRPD) and morphological analysis. The results indicated that many kinds of crystal habits exist in a solid form of LEV. To investigate the effects of LEV concentration, crystallization temperature, and crystallization type on crystallization and solid phase transformation of LEV, multiple methods were performed for LEV aqueous solution to determine if a new solid form exists in solid-state LEV. However, XRPD data demonstrate that the LEV solid forms possess same spatial arrangements that are similar to the original solid form. This result indicates that the LEV concentration, crystallization temperature, and crystallization type in aqueous solution have no influence on the crystallization and solid phase transformation of LEV. Moreover, crystallization by sublimation, melt cooling, and quench cooling, as well as mechanical effect, did not result in the formation of new LEV solid state. During melt cooling, the transformation of solid form LEV is a direct process from melting amorphous phase to the original LEV crystal phase, and the conversion rate is very quick. In addition, stability investigation manifested that LEV solid state is very stable under various conditions.

  5. Anisotropic crystal structure of magnetized neutron star crust

    Science.gov (United States)

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

    2017-09-01

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

  6. Structure of initial crystals formed during human amelogenesis

    Science.gov (United States)

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

    1992-02-01

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

  7. Structure and physical properties of EuTa2O6 tungsten bronze polymorph

    Science.gov (United States)

    Kolodiazhnyi, T.; Sakurai, H.; Vasylkiv, O.; Borodianska, H.; Forbes, S.; Mozharivskyj, Y.

    2014-08-01

    A tetragonal tungsten bronze (TTB) polymorph of EuTa2O6 was prepared and analyzed. EuTa2O6 crystallizes in the centrosymmetric Pnam space group (with unit cell: a = 12.3693, b = 12.4254, and c = 7.7228 Å) isomorphous with orthorhombic β-SrTa2O6. In contrast to early reports, we see no evidence of deviation from paramagnetic Curie-Weiss behavior among the Eu2+ 4f7spins in EuTa2O6 down to 2 K. Dielectric constant shows a broad peak at ca. 50 K with dielectric dispersion resembling diffuse phase transition. The relaxation time, however, follows a simple (non-freezing) thermally activated process with an activation energy of 92 meV and an attempt frequency of f0 = 5.79 × 1012 Hz. A thermal conductivity of EuTa2O6 shows a low-temperature (T ≈ 30 K) "plateau" region reminiscent of a glass-like behaviour in Nb-based TTB compounds. This behaviour can be attributed to the loosely bound Eu2+ ions occupying large tricapped trigonal prismatic sites in the EuTa2O6 structure.

  8. Single-Crystal Structure of a Covalent Organic Framework

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-06

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

  9. Crystal structure of 4-(4-methoxyphenoxybenzaldehyde

    Directory of Open Access Journals (Sweden)

    Andreas Schäfer

    2015-12-01

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

  10. The different conformations and crystal structures of dihydroergocristine

    Science.gov (United States)

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

    2016-02-01

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

  11. The formation of titania polymorphs under hydrothermal condition

    Institute of Scientific and Technical Information of China (English)

    ZHENG; Yanqing(郑燕青); SHI; Erwei(施尔畏); LI; Wenjun(李汶军); CHEN; Zhizhan(陈之战); ZHONG; Weizhuo(仲维卓); HU; Xingfang(胡行方)

    2002-01-01

    The formation process of crystal polymorphs of titania under hydrothermal condition is studied.According to the experimental results and theoretic analysis,the formation process of crystal polymorphs can be described as a unit process.It includes the formation of growth units,the formation of nuclei through the polymerization of growth unit,and the growth of crystallites.The influence of the environmental phase and growth conditions on the formation of polymorphs is reflected in the changes of the structures of growth units.For example,when changing the pH of the reaction medium,the structure of growth unit with the highest stable energy in the hydrothermal system changes.Then different titania polymorphs can be prepared.The absorption,movement,crystallization or desorption of the growth unit are related to crystalline structure.On the other hand,the formation of crystal inner defects is related to the disturbance of the crystallizing process.``

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

    Directory of Open Access Journals (Sweden)

    Alberto Cabrera

    2015-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

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

    Science.gov (United States)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

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

  15. Structure, Solubility and Stability of Orbifloxacin Crystal Forms: Hemihydrate versus Anhydrate.

    Science.gov (United States)

    Santos, Olimpia Maria Martins; Freitas, Jennifer Tavares Jacon; Cazedey, Edith Cristina Laignier; de Araújo, Magali Benjamim; Doriguetto, Antonio Carlos

    2016-03-09

    Orbifloxacin (ORBI) is a widely used antimicrobial drug of the fluoroquinolone class. In the official pharmaceutical compendia the existence of polymorphism in this active pharmaceutical ingredient (API) is reported. No crystal structure has been reported for this API and as described in the literature, its solubility is very controversial. Considering that different solid forms of the same API may have different physicochemical properties, these different solubilities may have resulted from analyses inadvertently carried out on different polymorphs. The solubility is the most critical property because it can affect the bioavailability and may compromise the quality of a drug product. The crystalline structure of ORBI determined by SCXRD is reported here for the first time. The structural analysis reveals that the ORBI molecule is zwitterionic and hemihydrated. ORBI hemihydrated form was characterized by the following techniques: TG/DTA, FTIR-ATR, and PXRD. A second crystalline ORBI form is also reported: the ORBI anhydrous form was obtained by heating the hemihydrate. These ORBI solid forms were isomorphous, since no significant change in unit cell and space group symmetry were observed. The solid-state phase transformation between these forms is discussed and the equilibrium solubility data were examined in order to check the impact of the differences observed in their crystalline structures.

  16. Structure, Solubility and Stability of Orbifloxacin Crystal Forms: Hemihydrate versus Anhydrate

    Directory of Open Access Journals (Sweden)

    Olimpia Maria Martins Santos

    2016-03-01

    Full Text Available Orbifloxacin (ORBI is a widely used antimicrobial drug of the fluoroquinolone class. In the official pharmaceutical compendia the existence of polymorphism in this active pharmaceutical ingredient (API is reported. No crystal structure has been reported for this API and as described in the literature, its solubility is very controversial. Considering that different solid forms of the same API may have different physicochemical properties, these different solubilities may have resulted from analyses inadvertently carried out on different polymorphs. The solubility is the most critical property because it can affect the bioavailability and may compromise the quality of a drug product. The crystalline structure of ORBI determined by SCXRD is reported here for the first time. The structural analysis reveals that the ORBI molecule is zwitterionic and hemihydrated. ORBI hemihydrated form was characterized by the following techniques: TG/DTA, FTIR-ATR, and PXRD. A second crystalline ORBI form is also reported: the ORBI anhydrous form was obtained by heating the hemihydrate. These ORBI solid forms were isomorphous, since no significant change in unit cell and space group symmetry were observed. The solid-state phase transformation between these forms is discussed and the equilibrium solubility data were examined in order to check the impact of the differences observed in their crystalline structures.

  17. Protein dynamics derived from clusters of crystal structures.

    OpenAIRE

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

    1997-01-01

    A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results ...

  18. Polymorph of dimethylacetamide-solvated crystals of 2,9-dichlorodithioketoquinacridone and their hydrogen bonding effect

    OpenAIRE

    Mizuguchi, Jin; Hoki, T.; Senju, T.

    2006-01-01

    2,9-Dichlorodithioketoquinacridone (DTQ-Cl) is a thionated derivative of industrially important 2,9-dichloroquinacridone used as colorants in painting and imaging industries. Crystallographic and electronic characterizations have been carried out on single crystals of DTQ-Cl recrystallized from solution in dimethylacetamide (DMA). Two kinds of DMA-solvated single crystals were isolated in the form of DTQ-Ci/(DMA)(2): modifications I and II. In both crystals, two DMA molecules are hydrogen-bon...

