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Sample records for crystal structure weak

  1. Weak crystallization theory of metallic alloys

    Science.gov (United States)

    Martin, Ivar; Gopalakrishnan, Sarang; Demler, Eugene A.

    2016-06-01

    Crystallization is one of the most familiar, but hardest to analyze, phase transitions. The principal reason is that crystallization typically occurs via a strongly first-order phase transition, and thus rigorous treatment would require comparing energies of an infinite number of possible crystalline states with the energy of liquid. A great simplification occurs when crystallization transition happens to be weakly first order. In this case, weak crystallization theory, based on unbiased Ginzburg-Landau expansion, can be applied. Even beyond its strict range of validity, it has been a useful qualitative tool for understanding crystallization. In its standard form, however, weak crystallization theory cannot explain the existence of a majority of observed crystalline and quasicrystalline states. Here we extend the weak crystallization theory to the case of metallic alloys. We identify a singular effect of itinerant electrons on the form of weak crystallization free energy. It is geometric in nature, generating strong dependence of free energy on the angles between ordering wave vectors of ionic density. That leads to stabilization of fcc, rhombohedral, and icosahedral quasicrystalline (iQC) phases, which are absent in the generic theory with only local interactions. As an application, we find the condition for stability of iQC that is consistent with the Hume-Rothery rules known empirically for the majority of stable iQC; namely, the length of the primary Bragg-peak wave vector is approximately equal to the diameter of the Fermi sphere.

  2. Weak Ferromagnetism below 41 K and Structural Transition at 395 K in CeIr3B2 Single Crystal

    Science.gov (United States)

    Kubota, Kazuhiro; Matsuoka, Eiichi; Funasako, Yusuke; Mochida, Tomoyuki; Sakurai, Takahiro; Ohta, Hitoshi; Onimaru, Takahiro; Takabatake, Toshiro; Sugawara, Hitoshi

    2013-10-01

    We report on the discovery of ferromagnetic behavior below TC = 41 K in CeIr3B2 single crystals by means of magnetization, electrical resistivity, and specific heat measurements. The ferromagnetic transition temperature is unusually high despite the lack of magnetic elements except Ce, which is the second highest transition temperature recorded after CeRh3B2 (TC˜ 120 K). The ferromagnetic ordered moment is estimated to be μs˜ 0.04 μB/Ce at 1.8 K, which lies in the c-plane of a monoclinic crystal structure. A structural phase transition from monoclinic to hexagonal occurs approximately at 395 K upon heating. The similarity and difference in physical properties between CeIr3B2 and CeRh3B2 are discussed.

  3. Planar versus non-planar: The important role of weak C—H...O hydrogen bonds in the crystal structure of 5-methylsalicylaldehyde

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    Ulrich Baisch

    2017-02-01

    Full Text Available The crystal structure of 5-methylsalicylaldehyde (5-MSA; systematic name 2-hydroxy-5-methylbenzaldehyde, C8H8O2, was discovered to be a textbook example of the drastic structural changes caused by just a few weak C—H...O interactions due to the additional methylation of the aromatic ring compared to salicylaldehyde SA. This weak intermolecular hydrogen bonding is observed between aromatic or methyl carbon donor atoms and hydroxyl or aldehyde acceptor oxygen atoms with d(D...A = 3.4801 (18 and 3.499 (11 Å. The molecule shows a distorted geometry of the aromatic ring with elongated bonds in the vicinity of substituted aldehyde and hydroxyl carbon atoms. The methyl hydrogen atoms are disordered over two sets of sites with occupancies of 0.69 (2 and 0.31 (2.

  4. Evidence for weakly bound electrons in non-irradiated alkane crystals. The electrons as a probe of structural differences in crystals

    CERN Document Server

    Pietrow, M; Misiak, L E; Kornarzynski, K; Szurkowski, J; Rochowski, P; Grzegorczyk, M

    2014-01-01

    It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents an evidence for the presence of these electrons in non-irradiated samples of docosane. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. The electrons from the former ones are bound more weakly than those from the latter ones. The origin of Vis absorption for the samples is explained. These spectra can be used as a probe indicating differences in the solid structures of hydrocarbons.

  5. Synthesis, Crystal Structure and Luminescent Property of a Novel Pt(II) Complex with Weak Metal-metal Interaction

    Institute of Scientific and Technical Information of China (English)

    YUE Cheng-Yang; JIANG Fei-Long; FENG Rui; HONG Mao-Chun

    2008-01-01

    The title complex cis-bis(tetrahydrothiophene)-bis(nitrate) platinum(II), (tht)2Pt(NO3)2, was the reducing product from potassium hexachloroplatinate(IV) K2PtCl6 where the platinum is tetra-valenced. Crystal data for C8H16N2O6PtS2: monoclinic, space group P21/c, a = 9.8833(5), b = 8.6744(4), c = 18.6407(9) (A), β = 114.401(3)°, V = 1455.35(12) (A)3, Z = 4, Mr = 495.44, Dc = 2.261 g/cm3, F(000) = 944, μ = 9.950 mm-1, λ(MoKα) = 0.71073 (A), T = 293(2) K, 2θmax = 54.96o, GOOF = 1.033, R = 0.0350 and wR = 0.0785 for 2572 observed reflections with I > 2σ(I). X-ray diffraction studies reveal that the title complex has interesting weak metal-metal interactions and two molecules linked by metal-metal interaction exist as a group. Luminescent spectrum illuminates red emission of the complex at room temperature.

  6. Landau Weak Crystallization Theory and its Applications

    Science.gov (United States)

    Kats, E. I.

    Aim of this lecture is to explain main features and ingredients of weak first order phase transitions between liquid-like (uniform in space) and solid-like (non-uniform with characteristic wave vector q0) states. We illustrate how this theory (traditionally termed as Landau weak crystallization theory) works. We consider two examples describing universal temperature dependence of shear viscosity in liquids, and so-called main phase transition in membranes. Our results are in a good qualitative agreement with experimental data, offering a deeper understanding of this kind of phase transitions. We discuss also why and where predicted universal effects can be masked.

  7. Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals

    Energy Technology Data Exchange (ETDEWEB)

    Pietrow, M., E-mail: mrk@kft.umcs.lublin.pl; Misiak, L. E. [Institute of Physics, M. Curie-Skłodowska University, ul. Pl. M. Curie-Skłodowskiej 1, 20-031 Lublin (Poland); Gagoś, M. [Department of Cell Biology, Institute of Biology and Biochemistry, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin (Poland); Kornarzyński, K. [Department of Physics, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin (Poland); Szurkowski, J.; Grzegorczyk, M. [Institute of Experimental Physics, University of Gdańsk, Wita Stwosza 57, 80-952 Gdańsk (Poland); Rochowski, P. [Institute of Experimental Physics, University of Gdańsk, Wita Stwosza 57, 80-952 Gdańsk (Poland); Pomeranian University in Słupsk, Arciszewskiego 22b, 76-200 Słupsk (Poland)

    2015-02-14

    It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra can be used as a probe indicating differences in the solid structures of hydrocarbons.

  8. X-Ray Crystal Structure and Properties of Phanta, a Weakly Fluorescent Photochromic GFP-Like Protein.

    Directory of Open Access Journals (Sweden)

    Craig Don Paul

    Full Text Available Phanta is a reversibly photoswitching chromoprotein (ΦF, 0.003, useful for pcFRET, that was isolated from a mutagenesis screen of the bright green fluorescent eCGP123 (ΦF, 0.8. We have investigated the contribution of substitutions at positions His193, Thr69 and Gln62, individually and in combination, to the optical properties of Phanta. Single amino acid substitutions at position 193 resulted in proteins with very low ΦF, indicating the importance of this position in controlling the fluorescence efficiency of the variant proteins. The substitution Thr69Val in Phanta was important for supressing the formation of a protonated chromophore species observed in some His193 substituted variants, whereas the substitution Gln62Met did not significantly contribute to the useful optical properties of Phanta. X-ray crystal structures for Phanta (2.3 Å, eCGP123T69V (2.0 Å and eCGP123H193Q (2.2 Å in their non-photoswitched state were determined, revealing the presence of a cis-coplanar chromophore. We conclude that changes in the hydrogen-bonding network supporting the cis-chromophore, and its contacts with the surrounding protein matrix, are responsible for the low fluorescence emission of eCGP123 variants containing a His193 substitution.

  9. X-Ray Crystal Structure and Properties of Phanta, a Weakly Fluorescent Photochromic GFP-Like Protein.

    Science.gov (United States)

    Don Paul, Craig; Traore, Daouda A K; Olsen, Seth; Devenish, Rodney J; Close, Devin W; Bell, Toby D M; Bradbury, Andrew; Wilce, Matthew C J; Prescott, Mark

    2015-01-01

    Phanta is a reversibly photoswitching chromoprotein (ΦF, 0.003), useful for pcFRET, that was isolated from a mutagenesis screen of the bright green fluorescent eCGP123 (ΦF, 0.8). We have investigated the contribution of substitutions at positions His193, Thr69 and Gln62, individually and in combination, to the optical properties of Phanta. Single amino acid substitutions at position 193 resulted in proteins with very low ΦF, indicating the importance of this position in controlling the fluorescence efficiency of the variant proteins. The substitution Thr69Val in Phanta was important for supressing the formation of a protonated chromophore species observed in some His193 substituted variants, whereas the substitution Gln62Met did not significantly contribute to the useful optical properties of Phanta. X-ray crystal structures for Phanta (2.3 Å), eCGP123T69V (2.0 Å) and eCGP123H193Q (2.2 Å) in their non-photoswitched state were determined, revealing the presence of a cis-coplanar chromophore. We conclude that changes in the hydrogen-bonding network supporting the cis-chromophore, and its contacts with the surrounding protein matrix, are responsible for the low fluorescence emission of eCGP123 variants containing a His193 substitution.

  10. The cohomology group of weak entwining structure

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In this paper, we reveal that a weak entwining structure admits a rich cohomology theory. As an application we compute the cohomology of a weak entwining structure associated to a weak coalgebra-Galois extension.

  11. Engineering molecular crystals with abnormally weak cohesion.

    Science.gov (United States)

    Maly, Kenneth E; Gagnon, Eric; Wuest, James D

    2011-05-14

    Adding astutely placed methyl groups to hexaphenylbenzene increases molecular weight but simultaneously weakens key C-H···π interactions, thereby leading to decreased enthalpies of sublimation and showing that materials with abnormally weak cohesion can be made by identifying and then obstructing interactions that help control association.

  12. 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.

  13. 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.

  14. Strong Connections and Invertible Weak Entwining Structures

    Institute of Scientific and Technical Information of China (English)

    J.N.ALONSO (A)LVAREZ; J.M.FERN(A)NDEZ VILABOA; R.GONZ(A)LEZ RODR(I)GUEZ

    2012-01-01

    In this paper we obtain a criterion under which the bijectivity of the canonical morphism of a weak Galois extension associated to a weak invertible entwining structure is equivalent to the existence of a strong connection form.Also we obtain an explicit formula for a strong connection under equivariant projective conditions or under coseparability conditions.

  15. 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.

  16. Structural features of sequential weak measurements

    Science.gov (United States)

    Diósi, Lajos

    2016-07-01

    We discuss the abstract structure of sequential weak measurement (WM) of general observables. In all orders, the sequential WM correlations without postselection yield the corresponding correlations of the Wigner function, offering direct quantum tomography through the moments of the canonical variables. Correlations in spin-1/2 sequential weak measurements coincide with those in strong measurements, they are constrained kinematically, and they are equivalent with single measurements. In sequential WMs with postselection, an anomaly occurs, different from the weak value anomaly of single WMs. In particular, the spread of polarization σ ̂ as measured in double WMs of σ ̂ will diverge for certain orthogonal pre- and postselected states.

  17. Higgs Boson Production and Weak Boson Structure

    OpenAIRE

    1995-01-01

    The influence of the QCD structure of the weak bosons on the Higgs boson production in $e$-$p$ scattering is studied. The energy and Higgs boson mass dependence of the cross-section, following from the new contributions, is calculated.

  18. 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...

  19. 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.

  20. 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.

  1. Strong eukaryotic IRESs have weak secondary structure.

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    Xuhua Xia

    Full Text Available BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. CONCLUSIONS: We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5'-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.

  2. Crystal structure of nuarimol

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    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.

  3. Crystal structure of pymetrozine

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    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.

  4. 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.)

  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. 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.

  7. Crystal structure of ruthenocenecarbonitrile

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    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.

  8. Elastic Wave Propagation in Two-Dimensional Ordered and Weakly Disordered Phononic Crystals

    Institute of Scientific and Technical Information of China (English)

    YUAN Zuo-Dong; CHENG Jian-Chun

    2005-01-01

    @@ Elastic wave propagation in two-dimensional solid-solid ordered and weakly disordered phononic crystals is studied by using finite-difference time-domain method.Theoretical results show that obvious band gaps in the ordered crystal could be found, while in the weakly disordered ones the band gaps could partially vanish.Furthermore,with increase of disorder, band gaps are destructed badly and prominently in the high frequency regime while slightly in the low regime.Comparing the energy transmission dependent on time, we find that the coda wave phenomenon is prominent in the ordered crystal while weakened in the weakly disordered ones, and the physical properties are discussed.

  9. Structures of cyano-biphenyl liquid crystals

    Science.gov (United States)

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

    1989-01-01

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

  10. 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.

  11. Crystal structure of fipronil

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    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.

  12. Crystal Structures of New Ammonium 5-Aminotetrazolates

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    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.

  13. 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...

  14. 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.

  15. 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

  16. 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)

  17. 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.

  18. Nuclear Dependence in Weak Structure Functions and the Determination of Weak Mixing Angle

    CERN Document Server

    Athar, M Sajjad; Simo, I Ruiz; Vacas, M J Vicente

    2013-01-01

    We have studied nuclear medium effects in the weak structure functions $F^A_2(x)$ and $F^A_3(x)$ and in the extraction of weak mixing angle using Paschos Wolfenstein(PW) relation. We have modified the PW relation for nonisoscalar nuclear target. We have incorporated the medium effects like Pauli blocking, Fermi motion, nuclear binding energy, nucleon correlations, pion $\\&$ rho cloud contributions, and shadowing and antishadowing effects.

  19. Algebraic structure and Poisson method for a weakly nonholonomic system

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The algebraic structure and the Poisson method for a weakly nonholonomic system are studied.The differential equations of motion of the system can be written in a contravariant algebra form and its algebraic structure is discussed.The Poisson theory for the systems which possess Lie algebra structure is generalized to the weakly nonholonomic system.An example is given to illustrate the application of the result.

  20. 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

  1. 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.

  2. The SAMPLE Experiment and Weak Nucleon Structure

    CERN Document Server

    Beise, E J; Spayde, D T

    2004-01-01

    One of the key elements to understanding the structure of the nucleon is the role of its quark-antiquark sea in its ground state properties such as charge, mass, magnetism and spin. In the last decade, parity-violating electron scattering has emerged as an important tool in this area, because of its ability to isolate the contribution of strange quark-antiquark pairs to the nucleon's charge and magnetism. The SAMPLE experiment at the MIT-Bates Laboratory, which has been focused on s-sbar contributions to the proton's magnetic moment, was the first of such experiments and its program has recently been completed. In this paper we give an overview of some of the experimental aspects of parity-violating electron scattering, briefly review the theoretical predictions for strange quark form factors, summarize the SAMPLE measurements, and place them in context with the program of experiments being carried out at other electron scattering facilities such as Jefferson Laboratory and the Mainz Microtron.

  3. 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.

  4. 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.

  5. 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.

  6. Small-core photonic crystal fibres with weakly disordered air-hole cladding

    DEFF Research Database (Denmark)

    Mortensen, Niels Asger; Nielsen, Martin Dybendal; Folkenberg, Jacob Riis;

    2004-01-01

    Motivated by recent experimental work by Folkenberg et al (2003 Opt. Lett. 28 1882–4) we consider the effect of weak disorder in the air-hole lattice of small-core photonic crystal fibres. We find that the broken symmetry leads to higher-order modes which have generic intensity distributions rese...

  7. 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.

  8. 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.

  9. Subharmonic energy-gap structure in superconducting weak links

    DEFF Research Database (Denmark)

    Flensberg, K.; Hansen, Jørn Bindslev; Octavio, M.

    1988-01-01

    We present corrected calculations of the subharmonic energy-gap structure using the model of Octavio, Tinkham, Blonder, and Klapwijk, which includes the effect of normal scattering in the weak link. We show that while the overall predictions of this model do not change qualitatively, the details ...

  10. Magnetic-Field-Induced Weak Order in Nematic Liquid Crystals Formed by Biaxial Molecules

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhi-Dong; ZHANG De-Xian; SUN Yu-Bao

    2000-01-01

    Nematic liquid crystal system of interacting biaxial particles via dispersion forces is studied. The molecular orienting potential form in a magnetic field is given for the first time. Weakly ordered isotropic phase is treated in the two-particle cluster approximation. Taking account of the molecular biaxiality, it is found that the ratio of the lowest supercooling temperature T* to the nematic-isotropic phase transition temperature TC approaches the observed value, and the validity of the mean field theory is clarified.

  11. Origin of weak ferroelectricity in semiconductive Sb2S3 crystal

    Science.gov (United States)

    Žigas, Leonardas; Audzijonis, Algirdas; Grigas, Jonas

    2017-02-01

    The paper presents the results of the investigations of electronic potential dependencies upon the normal co-ordinates of B1u mode in a large temperature range for the Sb2S3 crystal. The results revealed high anharmonicity of Sb and S atoms in this highly covalent semiconductive compound and B1u - mode polar distortion with temperature leading to appearance of weak ferroelectricity.