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2011-11-21

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

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

    Science.gov (United States)

    Jungblut, Swetlana; Dellago, Christoph

    2016-09-01

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

  2. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  3. Facts and fictions about polymorphism.

    Science.gov (United States)

    Cruz-Cabeza, Aurora J; Reutzel-Edens, Susan M; Bernstein, Joel

    2015-12-01

    We present new facts about polymorphism based on (i) crystallographic data from the Cambridge Structural Database (CSD, a database built over 50 years of community effort), (ii) 229 solid form screens conducted at Hoffmann-La Roche and Eli Lilly and Company over the course of 8+ and 15+ years respectively and (iii) a dataset of 446 polymorphic crystals with energies and properties computed with modern DFT-d methods. We found that molecular flexibility or size has no correlation with the ability of a compound to be polymorphic. Chiral molecules, however, were found to be less prone to polymorphism than their achiral counterparts and compounds able to hydrogen bond exhibit only a slightly higher propensity to polymorphism than those which do not. Whilst the energy difference between polymorphs is usually less than 1 kcal mol(-1), conformational polymorphs are capable of differing by larger values (up to 2.5 kcal mol(-1) in our dataset). As overall statistics, we found that one in three compounds in the CSD are polymorphic whilst at least one in two compounds from the Roche and Lilly set display polymorphism with a higher estimate of up to three in four when compounds are screened intensively. Whilst the statistics provide some guidance of expectations, each compound constitutes a new challenge and prediction and realization of targeted polymorphism still remains a holy grail of materials sciences.

  4. Crystal structure of 1-(4-formylbenzylidenethiosemicarbazone

    Directory of Open Access Journals (Sweden)

    Rosa Carballo

    2014-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Mohammed B. Alshammari

    2014-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Bronte J. Charette

    2015-03-01

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

  7. Crystal structure of 2-aminopyridinium 6-chloronicotinate

    Directory of Open Access Journals (Sweden)

    N. Jeeva Jasmine

    2015-09-01

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

  8. Idealized powder diffraction patterns for cellulose polymorphs

    Science.gov (United States)

    Cellulose samples are routinely analyzed by X-ray diffraction to determine their crystal type (polymorph) and crystallinity. However, the connection is seldom made between those efforts and the crystal structures of cellulose that have been determined with synchrotron X-radiation and neutron diffrac...

  9. Crystal Nucleation and Polymorph Control: Self-­association, Template Nucleation, Liquid‐Liquid, phase Separation

    NARCIS (Netherlands)

    Kulkarni, S.

    2014-01-01

    Crystallization is an essential step in many processes in chemical industries, ranging from bulk chemicals to special products. It is a separation and purification technique that results in a solid particulate product, which is generally preferred in the pharmaceutical industry. The crystal product

  10. Crystal Nucleation and Polymorph Control: Self-­association, Template Nucleation, Liquid‐Liquid, phase Separation

    NARCIS (Netherlands)

    Kulkarni, S.

    2014-01-01

    Crystallization is an essential step in many processes in chemical industries, ranging from bulk chemicals to special products. It is a separation and purification technique that results in a solid particulate product, which is generally preferred in the pharmaceutical industry. The crystal product

  11. Structural evolution of amino acid crystals under stress from a non-empirical density functional

    Science.gov (United States)

    Sabatini, Riccardo; Küçükbenli, Emine; Kolb, Brian; Thonhauser, T.; de Gironcoli, Stefano

    2012-10-01

    Use of the non-local correlation functional vdW-DF (from ‘van der Waals density functional’ Dion M et al 2004 Phys. Rev. Lett. 92 246401) has become a popular approach for including van der Waals interactions within density functional theory. In this work, we extend the vdW-DF theory and derive the corresponding stress tensor in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code. We then apply our methodology to investigate the structural evolution of amino acid crystals of glycine and l-alanine under pressure up to 10 GPa—with and without van der Waals interactions—and find that for an accurate description of intermolecular interactions and phase transitions in these systems, the inclusion of van der Waals interactions is crucial. For glycine, calculations including the vdW-DF (vdW-DF-c09x) functional are found to systematically overestimate (underestimate) the crystal lattice parameters, yet the stability ordering of the different polymorphs is determined accurately, at variance with the GGA case. In the case of l-alanine, our vdW-DF results agree with recent experiments that question the phase transition reported for this crystal at 2.3 GPa, as the a and c cell parameters happen to become equal but no phase transition is observed.

  12. Structure and properties of MTiOXO sub 4 crystals

    CERN Document Server

    Latham, T J

    2000-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  14. Electron Crystallographic Study on Structure Determination for Minute Crystals

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  15. A crystal structure prediction enigma solved

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  16. Solving Crystal Structures from Powder Diffraction Data

    DEFF Research Database (Denmark)

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

    1985-01-01

    High resolution powder data from both neutron and X-ray (synchrotron) sources have been used to estimate the possibility of direct structure determination from powder data. Two known structures were resolved by direct methods with neutron and X-ray data. With synchrotron X-ray data, the measured...... range of data was insufficient for a structure analysis, but the R-factor calculations showed the intensities extracted from the profile data to be of acceptable quality. The results were used to estimate the largest structure that might be solved using routine techniques. It was found that the limit...... would be near twenty atoms in the asymmetric part of a centro-symmetric structure....

  17. Prediction of protein-destabilizing polymorphisms by manual curation with protein structure.

    Directory of Open Access Journals (Sweden)

    Craig Alan Gough

    Full Text Available The relationship between sequence polymorphisms and human disease has been studied mostly in terms of effects of single nucleotide polymorphisms (SNPs leading to single amino acid substitutions that change protein structure and function. However, less attention has been paid to more drastic sequence polymorphisms which cause premature termination of a protein's sequence or large changes, insertions, or deletions in the sequence. We have analyzed a large set (n = 512 of insertions and deletions (indels and single nucleotide polymorphisms causing premature termination of translation in disease-related genes. Prediction of protein-destabilization effects was performed by graphical presentation of the locations of polymorphisms in the protein structure, using the Genomes TO Protein (GTOP database, and manual annotation with a set of specific criteria. Protein-destabilization was predicted for 44.4% of the nonsense SNPs, 32.4% of the frameshifting indels, and 9.1% of the non-frameshifting indels. A prediction of nonsense-mediated decay allowed to infer which truncated proteins would actually be translated as defective proteins. These cases included the proteins linked to diseases inherited dominantly, suggesting a relation between these diseases and toxic aggregation. Our approach would be useful in identifying potentially aggregation-inducing polymorphisms that may have pathological effects.

  18. Single-crystal field-effect transistors of new Cl₂-NDI polymorph processed by sublimation in air.

    Science.gov (United States)

    He, Tao; Stolte, Matthias; Burschka, Christian; Hansen, Nis Hauke; Musiol, Thomas; Kälblein, Daniel; Pflaum, Jens; Tao, Xutang; Brill, Jochen; Würthner, Frank

    2015-01-12

    Physical properties of active materials built up from small molecules are dictated by their molecular packing in the solid state. Here we demonstrate for the first time the growth of n-channel single-crystal field-effect transistors and organic thin-film transistors by sublimation of 2,6-dichloro-naphthalene diimide in air. Under these conditions, a new polymorph with two-dimensional brick-wall packing mode (β-phase) is obtained that is distinguished from the previously reported herringbone packing motif obtained from solution (α-phase). We are able to fabricate single-crystal field-effect transistors with electron mobilities in air of up to 8.6 cm(2) V(-1) s(-1) (α-phase) and up to 3.5 cm(2) V(-1) s(-1) (β-phase) on n-octadecyltriethoxysilane-modified substrates. On silicon dioxide, thin-film devices based on β-phase can be manufactured in air giving rise to electron mobilities of 0.37 cm(2) V(-1) s(-1). The simple crystal and thin-film growth procedures by sublimation under ambient conditions avoid elaborate substrate modifications and costly vacuum equipment-based fabrication steps.

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

    KAUST Repository

    Zhang, Chen

    2014-09-04

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

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-15

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

  2. Synthesis and Crystal Structure of Metronidazole-derived Compound

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2017-01-23

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

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

    National Research Council Canada - National Science Library

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

    2013-01-01

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

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

    National Research Council Canada - National Science Library

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

    2013-01-01

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

  7. Structural, elastic and thermodynamic properties of tetragonal and orthorhombic polymorphs of Sr2GeN2: an ab initio investigation

    Science.gov (United States)

    Bedjaoui, A.; Bouhemadou, A.; Bin-Omran, S.

    2016-04-01

    The structural, elastic and thermodynamic properties of the α (tetragonal) and β (orthorhombic) polymorphs of the Sr2GeN2 compound have been examined in detail using ab initio density functional theory pseudopotential plane-wave calculations. Apart the structural properties at the ambient conditions, all present reported results are predicted for the first time. The calculated equilibrium lattice parameters and inter-atomic bond-lengths of the considered polymorphs are in good agreement with the available experimental data. It is found that α-Sr2GeN2 is energetically more stable than β-Sr2GeN2. The two examined polymorphs are very similar in their crystal structures and have almost identical local environments. The single-crystal and polycrystalline elastic parameters and related properties - including elastic constants, bulk, shear and Young's moduli, Poisson's ratio, anisotropy indexes, Pugh's criterion, elastic wave velocities and Debye temperature - have been predicted. Temperature and pressure dependence of some macroscopic properties - including the unit-cell volume, bulk modulus, volume thermal expansion coefficient, heat capacity and Debye temperature - have been evaluated using ab initio calculations combined with the quasi-harmonic Debye model.

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

    Science.gov (United States)

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

    2011-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Hasna Yassine

    2015-10-01

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

  10. Synthesis and Crystal Structure of Isosteviol Derivatives

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  11. Crystal structure of benzene-1,3,5-tri-carb-oxy-lic acid-4-pyridone (1/3).

    Science.gov (United States)

    Staun, Selena L; Oliver, Allen G

    2015-11-01

    Slow co-crystallization of a solution of benzene-1,3,5-tri-carb-oxy-lic acid with a large excess of 4-hy-droxy-pyridine produces an inter-penetrating, three-dimensional, hydrogen-bonded framework consisting of three 4-pyridone and one benzene-1,3,5-tri-carb-oxy-lic acid mol-ecules, C9H6O6·3C5H5NO. This structure represents an ortho-rhom-bic polymorph of the previously reported C-centered, monoclinic structure [Campos-Gaxiola et al. (2014 ▸). Acta Cryst. E70, o453-o454].

  12. Photonics of liquid-crystal structures: A review

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-07-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  15. STRUCTURE FORMATION OF COLLOIDS IN NEMATIC LIQUID CRYSTALS

    Directory of Open Access Journals (Sweden)

    B.I.Lev

    2003-01-01

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

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

    Science.gov (United States)

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

    2012-11-01

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

  17. Tau protein assembles into isoform- and disulfide-dependent polymorphic fibrils with distinct structural properties.

    Science.gov (United States)

    Furukawa, Yoshiaki; Kaneko, Kumi; Nukina, Nobuyuki

    2011-08-05

    Tauopathies are neurodegenerative diseases in which insoluble fibrillar aggregates of a microtubule-binding protein, Tau, are abnormally accumulated. Pathological Tau fibrils often exhibit structural polymorphisms that differ among phenotypically distinct tauopathies; however, a molecular mechanism to generate polymorphic Tau fibrils remains obscure. Here, we note the formation of a disulfide bond in isoforms of full-length Tau and show that the thiol-disulfide status as well as the isoform composition determines structural and morphological properties of Tau fibrils in vitro. Mainly two regions in a Tau primary sequence are found to act as structural blocks for building a protease-resistant core of Tau fibrils. Interactions among those two blocks for building a core structure depend upon the thiol-disulfide status in each isoform of Tau, which results in the formation of polymorphic fibrils with distinct structural properties. Furthermore, we have found that more diverse structures of Tau fibrils emerge through a cross-seeded fibrillation between heterologous pairs of Tau isoforms. We thus propose that isoform- and disulfide-dependent combinatorial interactions among multiple regions in a Tau sequence endow Tau fibrils with various structures, i.e. polymorphism.

  18. Tau Protein Assembles into Isoform- and Disulfide-dependent Polymorphic Fibrils with Distinct Structural Properties*

    Science.gov (United States)

    Furukawa, Yoshiaki; Kaneko, Kumi; Nukina, Nobuyuki

    2011-01-01

    Tauopathies are neurodegenerative diseases in which insoluble fibrillar aggregates of a microtubule-binding protein, Tau, are abnormally accumulated. Pathological Tau fibrils often exhibit structural polymorphisms that differ among phenotypically distinct tauopathies; however, a molecular mechanism to generate polymorphic Tau fibrils remains obscure. Here, we note the formation of a disulfide bond in isoforms of full-length Tau and show that the thiol-disulfide status as well as the isoform composition determines structural and morphological properties of Tau fibrils in vitro. Mainly two regions in a Tau primary sequence are found to act as structural blocks for building a protease-resistant core of Tau fibrils. Interactions among those two blocks for building a core structure depend upon the thiol-disulfide status in each isoform of Tau, which results in the formation of polymorphic fibrils with distinct structural properties. Furthermore, we have found that more diverse structures of Tau fibrils emerge through a cross-seeded fibrillation between heterologous pairs of Tau isoforms. We thus propose that isoform- and disulfide-dependent combinatorial interactions among multiple regions in a Tau sequence endow Tau fibrils with various structures, i.e. polymorphism. PMID:21659525

  19. Comparative Analysis of Thermal Behavior, Isothermal Crystallization Kinetics and Polymorphism of Palm Oil Fractions

    OpenAIRE

    Zhang, Xia; Lin LI; Xie, He; Liang, Zhili; Su, Jianyu; Liu, Guoqin; LI, Bing

    2013-01-01

    Thermal behavior of palm stearin (PS) and palm olein (PO) was explored by monitoring peak temperature transitions by differential scanning calorimetry (DSC). The fatty acid composition (FAC), isothermal crystallization kinetics studied by pulsed Nuclear Magnetic Resonance (pNMR) and isothermal microstructure were also compared. The results indicated that the fatty acid composition had an important influence on the crystallization process. PS and PO both exhibited more multiple endotherms than...

  20. Hard Fats As Additives In Palm Oil And Its Relationships To Crystallization Process And Polymorphism

    OpenAIRE

    Oliveira, MR; Glazieli Marangoni; Ribeiro; Ana Paula Badan; dos Santos; Adenilson Oliveira; Cardoso; Lisandro Pavie; Kieckbusch; Theo Guenter

    2016-01-01

    The application of palm oil in fat-based product can be inappropriate due to its low crystallization rates and formation of crystalline clusters in post-processing stages. The adjustment of these properties can be achieved with the addition of hard fats, which are low-cost industrial products resulting from the process of total catalytic hydrogenation of liquid oils. During the crystallization of palm oil, these components can act as preferential nuclei in a crystalline ordering process, and ...