  12. Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

    Science.gov (United States)

    Prasanna, M. D.; Row, T. N. Guru

    2001-05-01

    The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

  13. 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.

  14. Electric-field-induced weakly chaotic transients in ferroelectric liquid crystals

    Science.gov (United States)

    Śliwa, I.; JeŻewski, W.; Kuczyński, W.

    2016-01-01

    Nonlinear dynamics induced in surface stabilized ferroelectric liquid crystals by strong alternating external electric fields is studied both theoretically and experimentally. As has already been shown, molecular reorientations induced by sufficiently strong fields of high-enough frequencies can reveal a long transient behavior that has a weakly chaotic character. The resulting complex dynamics of ferroelectric liquid crystals can be considered not only as a consequence of irregular motions of particular molecules but also as a repercussion of a surface-enforced partial decorrelation of nonlinear molecular motions within smectic layers. To achieve more insight into the nature of this phenomenon and to show that the underlying complex field-induced behavior of smectic liquid crystals is not exceptional, ranges of system parameters for which the chaotic behavior occurs are determined. It is proved that there exists a large enough set of initial phase trajectory points, for which weakly chaotic long-time transitory phenomena occur, and, thereby, it is demonstrated that such a chaotic behavior can be regarded as being typical for strongly field-driven thin liquid crystal systems. Additionally, the influence of low-amplitude random noise on the duration of the transient processes is numerically studied. The strongly nonlinear contribution to the electro-optic response, experimentally determined for liquid crystal samples at frequencies lower than the actual field frequency, is also analyzed for long-time signal sequences. Using a statistical approach to distinguish numerically response signals of samples from noise generated by measuring devices, it is shown that the distribution of sample signals distinctly differs from the device noise. This evidently corroborates the occurrence of the nonlinear low-frequency effect, found earlier for different surface stabilized liquid crystal samples.

  15. Electric-field-induced weakly chaotic transients in ferroelectric liquid crystals.

    Science.gov (United States)

    Śliwa, I; Jeżewski, W; Kuczyński, W

    2016-01-01

    Nonlinear dynamics induced in surface stabilized ferroelectric liquid crystals by strong alternating external electric fields is studied both theoretically and experimentally. As has already been shown, molecular reorientations induced by sufficiently strong fields of high-enough frequencies can reveal a long transient behavior that has a weakly chaotic character. The resulting complex dynamics of ferroelectric liquid crystals can be considered not only as a consequence of irregular motions of particular molecules but also as a repercussion of a surface-enforced partial decorrelation of nonlinear molecular motions within smectic layers. To achieve more insight into the nature of this phenomenon and to show that the underlying complex field-induced behavior of smectic liquid crystals is not exceptional, ranges of system parameters for which the chaotic behavior occurs are determined. It is proved that there exists a large enough set of initial phase trajectory points, for which weakly chaotic long-time transitory phenomena occur, and, thereby, it is demonstrated that such a chaotic behavior can be regarded as being typical for strongly field-driven thin liquid crystal systems. Additionally, the influence of low-amplitude random noise on the duration of the transient processes is numerically studied. The strongly nonlinear contribution to the electro-optic response, experimentally determined for liquid crystal samples at frequencies lower than the actual field frequency, is also analyzed for long-time signal sequences. Using a statistical approach to distinguish numerically response signals of samples from noise generated by measuring devices, it is shown that the distribution of sample signals distinctly differs from the device noise. This evidently corroborates the occurrence of the nonlinear low-frequency effect, found earlier for different surface stabilized liquid crystal samples.

  16. 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...

  17. EM vs Weak Structure Functions in DIS processes

    CERN Document Server

    Athar, M Sajjad; Simo, I Ruiz; Vacas, M J Vicente

    2013-01-01

    We obatin the ratio $F_i^A/F_i^{D}$(i=2,3, A=Be, C, Fe, Pb; D=Deuteron) in the case of weak and electromagnetic nuclear structure functions. For this, relativistic nuclear spectral function which incorporate the effects of Fermi motion, binding and nucleon correlations is used. We also consider the pion and rho meson cloud contributions and shadowing and antishadowing effects.

  18. Modulated magnetic phase of structurally heterogeneous easy-plane weak ferromagnets

    Science.gov (United States)

    Dzhuraev, D. R.; Niyazov, L. N.; Sokolov, B. Yu.

    2016-06-01

    The modulated magnetic phase of a structurally heterogeneous easy-plane weak ferromagnet is considered in terms of the thermodynamic Landau theory of phase transitions. The temperature and field dependences of the main magnetic order modulation parameters are determined. The results obtained are compared with the experimental data obtained for the orientational phase transition into a modulated magnetic state that occurs in hematite and iron borate crystals doped with diamagnetic ions to create structural heterogeneity. The proposed theoretical model is shown to describe the entire set of experimental results consistently with some exceptions.

  19. 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.

  20. 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.

  1. Weak first-order orientational transition in the Lebwohl-Lasher model for liquid crystals

    DEFF Research Database (Denmark)

    Zhang, Zhengping; Mouritsen, Ole G.; Zuckermann, Martin J.

    1992-01-01

    The nature of the orientational phase transition in the three-dimensional Lebwohl-Lasher model of liquid crystals has been studied by computer simulation using reweighting techniques and finite-size scaling analysis. Unambiguous numerical evidence is found in favor of a weak first-order transition...... and the presence of pseudospinodal points, T±*, which are extremely close to the equilibrium transition temperature, ‖Tc-T±*‖/Tc≲0.5×10-3, in good agreement with experimental data for the nematic-isotropic transition....

  2. Different supramolecular architectures mediated by different weak interactions in the crystals of three N-aryl-2,5-dimethoxybenzenesulfonamides.

    Science.gov (United States)

    Shakuntala, K; Naveen, S; Lokanath, N K; Suchetan, P A; Abdoh, M

    2017-10-01

    The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N-aryl-2,5-dimethoxybenzenesulfonamides, namely N-(2,3-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (I), N-(2,4-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (II), and N-(2,4-dimethylphenyl)-2,5-dimethoxybenzenesulfonamide, C16H19NO4S, (III), are described. The asymmetric unit of (I) consists of two symmetry-independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C-H...O interactions in (I), N-H...Cl and C-H...O interactions in (II), and C-H...O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C-H...O, C-H...Cl, C-H...π(aryl), π(aryl)-π(aryl) and Cl...Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The dnorm and shape-index surfaces of (I)-(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H...H contacts, followed by H...O/O...H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N-H...O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N-H...O hydrogen bonds form either C(4) chain motifs or R2(2)(8) rings. Further comparison reveals that the characteristics of the N-H...O hydrogen-bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Crystal structures of five 6-mercaptopurine derivatives

    Directory of Open Access Journals (Sweden)

    Lígia R. Gomes

    2016-03-01

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

  9. A-dependence of weak nuclear structure functions

    Energy Technology Data Exchange (ETDEWEB)

    Haider, H.; Athar, M. Sajjad [Department of Physics, Aligarh Muslim University, Aligarh-202 002 (India); Simo, I. Ruiz [Dipartimento di Fisica, Universitá degli studi di Trento Via Sommarive 14, Povo (Trento) I-38123 (Italy)

    2015-05-15

    Effect of nuclear medium on the weak structure functions F{sub 2}{sup A}(x, Q{sup 2}) and F{sub 3}{sup A}(x, Q{sup 2}) have been studied using charged current (anti)neutrino deep inelastic scattering on various nuclear targets. Relativistic nuclear spectral function which incorporate Fermi motion, binding and nucleon correlations are used for the calculations. We also consider the pion and rho meson cloud contributions calculated from a microscopic model for meson-nucleus self-energies. Using these structure functions, F{sub i}{sup A}/F{sub i}{sup proton} and F{sub i}{sup A}/F{sub i}{sup deuteron}(i=2,3, A={sup 12}C, {sup 16}O, CH and H{sub 2}O) are obtained.

  10. 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.

  11. THE CRYSTAL STRUCTURE OF ALPHA-DIMETHYLTELLURIUM DICHLORIDE,

    Science.gov (United States)

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

  12. Pinning features of the magnetic flux trapped by YBCO single crystals in weak constant magnetic fields

    Science.gov (United States)

    Monarkha, V. Yu.; Paschenko, V. A.; Timofeev, V. P.

    2013-02-01

    The dynamics of Abrikosov vortices and their bundles was experimentally investigated in weak constant magnetic fields, in the range of Earth's magnetic field. Characteristics of the isothermal magnetization relaxation in YBCO single-crystal samples with strong pinning centers were studied for different sample-field orientation. The obtained values of normalized relaxation rate S allowed us to estimate the effective pinning potential U in the bulk of the YBCO sample and its temperature dependence, as well as the critical current density Jc. A comparison between the data obtained and the results of similar measurements in significantly higher magnetic fields was performed. To compare different techniques for evaluation of Jc, the magnetization loop measurements M(H), which relate the loop width to the critical current, were carried out. These measurements provided important parameters of the samples under study (penetration field Hp and first critical field Hc1), which involve the geometrical configuration of the samples.

  13. Weak Anchoring and Surface Elasticity Effects in Electroosmotic Flow of Nematic Liquid Crystals Through Narrow Confinements

    CERN Document Server

    Poddar, Antarip; Chakraborty, Suman

    2016-01-01

    Advent of nematic liquid crystals flows have attracted renewed attention in view of microfluidic transport phenomena. Among various transport processes, electroosmosis stands as one of the efficient flow actuation method through narrow confinement. In the present study, we explore the electrically actuated flow of a nematic fluid with ionic inclusions taking into account the influences from surface induced elastic and electrical double layer phenomena. Influence of surface effects on the flow characteristics is known to get augmented in micro-confined environment and must be properly addressed. Towards this, we devise the coupled flow governing equations from fundamental free energy analysis considering the contributions from first and second-order elastic, dielectric, flexoelectric, ionic and entropic energies. We have further considered weak anchoring surface conditions with second order elasticity which helps us to more accurately capture the director deformations along the boundaries. The present study fo...

  14. Crystal Structure of Isoquinoline Derivatives

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  15. Crystal structure of 2-pentyloxybenzamide

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2014-10-01

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

  16. Method of fabricating patterned crystal structures

    KAUST Repository

    Yu, Liyang

    2016-12-15

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

  17. 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.

  18. Milliarcsecond radio structure of weak-lined T Tauri stars

    Science.gov (United States)

    Phillips, R. B.; Lonsdale, C. J.; Feigelson, E. D.

    1991-01-01

    VLBI and VLA observations of six radio-bright weak-lined T Taur (WTT) stars are reported, as well as direct measurements of the sizes of the emitting regions. VLBI measurements established that essentially all the radio emission from these premain-sequence stars originates in regions 15 stellar radii or less in size. Corresponding brightness temperatures ranged from 10 exp 7.5 to not less than 10 exp 9 K, ruling out a thermal process such as free-free bremsstrahlung radiation from a circumstellar wind. The radio luminosity and structure of several stars changed significantly between measurements separated by 1 day. HD 283447 showed intraday radio variability on time scales as short as 1 hr. Corresponding VLBI measurements show a new unresolved component appearing after an increase in flux density, possibly indicating that the driving agent for larger radio flares originates close to the star. The high conformation rate of nonthermal radio emission from this initial sample of radio-bright WTT stars show that these solar-type premain-sequence stars alter their immediate environments via magnetic processes to an extent comparable to that shown by RS CVn or Algol close binaries.

  19. 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.

  20. 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.

  1. 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

  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. Electro-osmosis of nematic liquid crystals under weak anchoring and second-order surface effects

    Science.gov (United States)

    Poddar, Antarip; Dhar, Jayabrata; Chakraborty, Suman

    2017-07-01

    Advent of nematic liquid crystal flows has attracted renewed attention in view of microfluidic transport phenomena. Among various transport processes, electro-osmosis stands as one of the efficient flow actuation mechanisms through narrow confinements. In the present study, we explore the electrically actuated flow of an ordered nematic fluid with ionic inclusions, taking into account the influences from surface-induced elasticity and electrical double layer (EDL) phenomena. Toward this, we devise the coupled flow governing equations from fundamental free-energy analysis, considering the contributions from first- and second-order elastic, dielectric, flexoelectric, charged surface polarization, ionic and entropic energies. The present study focuses on the influence of surface charge and elasticity effects in the resulting linear electro-osmosis through a slit-type microchannel whose surfaces are chemically treated to display a homeotropic-type weak anchoring state. An optical periodic stripe configuration of the nematic director has been observed, especially for higher electric fields, wherein the Ericksen number for the dynamic study is restricted to the order of unity. Contrary to the isotropic electrolytes, the EDL potential in this case was found to be dependent on the external field strength. Through a systematic investigation, we brought out the fact that the wavelength of the oscillating patterns is dictated mainly by the external field, while the amplitude depends on most of the physical variables ranging from the anchoring strength and the flexoelectric coefficients to the surface charge density and electrical double layer thickness.

  4. Nucleation and structural growth of cluster crystals

    CERN Document Server

    Leitold, Christian

    2016-01-01

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

  5. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

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

  6. Structure of 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.

  7. Crystal Structure of Macrocalyxin J

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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...

  14. Crystal structure of N,N-dimethyl-2-[(4-methylbenzylsulfonyl]ethanamine

    Directory of Open Access Journals (Sweden)

    Alan R. Kennedy

    2015-07-01

    Full Text Available In the crystal, the title compound, C12H19NO2S, has a disordered structure with two equally populated conformations of the amine fragment. A pair of weak C—H...O intermolecular interactions between the CH2 and SO2 groups gives a one-dimensional supramolecular structure that propagates through translation along the a-axis direction.

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Modular crystals as modulated structures

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  3. Analogical Reasoning as a Decision Support Principle for Weakly-Structured Marketing Problems

    NARCIS (Netherlands)

    N.A.P. Althuizen (Niek)

    2006-01-01

    textabstractMany marketing problems are weakly-structured. From the psychological literature, we know that analogical reasoning is an effective problem-solving method in weakly-structured decision situations. That is, when confronted with such a problem, one of the first things managers will natural

  4. 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.

  5. A research of weak absorption measurements in crystal based on photothermal interferometry

    Science.gov (United States)

    Chen, Bing; Liu, Zongkai; Wang, Shiwu

    2013-07-01

    It is important for testing the process of crystal growing and crystal quality. This paper built a mathematical model based on principle of photothermal common-path interferometry, the index change induced in the crystal by the heating pump beam and the phase distortion of probe beam in the heated area are presented then obtain the intensity distribution of the interference in the near filed. Optical geometry of focusing pump beam and intersecting pump and probe beams at waist position of the pump beam is used. This optical instruction can be adjusted easily and stabilized. Now CRYSTECH have the largest NLO crystals product line in the world, especially KTP crystals. With absorption measurements in nonlinear laser crystal KTP as an example to investigate the experimental parameters affecting the photothermal interference signal and high measuring precision. The analysis of experimental data showed this kind of instruction can reach the measurement accuracy of 0.1ppm.

  6. 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.

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

    Science.gov (United States)

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

    2015-11-19

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

  8. 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.

  9. 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...

  10. 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...

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Universal homogeneous constraint structures and the hom-equivalence classes of weakly oligomorphic structures

    CERN Document Server

    Pech, Christian

    2012-01-01

    We derive a new sufficient condition for the existence of {\\omega}-categorical universal structures in classes of relational structures with constraints, augmenting results by Cherlin, Shelah, Chi, and Hubi\\v{c}ka and Ne\\v{s}et\\v{r}il. Using this result we show that the hom-equivalence class of any countable weakly oligomorphic structure has up to isomorphism a unique model-complete smallest and greatest element, both of which are {\\omega}-categorical. As the main tool we introduce the category of constraint structures, show the existence of universal homogeneous objects, and study their automorphism groups. All constructions rest on a category-theoretic version of Fra\\"iss\\'e's Theorem due to Droste and G\\"obel. We derive sufficient conditions for a comma category to contain a universal homogeneous object. This research is motivated by the observation that all countable models of the theory of a weakly oligomorphic structure are hom-equivalent---a result akin to (part of) the Ryll-Nardzewski Theorem.

  18. 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.

  19. 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...

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

    Directory of Open Access Journals (Sweden)

    Hasna Yassine

    2015-10-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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'.

  6. Magnetoresistive study of the antiferromagnetic-weak ferromagnetic transition in single-crystal La2CuO4+δ

    Science.gov (United States)

    Belevtsev, B. I.; Dalakova, N. V.; Savitsky, V. N.; Panfilov, A. S.; Braude, I. S.; Bondarenko, A. V.

    2004-05-01

    Resistive measurements were made to study the magnetic field-induced antiferromagnetic (AF)—weak ferromagnetic (WF) transition in the La2CuO4 single crystal. The magnetic field (dc or pulsed) was applied normally to the CuO2 layers. The transition manifested itself in a drastic decrease of the resistance in critical fields of 5-7 T. The study is the first to display the effect of the AF-WF transition on the conductivity of the La2CuO4 single crystal in the direction parallel to the CuO2 layers. The results provide support for the three-dimensional nature of the hopping conduction of this layered oxide.