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

    Institute of Scientific and Technical Information of China (English)

    周秋生; 李小斌; 彭志宏; 刘桂华

    2004-01-01

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

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

    Science.gov (United States)

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

    2007-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-03-15

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

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

    CERN Document Server

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

    2015-01-01

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

  5. Synthesis and crystal structures of three new benzotriazolylpropanamides

    Directory of Open Access Journals (Sweden)

    Donna S. Amenta

    2017-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Dichen Li

    2012-05-01

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

  7. Crystal structures of human 108V and 108M catechol O-methyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Rutherford, K.; Le Trong, I.; Stenkamp, R.E.; Parson, W.W. (UWASH)

    2008-08-01

    Catechol O-methyltransferase (COMT) plays important roles in the metabolism of catecholamine neurotransmitters and catechol estrogens. The development of COMT inhibitors for use in the treatment of Parkinson's disease has been aided by crystallographic structures of the rat enzyme. However, the human and rat proteins have significantly different substrate specificities. Additionally, human COMT contains a common valine-methionine polymorphism at position 108. The methionine protein is less stable than the valine polymorph, resulting in decreased enzyme activity and protein levels in vivo. Here we describe the crystal structures of the 108V and 108M variants of the soluble form of human COMT bound with S-adenosylmethionine (SAM) and a substrate analog, 3,5-dinitrocatechol. The polymorphic residue 108 is located in the {alpha}5-{beta}3 loop, buried in a hydrophobic pocket {approx}16 {angstrom} from the SAM-binding site. The 108V and 108M structures are very similar overall [RMSD of C{sup {alpha}} atoms between two structures (C{sup {alpha}} RMSD) = 0.2 {angstrom}], and the active-site residues are superposable, in accord with the observation that SAM stabilizes 108M COMT. However, the methionine side chain is packed more tightly within the polymorphic site and, consequently, interacts more closely with residues A22 ({alpha}2) and R78 ({alpha}4) than does valine. These interactions of the larger methionine result in a 0.7-{angstrom} displacement in the backbone structure near residue 108, which propagates along {alpha}1 and {alpha}5 toward the SAM-binding site. Although the overall secondary structures of the human and rat proteins are very similar (C{sup {alpha}} RMSD = 0.4 {angstrom}), several nonconserved residues are present in the SAM-(I89M, I91M, C95Y) and catechol- (C173V, R201M, E202K) binding sites. The human protein also contains three additional solvent-exposed cysteine residues (C95, C173, C188) that may contribute to intermolecular disulfide bond

  8. Crystal structure and Hirshfeld surface analysis of 1-carb­oxy-2-(3,4-di­hydroxy­phen­yl)ethan-1-aminium chloride 2-ammonio-3-(3,4-di­hydroxy­phen­yl)propano­ate: a new polymorph of l-dopa HCl and isotypic with its bromide counterpart

    Science.gov (United States)

    Kathiravan, Perumal; Balakrishnan, Thangavelu; Venkatesan, Perumal; Ramamurthi, Kandasamy; Percino, María Judith; Thamotharan, Subbiah

    2016-01-01

    The title mol­ecular salt, C9H12NO4 +·Cl−·C9H11NO4, is isotypic with that of the bromide counterpart [Kathiravan et al. (2016 ▸). Acta Cryst. E72, 1544–1548]. The title salt is a second monoclinic polymorph of the l-dopa HCl structure reported earlier in the monoclinic space group P21 [Jandacek & Earle (1971 ▸). Acta Cryst. B27, 841–845; Mostad & Rømming (1974 ▸). Acta Chemica Scand. B28, 1161–1168]. In the title compound, monoclinic space group I2, one of the dopa mol­ecules has a positive charge with a protonated α-amino group and the α-carb­oxy­lic acid group uncharged, while the second dopa mol­ecule has a neutral charge, the α-amino group is protonated and the α-carb­oxy­lic acid is deprotonated. In the previously reported form, a single dopa mol­ecule is observed in which the α-amino group is protonated and the α-carb­oxy­lic acid group is uncharged. The invariant and variations of various types of inter­molecular inter­actions present in these two forms of dopa HCl structures are discussed with the aid of two-dimensional fingerprint plots. PMID:27840723

  9. Crystal structure and Hirshfeld surface analysis of 1-carb-oxy-2-(3,4-di-hydroxy-phen-yl)ethan-1-aminium chloride 2-ammonio-3-(3,4-di-hydroxy-phen-yl)propano-ate: a new polymorph of l-dopa HCl and isotypic with its bromide counterpart.

    Science.gov (United States)

    Kathiravan, Perumal; Balakrishnan, Thangavelu; Venkatesan, Perumal; Ramamurthi, Kandasamy; Percino, María Judith; Thamotharan, Subbiah

    2016-11-01

    The title mol-ecular salt, C9H12NO4(+)·Cl(-)·C9H11NO4, is isotypic with that of the bromide counterpart [Kathiravan et al. (2016 ▸). Acta Cryst. E72, 1544-1548]. The title salt is a second monoclinic polymorph of the l-dopa HCl structure reported earlier in the monoclinic space group P21 [Jandacek & Earle (1971 ▸). Acta Cryst. B27, 841-845; Mostad & Rømming (1974 ▸). Acta Chemica Scand. B28, 1161-1168]. In the title compound, monoclinic space group I2, one of the dopa mol-ecules has a positive charge with a protonated α-amino group and the α-carb-oxy-lic acid group uncharged, while the second dopa mol-ecule has a neutral charge, the α-amino group is protonated and the α-carb-oxy-lic acid is deprotonated. In the previously reported form, a single dopa mol-ecule is observed in which the α-amino group is protonated and the α-carb-oxy-lic acid group is uncharged. The invariant and variations of various types of inter-molecular inter-actions present in these two forms of dopa HCl structures are discussed with the aid of two-dimensional fingerprint plots.

  10. Single crystal surface structure by bragg scattering

    DEFF Research Database (Denmark)

    Nielsen, Mogens

    1985-01-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Mohamed H Abd El-Razek

    2010-01-01

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

  13. Ultrafast investigations of slow light in photonic crystal structures

    NARCIS (Netherlands)

    Engelen, Rob Jacques Paul

    2008-01-01

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

  14. Topology optimization for transient response of photonic crystal structures

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  15. Redetermination of the Crystal Structure of Al2Br6

    DEFF Research Database (Denmark)

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

    1997-01-01

    The structure of aluminium bromide has been reinvestigated by X-ray diffraction in three different ways: (a) on a single crystal grown in a glass capillary, (b) on powder in a Debye-Scherrer glass capillary and (c) on an area of powder placed in a protective container for Bragg-Brentano geometry....

  16. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.

    NARCIS (Netherlands)

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

    2004-01-01

    Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and a-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphoryla

  17. Crystal structure of the sodium-potassium pump

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  18. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

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

    2012-01-01

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

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

    Science.gov (United States)

    1975-01-01

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

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

    Science.gov (United States)

    Douglas, Bodie

    2009-01-01

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

  1. A unified picture of the crystal structures of metals

    Science.gov (United States)

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

    1995-04-01

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

  2. Crystal structure and magnetization of a Co3B2O6 single crystal

    Science.gov (United States)

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

    2013-07-01

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

  3. Band structures in Sierpinski triangle fractal porous phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Vasily F. Shabanov

    2013-08-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  7. Hydrothermal descriptive chemistry and single crystal structure determination of cesium and rubidium thorium fluorides.

    Science.gov (United States)

    Underwood, Christopher C; Mann, Matthew; McMillen, Colin D; Kolis, Joseph W

    2011-11-21

    Two new cesium thorium fluorides and three new rubidium thorium fluorides have been synthesized hydrothermally and structurally characterized. The structures of two polymorphs of CsTh(3)F(13) are described in space group P6/mmm with a = 8.2608(14) and c = 8.6519(17) and space group Pmc2(1) with a = 8.1830(16), b = 7.5780(15), and c = 8.6244(17). The analogous orthorhombic compound RbTh(3)F(13), with a = 8.1805(16), b = 7.4378(15), and c = 8.6594(17) in space group Pmc2(1), is also reported. Two other rubidium thorium fluorides are also described: RbTh(2)F(9) crystallizes in the space group Pnma where a = 8.9101(18), b = 11.829(2), and c = 7.4048(15), and Rb(7)Th(6)F(31) crystallizes in the space group R3 where a = 15.609(2) and c = 10.823(2). Comparison of these materials was made on the basis of their structures and synthesis conditions. The formation of these species in hydrothermal fluids appears to be dependent upon the concentration of the alkali fluoride mineralizer solution and, thus, the ratio of alkali ions to thorium in the system.

  8. Crystal structures at high pressures and temperatures

    Science.gov (United States)

    Caldwell, Wendel Alexander

    2000-10-01

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

  9. Crystal Structure of Cold Compressed Graphite

    Science.gov (United States)

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

    2012-02-01

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

  10. Single-crystal diffuse scattering studies on polymorphs of molecular crystals. I. The room-temperature polymorphs of the drug benzocaine.

    Science.gov (United States)

    Chan, E J; Welberry, T R; Goossens, D J; Heerdegen, A P; Beasley, A G; Chupas, P J

    2009-06-01

    The drug benzocaine (ethyl 4-aminobenzoate), commonly used as a local anaesthetic, is a bimorphic solid at room temperature. Form (I) is monoclinic P2(1)/c, while the metastable form (II) is orthorhombic P2(1)2(1)2(1). Three-dimensional diffuse X-ray scattering data have been collected for the two forms on the 11-ID-B beamline at the Advanced Photon Source (APS). Both forms show strong and highly structured diffuse scattering. The data have been interpreted and analysed using Monte Carlo (MC) modelling on the basis that the scattering is purely thermal in origin and indicates the presence of highly correlated molecular motions. In both forms (I) and (II) broad diffuse streaks are observed in the 0kl section which indicate strong longitudinal displacement correlations between molecules in the 031 directions, extending over distances of up to 50 A. Streaks extending between Bragg peaks in the hk0 section normal to [100] correspond to correlated motions of chains of molecules extending along a that are linked by N-H...O=C hydrogen bonds and which occur together as coplanar ribbon pairs. The main difference between the two forms is in the dynamical behaviour of the ribbon pairs and in particular how they are able to slide relative to each other. While for form (I) a model involving harmonic springs is able to describe the motion satisfactorily, as simple excursions away from the average structure, there is evidence in form (II) of anharmonic effects that are precursors of a phase transition to a new low-temperature phase, form (III), that was subsequently found.

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

    Science.gov (United States)

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

    2004-03-01

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

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

    Directory of Open Access Journals (Sweden)

    J. Piątkowski

    2009-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-15

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

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

    Science.gov (United States)

    Neumann, Marcus A

    2008-08-14

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

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

    Science.gov (United States)

    Kubo, S.; Wunderlich, B.

    1971-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-07-01

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

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

    Science.gov (United States)

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

    1999-08-01

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

  18. Modeling liquid crystal bilayer structures with minimal surfaces.

    Science.gov (United States)

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

    2004-01-22

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

  19. Physicochemical properties of Brazilian cocoa butter and industrial blends. Part II Microstructure, polymorphic behavior and crystallization characteristics

    Directory of Open Access Journals (Sweden)

    Ribeiro, A. P. B.

    2012-03-01

    Full Text Available The microstructural behavior of industrial standardized cocoa butter samples and cocoa butter samples from three different Brazilian states is compared. The cocoa butters were characterized by their microstructural patterns, crystallization kinetics and polymorphic habits. The evaluation of these parameters aided in establishing relationships between the chemical compositions and crystallization behavior of the samples, as well as differentiating them in terms of technological and industrial potential for use in tropical regions.

    En este trabajo se presenta el comportamiento de la microestructura y la cristalización de mantecas de cacao representativas de las mezclas industriales, y de la manteca de cacao original de tres regiones geográficas diferentes de Brasil. Las muestras se evaluaron de acuerdo a la microestructura, la cinética de cristalización y el comportamiento polimórfico. La evaluación de estos parámetros nos permite establecer relaciones entre la composición química y el comportamiento de la cristalización de las muestras, así como las diferencias sobre la adecuación del potencial tecnológico e industrial para su aplicación en las regiones tropicales.

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

    Directory of Open Access Journals (Sweden)

    Anuruddha Rajapakse

    2014-11-01

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

  1. Crystal structure and density of helium to 232 kbar

    Science.gov (United States)

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

    1988-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Rikako Tanaka

    2017-02-01

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

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

    Institute of Scientific and Technical Information of China (English)

    周堃; 李军; 罗建洪; 金央

    2012-01-01

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

  4. Synthesis and Crystal Structure of Tetranuclear Zinc Benzoate

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  5. Assembly of 4-, 6- and 8-connected Cd(II) pseudo-polymorphic coordination polymers: Synthesis, solvent-dependent structural variation and properties

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhao-Hao [College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934 (China); Xue, Li-Ping, E-mail: lpxue@163.com [College of Food and Drug, Luoyang Normal University, Luoyang 471934 (China); Miao, Shao-Bin [College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934 (China); Zhao, Bang-Tun, E-mail: zbt@lynu.edu.cn [College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934 (China)

    2016-08-15

    The reaction of Cd(NO{sub 3}){sub 2}·4H{sub 2}O, 2,5-thiophenedicarboxylic acid (H{sub 2}tdc) and 1,2-bis(imidazol-1′-yl)methane (bimm) by modulating solvent systems yielded three highly connected pseudo-polymorphic coordination polymers based on different dinuclear [Cd{sub 2}(CO{sub 2}){sub 2}] subunits bridged by carboxylate groups. Single crystal structural analyses reveal structural variation from 4-connected 2D sql layer, 6-connected 2-fold interpenetrated 3D pcu to 8-connected 3D bcu-type network in compounds 1–3. The structural dissimilarity in the structures dependent on the coordination environments of Cd(II) ions and linking modes of mixed ligand influenced by different solvent systems during the synthesis process. Moreover, thermogravimetric and photoluminescence behaviors of 1–3 were also investigated for the first time, and all the complexes emit blue luminescence in the solid state. - Graphical abstract: Key Topic. Different solvent systems modulated three Cd(II) pseudo-polymorphic coordination polymers based on thiophene-2,5-dicarboxylate and 1,2-bis(imidazol-1′-yl)methane mixed ligands. Display Omitted - Highlights: • Three solvent-dependent Cd(II) pseudo-polymorphic coordination polymers have been synthesized. • Structural variation from 4-connected 2D layer, 6-connected 2-fold interpenetrated 3D net to 8-connected 3D net. • All complexes emit blue luminescence.