  7. Comparison of thermomagnetic history effects in weakly pinned single crystals of 3Rh4Sn13(R=Yb, Ca)

    Indian Academy of Sciences (India)

    S Sarkar; S Ramakrishnan; A K Grover; C V Tomy; G Balakrishnan; D McK Paul

    2002-05-01

    A comparative study of the thermomagnetic memory effects of c in two weakly pinned low c superconductors, Ca3Rh4Sn13 (CaRhSn) and Yb3Rh4Sn13 (YbRhSn), is presented. In both the systems, the peak effect (PE) phenomenon appears as an order–disorder transformation through stepwise amorphization of the flux line lattice (FLL). However, in CaRhSn, we can witness another disorder-driven transition (Bragg glass (BG) to a vortex glass (VG)) in a distinct manner as in a single crystal of high c YBa2Cu3O7- for $H||c$.

  8. Orientational instabilities in nematic liquid crystals with weak anchoring under combined action of steady flow and external fields.

    Science.gov (United States)

    Nasibullayev, I Sh; Tarasov, O S; Krekhov, A P; Kramer, L

    2005-11-01

    We study the homogeneous and the spatially periodic instabilities in a nematic liquid crystal layer subjected to steady plane Couette or Poiseuille flow. The initial director orientation is perpendicular to the flow plane. Weak anchoring at the confining plates and the influence of the external electric and/or magnetic field are taken into account. Approximate expressions for the critical shear rate are presented and compared with semianalytical solutions in case of Couette flow and numerical solutions of the full set of nematodynamic equations for Poiseuille flow. In particular the dependence of the type of instability and the threshold on the azimuthal and the polar anchoring strength and external fields is analyzed.

  9. 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.

  10. 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)

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

    Indian Academy of Sciences (India)

    Okram Mukherjee Singh; Laishram Ronibala Devi; Neeladri Das

    2013-09-01

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

  12. Method and apparatus for evaluating structural weakness in polymer matrix composites

    Science.gov (United States)

    Wachter, E.A.; Fisher, W.G.

    1996-01-09

    A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image. 6 figs.

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

    Science.gov (United States)

    Clark, Noel A.

    2000-01-01

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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Crystal structure of 2,5-dimethylanilinium salicylate

    Directory of Open Access Journals (Sweden)

    A. Mani

    2015-09-01

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

  1. 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.

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

    Science.gov (United States)

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

    2014-09-01

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

  3. 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...

  4. 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.

  5. 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.

  6. [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.

  7. 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].

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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).

  13. Structure and Dynamics of Freely Suspended Liquid Crystals

    Science.gov (United States)

    Clark, Noel A.

    2004-01-01

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

  14. Critical points in the Bragg glass phase of a weakly pinned crystal of Ca3Rh4Sn13

    Indian Academy of Sciences (India)

    S Sarkar; A D Thakur; C V Tomy; G Balakrishnan; D McK Paul; S Ramakrishnan; A K Grover

    2006-01-01

    New experimental data are presented on the scan rate dependence of the magnetization hysteresis width () (∝ critical current density c()) in isothermal - scans in a weakly pinned single crystal of Ca3Rh4Sn13, which displays second magnetization peak (SMP) anomaly as distinct from the peak effect (PE). We observe an interesting modulation in the field dependence of a parameter which purports to measure the dynamical annealing of the disordered bundles of vortices injected through the sample edges towards the destined equilibrium vortex state at a given . These data, in conjunction with the earlier observations made while studying the thermomagnetic history dependence in c() in the tracing of the minor hysteresis loops, imply that the partially disordered state heals towards the more ordered state between the peak field of the SMP anomaly and the onset field of the PE. The vortex phase diagram in the given crystal of Ca3Rh4Sn13 has been updated in the context of the notion of the phase coexistence of the ordered and disordered regions between the onset field of the SMP anomaly and the spinodal line located just prior to the irreversibility line. A multi-critical point and a critical point in the (, ) region of the Bragg glass phase have been marked in this phase diagram and the observed behavior is discussed in the light of recent data on multi-critical point in the vortex phase diagram in a single crystal of Nb.

  15. 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.

  16. 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.

  17. Single-borehole measuring method for broken rock zone in gently inclined thin layer weakness structure

    Institute of Scientific and Technical Information of China (English)

    CHEN Qing-fa; ZHOU Ke-ping; LONG Teng-teng; GAO Feng

    2008-01-01

    According to the structural characteristics of gently inclined thin layer rock mass in which lots of weak interlayer existed, the concept of gently inclined thin layer weakness structure was proposed. If single-borehole measuring method of the acoustic along the conventional arrangement mode was used in measuring the broken rock zone in this structure, the change of the relationship curves (Vp-L) between acoustic p-wave velocity (Vp) and borehole depth (L) would present the irregular feature due to the mechanical characteristics of layered rock mass and harmful effects of weak interlayers, and the scope of broken rock zone couldn't be defined quickly. Based on the analysis of the mechanical characteristics of layered rock mass, the propagation rule of acoustic and distributions characteristics of plastic zone and slip zone in layered rock mass, new arrangement mode of acoustic measuring boreholes for broken rock zone in gently inclined thin layer weakness structure was proposed. Namely, the measuring boreholes in two sides were parallel to the strata, the measuring boreholes in the roof and floor perpendicular to the strata. Besides the controlling depth of the measuring boreholes in the scope of the large plastic zones or the large slip zones should be increased. Engineering exampleshowed that new acoustic measuring boreholes arrangement mode had the better applicability and could determine the scope of the broken rock zone in the gently inclined thin layer weakness structure quickly.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Crystal and mol-ecular structure of aflatrem.

    Science.gov (United States)

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

    2015-11-01

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

  5. A Sensitive Scheme to Observe Weak Photo-Refraction Effects in Some Nonlinear Optical Crystals Pumped by Ultrashort Optical Pulses

    Institute of Scientific and Technical Information of China (English)

    XU Shi-Xiang; GAO Yan-Xia; CAI Hua; LI Jing-Zhen

    2009-01-01

    We present a sensitive scheme, for the first time to our knowledge, to observe photo-refraction (PR) effects in some nonlinear optical crystals, e.g.β-BBO, LBO and BIBO, pumped by an intense ultrashort laser pulse chain. These quite weak effects are "amplified" by sensitive cw intracavity loss modulation. Our results show that they are repeatable and are dependent on pumping power and wavelength, and their response time ranges from tens of seconds to several minutes. The recorded dynamical transitions between the self-focusing to the self-defocusing (or vice versa) induced by the PR effect may be critically important for us to give more insight into the stability of some cascade nonlinear frequency conversions, e.g. multi-stage optical parametric amplifiers.

  6. 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.

  7. Weak antibody-cyclodextrin interactions determined by quartz crystal microbalance and dynamic/static light scattering.

    Science.gov (United States)

    Härtl, Elisabeth; Dixit, Nitin; Besheer, Ahmed; Kalonia, Devendra; Winter, Gerhard

    2013-11-01

    In a quest to elucidate the mechanism by which hydroxypropyl β-cyclodextrin (HPβCD) stabilizes antibodies against shaking stress, two heavily debated hypotheses exist, namely that stabilization is due to HPβCD's surface activity, or due to specific interactions with proteins. In a previous study by Serno et al. (Pharm. Res. 30 (2013) 117), we could refute the first hypothesis by proving that, although HPβCD is slightly surface active, it does not displace the antibody at the air-water interface, and accordingly, its surface activity is not the underlying stabilizing mechanism. In the present study, we investigated the possibility of interactions between HPβCD and monoclonal antibodies as the potential stabilization mechanism using quartz crystal microbalance (QCM) and static as well as dynamic light scattering. In the presence of HPβCD, the adsorption of IgG antibodies in the native state (IgG A) and the unfolded state (IgG A and IgG B) on gold-coated quartz crystals was studied by QCM. Results show that HPβCD causes a reduction in protein adsorption in both the folded and the unfolded states, probably due to an interaction between the protein and the cyclodextrin, leading to a reduced hydrophobicity of the protein and consequently a lower extent of adsorption. These results were supported by investigation of the interaction between the native protein and HPβCD using static and dynamic light scattering experiments, which provide the protein-protein interaction parameters, B22 and kD, respectively. Both B22 and kD showed an increase in magnitude with increasing HPβCD-concentrations, indicating a rise in net repulsive forces between the protein molecules. This is further evidence for the presence of interactions between HPβCD and the studied antibodies, since an association of HPβCD on the protein surface leads to a change in the intermolecular forces between the protein molecules. In conclusion, this study provides evidence that the previously observed

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Algorithms for singularities and real structures of weak Del Pezzo surfaces

    KAUST Repository

    Lubbes, Niels

    2014-08-01

    In this paper, we consider the classification of singularities [P. Du Val, On isolated singularities of surfaces which do not affect the conditions of adjunction. I, II, III, Proc. Camb. Philos. Soc. 30 (1934) 453-491] and real structures [C. T. C. Wall, Real forms of smooth del Pezzo surfaces, J. Reine Angew. Math. 1987(375/376) (1987) 47-66, ISSN 0075-4102] of weak Del Pezzo surfaces from an algorithmic point of view. It is well-known that the singularities of weak Del Pezzo surfaces correspond to root subsystems. We present an algorithm which computes the classification of these root subsystems. We represent equivalence classes of root subsystems by unique labels. These labels allow us to construct examples of weak Del Pezzo surfaces with the corresponding singularity configuration. Equivalence classes of real structures of weak Del Pezzo surfaces are also represented by root subsystems. We present an algorithm which computes the classification of real structures. This leads to an alternative proof of the known classification for Del Pezzo surfaces and extends this classification to singular weak Del Pezzo surfaces. As an application we classify families of real conics on cyclides. © World Scientific Publishing Company.

  13. 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.

  14. 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.

  15. 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 .

  16. 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.

  17. Local structural ordering in surface-confined liquid crystals

    Science.gov (United States)

    Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

    2017-06-01

    The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

  18. 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...

  19. 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.

  20. 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)

  1. Unusual weak magnetic exchange in two different structure types: YbPt2Sn and YbPt2In.

    Science.gov (United States)

    Gruner, T; Jang, D; Steppke, A; Brando, M; Ritter, F; Krellner, C; Geibel, C

    2014-12-03

    We present the structural, magnetic, thermodynamic and transport properties of the two new compounds YbPt(2)Sn and YbPt(2)In. X-ray powder diffraction shows that they crystallize in different structure types, the hexagonal ZrPt(2)Al and the cubic Heusler type, respectively. Despite quite different lattice types, both compounds present very similar magnetic properties: a stable trivalent Yb(3+), no evidence for a sizeable Kondo interaction and very weak exchange interactions with a strength below 1 K as deduced from specific heat C(T). Broad anomalies in C(T) suggest short range magnetic ordering at about 250 mK and 180 mK for YbPt(2)Sn and YbPt(2)In, respectively. The weak exchange and the low ordering temperature result in a large magnetocaloric effect as deduced from the magnetic field dependence of C(T), making these compounds interesting candidates for magnetic cooling. In addition we found in YbPt(2)In evidences for a charge density wave transition at about 290 K. The occurrence of such transitions within several RET2X compound series (RE = rare earth, T = noble metal, X = In, Sn) is analyzed.

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

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2017-03-01

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

  3. Mechanizing Weakly Ground Termination Proving of Term Rewriting Systems by Structural and Cover-Set Inductions

    Institute of Scientific and Technical Information of China (English)

    Su Feng

    2005-01-01

    The paper presents three formal proving methods for generalized weakly ground terminating property, i.e.,weakly terminating property in a restricted domain of a term rewriting system, one with structural induction, one with cover-set induction, and the third without induction, and describes their mechanization based on a meta-computation model for term rewriting systems-dynamic term rewriting calculus. The methods can be applied to non-terminating, nonconfluent and/or non-left-linear term rewriting systems. They can do "forward proving" by applying propositions in the proof, as well as "backward proving" by discovering lemmas during the proof.

  4. Weak Uniform Normal Structure and Fixed Points of Asymptotically Regular Semigroups

    Institute of Scientific and Technical Information of China (English)

    Lu Chuan ZENG

    2004-01-01

    Let X be a Banach space with a weak uniform normal structure and C a non-empty convexweakly compact subset of X. Under some suitable restriction, we prove that every asymptoticallyregular semigroup T = {T(t): t ∈ S} of selfmappings on C satisfyinglim inf |‖T(t)‖| < WCS(X)S(∈)t→∞has a common fixed point, where WCS(X) is the weakly convergent sequence coefficient of X, and |‖T(t) ‖ | is the exact Lipschitz constant of T(t).

  5. 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.

  6. 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.

  7. Crystal structure of 2,4,6-tris(cyclohexyloxy-1,3,5-triazine

    Directory of Open Access Journals (Sweden)

    Ravish Sankolli

    2015-11-01

    Full Text Available The title compound, C21H33N3O3, is a tri-substituted cyclohexyloxy triazine. In the crystal, the triazine rings form (C3i-PU Piedfort units. The inter-centroid distance of the π–π interaction involving the triazine rings is 3.3914 (10 Å. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming ribbons propagating along [1-10]. There are also weak C—H...N and C—H...O contacts present, linking inversion-related ribbons, forming a three-dimensional structure.

  8. 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.

  9. 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...

  10. 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…

  11. 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...

  12. 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.

  13. Origin of weak layer contraction in de Vries smectic liquid crystals

    Science.gov (United States)

    Agra-Kooijman, Dena M.; Yoon, HyungGuen; Dey, Sonal; Kumar, Satyendra

    2014-03-01

    Structural investigations of the de Vries smectic-A (SmA) and smectic-C (SmC) phases of four mesogens containing a trisiloxane end segment reveal a linear molecular conformation in the SmA phase and a bent conformation resembling a hockey stick in the SmC phase. The siloxane and the hydrocarbon parts of the molecule tilt at different angles relative to the smectic layer normal and are oriented along different directions. For the compounds investigated, the shape of orientational distribution function (ODF) is found to be sugarloaf shaped and not the widely expected volcano like with positive orientational order parameters: ⟨P2⟩ = 0.53-0.78, ⟨P4⟩ = 0.14-0.45, and ⟨P6⟩˜0.10. The increase in the effective molecular length, and consequently in the smectic layer spacing caused by reduced fluctuations and the corresponding narrowing of the ODF, counteracts the effect of molecular tilt and significantly reduces the SmC layer contraction. Maximum tilt of the hydrocarbon part of the molecule lies between approximately 18° and 25° and between 6° and 12° for the siloxane part. The critical exponent of the tilt order parameter, β˜0.25, is in agreement with tricritical behavior at the SmA-SmC transition for two compounds and has lower value for first-order transition in the other compounds with finite enthalpy of transition.

  14. 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)

  15. 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.

  16. 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...

  17. 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...

  18. 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.

  19. Atomic density functional and diagram of structures in the phase field crystal model

    Science.gov (United States)

    Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.

    2016-02-01

    The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. New Limits on Interactions between Weakly Interacting Massive Particles and Nucleons Obtained with CsI(Tl) Crystal Detectors

    CERN Document Server

    Kim, S C; Choi, J H; Kang, W G; Kim, B H; Kim, H J; Kim, K W; Kim, S K; Kim, Y D; Lee, J; Lee, J H; Lee, J K; Lee, M J; Lee, S J; Li, J; Li, J; Li, X R; Li, Y J; Myung, S S; Olsen, S L; Ryu, S; Seong, I S; So, J H; Yue, Q

    2012-01-01

    New limits are presented on the cross section for Weakly Interacting Massive Particle (WIMP) nucleon scattering in the KIMS CsI(T) detector array at the Yangyang Underground Laboratory. The exposure used for these results is 24524.3 kg\\cdotdays. Nuclei recoiling from WIMP interactions are identified by a pulse shape discrimination method. A low energy background due to alpha emitters on the crystal surfaces is identified and taken into account in the analysis. The detected numbers of nuclear recoils are consistent with zero and 90% confidence level upper limits on the WIMP interaction rates are set for electron equivalent energies from 3 keV to 11 keV. The 90% upper limit of NR event rate for 3.6-5.8 keV corresponding to 2-4 keV in NaI(T) is 0.0098 counts/kg/keV/day which is below the annual modulation amplitude reported by DAMA. This is incompatible with interpretations that enhance the modulation amplitude such as inelastic dark matter models. We establish the most stringent cross section limits on spin-dep...

  5. On Spectral Invariance of Single Scattering Albedo for Water Droplets and Ice Crystals at Weakly Absorbing Wavelengths

    Science.gov (United States)

    Marshak, Alexander; Knyazikhin, Yuri; Chiu, J. Christine; Wiscombe, Warren J.

    2012-01-01

    The single scattering albedo omega(sub O lambda) in atmospheric radiative transfer is the ratio of the scattering coefficient to the extinction coefficient. For cloud water droplets both the scattering and absorption coefficients, thus the single scattering albedo, are functions of wavelength lambda and droplet size r. This note shows that for water droplets at weakly absorbing wavelengths, the ratio omega(sub O lambda)(r)/omega(sub O lambda)(r (sub O)) of two single scattering albedo spectra is a linear function of omega(sub O lambda)(r). The slope and intercept of the linear function are wavelength independent and sum to unity. This relationship allows for a representation of any single scattering albedo spectrum omega(sub O lambda)(r) via one known spectrum omega(sub O lambda)(r (sub O)). We provide a simple physical explanation of the discovered relationship. Similar linear relationships were found for the single scattering albedo spectra of non-spherical ice crystals.

  6. 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.

  7. 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.

  8. 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.

  9. Prediction of Shock Wave Structure in Weakly Ionized Gas Flow by Solving MGD Equation

    Science.gov (United States)

    Deng, Z. T.; Oviedo-Rojas, Ruben; Chow, Alan; Litchford, Ron J.; Cook, Stephen (Technical Monitor)

    2002-01-01

    This paper reports the recent research results of shockwave structure predictions using a new developed code. The modified Rankine-Hugoniot relations across a standing normal shock wave are discussed and adopted to obtain jump conditions. Coupling a electrostatic body force to the Burnett equations, the weakly ionized flow field across the shock wave was solved. Results indicated that the Modified Rankine-Hugoniot equations for shock wave are valid for a wide range of ionization fraction. However, this model breaks down with small free stream Mach number and with large ionization fraction. The jump conditions also depend on the value of free stream pressure, temperature and density. The computed shock wave structure with ionization provides results, which indicated that shock wave strength may be reduced by existence of weakly ionized gas.

  10. 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.

  11. 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.

  12. 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...

  13. 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.

  14. 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...

  15. Crystal structures of two thiacalix[4]arene derivatives anchoring four thiadiazole groups

    Indian Academy of Sciences (India)

    Bang-Tun Zhao; Zhen Zhou; Zhen-Ning Yan

    2009-11-01

    The crystal structures of two thiacalixarene derivatives anchoring thiadiazole functional groups at lower rim, C60H72O4S12N8 (1), C64H80O4S12N8 (2), have been determined by single crystal X-ray diffraction. The thiacalix[4]arene framework in both 1 and 2 adopts the 1,3-alternate conformation. Compound 1 forms a 1-D chain by weak hydrogen bonding (C-H$\\cdots$N) interactions between two thiadiazole groups in two different molecules. The chains are further connected to form a 2-D network through sulfur-sulfur (S$\\cdots$S) interactions. The lattice water molecules which exist as dimers by forming hydrogen bonds (O-H$\\cdots$O) promote a 3-D supramolecular structure through weak hydrogen bonding (O-H$\\cdots$S) interactions between the lattice water dimers and the 2-D networks. On the other hand, compound 2, based on dimer which is formed by weak hydrogen bonding (C-H$\\cdots$S) interactions, is extended to a 1-D chain through sulfur-sulfur (S$\\cdots$S) interactions. The dimers of lattice methanol molecules linked by hydrogen bonds (O-H$\\cdots$O) act as bridges to link the 1-D chains into a 2-D network through weak hydrogen bonding (C-H$\\cdots$N) interactions.

  16. Classical integrability for three-point functions: cognate structure at weak and strong couplings

    Energy Technology Data Exchange (ETDEWEB)

    Kazama, Yoichi [Research Center for Mathematical Physics, Rikkyo University,Toshima-ku, Tokyo 171-8501 (Japan); Quantum Hadron Physics Laboratory, RIKEN Nishina Center, Wako 351-0198 (Japan); Institute of Physics, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Komatsu, Shota [Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo, Ontario, N2L 2Y5 (Canada); Nishimura, Takuya [Institute of Physics, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2016-10-10

    In this paper, we develop a new method of computing three-point functions in the SU(2) sector of the N=4 super Yang-Mills theory in the semi-classical regime at weak coupling, which closely parallels the strong coupling analysis. The structure threading two disparate regimes is the so-called monodromy relation, an identity connecting the three-point functions with and without the insertion of the monodromy matrix. We shall show that this relation can be put to use directly for the semi-classical regime, where the dynamics is governed by the classical Landau-Lifshitz sigma model. Specifically, it reduces the problem to a set of functional equations, which can be solved once the analyticity in the spectral parameter space is specified. To determine the analyticity, we develop a new universal logic applicable at both weak and strong couplings. As a result, compact semi-classical formulas are obtained for a general class of three-point functions at weak coupling including the ones whose semi-classical behaviors were not known before. In addition, the new analyticity argument applied to the strong coupling analysis leads to a modification of the integration contour, producing the results consistent with the recent hexagon bootstrap approach. This modification also makes the Frolov-Tseytlin limit perfectly agree with the weak coupling form.

  17. Crystal structure of 2-amino-5-nitro-pyridinium sulfamate.

    Science.gov (United States)

    Rajkumar, M Ambrose; NizamMohideen, M; Xavier, S Stanly John; Anbarasu, S; Devarajan, Dr Prem Anand

    2015-02-01

    The title mol-ecular salt, C5H6N3O2 (+) ·H2NO3S(-), was obtained from the reaction of sulfamic acid with 2-amino-5-nitro-pyridine. A proton transfer from sulfamic acid to the pyridine N atom occurred, resulting in the formation of a salt. As expected, this protonation leads to the widening of the C-N-C angle of the pyridine ring, to 122.9 (3)°, with the pyridinium ring being essentially planar (r.m.s. deviation = 0.025 Å). In the crystal, the ion pairs are joined by three N-H⋯O and one N-H⋯N hydrogen bonds in which the pyridinium N atom and the amino N atom act as donors, and are hydrogen bonded to the carboxyl-ate O atoms and the N atom of the sulfamate anion, thus generating an R (3) 3(22) ring motif. These motifs are linked by further N-H⋯O hydrogen bonds enclosing R (3) 3(8) loops, forming sheets parallel to (100). The sheets are linked via weak C-H⋯O hydrogen bonds, forming a three-dimensional structure. The O atoms of the nitro group are disordered over two sets of sites with a refined occupancy ratio of 0.737 (19):0.263 (19).

  18. 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,

  19. 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.

  20. 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.

  1. 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.

  2. 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...

  3. Reactions of a cyclodimethylsiloxane (Me2SiO)6 with silver salts of weakly coordinating anions; crystal structures of [Ag(Me2SiO)6][Al] ([Al] = [FAl{OC(CF3)3}3], [Al{OC(CF3)3}4]) and their comparison with [Ag(18-crown-6)]2[SbF6]2.

    Science.gov (United States)

    Cameron, T Stanley; Decken, Andreas; Krossing, Ingo; Passmore, Jack; Rautiainen, J Mikko; Wang, Xinping; Zeng, Xiaoqing

    2013-03-18

    Two silver-cyclodimethylsiloxane cation salts [AgD6][Al] ([Al] = [Al(ORF)4](1) or [FAl(OR(F))3](2), R(F) = C(CF3)3, D = Me2SiO) were prepared by the reactions of Ag[Al] with D6 in SO2(l). For a comparison the [Ag(18-crown-6)]2[SbF6]2(3) salt was prepared by the reaction of Ag[SbF6] and 18-crown-6 in SO2(l). The compounds were characterized by IR, multinuclear NMR, and single crystal X-ray crystallography. The structures of 1 and 2 show that D6 acts as a pseudo crown ether toward Ag(+). The stabilities and bonding of [MDn](+) and [M(18-crown-6)](+) (M = Ag, Li, n = 4-8) complexes were studied with theoretical calculations. The calculations predicted that D6 adopts a puckered C(i) symmetric structure in the gas phase in contrast to previous reports. 18-Crown-6 was calculated to bind more strongly to Li(+) and Ag(+) than D6. (29)Si[(1)H] NMR results in solution, and calculations in the gas phase established that a hard Lewis acid Li(+) binds more strongly to D6 than Ag(+). A comparison of the [MD(n)](+) complex stabilities showed D7 to form the most stable metal complexes in the gas phase and the solid state and explained why [AgD7][SbF6] was isolated in a previous reaction where ring transformations resulted in an equilibrium of [AgD(n)](+) complexes. In contrast, the isolations of 1 and 2 were possible because the corresponding equilibrium of [AgD(n)](+) complexes was not observed with [Al](-) anions. The formation of the dinuclear complex salt 3 instead of the corresponding mononuclear complex salt was shown to be driven by the gain in lattice enthalpy in the solid state. The bonding to Li(+) in D6 and 18-crown-6 metal complexes was described by a quantum theory of atoms in molecules (QTAIM) analysis to be mostly electrostatic while the bonding to Ag(+) also had a significant charge transfer component. The charge transfer from both D6 and 18-crown-6 to Ag(+) and Li(+) metal ions was depicted by the QTAIM analysis to be of similar strength, and the difference in the

  4. 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)

  5. 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.

  6. 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.

  7. 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.

  8. Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermodynamic Stability

    Science.gov (United States)

    2015-01-01

    Folding dynamics are ubiquitously involved in controlling the multivariate functions of RNAs. While the high thermodynamic stabilities of some RNAs favor purely native states at equilibrium, it is unclear whether weakly stable RNAs exist in random, partially folded states or sample well-defined, globally folded conformations. Using a folding assay that precisely tracks the formation of native aminoacylable tRNA, we show that the folding of a weakly stable human mitochondrial (hmt) leucine tRNA is hierarchical with a distinct kinetic folding intermediate. The stabilities of the native and intermediate conformers are separated by only about 1.2 kcal/mol, and the species are readily interconvertible. Comparison of folding dynamics between unmodified and fully modified tRNAs reveals that post-transcriptional modifications produce a more constrained native structure that does not sample intermediate conformations. These structural dynamics may thus be crucial for recognition by some modifying enzymes in vivo, especially those targeting the globular core region, by allowing access to pretransition state conformers. Reduced conformational sampling of the native, modified tRNAs could then permit improved performance in downstream processes of translation. More generally, weak stabilities of small RNAs that fold in the absence of chaperone proteins may facilitate conformational switching that is central to biological function. PMID:24520994

  9. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    Energy Technology Data Exchange (ETDEWEB)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I., E-mail: igalsz@northwestern.edu [Department of Biomedical Engineering, Department of Chemistry, and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3100 (United States)

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  10. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    Science.gov (United States)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-01

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  11. Phase Structure of Weak MgII Absorbers Star Forming Pockets Outside of Galaxies

    CERN Document Server

    Charlton, J C; Ding, J; Zonak, S G; Bond, N; Rigby, J R; Charlton, Jane C.; Churchill, Christopher W.; Ding, Jie; Zonak, Stephanie; Bond, Nicholas; Rigby, Jane R.

    2001-01-01

    A new and mysterious class of object has been revealed by the detection of numerous weak MgII doublets in quasar absorption line spectra. The properties of these objects will be reviewed. They are not in close proximity to luminous galaxies, yet they have metallicities close to the solar value; they are likely to be self-enriched. A significant fraction of the weak MgII absorbers are constrained to be less than 10 parsecs in size, yet they present a large cross-section for absorption, indicating that there are more than a million times more of them than there are luminous galaxies. They could be remnants of Population III star clusters or tracers of supernova remnants in a population of "failed dwarf galaxies" expected in cold dark matter structure formation scenarios.

  12. Crystal structure of triphenylphosphonium-meth-yl-enetrifluoroborate.

    Science.gov (United States)

    Bateman, Christopher M; Zakharov, Lev N; Abbey, Eric R

    2017-07-01

    The title compound, C19H17BF3P {alternative name: triphen-yl[(tri-fluoro-boran-yl)meth-yl]phosphanium}, was formed by the reaction of tri-phenyl-phosphine with potassium iodo-methyl-tri-fluoro-borate. The mol-ecule features a nearly staggered conformation along the P-C bond and a less than staggered conformation along the C-B bond. In the crystal, weak C-H⋯F hydrogen bonds between the meta-phenyl C-H groups and the tri-fluoro-borate B-F groups form chains of R2(2)(16) rings along [100]. These chains are are further stabilized by weak C-H⋯π inter-actions. A weak intra-molecular C-H⋯F hydrogen bond is also observed.

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

    Science.gov (United States)

    Jariwala, Bhakti; Thamizhavel, Arumugum; Bhattacharya, Arnab

    2017-02-01

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

  14. 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.

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

    Science.gov (United States)

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

    2017-04-01

    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.

  16. 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.

  17. 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.

  18. 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....

  19. 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°

  20. 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.

  1. Classical Integrability for Three-point Functions: Cognate Structure at Weak and Strong Couplings

    CERN Document Server

    Kazama, Y; Nishimura, T

    2016-01-01

    In this paper, we develop a new method of computing three-point functions in the SU(2) sector of the $\\mathcal{N}=4$ super Yang-Mills theory in the semi-classical regime at weak coupling, which closely parallels the strong coupling analysis. The structure threading two disparate regimes is the so-called monodromy relation, an identity connecting the three-point functions with and without the insertion of the monodromy matrix. We shall show that this relation can be put to use directly for the semi-classical regime, where the dynamics is governed by the classical Landau-Lifshitz sigma model. Specifically, it reduces the problem to a set of functional equations, which can be solved once the analyticity in the spectral parameter space is specified. To determine the analyticity, we develop a new universal logic applicable at both weak and strong couplings. As a result, compact semi-classical formulas are obtained for a general class of three-point functions at weak coupling including the ones whose semi-classical...

  2. 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...

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

    Science.gov (United States)

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

    2010-06-21

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

  4. 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.

  5. Aging population in change – a crucial challenge for structurally weak rural areas in Austria

    Directory of Open Access Journals (Sweden)

    Fischer Tatjana

    2014-03-01

    Full Text Available Besides population decline, structurally weak rural areas in Austria face a new challenge related to demographic change: the increasing heterogeneity of their aging population. From the example of the so-called ‘best agers’ - comprising people aged 55 to 65 years - this contribution makes visible patterns and consequences of growing individualized spatial behaviour and spatial perception. Furthermore, contradictions between claims, wishes and expectations and actual engagement and commitment to their residential rural municipalities are being pointed out. These empirically-based facts are rounded off by considerations on the best agers’ future migration-behaviour and the challenges for spatial planning at the municipal level.

  6. Energy-band structure and intrinsic coherent properties in two weakly linked Bose-Einstein condensates

    Science.gov (United States)

    Li, Wei-Dong; Zhang, Yunbo; Liang, J.-Q.

    2003-06-01

    The energy-band structure and energy splitting due to quantum tunneling in two weakly linked Bose-Einstein condensates were calculated by using the instanton method. The intrinsic coherent properties of Bose-Josephson junction (BJJ) were investigated in terms of energy splitting. For EC/EJ≪1, the energy splitting is small and the system is globally phase coherent. In the opposite limit, EC/EJ≫1, the energy splitting is large and the system becomes phase dissipated. Our results suggest that one should investigate the coherence phenomena of BJJ in proper condition such as EC/EJ˜1.

  7. On-line spectrophotometric method for monitoring weak residual absorption of CaMoO{sub 4} single crystals near the intrinsic luminescence peak

    Energy Technology Data Exchange (ETDEWEB)

    Buzanov, O. A., E-mail: fedorov-metrology@yandex.ru [OAO Fomos-Materials (Russian Federation); Kanevskii, V. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Kornoukhov, V. N. [OAO Fomos-Materials (Russian Federation); Nabatov, B. V.; Nabatov, V. V.; Fedorov, V. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2013-11-15

    The optical and spectral characteristics of isotopically enriched Czochralski-grown {sup 40}Ca{sup 100}MoO{sub 4} single crystals have been investigated. This material is promising for detecting double neutrinoless {beta} decay. The possibility and the technique of spectrophotometric monitoring of weak residual absorption near the intrinsic luminescence peak of this scintillation material, which is designed for developing new-generation detectors of elementary particles, are considered.

  8. On-line spectrophotometric method for monitoring weak residual absorption of CaMoO4 single crystals near the intrinsic luminescence peak

    Science.gov (United States)

    Buzanov, O. A.; Kanevskii, V. M.; Kornoukhov, V. N.; Nabatov, B. V.; Nabatov, V. V.; Fedorov, V. A.

    2013-11-01

    The optical and spectral characteristics of isotopically enriched Czochralski-grown 40Ca100MoO4 single crystals have been investigated. This material is promising for detecting double neutrinoless β decay. The possibility and the technique of spectrophotometric monitoring of weak residual absorption near the intrinsic luminescence peak of this scintillation material, which is designed for developing new-generation detectors of elementary particles, are considered.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Crystal structure of 3-{1′-[3,5-bis(trifluoromethylphenyl]ferrocenyl}-4-bromothiophene

    Directory of Open Access Journals (Sweden)

    Elisabeth A. Poppitz

    2014-10-01

    Full Text Available The molecular structure of the title compound, [Fe(C9H6BrS(C13H7F6], consists of a ferrocene backbone with a bis(trifluoromethylphenyl group at one cyclopentadienyl ring and a thiophene heterocycle at the other cyclopentadienyl ring. The latter is disordered over two sets of sites in a 0.6:0.4 ratio. In the crystal structure, intramolecular π–π interactions between the thienyl and the phenyl substituent [centroid–centroid distance 3.695 (4 Å] and additional weak T-shaped π–π interactions between the thienyl and the phenyl-substituted cyclopentadienyl ring [4.688 (6 Å] consolidate the crystal packing.

  14. Sliding surface searching method for slopes containing a potential weak structural surface

    Directory of Open Access Journals (Sweden)

    Aijun Yao

    2014-06-01

    Full Text Available Weak structural surface is one of the key factors controlling the stability of slopes. The stability of rock slopes is in general concerned with set of discontinuities. However, in soft rocks, failure can occur along surfaces approaching to a circular failure surface. To better understand the position of potential sliding surface, a new method called simplex-finite stochastic tracking method is proposed. This method basically divides sliding surface into two parts: one is described by smooth curve obtained by random searching, the other one is polyline formed by the weak structural surface. Single or multiple sliding surfaces can be considered, and consequently several types of combined sliding surfaces can be simulated. The paper will adopt the arc-polyline to simulate potential sliding surface and analyze the searching process of sliding surface. Accordingly, software for slope stability analysis using this method was developed and applied in real cases. The results show that, using simplex-finite stochastic tracking method, it is possible to locate the position of a potential sliding surface in the slope.