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

    Science.gov (United States)

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

    2015-07-15

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

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

    Science.gov (United States)

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

    2010-01-01

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

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

    CERN Document Server

    McBride, L

    2000-01-01

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

  9. Structural engineering of three-dimensional phononic crystals

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

    ZHANG GangSheng

    2007-01-01

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

  13. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-28

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

  14. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

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

    1992-01-01

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

  15. Improved switching using Fano resonances in photonic crystal structures

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2015-11-14

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

  17. Crystal structure optimisation using an auxiliary equation of state

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-14

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

  18. Isolation and Crystal Structure of Xanthones from Swertia Chirayita

    Institute of Scientific and Technical Information of China (English)

    史高峰; 鲁润华; 杨云裳; 李春雷; 杨爱梅; 蔡立祥

    2004-01-01

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

  19. Role of Dispersion Interactions in the Polymorphism and Entropic Stabilization of the Aspirin Crystal

    Science.gov (United States)

    Reilly, Anthony M.; Tkatchenko, Alexandre

    2014-08-01

    Aspirin has been used and studied for over a century but has only recently been shown to have an additional polymorphic form, known as form II. Since the two observed solid forms of aspirin are degenerate in terms of lattice energy, kinetic effects have been suggested to determine the metastability of the less abundant form II. Here, first-principles calculations provide an alternative explanation based on free-energy differences at room temperature. The explicit consideration of many-body van der Waals interactions in the free energy demonstrates that the stability of the most abundant form of aspirin is due to a subtle coupling between collective electronic fluctuations and quantized lattice vibrations. In addition, a systematic analysis of the elastic properties of the two forms of aspirin rules out mechanical instability of form II as making it metastable.

  20. The crystal structure of synthetic kutinaite, Cu14Ag6As7

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-12-31

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

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

    Science.gov (United States)

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

    2011-03-15

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

  3. Crystal structure and physicochemical characterization of 3β-hydroxyolea-12-en-28-oic acid-3,5,6-trimethylpyrazin-2-methyl ester

    Science.gov (United States)

    Fu, Jing; Dong, Xiaoxv; Yin, Xinbing; Cao, Sali; Yang, Chunjing; He, Huyiligeqi; Ni, Jian

    2017-02-01

    3β-hydroxyolea-12-en-28-oic acid-3,5,6-trimethylpyrazin-2-methyl ester (T-OA) is a newly discovered potential antitumor compound. However, the poor solubility of T-OA leads to poor dissolution and limited clinical application. So as to enhance the dissolution and bioavailability of T-OA, an investigation of the polymorphism of T-OA was successfully undertaken. A new solvate and an amorphous form of T-OA were discovered through a comprehensive polymorph screening experiments. Their structures were elucidated by single-crystal structure analysis and extensively characterized by PXRD, DSC and SEM. The powder dissolution rates were compared with those of the previously known polymorph. Thermodynamic stability and phase transformation are also discussed in detail.

  4. Crystal structure of Pb3(IO4(OH22

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-07-01

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

  5. Solid State Synthesis and Crystal Structure of K3SI

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2015-11-01

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

  7. Crystal Structure of the Human Laminin Receptor Precursor

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-01

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

  8. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatezinc

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-03-01

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

  9. Dispersion Based Photonic-Crystal Structures for RF Applications

    Science.gov (United States)

    2006-06-01

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

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

    OpenAIRE

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

    2016-01-01

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

  11. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

  12. Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.

    Science.gov (United States)

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

    2006-12-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

  16. Nanoconfinement-induced structures in chiral liquid crystals.

    Science.gov (United States)

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

    2013-08-28

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

  17. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Carol K. Hall

    2013-08-01

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

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

    Institute of Scientific and Technical Information of China (English)

    叶军; 茅毓新; 桂璐璐; 常文瑞; 梁栋材

    2000-01-01

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

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

    Science.gov (United States)

    Weil, Matthias

    2015-01-01

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

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

    Science.gov (United States)

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

    2014-09-16

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

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

    Science.gov (United States)

    Kilby, Gregory R; Gaylord, Thomas K

    2009-07-01

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

  2. Crystal structure of tetra-wickmanite, Mn(2+)Sn(4+)(OH)6.

    Science.gov (United States)

    Lafuente, Barbara; Yang, Hexiong; Downs, Robert T

    2015-02-01

    The crystal structure of tetra-wickmanite, ideally Mn(2+)Sn(4+)(OH)6 [mangan-ese(II) tin(IV) hexa-hydroxide], has been determined based on single-crystal X-ray diffraction data collected from a natural sample from Långban, Sweden. Tetra-wickmanite belongs to the octa-hedral-framework group of hydroxide-perovskite minerals, described by the general formula BB'(OH)6 with a perovskite derivative structure. The structure differs from that of an ABO3 perovskite in that the A site is empty while each O atom is bonded to an H atom. The perovskite B-type cations split into ordered B and B' sites, which are occupied by Mn(2+) and Sn(4+), respectively. Tetra-wickmanite exhibits tetra-gonal symmetry and is topologically similar to its cubic polymorph, wickmanite. The tetra-wickmanite structure is characterized by a framework of alternating corner-linked [Mn(2+)(OH)6] and [Sn(4+)(OH)6] octa-hedra, both with point-group symmetry -1. Four of the five distinct H atoms in the structure are statistically disordered. The vacant A site is in a cavity in the centre of a distorted cube formed by eight octa-hedra at the corners. However, the hydrogen-atom positions and their hydrogen bonds are not equivalent in every cavity, resulting in two distinct environments. One of the cavities contains a ring of four hydrogen bonds, similar to that found in wickmanite, while the other cavity is more distorted and forms crankshaft-type chains of hydrogen bonds, as previously proposed for tetra-gonal stottite, Fe(2+)Ge(4+)(OH)6.

  3. Crystal structure of tetra­wickmanite, Mn2+Sn4+(OH)6

    Science.gov (United States)

    Lafuente, Barbara; Yang, Hexiong; Downs, Robert T.

    2015-01-01

    The crystal structure of tetra­wickmanite, ideally Mn2+Sn4+(OH)6 [mangan­ese(II) tin(IV) hexa­hydroxide], has been determined based on single-crystal X-ray diffraction data collected from a natural sample from Långban, Sweden. Tetra­wickmanite belongs to the octa­hedral-framework group of hydroxide-perovskite minerals, described by the general formula BB’(OH)6 with a perovskite derivative structure. The structure differs from that of an ABO3 perovskite in that the A site is empty while each O atom is bonded to an H atom. The perovskite B-type cations split into ordered B and B′ sites, which are occupied by Mn2+ and Sn4+, respectively. Tetra­wickmanite exhibits tetra­gonal symmetry and is topologically similar to its cubic polymorph, wickmanite. The tetra­wickmanite structure is characterized by a framework of alternating corner-linked [Mn2+(OH)6] and [Sn4+(OH)6] octa­hedra, both with point-group symmetry -1. Four of the five distinct H atoms in the structure are statistically disordered. The vacant A site is in a cavity in the centre of a distorted cube formed by eight octa­hedra at the corners. However, the hydrogen-atom positions and their hydrogen bonds are not equivalent in every cavity, resulting in two distinct environments. One of the cavities contains a ring of four hydrogen bonds, similar to that found in wickmanite, while the other cavity is more distorted and forms crankshaft-type chains of hydrogen bonds, as previously proposed for tetra­gonal stottite, Fe2+Ge4+(OH)6. PMID:25878828

  4. Influence of morphology and polymorphic transformation of fat crystals on the freeze-thaw stability of mayonnaise-type oil-in-water emulsions.