  15. Sliding surface searching method for slopes containing a potential weak structural surface

    Institute of Scientific and Technical Information of China (English)

    Aijun Yao; Zhizhou Tian; Yongjun Jin

    2014-01-01

    Weak structural surface is one of the key factors controlling the stability of slopes. The stability of rock slopes is in general concerned with set of discontinuities. However, in soft rocks, failure can occur along surfaces approaching to a circular failure surface. To better understand the position of potential sliding surface, a new method called simplex-finite stochastic tracking method is proposed. This method basically divides sliding surface into two parts: one is described by smooth curve obtained by random searching, the other one is polyline formed by the weak structural surface. Single or multiple sliding surfaces can be considered, and consequently several types of combined sliding surfaces can be simu-lated. The paper will adopt the arc-polyline to simulate potential sliding surface and analyze the searching process of sliding surface. Accordingly, software for slope stability analysis using this method was developed and applied in real cases. The results show that, using simplex-finite stochastic tracking method, it is possible to locate the position of a potential sliding surface in the slope.

  16. Structure and magnetic properties of the weak ferromagnet Sr{sub 2-x}La{sub x}IrO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Cosio-Castaneda, Carlos [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria 04510, Mexico, DF (Mexico); Tavizon, Gustavo [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria 04510, Mexico, DF (Mexico); Baeza, Alejandro [Departamento de Quimica AnalItica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria 04510, Mexico, DF (Mexico); Mora, Pablo de la [Departamento de Fisica, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria 04510, Mexico, DF (Mexico); Escudero, Roberto [Instituto de Investigaciones en Materiales, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria 04510, Mexico, DF (Mexico)

    2007-11-07

    The 5d electron-based Sr{sub 2-x}La{sub x}IrO{sub 4} system (0{<=}x{<=}0.2) has been synthesized by a solid-state route. The x = 0 composition is a nonmetallic weak ferromagnet with a Curie temperature at about 240 K. The crystal structure behaviour and magnetic properties exhibited by this Sr{sub 2-x}La{sub x}IrO{sub 4} system can be explained on the basis of the extended character of the 5d electrons of the Ir cation and its valence states. Rietveld analysis of x-ray powder diffraction on Sr{sub 2}IrO{sub 4} agrees well with previous structural neutron experiments. Furthermore, density functional theory (DFT) calculations predict that I4{sub 1}/acd represents a more stable crystal structure than K{sub 2}NiF{sub 4} (I4/mmm). Electrical resistivity and magnetic properties of Sr{sub 2-x}La{sub x}IrO{sub 4} are strongly dependent on the Ir{sup 3+} content. The Sr{sub 2-x}La{sub x}IrO{sub 4} magnetic behaviour in the range of 2-240 K can be ascribed to a weak ferromagnet, produced by an array of canted antiferromagnetically ordered Ir{sup 4+} magnetic moments.

  17. First-order Freedericksz transition at the threshold point for weak anchoring nematic liquid crystal cell under external electric and magnetic fields

    Institute of Scientific and Technical Information of China (English)

    关荣华; 杨国琛

    2003-01-01

    Based on the modified formula of Rapini-Papoular, the equilibrium equation and boundary condition of the director have been obtained and the behaviour of the Freedericksz transition at the threshold point has been studied for weak-anchoring nematic liquid crystal cells under external electric and magnetic fields with the methods of analytical derivation and numerical calculation. The results show that, except for the usual second-order transition, the first-order Freedericksz transition can also be induced by a suitable surface anchoring technique for the liquid crystal cell given in the paper. The conditions for the existence of the first-order Freedericksz transition are obtained. They are related to the material elastic coefficient k11, k33 the thickness of the liquid crystal cell, the external electric field and the strength of surface anchoring, etc.

  18. Synthesis, X-ray powder structure, and magnetic properties of the new, weak ferromagnet iron(II) phenylphosphonate.

    Science.gov (United States)

    Bellitto, C; Federici, F; Altomare, A; Rizzi, R; Ibrahim, S A

    2000-04-17

    A new molecule-based weak ferromagnet of formula Fe[C6H5PO3].H2O was synthesized. It was characterized by thermogravimetric analysis and UV-visible and infrared spectroscopy, and the magnetic properties were studied using a superconducting quantum interference device magnetometer. The crystal structure of the compound was determined "ab initio" from X-ray powder diffraction data and refined by the Rietveld method. The crystals of Fe[C6H5PO3].H2O are orthorhombic, space group Pmn2(1), with a = 5.668(8) A, b = 14.453(2) A, c = 4.893(7) A, and Z = 2. The title compound is isostructural with the previously reported lamellar M[C6H5PO3].H2O, M = Mn(II), Zn(II), and Cd(II). The inorganic layers are made of Fe(II) ions octahedrally coordinated by five phosphonate oxygen atoms and one from oxygen of the water molecule. These layers are then separated by bilayers of the phenyl groups, and van der Waals contacts are established between them. The refinement has shown that the phenyl rings are disordered in the lattice. The oxidation state of the metal ion is +2, and the electronic configuration is d6 (S = 2) high-spin, as determined from dc magnetic susceptibility measurements from 150 K to room temperature. Below 100 K, the magnetic moment of Fe[C6H5PO3].H2O rises rapidly to a maximum at TN = 21.5 K, and then it decreases again. The peak at TN is associated with the 3D antiferromagnetic long-range ordering. Below the critical temperature, the title compound behaves as a "weak" ferromagnet, which represents the third type of magnetic materials characterized by having a finite zero-field magnetization, ferromagnets and ferrimagnets being the other two types. The large coercive field (i.e., 6400 G) observed in the hysteresis loop at T = 10 K is rare in molecule-based materials; it can be ascribed to a pronounced spin-orbit coupling for the 5T2g ground state of the Fe(II) ion in the octahedral environment.

  19. Computation of Large-Scale Structure Jet Noise Sources With Weak Nonlinear Effects Using Linear Euler

    Science.gov (United States)

    Dahl, Milo D.; Hixon, Ray; Mankbadi, Reda R.

    2003-01-01

    An approximate technique is presented for the prediction of the large-scale turbulent structure sound source in a supersonic jet. A linearized Euler equations code is used to solve for the flow disturbances within and near a jet with a given mean flow. Assuming a normal mode composition for the wave-like disturbances, the linear radial profiles are used in an integration of the Navier-Stokes equations. This results in a set of ordinary differential equations representing the weakly nonlinear self-interactions of the modes along with their interaction with the mean flow. Solutions are then used to correct the amplitude of the disturbances that represent the source of large-scale turbulent structure sound in the jet.

  20. 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.

  1. The different conformations and crystal structures of dihydroergocristine

    Science.gov (United States)

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

    2016-02-01

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

  2. 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.

  3. 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.

  4. 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 ...

  5. Recovery of weak factor loadings when adding the mean structure in confirmatory factor analysis: A simulation study

    Directory of Open Access Journals (Sweden)

    Carmen eXiménez

    2016-01-01

    Full Text Available This article extends previous research on the recovery of weak factor loadings in confirmatory factor analysis by exploring the effects of adding the mean structure. This issue has not been examined in previous research. This study is based on the framework of Yung and Bentler (1999 and aims to examine the conditions that affect the recovery of weak factor loadings when the model includes the mean structure, compared to analyzing the covariance structure alone. A simulation study was conducted in which several constraints were defined for one-, two-, and three-factor models. Results show that adding the mean structure improves the recovery of weak factor loadings and reduces the asymptotic variances for the factor loadings, particularly for the models with a smaller number of factors and a small sample size. Therefore, under certain circumstances, modeling the means should be seriously considered for covariance models containing weak factor loadings.

  6. 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...

  7. 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.

  8. 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.

  9. Crystal structure of 7,8-benzocoumarin-4-acetic acid

    Directory of Open Access Journals (Sweden)

    R. Ranga Swamy

    2015-08-01

    Full Text Available The fused-ring system in the title compound [systematic name: 2-(2-oxo-2H-benzo[h]chromen-4-ylacetic acid], C15H10O4, is almost planar (r.m.s. deviation = 0.031 Å and the Car—C—C=O (ar = aromatic torsion angle for the side chain is −134.4 (3°. In the crystal, molecules are linked by O—H...O hydrogen bonds, generating [100] C(8 chains, where the acceptor atom is the exocyclic O atom of the fused-ring system. The packing is consolidated by a very weak C—H...O hydrogen bond to the same acceptor atom. Together, these interactions lead to undulating (001 layers in the crystal.

  10. Crystal structure and Raman spectra of rubidium hydrogen squarate

    Science.gov (United States)

    Georgopoulos, Stéfanos L.; Diniz, Renata; Rodrigues, Bernardo L.; de Oliveira, Luiz F. C.

    2005-05-01

    Rubidium hydrogen squarate (RbHC 4O 4, RbHSQ) crystallized in monoclinic space group P2 1/ c. This compound form a short asymmetric intermolecular hydrogen bond whose O-O distance is 2.482(4) Å. The hydrogen squarate anions are forming head-to-tail infinite chain hydrogen-bonding motifs. A long interplanar separation (4.15 Å) indicates that a weak π interaction occurs between hydrogen squarate anions in RbHSQ. The hydrogen bond and cation-anion interactions are the predominant driving forces in the crystal packing. The Raman spectrum of RbHSQ shows an average behaviour between squaric acid and squarate dianion, however, the vibrational modes at ca. 1800 cm -1 (CO stretching mode) and in the region 1500-1700 cm -1 (CO+CC stretching modes) are the most affected by the presence of strong hydrogen bonding interactions.

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

    Directory of Open Access Journals (Sweden)

    Assane Toure

    2016-12-01

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

  12. Crystal structure of C-2-benzothiazole-N-methylnitrone

    Directory of Open Access Journals (Sweden)

    Roman Doroschuk

    2015-08-01

    Full Text Available The molecule of the title compound {systematic name: N-[(benzothiazol-2-ylmethylidene]methylamine N-oxide}, C9H8N2OS, is close to planar [maximum deviation from the mean plane = 0.081 (2 Å], its conformation being stabilized by a strong intramolecular attractive S...O interaction [2.6977 (16 Å]. In the crystal, molecules are linked into centrosymmetric dimers by pairs of weak C—H...O hydrogen bonds.

  13. 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.

  14. 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.

  15. 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.

  16. Weak links between fast mobility and local structure in molecular and atomic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Bernini, S. [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Puosi, F. [Laboratoire de Physique de l’École Normale Supérieure de Lyon, UMR CNRS 5672, 46 allée d’Italie, 69007 Lyon (France); Leporini, D., E-mail: dino.leporini@df.unipi.it [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); IPCF-CNR, UOS Pisa, Pisa (Italy)

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  17. The weak core and the structure of elites in social multiplex networks

    CERN Document Server

    Corominas-Murtra, Bernat

    2014-01-01

    Recent approaches on elite identification highlighted the important role of {\\em intermediaries}, by means of a new definition of the core of a multiplex network, the {\\em generalised} $K$-core. This newly introduced core subgraph crucially incorporates those individuals who, in spite of not being very connected, maintain the cohesiveness and plasticity of the core. Interestingly, it has been shown that the performance on elite identification of the generalised $K$-core is sensibly better that the standard $K$-core. Here we go further: Over a multiplex social system, we isolate the community structure of the generalised $K$-core and we identify the weakly connected regions acting as bridges between core communities, ensuring the cohesiveness and connectivity of the core region. This gluing region is the {\\em Weak core} of the multiplex system. We test the suitability of our method on data from the society of 420.000 players of the Massive Multiplayer Online Game {\\em Pardus}. Results show that the generalised...

  18. Experimental Observation of Exact Coherent Structures in a Weakly Turbulent Quasi-Two-Dimensional Flow

    Science.gov (United States)

    Suri, Balachandra; Tithof, Jeffrey; Pallantla, Ravi Kumar; Grigoriev, Roman; Schatz, Michael

    2015-11-01

    The dynamical systems approach to fluid turbulence relies on understanding the role of unstable, non-chaotic solutions - such as equilibria, traveling waves, and periodic orbits - of the Navier-Stokes equations. These solutions, called Exact Coherent Structures, exist in the same parameter regime as turbulence, but being unstable, are observed in experiments only as short transients. In this talk, we present experimental evidence for the existence and dynamical relevance of unstable equilibria in a weakly turbulent quasi-two-dimensional (Q2D) Kolmogorov flow. In the experiment, this Q2D flow is generated in an electromagnetically driven shallow layer of electrolyte. The numerical simulations, however, use a strictly 2D model which incorporates the effects of the finite thickness of the fluid layer in the experiment. During its evolution, there are instances when the dynamics of a weakly turbulent flow slow down, rather dramatically. Using experimental flow fields from such instances, and by means of a Newton-Solver, we numerically compute several unstable equilibria. Additionally, using numerical simulations, we show that the dynamics of a turbulent flow in the neighbourhood of an equilibrium are accurately described by the unstable manifold of the equilibrium. This work is supported in part by the National Science Foundation under grants CBET-0900018, and CMMI-1234436.

  19. Structural study of quasi-one-dimensional vanadium pyroxene LiVSi2O6 single crystals

    Science.gov (United States)

    Ishii, Yuto; Matsushita, Yoshitaka; Oda, Migaku; Yoshida, Hiroyuki

    2017-02-01

    Single crystals of quasi-one-dimensional vanadium pyroxene LiVSi2O6 were synthesized and the crystal structures at 293 K and 113 K were studied using X-ray diffraction experiments. We found a structural phase transition from the room-temperature crystal structure with space group C2/c to a low-temperature structure with space group P21/c, resulting from a rotational displacement of SiO4 tetrahedra. The temperature dependence of magnetic susceptibility shows a broad maximum around 116 K, suggesting an opening of the Haldane gap expected for one-dimensional antiferromagnets with S=1. However, an antiferromagnetic long-range order was developed below 24 K, probably caused by a weak inter-chain magnetic coupling in the compound.

  20. 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-...

  1. Weakly nonlinear analysis and localised structures in nonlinear cavities with metamaterials

    Science.gov (United States)

    Slimani, N.; Makhoute, A.; Tlidi, M.

    2016-04-01

    We consider an optical ring cavity filled with a metamaterial and with a Kerr medium. The cavity is driven by a coherent radiation beam. The modelling of this device leads to the well known Lugiato-Lefever equation with high order diffraction term. We assume that both left-handed and right-handed materials possess a Kerr focusing type of nonlinearity. We show that close to the zero-diffraction regime, high-order diffraction effect allows us to stabilise dark localised structures in this device. These structures consist of dips or holes in the transverse profile of the intracavity field and do not exist without high-order diffraction effects. We show that high order diffraction effects alter in depth the space-time dynamics of this device. A weakly nonlinear analysis in the vicinity of the first threshold associated with the Turing instability is performed. This analysis allows us to determine the parameter regime where the transition from super- to sub-critical bifurcation occurs. When the modulational instability appears subcritically, we show that bright localised structures of light may be generated in two-dimensional setting. Close to the second threshold associated with the Turing instability, dark localised structures are generated.

  2. 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.

  3. 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.

  4. 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. ...

  5. 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....

  6. 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

  7. 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.

  8. Eikonal approximation, Finsler structures, and implications for Lorentz-violating photons in weak gravitational fields

    CERN Document Server

    Schreck, M

    2015-01-01

    The current article shall contribute to understanding the classical analogue of the minimal photon sector in the Lorentz-violating Standard-Model Extension (SME). It is supposed to complement all studies performed on classical point-particle equivalents of SME fermions. The classical analogue of a photon is not a massive particle being described by a usual equation of motion, but a geometric ray underlying the eikonal equation. The first part of the paper will set up the necessary tools to understand this correspondence for interesting cases of the minimal SME photon sector. In conventional optics the eikonal equation follows from an action principle, which is demonstrated to work in most (but not all) Lorentz-violating cases as well. The integrands of the action functional correspond to Finsler structures, which establishes the connection to Finsler geometry. The second part of the article treats Lorentz-violating light rays in a weak gravitational background by implementing the principle of minimal coupling...

  9. 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.

  10. 3D modeling method for computer animate based on modified weak structured light method

    Science.gov (United States)

    Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

    2010-11-01

    A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.

  11. The role of weak intermolecular C-H…F interactions in supramolecular assembly: Structural investigations on 3,5- dibenzylidene-piperidin-4-one and database analysis

    Indian Academy of Sciences (India)

    R S Rathore; N S Karthikeyan; Y Alekhya; K Sathiyanarayanan; P G Aravindan

    2011-07-01

    The fluorinated and non-fluorinated dibenzylidene-4-piperidones were synthesized and their structures examined using X-ray crystallography. Interestingly, the para-fluorosubstituted dibenzylidene compound, in contrast to other analogs, is characterized by C-H…F bonded one-dimensional packing motif. To evaluate the ability of hydrogen bond donors and acceptors for forming interactions, in general and competitive situation, we have defined statistical descriptors. Analysis of Cambridge Structural Database using these newly defined parameters reveals high propensity of C-H…F interactions in organic crystals. The present structural study suggests much larger role of fluorine driven intermolecular interactions that are even though weak, but possess significant ability to direct and alter the packing.

  12. [Iliopsoas muscle syndrome. Functional disorders: shortening, spasm and weakness of a structurally unchanged muscle].

    Science.gov (United States)

    Grgić, Vjekoslav

    2009-01-01

    Functional (non-organic) disorders of the iliopsoas muscle (IPM), i.e. the shortening, spasm and weakness of the structurally unchanged IPM, can be manifested as abdominal and/or pelvic pain, pain in areas of the thoracolumbar (ThL) and lumbosacral (LS) spine, sacroiliac (SI) joint, hip, groin and anterior thigh on the side of the affected muscle as well as gait disturbances (iliopsoas muscle syndrome). By clinical examination of the IPM, including the transabdominal palpation, stretch and strength tests, pathological masses, shortening, painful spasm, weakness and tendon tenderness of that muscle can be diagnosed. The IPM is, like other postural muscles, inclined to shortening. The weakness of the IPM can be a consequence of the lesion of the lumbar plexus or femoral nerve that innervate the IPM, as well as a consequence of certain organic diseases of the IPM. Painful stimuli coming from somatic and visceral structures that are innervated from Th12-L4 nerve roots, from which the IPM segmental innervation also originates, can cause a reflex spasm of the IPM. A painful spasm of the IPM caused by disorders of the ThL and LS spine, SI and hip joint, can mimic diseases of the abdominal and pelvic organs. In the differential diagnosis of the IPM painful spasm, organic diseases of that muscle should be considered foremost (abscess, hematoma, tumor, metastase), as they can result in spasm, and the diseases of the abdominal and pelvic organs that can cause an IPM reflex spasm. The IPM functional disorders, which are not rare, are often overlooked during a clinical examination of a patient. Reasons for overlooking these disorders are: 1) a nonspecific and variable clinical picture presenting the IPM functional disorders, 2) the IPM functional disorders are a neglected source of pain, 3) the inaccessibility of the IPM for inspection, 4) the lack of knowledge of the IPM examination techniques and 5) the IPM functional disorders cannot be discovered by radiological

  13. 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.

  14. 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)

  15. 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.

  16. 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....

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. 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.

  2. Crystal structure and Hirshfeld surface analysis of ethyl 5-phenylisoxazole-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Althaf Shaik

    2017-04-01

    Full Text Available The title compound, C12H11NO3, is an intermediate used in the synthesis of many drug-like molecules. The molecule is almost planar, with the phenyl ring inclined to the isoxazole ring by 0.5 (1°. The ester moiety has an extended conformation and is almost in the same plane with respect to the isoxazole ring, as indicated by the O—C—C—N torsion angle of −172.86 (18°. In the crystal, molecules are linked via pairs of C—H...O hydrogen bonds with the same acceptor atom, forming inversion dimers with two R21(7 ring motifs. The molecules stack in layers lying parallel to (10-3. Analysis using Hirshfeld surface generation and two-dimensional fingerprint plots explores the distribution of weak intermolecular interactions in the crystal structure.

  3. 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.

  4. Synthesis,Crystal Structure and Magnetic Properties of Novel Three-dimensional Frameworks [Mn(PDC)H2O]n

    Institute of Scientific and Technical Information of China (English)

    GAO En-Jun; GU Xiao-Fu; SUN Ya-Guang; YIN Hong-Xi; WU Qiong; LIU Lei; ZHU Ming-Chang; ZHANG Wan-Zhong

    2008-01-01

    A novel coordination polymer,[Mn(PDC)H2O]n(1)(H2PDC=pyridine-2,3-dicarboxylic acid),has been hydrothermally synthesized and characterized by elemental analysis,IR and single crystal X-ray diffraction.X-ray single crystal structural analyses revealed that two-dimensional frameworks were formed,and further assembled into a three-dimensional supramolecular structure bridged by PDC ligands.Moreover,the magnetic study of complex 1 shows weak antiferromagnetic interaction between the neighboring Mn(Ⅱ)centers within the chains and even weak ferromagnetic interactions between the Mn(Ⅱ)centers in different chains.

  5. 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)

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.)

  12. 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...

  13. 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.

  14. 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.

  15. Nuclear structure properties and stellar weak rates for 76Se: Unblocking of the Gamow Teller strength

    Science.gov (United States)

    Nabi, Jameel-Un; Ishfaq, Mavra; Böyükata, Mahmut; Riaz, Muhammad

    2017-10-01

    At finite temperatures (≥ 107K), 76Se is abundant in the core of massive stars and electron capture on 76Se has a consequential role to play in the dynamics of core-collapse. The present work may be classified into two main categories. In the first phase we study the nuclear structure properties of 76Se using the interacting boson model-1 (IBM-1). The IBM-1 investigations include the energy levels, B (E 2) values and the prediction of the geometry. We performed the extended consistent-Q formalism (ECQF) calculation and later the triaxial formalism calculation (constructed by adding the cubic term to the ECQF). The geometry of 76Se can be envisioned within the formalism of the potential energy surface based on the classical limit of IBM-1 model. In the second phase, we reconfirm the unblocking of the Gamow-Teller (GT) strength in 76Se (a test case for nuclei having N > 40 and Z < 40). Using the deformed pn-QRPA model we calculate GT transitions, stellar electron capture cross section (within the limit of low momentum transfer) and stellar weak rates for 76Se. The distinguishing feature of our calculation is a state-by-state evaluation of stellar weak rates in a fully microscopic fashion. Results are compared with experimental data and previous calculations. The calculated GT distribution fulfills the Ikeda sum rule. Rates for β-delayed neutrons and emission probabilities are also calculated. Our study suggests that at high stellar temperatures and low densities, the β+-decay on 76Se should not be neglected and needs to be taken into consideration along with electron capture rates for simulation of presupernova evolution of massive stars.

  16. Arthritis induces early bone high turnover, structural degradation and mechanical weakness.

    Directory of Open Access Journals (Sweden)

    Bruno Vidal

    Full Text Available We have previously found in the chronic SKG mouse model of arthritis that long standing (5 and 8 months inflammation directly leads to high collagen bone turnover, disorganization of the collagen network, disturbed bone microstructure and degradation of bone biomechanical properties. The main goal of the present work was to study the effects of the first days of the inflammatory process on the microarchitecture and mechanical properties of bone.Twenty eight Wistar adjuvant-induced arthritis (AIA rats were monitored during 22 days after disease induction for the inflammatory score, ankle perimeter and body weight. Healthy non-arthritic rats were used as controls for compar-ison. After 22 days of disease progression rats were sacrificed and bone samples were collected for histomorphometrical, energy dispersive X-ray spectroscopical analysis and 3-point bending. Blood samples were also collected for bone turnover markers.AIA rats had an increased bone turnover (as inferred from increased P1NP and CTX1, p = 0.0010 and p = 0.0002, respectively and this was paralleled by a decreased mineral content (calcium p = 0.0046 and phos-phorus p = 0.0046. Histomorphometry showed a lower trabecular thickness (p = 0.0002 and bone volume (p = 0.0003 and higher trabecular sepa-ration (p = 0.0009 in the arthritic group as compared with controls. In addition, bone mechanical tests showed evidence of fragility as depicted by diminished values of yield stress and ultimate fracture point (p = 0.0061 and p = 0.0279, re-spectively in the arthritic group.We have shown in an AIA rat model that arthritis induc-es early bone high turnover, structural degradation, mineral loss and mechanical weak-ness.

  17. Arthritis induces early bone high turnover, structural degradation and mechanical weakness.

    Science.gov (United States)

    Vidal, Bruno; Cascão, Rita; Vale, Ana Catarina; Cavaleiro, Inês; Vaz, Maria Fátima; Brito, José Américo Almeida; Canhão, Helena; Fonseca, João Eurico

    2015-01-01

    We have previously found in the chronic SKG mouse model of arthritis that long standing (5 and 8 months) inflammation directly leads to high collagen bone turnover, disorganization of the collagen network, disturbed bone microstructure and degradation of bone biomechanical properties. The main goal of the present work was to study the effects of the first days of the inflammatory process on the microarchitecture and mechanical properties of bone. Twenty eight Wistar adjuvant-induced arthritis (AIA) rats were monitored during 22 days after disease induction for the inflammatory score, ankle perimeter and body weight. Healthy non-arthritic rats were used as controls for compar-ison. After 22 days of disease progression rats were sacrificed and bone samples were collected for histomorphometrical, energy dispersive X-ray spectroscopical analysis and 3-point bending. Blood samples were also collected for bone turnover markers. AIA rats had an increased bone turnover (as inferred from increased P1NP and CTX1, p = 0.0010 and p = 0.0002, respectively) and this was paralleled by a decreased mineral content (calcium p = 0.0046 and phos-phorus p = 0.0046). Histomorphometry showed a lower trabecular thickness (p = 0.0002) and bone volume (p = 0.0003) and higher trabecular sepa-ration (p = 0.0009) in the arthritic group as compared with controls. In addition, bone mechanical tests showed evidence of fragility as depicted by diminished values of yield stress and ultimate fracture point (p = 0.0061 and p = 0.0279, re-spectively) in the arthritic group. We have shown in an AIA rat model that arthritis induc-es early bone high turnover, structural degradation, mineral loss and mechanical weak-ness.

  18. Growth and characterization of large weak topological insulator Bi2TeI single crystal by Bismuth self-flux method

    Science.gov (United States)

    Ryu, Gihun; Son, Kwanghyo; Schütz, Gisela

    2016-04-01

    Two dimensional (2D) topological insulators (TIs) with a quantum spin Hall (QSH) effect feature edge states (ESs) that are topologically protected from backscattering. Bi2TeI with 2D Bismuth bilayer is one of the representative compounds of weak topological insulator. However, nobody has prepared a high quality single crystal with a millimeter size so far. Here, we have successfully synthesized a large single crystal sized up to "millimeter (~5×5 mm2)" using the Bismuth self-flux method. And we also found its giant anisotropy transport behavior in Bi2TeI of a 2D TI constructed from nontrivial Bi bilayers (Quantum Spin Hall phase) capped by a trivial Te-Bi-I layer.

  19. 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....

  20. 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....

  1. 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.

  2. 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

  3. 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...

  4. 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....

  5. 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

  6. 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...

  7. 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...

  8. 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.

  9. 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.…

  10. Network structural analysis using directed graph for chemical reaction analysis in weakly-ionized plasmas

    Science.gov (United States)

    Nobuto, Kyosuke; Mizui, Yasutaka; Miyagi, Shigeyuki; Sakai, Osamu; Murakami, Tomoyuki

    2016-09-01

    We visualize complicated chemical reaction systems in weakly-ionized plasmas by analysing network structure for chemical processes, and calculate some indexes by assuming interspecies relationships to be a network to clarify them. With the current social evolution, the mean size of general data which we can use in computers grows huge, and significance of the data analysis increases. The methods of the network analysis which we focus on in this study do not depend on a specific analysis target, but the field where it has been already applied is still limited. In this study, we analyse chemical reaction systems in plasmas for configuring the network structure. We visualize them by expressing a reaction system in a specific plasma by a directed graph and examine the indexes and the relations with the characteristic of the species in the reaction system. For example, in the methane plasma network, the centrality index reveals importance of CH3 in an influential position of species in the reaction. In addition, silane and atmospheric pressure plasmas can be also visualized in reaction networks, suggesting other characteristics in the centrality indexes.

  11. A unified picture of the crystal structures of metals

    Science.gov (United States)

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

    1995-04-01

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

  12. Crystal structure of 2,4,6-tris-(cyclo-hex-yloxy)-1,3,5-triazine.

    Science.gov (United States)

    Sankolli, Ravish; Hauser, Jürg; Row, T N Guru; Hulliger, Jürg

    2015-11-01

    The title compound, C21H33N3O3, is a tri-substituted cyclo-hex-yloxy triazine. In the crystal, the triazine rings form (C3i-PU) Piedfort units. The inter-centroid distance of the π-π inter-action involving the triazine rings is 3.3914 (10) Å. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming ribbons propagating along [1-10]. There are also weak C-H⋯N and C-H⋯O contacts present, linking inversion-related ribbons, forming a three-dimensional structure.

  13. Synthesis, Crystal Structure and Theoretically Study of 2-(Dimethylamino)-1,3-dithiocyanatopropane and Its Isomer

    Institute of Scientific and Technical Information of China (English)

    YU Guan-ping; MA Yi; LIU Zhuo; WANG Gang; LI Zheng-ming

    2011-01-01

    2-(Dimethylamino)-1,3-dithiocyanatopropane(1)has been prepared as a key intermediate synthesizing a natural insecticide Cartap by the reaction of 1-dimethylamino-2,3-dichloropropane with sodium thiocyanate.The crystal structures of compound 1 and its isomer 1-(dimethylamino)-2,3-dithiocyanotopropane(2)formed during the reaction were determined by X-ray single-crystal diffraction.Bond lengths in both the compounds are common and fall within normal ranges.There are some weak C-H…N hydrogen bonds in the lattice of compound 1,which makes it form a three-dimensional network,which stabilize the crystal structure.No classic hydrogen bonds were founded in its isomer(2),only van der Waals forces contribute to the stability of the structure.In addition,DFT and MP2 calculations with 6-311+G(d,p)basis set have also been carried out to investigate the thermodynamic properties of compounds 1 and 2.The research will be applied to the further investigation of the tautomerization of compounds 1 and 2.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Synthesis, crystal structure and magnetic properties of U 2Co 6Al 19

    Science.gov (United States)

    Tougait, O.; Stêpieň-Damm, J.; Zaremba, V.; Noël, H.; Troc, R.

    2003-08-01

    The new compound U 2Co 6Al 19 was prepared by reaction of the elemental components in an arc-melting furnace followed by a heat treatment at 1050°C for 500 h. Its chemical composition was checked by energy-dispersive X-ray analyses and its crystal structure was determined by single crystal X-ray diffraction experiments. It crystallizes with four formula units in the monoclinic space group C2/ m in a unit cell of dimensions a=17.4617(3) Å, b=12.0474(2) Å, c=8.2003(1) Å, β=103.915(1)°. The crystal structure of U 2Co 6Al 19 can be regarded as a superstructure of NdCo 4- xGa 9 structure type. This complex structure consists of a three-dimensional Co-Al framework delimiting tunnels where the U atoms reside. The shortest U-U distances are found in the c direction with alternating values of 3.98(1) and 4.22(1) Å. Temperature-dependent magnetization shows a first peak at 12.5 K and a weak ferromagnetic character below the temperature TC=8 K. Magnetization at 1.9 K reaches almost saturation in 5 T with the moment of 0.36 μ B/U atom. The complex magnetic behavior of U 2Co 6Al 19 may be ascribed to a canted spin structure resulting from an antiparallel arrangement of the magnetic moments not fully compensated at low temperature. At higher temperature, the compound displays simple paramagnetic behavior.

  7. 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.

  8. 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.).

  9. 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.

  10. 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.

  11. 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.

  12. 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−.

  13. 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.

  14. 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.

  15. Crystal structures of three N-(aryl-sulfon-yl)-4-fluoro-benzamides.

    Science.gov (United States)

    Suchetan, P A; Naveen, S; Lokanath, N K; Srivishnu, K S; Supriya, G M; Lakshmikantha, H N

    2016-04-01

    The crystal structures of three N-aryl-sulfonyl-4-fluoro-benzamides, namely 4-fluoro-N-(2-methyl-phenyl-sulfon-yl)benzamide, C14H12FNO3S, (I), N-(2-chloro-phenyl-sulfon-yl)-4-fluorobenzamide, C13H9ClFNO3S, (II), and N-(4-chloro-phenyl-sulfon-yl)-4-fluoro-benzamide monohydrate, C13H9ClFNO3S·H2O, (III), are described and compared with related structures. The asymmetric unit of (I) contains two independent mol-ecules (A and B), while that of (II) contains just one mol-ecule, and that of (III) contains a mol-ecule of water in addition to one main mol-ecule. The dihedral angle between the benzene rings is 82.83 (11)° in mol-ecule A and 85.01 (10)° in mol-ecule B of (I), compared to 89.91 (10)° in (II) and 81.82 (11)° in (III). The crystal structure of (I) features strong N-H⋯O hydrogen bonds between the A and B mol-ecules, resulting in an R 4 (4)(16) tetra-meric unit. These tetra-meric units are connected into sheets in the bc plane by various C-H⋯O inter-actions, and adjacent sheets are further inter-linked via C-H⋯πar-yl inter-actions, forming a three-dimensional architecture. The crystal structure is further stabilized by πar-yl-πar-yl and S=O⋯πar-yl inter-actions. In the crystal of (II), mol-ecules are connected into R 2 (2)(8) and R 2 (2)(14) dimers via N-H⋯O hydrogen bonds and C-H⋯O inter-actions, respectively; the dimers are further inter-connected via a weak C=O⋯πar-yl inter-action, leading to the formation of chains along [1-10]. In the crystal of (III), N-H⋯O and O-H⋯O hydrogen bonds involving both the main mol-ecule and the solvent water mol-ecule results in the formation of sheets parallel to the bc plane. The sheets are further connected by C-H⋯O inter-actions and weak C-Cl⋯πar-yl, C-F⋯πar-yl and S=O⋯πar-yl inter-actions, forming a three-dimensional architecture.

  16. Optical bistability and four-wave mixing with a single nitrogen-vacancy center coupled to a photonic crystal nanocavity in the weak-coupling regime.