    Science.gov (United States)

    Ishibashi, C; Hondoh, H; Ueno, S

    2016-11-01

    This study examined the destabilization of an oil-in-water (O/W) emulsion by freeze-thawing with a focus on the influence of the morphology and polymorph of fat crystals. For a model of food emulsion, this study used a mayonnaise-type O/W emulsion containing 70wt% canola oil (canola emulsion) or soybean oil (soybean emulsion) stored at -15, -20, and -30°C. The freeze-thaw stabilities of the emulsions were evaluated by measuring the upper oil layer after freeze-thawing. The soybean emulsion kept at -20°C had the highest stability; the other emulsions were destabilized during 6h of storage. Crystallization in the emulsions was determined using differential scanning calorimetry (DSC), time variation of temperature, X-ray diffraction measurement, and polarized light microscopy. DSC thermograms indicated that crystallization in emulsions occurred first in the high-melting fraction of oil, followed by water and, last, in the low-melting fraction of oil during cooling to -40°C. In the canola emulsion, the amount of fat crystals derived from the low-melting fraction of oil increased during storage at all temperatures, resulting in partial coalescence. The soybean emulsion was expected to be destabilized by polymorphic transformation (sub-α to β' and β) of fat crystals derived from the high-melting fraction during storage at -15 and -20°C. However, the soybean emulsion did not exhibit polymorphic transformation stored at -30°C, and the amount of fat crystals did not increase during freezing; thus, it was destabilized via a different mechanism. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-02-24

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

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

    Science.gov (United States)

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

    2013-09-01

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

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

    Directory of Open Access Journals (Sweden)

    A.V. Mukhametshin

    2017-03-01

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

  8. Crystal Structure of an Ammonia-Permeable Aquaporin

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Science.gov (United States)

    Smirnov, M; Saint-Grégoire, P

    2014-05-01

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

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

    Science.gov (United States)

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

    2016-03-15

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

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

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2015-05-01

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

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

    Science.gov (United States)

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

    1994-01-01

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

  13. Crystal structure of seleno-l-cystine dihydrochloride

    OpenAIRE

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

    2015-01-01

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

  14. Band structures in the nematic elastomers phononic crystals

    Science.gov (United States)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    2017-02-01

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

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

    Science.gov (United States)

    Allen, Frank H

    2002-06-01

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

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

    Science.gov (United States)

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

    1987-01-01

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

  17. How important is thermal expansion for predicting molecular crystal structures and thermochemistry at finite temperatures?

    Science.gov (United States)

    Heit, Yonaton N; Beran, Gregory J O

    2016-08-01

    Molecular crystals expand appreciably upon heating due to both zero-point and thermal vibrational motion, yet this expansion is often neglected in molecular crystal modeling studies. Here, a quasi-harmonic approximation is coupled with fragment-based hybrid many-body interaction calculations to predict thermal expansion and finite-temperature thermochemical properties in crystalline carbon dioxide, ice Ih, acetic acid and imidazole. Fragment-based second-order Möller-Plesset perturbation theory (MP2) and coupled cluster theory with singles, doubles and perturbative triples [CCSD(T)] predict the thermal expansion and the temperature dependence of the enthalpies, entropies and Gibbs free energies of sublimation in good agreement with experiment. The errors introduced by neglecting thermal expansion in the enthalpy and entropy cancel somewhat in the Gibbs free energy. The resulting ∼ 1-2 kJ mol(-1) errors in the free energy near room temperature are comparable to or smaller than the errors expected from the electronic structure treatment, but they may be sufficiently large to affect free-energy rankings among energetically close polymorphs.

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

    Science.gov (United States)

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

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

  19. Crystal structure of the 80S yeast ribosome.

    Science.gov (United States)

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

    2012-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Luca eRonda

    2015-04-01

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

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

    Science.gov (United States)

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

    2013-09-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Science.gov (United States)

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

    2015-10-01

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

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

    Science.gov (United States)

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

    2012-06-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

  6. Crystal structure of the Fe-member of usovite

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2015-06-01

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

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

    Science.gov (United States)

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

    2005-02-21

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

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

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    金轶; 车云霞; 魏荣敏; 郑吉民

    2004-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2000-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Diana Dragancea, Vladimir B. Arion, Sergiu Shova

    2008-12-01

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

  12. Crystal structure and magnetism of UOsAl

    Science.gov (United States)

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

    2017-04-01

    Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn2 type, space group P63/mmc, with lattice parameters a=536.4 pm, c=845.3 pm. Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). The compound is a weakly temperature-dependent paramagnet with magnetic susceptibility of ≈1.5*10-8 m3 mol-1 (at T=2 K), which is slightly higher with magnetic field along the a-axis compared to the c-axis. The Sommerfeld coefficient of electronic specific heat has moderate value of γ=36 mJ mol-1 K-2.

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

    Institute of Scientific and Technical Information of China (English)

    Xiao-qing Niu; Ji-chun Chen

    2014-01-01

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

  14. Crystal structures and conformers of CyMe4-BTBP

    Directory of Open Access Journals (Sweden)

    Lyczko Krzysztof

    2015-12-01

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

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

    Science.gov (United States)

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

    2006-05-19

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

  16. Double-bridge bonding of aluminium and hydrogen in the crystal structure of gamma-AlH3.

    Science.gov (United States)

    Yartys, Volodymyr A; Denys, Roman V; Maehlen, Jan Petter; Frommen, Christoph; Fichtner, Maximilian; Bulychev, Boris M; Emerich, Hermann

    2007-02-19

    Aluminum trihydride (alane) is one of the most promising among the prospective solid hydrogen-storage materials, with a high gravimetric and volumetric density of hydrogen. In the present work, the alane, crystallizing in the gamma-AlH3 polymorphic modification, was synthesized and then structurally characterized by means of synchrotron X-ray powder diffraction. This study revealed that gamma-AlH3 crystallizes with an orthorhombic unit cell (space group Pnnm, a = 5.3806(1) A, b = 7.3555(2) A, c = 5.77509(5) A). The crystal structure of gamma-AlH3 contains two types of AlH6 octahedra as the building blocks. The Al-H bond distances in the structure vary in the range of 1.66-1.79 A. A prominent feature of the crystal structure is the formation of the bifurcated double-bridge bonds, Al-2H-Al, in addition to the normal bridge bonds, Al-H-Al. This former feature has not been previously reported for Al-containing hydrides so far. The geometry of the double-bridge bond shows formation of short Al-Al (2.606 A) and Al-H (1.68-1.70 A) bonds compared to the Al-Al distances in Al metal (2.86 A) and Al-H distances for Al atoms involved in the formation of normal bridge bonds (1.769-1.784 A). The crystal structure of gamma-AlH3 contains large cavities between the AlH6 octahedra. As a consequence, the density is 11% less than for alpha-AlH3.

  17. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-13

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

  18. Crystal structure and conformational analysis of angiotensinogen fragments.

    Science.gov (United States)

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

    1989-12-01

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

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

    CERN Document Server

    Vetrov, Stepan Ya; Timofeev, Ivan V

    2015-01-01

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

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

    Science.gov (United States)

    Clark, Noel A.

    2000-01-01

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

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

    Science.gov (United States)

    Hornfeck, Wolfgang; Hoch, Constantin

    2015-12-01

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

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

    OpenAIRE

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

    2015-01-01

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

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

    CERN Document Server

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

    2003-01-01

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

  4. Crystal structures and dynamical properties of dense CO2.

    Science.gov (United States)

    Yong, Xue; Liu, Hanyu; Wu, Min; Yao, Yansun; Tse, John S; Dias, Ranga; Yoo, Choong-Shik

    2016-10-04

    Structural polymorphism in dense carbon dioxide (CO2) has attracted significant attention in high-pressure physics and chemistry for the past two decades. Here, we have performed high-pressure experiments and first-principles theoretical calculations to investigate the stability, structure, and dynamical properties of dense CO2 We found evidence that CO2-V with the 4-coordinated extended structure can be quenched to ambient pressure below 200 K-the melting temperature of CO2-I. CO2-V is a fully coordinated structure formed from a molecular solid at high pressure and recovered at ambient pressure. Apart from confirming the metastability of CO2-V (I-42d) at ambient pressure at low temperature, results of ab initio molecular dynamics and metadynamics (MD) simulations provided insights into the transformation processes and structural relationship from the molecular to the extended phases. In addition, the simulation also predicted a phase V'(Pna21) in the stability region of CO2-V with a diffraction pattern similar to that previously assigned to the CO2-V (P212121) structure. Both CO2-V and -V' are predicted to be recoverable and hard with a Vicker hardness of ∼20 GPa. Significantly, MD simulations found that the CO2 in phase IV exhibits large-amplitude bending motions at finite temperatures and high pressures. This finding helps to explain the discrepancy between earlier predicted static structures and experiments. MD simulations clearly indicate temperature effects are critical to understanding the high-pressure behaviors of dense CO2 structures-highlighting the significance of chemical kinetics associated with the transformations.

  5. Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease.

    Science.gov (United States)

    Apostol, Marcin I; Sawaya, Michael R; Cascio, Duilio; Eisenberg, David

    2010-09-24

    A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are "steric zippers," pairs of interacting β-sheets. Both structures of these "homozygous steric zippers" reveal direct intermolecular interactions between Met or Val in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.

  6. Assembly of 4-, 6- and 8-connected Cd(II) pseudo-polymorphic coordination polymers: Synthesis, solvent-dependent structural variation and properties

    Science.gov (United States)

    Li, Zhao-Hao; Xue, Li-Ping; Miao, Shao-Bin; Zhao, Bang-Tun

    2016-08-01

    The reaction of Cd(NO3)2·4H2O, 2,5-thiophenedicarboxylic acid (H2tdc) and 1,2-bis(imidazol-1‧-yl)methane (bimm) by modulating solvent systems yielded three highly connected pseudo-polymorphic coordination polymers based on different dinuclear [Cd2(CO2)2] subunits bridged by carboxylate groups. Single crystal structural analyses reveal structural variation from 4-connected 2D sql layer, 6-connected 2-fold interpenetrated 3D pcu to 8-connected 3D bcu-type network in compounds 1-3. The structural dissimilarity in the structures dependent on the coordination environments of Cd(II) ions and linking modes of mixed ligand influenced by different solvent systems during the synthesis process. Moreover, thermogravimetric and photoluminescence behaviors of 1-3 were also investigated for the first time, and all the complexes emit blue luminescence in the solid state.

  7. Crystallographic Studies of Prion Protein (PrP) Segments Suggest How Structural Changes Encoded by Polymorphism at Residue 129 Modulate Susceptibility to Human Prion Disease

    Energy Technology Data Exchange (ETDEWEB)

    Apostol, Marcin I.; Sawaya, Michael R.; Cascio, Duilio; Eisenberg, David (UCLA)

    2010-09-23

    A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are 'steric zippers,' pairs of interacting {beta}-sheets. Both structures of these 'homozygous steric zippers' reveal direct intermolecular interactions between Met or Val in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.

  8. Molecular structure and polymorphism of a cyclohexanediol: trans-1,4-cyclohexanedimethanol

    OpenAIRE

    Rosado, Mário T. S.; Maria, Teresa M. R.; Castro, Ricardo A. E.; Canotilho, João; Silva, Manuela Ramos; Eusébio,M. Ermelinda S.

    2014-01-01

    This study aims to investigate the molecular structure and polymorphism of trans-1,4-cyclohexanedimethanol, including the bi-axial/bi-equatorial equilibrium and the nature of the intermolecular H-bond networks in condensed phases created by the hydroxyl group torsions. The full conformational space of the single molecule was explored by MP2 calculations, showing that the optimized bi-equatorial conformers have similar stability and the bi-axial ones have much higher energies. The ...

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

    Directory of Open Access Journals (Sweden)

    Amy Wernimont

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

  10. Effects of APOE promoter polymorphism on the topological organization of brain structural connectome in nondemented elderly.

    Science.gov (United States)

    Shu, Ni; Li, Xin; Ma, Chao; Zhang, Junying; Chen, Kewei; Liang, Ying; Chen, Yaojing; Zhang, Zhanjun

    2015-12-01

    The polymorphism of the Apolipoprotein E (APOE) promoter rs405509 can regulate the transcriptional activity of the APOE gene and is related to Alzheimer's disease (AD). However, its effects on cognitive performance and the underlying brain mechanisms remain unknown. Here, we performed a battery of neuropsychological tests in a large sample (837 subjects) of nondemented elderly Chinese people, and explored the related brain mechanisms via the construction of diffusion MRI-based structural connectome and graph analysis from a subset (84 subjects) of the sample. Cognitively, the rs405509 risk allele (TT) carriers showed decreased attention and execution functions compared with noncarriers (GG/GT). Regarding the topological alterations of the brain connectome, the risk allele group exhibited reduced global and local efficiency of white matter structural networks, mainly in the left anterior and posterior cingulate cortices (PCC). Importantly, the efficiency of the left PCC is correlated with the impaired attention function and mediates the impacts of the rs405509 genotype on attention. These results demonstrated that the rs405509 polymorphism affects attention function in nondemented elderly people, possibly by modulating brain structural connectivity of the PCC. This polymorphism may help us to understand the neural mechanisms of cognitive aging and to serve as a potential marker assessing the risk of AD.

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

    Science.gov (United States)

    Bindel, Thomas H.

    2008-01-01

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

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

    Science.gov (United States)

    Bindel, Thomas H.

    2008-01-01

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

  13. Crystal Structure of Borophosphate with 61 Screw Axis Helices

    Institute of Scientific and Technical Information of China (English)

    石恒真; 单永奎; 戴立益; 刘煜炎; 翁林红

    2003-01-01

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

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

    Indian Academy of Sciences (India)

    M P BINITHA; P P PRADYUMNAN

    2017-09-01

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

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

    Science.gov (United States)

    Fortes, A Dominic; Suard, Emmanuelle

    2011-12-21

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

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

    Science.gov (United States)

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

    2015-11-30

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

  17. Crystal structure of Homo sapiens protein LOC79017

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-02-08

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

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

    Science.gov (United States)

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

    2010-01-13

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

  19. Patterns of DNA structural polymorphism and their evolutionary implications.

    Science.gov (United States)

    Keene, M A; Elgin, S C

    1984-01-01

    The pattern of sites within purified DNA that are highly susceptible to double-stranded cleavage by micrococcal nuclease has been analyzed in the vicinity of over 20 genes from widely separated loci in Drosophila. These genes have uniformly exhibited a distinctive organization of cleavage sites such that at early times of digestion major sites are observed in the spacer regions surrounding the genes, but not within the protein coding regions themselves. Examples examined include Drosophila genes for heat-shock proteins, cytoplasmic actin, ribosomal protein 49, alcohol dehydrogenase, Sgs 4 glue protein, and other developmentally regulated transcripts, a human beta-globin gene, and mouse alpha 3-globin pseudogene. It seems probable that this gene/spacer pattern will be a general one in the genomes of eucaryotes, but not in the genomes of procaryotes, since neither pBR322 nor phage lambda DNA display such a pattern. One observes a nonrandom spacing of strong cleavage sites in Drosophila DNA, with the most frequent intervals being 195 bp and 411 bp. Such a pattern of variation in DNA structure may have evolved to facilitate the packaging of eucaryotic DNA into chromatin.

  20. Crystal structure of Ca5Nb5O17

    Science.gov (United States)

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

    2005-09-01

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