    Science.gov (United States)

    Li, Jiahua; Yu, Rong; Ding, Chunling; Wu, Ying

    2014-06-16

    We explore optical bistability and degenerate four-wave mixing of a hybrid optical system composed of a photonic crystal nanocavity, a single nitrogen-vacancy center embedded in the cavity, and a nearby photonic waveguide serving for in- and outcoupling of light into the cavity in the weak-coupling regime. Here the hybrid system is coherently driven by a continuous-wave bichromatic laser field consisting of a strong control field and a weak probe field. We take account of the nonlinear nature of the nitrogen-vacancy center in the Heisenberg-Langevin equations and give an effective perturbation method to deal with such problems in the continuous-wave-operation regime. The results clearly show that the bistability region of the population inversion and the intensity of the generated four-wave mixing field can be well controlled by properly adjusting the system practical parameters. The nanophotonic platform can be used to implement our proposal. This investigation may be useful for gaining further insight into the properties of solid-state cavity quantum electrodynamics system and find applications in all-optical wavelength converter and switch in a photonic crystal platform.

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

    Science.gov (United States)

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

    2015-07-15

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

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

    Science.gov (United States)

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

    2010-01-01

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

  19. Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

    Science.gov (United States)

    Cherifi, Youcef Amine; Gaouar, Suheil Bechir Semir; Guastamacchia, Rosangela; El-Bahrawy, Khalid Ahmed; Abushady, Asmaa Mohammed Aly; Sharaf, Abdoallah Aboelnasr; Harek, Derradji; Lacalandra, Giovanni Michele; Saïdi-Mehtar, Nadhira

    2017-01-01

    Knowledge on genetic diversity and structure of camel populations is fundamental for sustainable herd management and breeding program implementation in this species. Here we characterized a total of 331 camels from Northern Africa, representative of six populations and thirteen Algerian and Egyptian geographic regions, using 20 STR markers. The nineteen polymorphic loci displayed an average of 9.79 ± 5.31 alleles, ranging from 2 (CVRL8) to 24 (CVRL1D). Average He was 0.647 ± 0.173. Eleven loci deviated significantly from Hardy-Weinberg proportions (P<0.05), due to excess of homozygous genotypes in all cases except one (CMS18). Distribution of genetic diversity along a weak geographic gradient as suggested by network analysis was not supported by either unsupervised and supervised Bayesian clustering. Traditional extensive/nomadic herding practices, together with the historical use as a long-range beast of burden and its peculiar evolutionary history, with domestication likely occurring from a bottlenecked and geographically confined wild progenitor, may explain the observed genetic patterns. PMID:28103238

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

    CERN Document Server

    McBride, L

    2000-01-01

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

  1. Weak Galois and Weak Cocleft Coextensions

    Institute of Scientific and Technical Information of China (English)

    J.N. Alonso (A)lvarez; J.M. Fernández Vilaboa; R. González Rodríguez; A.B. Rodríguez Raposo

    2007-01-01

    For a weak entwining structure (A, C,ψ) living in a braided monoidal category with equalizers and coequalizers, we formulate the notion of weak A-Galois coextension with normal basis and we show that these Galois coextensions are equivalent to the weak A-cocleft coextensions introduced by the authors.

  2. Effect of crystal structure of manganese dioxide on response for electrolyte of ahydrogen sensor operative at room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Koyanaka, Hideki [Forward Science Laboratory Ltd, Oita, Japan; Ueda, Yoshikatsu [Kyoto University, Japan; Takeuchi, K [Tokyo University of Science, Oshamanbe Hokkaido, Japan; Kolesnikov, Alexander I [ORNL

    2013-01-01

    Sensoring properties of a hydrogen sensor that used electrolytes made of different crystal type manganese dioxides were compared. An electrolyte made of a manganese dioxide, which has a high purity of ramsdellite-type crystal structure, provided the best characteristics for the hydrogen sensor. To explain the sensor property, network model of oxygen-pairs to store protons with a weak covalent bond and to conduct protons along the network in the ideal crystal structure of ramsdellite manganese dioxide was proposed. The inter-atomic distance of those oxygen-pairs in the high purity of ramsdellite manganese dioxide was estimated between 2.57 and 2.60 A using inelastic neutron scattering measurements. The property of the hydrogen sensor supported the unique proton conduction based on the network model.

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

    Directory of Open Access Journals (Sweden)

    Rodolfo Moreno-Fuquen

    2015-06-01

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

  4. Crystal structure of 3-benzamido-1-(4-nitrobenzylquinolinium trifluoromethanesulfonate

    Directory of Open Access Journals (Sweden)

    Mariana Nicolas-Gomez

    2016-05-01

    Full Text Available In the title compound, C23H18N3O3+·CF3SO3−, the asymmetric unit contains two crystallographically independent organic cations with similar conformations. Each cation shows a moderate distortion between the planes of the amide groups and the quinolinium rings with dihedral angles of 14.90 (2 and 31.66 (2°. The quinolinium and phenyl rings are slightly twisted with respect to each other at dihedral angles of 6.99 (4 and 8.54 (4°. The trifluoromethanesulfonate anions are linked to the organic cations via N—H...O hydrogen-bonding interactions involving the NH amide groups. In the crystal, the organic cations are linked by weak C—H...O(nitro group interactions into supramolecular chains propagating along the b-axis direction.

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

    Directory of Open Access Journals (Sweden)

    Min Wu

    2015-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Muhammad Shahid

    2015-07-01

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

  7. 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.

  8. 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.

  9. 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.)

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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·.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Synthesis, crystal structure, Hirshfeld surface analysis, electronic structure through DFT study and fluorescence properties of a new anthracene based organic tecton

    Science.gov (United States)

    Pal, Nilasish; Singha, Debabrata; Jana, Atish Dipankar

    2017-10-01

    A new organic molecule 9,10-bis((2-(pyridin-2-yl)-1H-imidazol-1-yl)methyl)anthracene (APIM) has been synthesized. Crystal structure analysis of the molecular solid reveals that CH⋯π and π⋯π interactions are the molecular packing forces in the solid state. Thermal analysis of the molecular solid shows relatively higher decomposition temperature of the crystalline molecular solid that correlates well with the cooperative nature of CH⋯π and π⋯π interactions. Density Functional Theory (DFT) optimized structure of the molecule closely correlates with that found in the crystal. DFT optimizations also lead to the similar CH⋯π and π⋯π interaction motifs that are found within the crystal. Hirshfeld surface analysis provides detailed insight into the relative importance of various weak forces in the molecular packing. Study of the fluorescence behavior of the molecules shows quenching in the presence of metal ions.

  19. Coexistence of Weak Ferromagnetism and Polar Lattice Distortion in Epitaxial NiTiO3 thin films of the LiNbO3-Type Structure

    Energy Technology Data Exchange (ETDEWEB)

    Varga, Tamas [Environmental Molecular Sciences Lab., Richland, WA (United States); Droubay, Timothy C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bowden, Mark E. [Environmental Molecular Sciences Lab., Richland, WA (United States); Colby, Robert J. [Environmental Molecular Sciences Lab., Richland, WA (United States); Manandhar, Sandeep [Environmental Molecular Sciences Lab., Richland, WA (United States); Shutthanandan, Vaithiyalingam [Environmental Molecular Sciences Lab., Richland, WA (United States); Hu, Dehong [Environmental Molecular Sciences Lab., Richland, WA (United States); Kabius, Bernd C. [Environmental Molecular Sciences Lab., Richland, WA (United States); Apra, Edoardo [Environmental Molecular Sciences Lab., Richland, WA (United States); Shelton, William A. [Environmental Molecular Sciences Lab., Richland, WA (United States); Chambers, Scott A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-04-15

    We report the magnetic and structural characteristics of epitaxial NiTiO3 films grown by pulsed laser deposition that are isostructural with acentric LiNbO3 (space group R3c). Optical second harmonic generation and magnetometry demonstrate lattice polarization at room temperature and weak ferromagnetism below 250 K, respectively. These results appear to be consistent with earlier predictions from first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LiNbO3 structure. This acentric form of NiTiO3 is believed to be one of the rare examples of ferroelectrics exhibiting weak ferromagnetism generated by a Dzyaloshinskii-Moriya interaction.

  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. The structure of weak Pareto solution sets in piecewise linear multiobjective optimization in normed spaces

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In general normed spaces,we consider a multiobjective piecewise linear optimization problem with the ordering cone being convex and having a nonempty interior.We establish that the weak Pareto optimal solution set of such a problem is the union of finitely many polyhedra and that this set is also arcwise connected under the cone convexity assumption of the objective function.Moreover,we provide necessary and suffcient conditions about the existence of weak(sharp) Pareto solutions.

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

    Science.gov (United States)

    Thomas, Noel W

    2015-08-01

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

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

    Science.gov (United States)

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

    2014-09-16

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

  2. 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.

  3. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-02-24

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

  4. On Weak Regular *-semigroups

    Institute of Scientific and Technical Information of China (English)

    Yong Hua LI; Hai Bin KAN; Bing Jun YU

    2004-01-01

    In this paper, a special kind of partial algebras called projective partial groupoids is defined.It is proved that the inverse image of all projections of a fundamental weak regular *-semigroup under the homomorphism induced by the maximum idempotent-separating congruence of a weak regular *-semigroup has a projective partial groupoid structure. Moreover, a weak regular *-product which connects a fundamental weak regular *-semigroup with corresponding projective partial groupoid is defined and characterized. It is finally proved that every weak regular *-product is in fact a weak regular *-semigroup and any weak regular *-semigroup is constructed in this way.

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    A.V. Mukhametshin

    2017-03-01

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

  7. Crystal 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...

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. 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.

  14. 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.

  15. 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.

  16. Far-infrared optical constants of a selection of zincblende structure crystals at 300 K

    Science.gov (United States)

    Maslin, K. A.; Parker, T. J.; Patel, C.

    The far-infrared amplitude and phase reflection spectra of six group III-V single crystal compounds (GaP, GaAs, GaSb, InP, InAs, and InSb) and two group II-VI single crystal compounds (CdTe and ZnSe) with the zincblende structure have been determined at room temperature in the region of their reststrahlen bands by reflection dispersive Fourier transform spectroscopy. The measured amplitude and phase reflection spectra and values of the optical constants calculated from them are presented. As an illustration of weak mode anharmonicity in these crystals, the imaginary part of the anharmonic self-energy of the infrared-active transverse optic mode of ZnSe at the center of the Brillouin zone is calculated from its measured dielectric functions. Prominent features in the self-energy function in the region of the reststrahlen band are assigned as phonon combination bands with the aid of critical point phonon frequencies derived from an 11-parameter rigid-ion model.

  17. 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'.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Hydrogen bonded helices: Synthesis, crystal structure and self-assembled microtubes

    Science.gov (United States)

    Mosae Selvakumar, P.; Suresh, E.; Subramanian, P. S.

    2009-02-01

    Dicarboxylic bola-shaped compounds 1- 3, possessing phthalyl head groups and diol spacers are synthesized and characterized. Keeping phthalyl head group common for all three diester-dicarboxylic acids, the spacer moiety is systematically altered by two and four carbon atoms in 1 and 2, 3, respectively. The flexible spacer moiety ethane-1,2-diol in compound 1 is replaced by cis-but-2-ene-1,4-diol and 1,4-butane diol in 2 and 3, respectively, to study the effect on the morphology of the microcrystal grown on them. Thus compound 2 and 3 though posses four carbon atoms in their respective spacer moiety, they differ by their rigidity. The single crystal X-ray structure obtained for 1, 2 and 3 indicates the formation of self-assembled single stranded helical structure mediated through O-H…O interaction of the end carboxylic acids. Interestingly compound 1 self-assembled into microtubes in ethanol:water solvent mixture. The solvent and the O-H…O; C-H…O interaction combinedly play crucial role in molecular self-assembly process and defines the morphology for 1 into "microtube" whereas 2 and 3 forming "bar" fails to produce such tubular texture though their respective crystal structure shows single stranded helices. The role of weak C-H...O interaction, incorporation of rigid spacer and various other factors such as polarity of the solvents are discussed in detail to explore the difference in the morphology.

  4. Inkjet Printing Based Mono-layered Photonic Crystal Patterning for Anti-counterfeiting Structural Colors

    Science.gov (United States)

    Nam, Hyunmoon; Song, Kyungjun; Ha, Dogyeong; Kim, Taesung

    2016-08-01

    Photonic crystal structures can be created to manipulate electromagnetic waves so that many studies have focused on designing photonic band-gaps for various applications including sensors, LEDs, lasers, and optical fibers. Here, we show that mono-layered, self-assembled photonic crystals (SAPCs) fabricated by using an inkjet printer exhibit extremely weak structural colors and multiple colorful holograms so that they can be utilized in anti-counterfeit measures. We demonstrate that SAPC patterns on a white background are covert under daylight, such that pattern detection can be avoided, but they become overt in a simple manner under strong illumination with smartphone flash light and/or on a black background, showing remarkable potential for anti-counterfeit techniques. Besides, we demonstrate that SAPCs yield different RGB histograms that depend on viewing angles and pattern densities, thus enhancing their cryptographic capabilities. Hence, the structural colorations designed by inkjet printers would not only produce optical holograms for the simple authentication of many items and products but also enable a high-secure anti-counterfeit technique.

  5. 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°.

  6. 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.

  7. Crystal structure of the Fe-member of usovite

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2015-06-01

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

  8. 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.

  9. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatecobalt(II

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-01-01

    Full Text Available The structure of the mononuclear title complex, [{(H3CS2C=NC[triple-bond] N}2CoCl2], consists of a CoII atom coordinated in a distorted tetrahedral manner by two Cl− ligands and the terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515 (su? Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.

  10. 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.

  11. 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.

  12. 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.

  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. X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.

    Science.gov (United States)

    Catalano, Alessia; Luciani, Rosaria; Carocci, Alessia; Cortesi, Debora; Pozzi, Cecilia; Borsari, Chiara; Ferrari, Stefania; Mangani, Stefano

    2016-11-10

    Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that species-specific inhibition of the protein can be achieved despite the relatively high structural similarity among bacterial TSs and human TS. We had previously obtained the EfTS crystal structure of the protein in complex with the metabolite 5-formyl-tetrahydrofolate (5-FTHF) suggesting the protein role as metabolite reservoir; however, protein-inhibitors complexes were still missing. In the present work we identified some inhibitors bearing the phthalimidic core from our in-house library and we performed crystallographic screening towards EfTS. We obtained two X-ray crystallographic structures: the first with a weak phthalimidic inhibitor bound in one subunit and 5-hydroxymethylene-6-hydrofolic acid (5-HMHF) in the other subunit; a second X-ray structure complex with methotrexate. The structural information achieved confirm the role of EfTS as an enzyme involved in the folate pool system and provide a structural basis for structure-based drug design.

  17. Quadriceps Weakness, Patella Alta and Structural Features of Patellofemoral Osteoarthritis: The Multicenter Osteoarthritis Study

    Science.gov (United States)

    Stefanik, Joshua J.; Guermazi, Ali; Zhu, Yanyan; Zumwalt, Ann C.; Gross, K. Douglas; Clancy, Margaret; Lynch, John A.; Segal, Neil A.; Lewis, Cora E.; Roemer, Frank W.; Powers, Christopher M.; Felson, David T.

    2011-01-01

    Objective To determine the relationship between quadriceps weakness and cartilage damage and bone marrow lesions (BMLs) in the patellofemoral joint (PFJ), and if this relationship is modified by patella alta. Methods The Multicenter Osteoarthritis (MOST) Study is a cohort study of persons aged 50–79 years with or at risk for knee OA. Concentric knee extensor strength was measured using an isokinetic dynamometer. Patella alta was measured using the Insall-Salvati ratio (ISR) on the lateral radiograph, and cartilage damage and bone marrow lesions (BMLs) were graded on MRI in the PFJ. We determined the association between quadriceps weakness with cartilage damage and BMLs in the PFJ among those knees with (ISR≥1.2) and without patella alta (ISRpatella alta in the lateral PFJ. Conclusion Quadriceps weakness was associated with PFJ cartilage damage and BMLs. While both patella alta and quadriceps weakness are associated with PFJ damage, the combination of the two was not associated with more damage than either of these factors alone. PMID:21702087

  18. 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.

  19. 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).

  20. 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)

  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. 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.

  5. Magnetic properties of weakly exchange-coupled high spin Co(II) ions in pseudooctahedral coordination evaluated by single crystal X-band EPR spectroscopy and magnetic measurements.

    Science.gov (United States)

    Neuman, Nicolás I; Winkler, Elín; Peña, Octavio; Passeggi, Mario C G; Rizzi, Alberto C; Brondino, Carlos D

    2014-03-01

    We report single-crystal X-band EPR and magnetic measurements of the coordination polymer catena-(trans-(μ2-fumarato)tetraaquacobalt(II)), 1, and the Co(II)-doped Zn(II) analogue, 2, in different Zn:Co ratios. 1 presents two magnetically inequivalent high spin S = 3/2 Co(II) ions per unit cell, named A and B, in a distorted octahedral environment coordinated to four water oxygen atoms and trans coordinated to two carboxylic oxygen atoms from the fumarate anions, in which the Co(II) ions are linked by hydrogen bonds and fumarate molecules. Magnetic susceptibility and magnetization measurements of 1 indicate weak antiferromagnetic exchange interactions between the S = 3/2 spins of the Co(II) ions in the crystal lattice. Oriented single crystal EPR experiments of 1 and 2 were used to evaluate the molecular g-tensor and the different exchange coupling constants between the Co(II) ions, assuming an effective spin S′= 1/2. Unexpectedly, the eigenvectors of the molecular g-tensor were not lying along any preferential bond direction, indicating that, in high spin Co(II) ions in roughly octahedral geometry with approximately axial EPR signals, the presence of molecular pseudo axes in the metal site does not determine preferential directions for the molecular g-tensor. The EPR experiment and magnetic measurements, together with a theoretical analysis relating the coupling constants obtained from both techniques, allowed us to evaluate selectively the exchange coupling constant associated with hydrogen bonds that connect magnetically inequivalent Co(II) ions (|JAB(1/2)| = 0.055(2) cm(–1)) and the exchange coupling constant associated with a fumarate bridge connecting equivalent Co(II) ions (|JAA(1/2)| ≈ 0.25 (1) cm(–1)), in good agreement with the average J(3/2) value determined from magnetic measurements.

  6. Crystal structure of bis[4-(4-chlorobenzylpyridine-κN]bis(thiocyanato-κNzinc

    Directory of Open Access Journals (Sweden)

    Julia Werner

    2014-10-01

    Full Text Available In the crystal structure of the title compound, [Zn(NCS2(C12H10ClN2], the Zn2+ cation is N-coordinated by two terminally bonded thiocyante anions and by two 4-(4-chlorobenzylpyridine ligands within a slightly distorted tetrahedron. The asymmetric unit consists of half of the discrete complex, the central Zn2+ cation of which is located on a twofold rotation axis. The discrete complexes are linked into layers via a weak intermolecular hydrogen-bonding interaction, with a H...Cl distance of 2.85 Å and a C—H...Cl angle of 151°. These layers extend parallel to the ab plane and are held together by dispersion forces only.

  7. Crystal structure of dimethyl 4,4′-dimethoxybiphenyl-3,3′-dicarboxylate

    Directory of Open Access Journals (Sweden)

    Fredrik Lundvall

    2016-03-01

    Full Text Available In the title compound, C18H18O6, the benzene rings are coplanar due to the centrosymmetric nature of the molecule, with an inversion centre located at the midpoint of the C—C bond between the two rings. Consequently, the methyl carboxylate substituents are oriented in a trans fashion with regards to the bond between the benzene rings. The methyl carboxylate and methoxy substituents are rotated slightly out of plane relative to their parent benzene rings, with dihedral and torsion angles of 18.52 (8 and −5.22 (15°, respectively. The shortest O...H contact between neighbouring molecules is about 2.5 Å. Although some structure-directing contributions from C—H...O hydrogen-bonding interactions are possible, the crystal packing seems primarily directed by weak van der Waals forces.

  8. Crystal structure of bis{μ-2-[(dimethylaminomethyl]ferroceneselenolato}bis[chloridopalladium(II

    Directory of Open Access Journals (Sweden)

    Esther M. Takaluoma

    2014-10-01

    Full Text Available The dinuclear title compound, [PdCl{Se[(C5H5Fe(C5H32CH2N(CH32]}]2 was obtained by the reaction of [PdCl2(NCPh2] with 2-[(N,N′-dimethylaminomethyl]ferroceneselenolate and the crystals for the structure determination were grown from a mixture of THF and n-hexane. Both PdII atoms are coordinated by the bridging Se atoms and by the amino N atoms of the bidentate 2-[(N,N′-dimethylaminomethyl]ferroceneselenolate ligand, as well as by Cl atoms, and show a distorted square-planar coordination. The angle between the Pd—Se—Se planes of the two Pd atoms is 149.31 (3°. Weak Cl...H hydrogen bonds link the binuclear complexes into a three-dimensional network.

  9. Crystal structure of [NiHg(SCN4(CH3OH2]n

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-08-01

    Full Text Available The title compound, catena-poly[[bis(methanol-κOnickel(II]-di-μ-thiocyanato-κ4N:S-mercurate(II-di-μ-thiocyanato-κ4N:S], was obtained from a gel-growth method using tetramethoxysilane as gelling agent. The crystal structure is composed of rather regular HgS4 tetrahedra (point group symmetry .2. and trans-NiN4O2 octahedra (point group symmetry 2.. that are linked through thiocyanato bridges into a three-dimensional framework. The methanol molecules coordinate via the O atom to the Ni2+ cations and point into the voids of this arrangement while a weak O—H...S hydrogen bond to an adjacent S atom stabilizes it.

  10. X-ray crystal and computational structural study of (E-2-[(2-chlorophenyliminomethyl]-4-methoxyphenol

    Directory of Open Access Journals (Sweden)

    Arzu Özek

    2008-08-01

    Full Text Available In the molecule of the title compound, C14H12ClNO, the two aromatic rings are oriented at a dihedral angle of 12.28 (7°. An intramolecular O—H...N hydrogen bond results in the formation of a nearly planar six-membered ring, which is oriented with respect to the aromatic rings at dihedral angles of 0.18 (5 and 12.10 (6°. In the crystal structure, weak intermolecular C—H...O hydrogen bonds link the molecules into chains along the c axis. There is a C—H...π contact between the methyl group and the chlorophenyl ring and a π–π contact between the two benzene rings [centroid–centroid distance = 3.866 (1 Å].

  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. The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix

    Science.gov (United States)

    Landis, W. J.

    1995-01-01

    High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

  16. The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix

    Science.gov (United States)

    Landis, W. J.

    1995-01-01

    High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

  17. 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.

  18. 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).

  19. 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.

  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.

  1. Potassium and magnesium succinatouranilates - Synthesis and crystal structure

    Science.gov (United States)

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

    2017-04-01

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

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

    Science.gov (United States)

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

    2017-06-20

    The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl(-)2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-26

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

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

    Science.gov (United States)

    Orlando, Benjamin J; Malkowski, Michael G

    2016-10-01

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

  5. Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.

    Science.gov (United States)

    Clausen, Johannes D; Bublitz, Maike; Arnou, Bertrand; Olesen, Claus; Andersen, Jens Peter; Møller, Jesper Vuust; Nissen, Poul

    2016-04-05

    Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase with bound vanadate in the absence of Ca(2+). Vanadate is bound at the catalytic site as a planar VO3(-) in complex with water and Mg(2+) in a dephosphorylation transition-state-like conformation. Validating bound VO3(-) by anomalous difference Fourier maps using long-wavelength data we also identify a hitherto undescribed Cl(-) site near the dephosphorylation site. Crystallization was facilitated by trinitrophenyl (TNP)-derivatized nucleotides that bind with the TNP moiety occupying the binding pocket that normally accommodates the adenine of ATP, rationalizing their remarkably high affinity for E2P-like conformations of the Ca(2+)-ATPase. A comparison of the configurations of bound nucleotide analogs in the E2·VO3(-) structure with that in E2·BeF3(-) (E2P ground state analog) reveals multiple binding modes to the Ca(2+)-ATPase.

  6. The local structure and ferromagnetism in Fe-implanted SrTiO3 single crystals

    Science.gov (United States)

    Lobacheva, O.; Chavarha, M.; Yiu, Y. M.; Sham, T. K.; Goncharova, L. V.

    2014-07-01

    We report a connection between the local structure of low-level Fe impurities and vacancies as the cause of ferromagnetic behavior observed in strontium titanate single crystals (STO), which were implanted with Fe and Si ions at different doses then annealed in oxygen. The effects of Fe doping and post-implantation annealing of STO were studied by X-ray Absorption Near Edge Structure (XANES) spectroscopy and Superconducting Quantum Interference Device magnetometry. XANES spectra for Fe and Ti K- and L-edge reveal the changes in the local environment of Fe and Ti following the implantation and annealing steps. The annealing in oxygen atmosphere partially healed implantation damages and changed the oxidation state of the implanted iron from metallic Fe0 to Fe2+/Fe3+ oxide. The STO single crystals were weak ferromagnets prior to implantation. The maximum saturation moment was obtained after our highest implantation dose of 2 × 1016 Fe atom/cm2, which could be correlated with the metallic Fe0 phases in addition to the presence of O/Ti vacancies. After recrystallization annealing, the ferromagnetic response disappears. Iron oxide phases with Fe2+ and Fe3+ corresponding to this regime were identified and confirmed by calculations using Real Space Multiple Scattering program (FEFF9).

  7. Crystal structure of 2-bromobenzoic acid at 120 K: a redetermination

    Directory of Open Access Journals (Sweden)

    Kornelia Kowalska

    2014-10-01

    Full Text Available The crystal structure of the title compound, C7H5BrO2, was originally studied using photographic data at room temperature with Cu Kα radiation [Ferguson & Sim (1962. Acta Cryst. 15, 346–350]. The present study was undertaken at 120 K with a CCD diffractometer using Cu Kα radiation, and resulted in improved geometrical parameters. In the molecule, the carboxy group is inclined to the benzene ring by 18.7 (2° and there is a close intramolecular Br...O contact of 3.009 (3 Å. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers with the classical R22(8 ring motif for carboxylic acids. Neighbouring dimers are linked by weak C—H...O hydrogen bonds, forming tapes propagating in [1-10]. Adjacent tapes interact by slipped parallel π–π interactions [inter-centroid distance = 3.991 (2, interplanar distance = 3.509 (2 Å, slippage = 1.900 Å] to form columns approximately along the b-axis direction. Neighbouring columns interact dispersively, forming a three-dimensional framework structure.

  8. Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-07

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

  9. Photonic crystal digital alloys and their band structure properties.

    Science.gov (United States)

    Lee, Jeongkug; Kim, Dong-Uk; Jeon, Heonsu

    2011-09-26

    We investigated semi-disordered photonic crystals (PCs), digital alloys, and made thorough comparisons with their counterparts, random alloys. A set of diamond lattice PC digital alloys operating in a microwave regime were prepared by alternately stacking two kinds of sub-PC systems composed of alumina and silica spheres of the same size. Measured transmission spectra as well as calculated band structures revealed that when the digital alloy period is short, band-gaps of the digital alloys are practically the same as those of the random alloys. This study indicates that the concept of digital alloys holds for photons in PCs as well.

  10. Crystal structure of pure ZrO{sub 2} nanopowders

    Energy Technology Data Exchange (ETDEWEB)

    Lamas, D.G. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina)]. E-mail: dlamas@citefa.gov.ar; Rosso, A.M. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Anzorena, M. Suarez [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Fernandez, A. [DEICOR - Departamento de Investigaciones en Corrosion, CITEFA, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Bellino, M.G. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Cabezas, M.D. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Walsoee de Reca, N.E. [CINSO - Centro de Investigaciones en Solidos, CITEFA-CONICET, J.B. de La Salle 4397 (1603) Villa Martelli, Pcia. de Buenos Aires (Argentina); Craievich, A.F. [Instituto de Fisica, FAP, USP, Travessa R da Rua do Matao, No.187, Cidade Universitaria (05508-900) Sao Paulo (Brazil)

    2006-09-15

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

  11. Crystal structure determination of anti-DNA Fab A52.

    Science.gov (United States)

    Stanfield, Robyn L; Eilat, Dan

    2014-08-01

    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  12. Crystal structure of hexa-aqua-dichlorido-ytterbium(III) chloride.

    Science.gov (United States)

    Knopf, Kevin M; Crundwell, Guy; Westcott, Barry L

    2015-06-01

    The crystal structure of the title compound, [YbCl2(H2O)6]Cl, was determined at 110 K. Samples were obtained from evaporated aceto-nitrile solutions containing the title compound, which consists of a [YbCl2(H2O)6](+) cation and a Cl(-) anion. The cations in the title compound sit on a twofold axis and form O-H⋯Cl hydrogen bonds with the nearby Cl(-) anion. The coordination geometry around the metal centre forms a distorted square anti-prism. The ytterbium complex is isotypic with the europium complex [Tambrornino et al. (2014 ▶). Acta Cryst. E70, i27].

  13. 9R structure in drawn industrial single crystal copper wires

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian; YAN Wen; FAN Xin-hui

    2009-01-01

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

  14. Topological Structure of Knotted Vortex Lines in Liquid Crystals

    Institute of Scientific and Technical Information of China (English)

    DUAN Yi-Shi; ZHAO Li; ZHANG Xin-Hui

    2007-01-01

    In this paper, a novel decomposition expression for the U(1) gauge field in liquid crystals (LCs) is derived.Using this decomposition expression and the φ-mapping topological current theory,.we investigate the topological structure of the vortex lines in LCs in detail. A topological invariant, i.e., the Chern-Simons (CS) action for the knotted vortex lines is presented, and the CS action is shown to be the total sum of all the self-linking and linking numbers of the knot family. Moreover, it is pointed out that the CS action is preserved in the branch processes of the knotted vortex lines.

  15. Synthesis, Crystal Structural Investigations, and DFT Calculations of Novel Thiosemicarbazones

    Directory of Open Access Journals (Sweden)

    Brian J. Anderson

    2016-02-01

    Full Text Available The crystal and molecular structures of three new thiosemicarbazones, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide monohydrate (1, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide (2 and 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide acetonitrile solvate (3, are reported and confirmed by single crystal X-ray diffraction, NMR and UV-vis spectroscopic data. Compound (1, C11H15N3O2S·H2O, crystallizes in the monoclinic with space group P21/c, with cell parameters a = 8.2304(3 Å, b = 16.2787(6 Å, c = 9.9708(4 Å, and β = 103.355(4°. Compound (2, C12H17N3O2S, crystallizes in the C2/c space group with cell parameters a = 23.3083(6 Å, b = 8.2956(2 Å, c = 13.5312(3 Å, β = 91.077(2°. Compound (3, C11H15N3O2S·C2H3N, crystallizes in the triclinic P-1 space group with cell constants a = 8.9384(7 Å, b = 9.5167(8 Å, c = 10.0574(8 Å, α = 110.773(7°, β = 92.413(6°, and γ = 90.654(7°. DFT B3LYP/6-31(G geometry optimized molecular orbital calculations were also performed and frontier molecular orbitals of each compound are displayed. The correlations between the calculated molecular orbital energies (eV for the surfaces of the frontier molecular orbitals to the electronic excitation transitions from the absorption spectra of each compound have been proposed. Additionally, similar correlations observed among three closely related compounds, (4, 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide, (5, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide acetonitrile monosolvate and (6, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide, examining structural differences from the substitution of the methoxy group from the phenyl ring (4, 5, or 6 position and the substitution of the terminal amine (methyl or ethyl to their frontier molecular orbital surfaces and from their Density Functional

  16. Syntheses, Crystal Structures and Bioactivities of Two Novel Isatin Derivatives

    Institute of Scientific and Technical Information of China (English)

    SHANG Jian-li; LI Hui-dong; SHANG Jun; SONG Hai-bin; LI Zheng-ming; WANG Jian-guo

    2011-01-01

    Two novel compoundsl-(4-fluorobenzyl)-4-chloro-(Z)-3-benzoylhydrazono-2-indolinone(1) and 1-(4-methoxybenzyl)-(Z)-3-benzoylhydrazono-2-indolinone(2) were synthesized and their crystal structures were determined by single-crystal X-ray diffraction.Compound 1(C22H15ClFN3O2) crystallized in the triclinic system,space group P1- with a=0.94198(19) nm,b=1.4339(3) nm,c=1.5018(3) nm,a=101.58(3)°,β=102.96(3)°,γ=102.73°,V=1.8602(6) nm3,Mr=407.82,Dc=1.456 g/cm3,μ=0.240 mm-1,F(000)=840,Z=4,R1=0.0442 and wR2=0.1064.Compound 2(C23H19N3O3) crystallized in the triclinic system,space group P1- with a=1.0022(2) nm,b=1.0192(2) nm,c=1.0461(2) nm,a=99.86(3)°,β=117.30(3)°,γ=94.13(3)°,V=0.9215(3) nm3,Mr=385.41,Dc=1.389 g/cm3,μ=0.094mm-1,F(000)=404,Z=2,R1=0.0403 and wR2=0.1142.The preliminary herbicidal activities of the two compounds were also evaluated.

  17. Electromagnetic structure and weak decay of meson K in a light-front QCD-inspired

    CERN Document Server

    Pereira, Fabiano P; Frederico, T; Tomio, Lauro

    2007-01-01

    The kaon electromagnetic (e.m.) form factor is reviewed considering a light-front constituent quark model. In this approach, it is discussed the relevance of the quark-antiquark pair terms for the full covariance of the e.m. current. It is also verified, by considering a QCD dynamical model, that a good agreement with experimental data can be obtained for the kaon weak decay constant once a probability of about 80% of the valence component is taken into account.

  18. Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

    Science.gov (United States)

    Koley, Biplab; Chatterjee, S.; Jana, Partha P.

    2017-02-01

    A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

  19. Crystal structures of three 6-substituted coumarin-3-carboxamide derivatives.

    Science.gov (United States)

    Gomes, Lígia R; Low, John Nicolson; Fonseca, André; Matos, Maria João; Borges, Fernanda

    2016-07-01

    Three coumarin derivatives, viz. 6-methyl-N-(3-methyl-phen-yl)-2-oxo-2H-chromene-3-carboxamide, C18H15NO3 (1), N-(3-meth-oxy-phen-yl)-6-methyl-2-oxo-2H-chromene-3-carboxamide, C18H15NO4 (2), and 6-meth-oxy-N-(3-meth-oxy-phen-yl)-2-oxo-2H-chromene-3-carboxamide, C18H15NO5 (3), were synthesized and structurally characterized. The mol-ecules display intra-molecular N-H⋯O and weak C-H⋯O hydrogen bonds, which probably contribute to the approximate planarity of the mol-ecules. The supra-molecular structures feature C-H⋯O hydrogen bonds and π-π inter-actions, as confirmed by Hirshfeld surface analyses.

  20. Crystal structure of 2-(thiophen-3-ylethyl pyrene-1-carboxylate

    Directory of Open Access Journals (Sweden)

    Bianca X. Valderrama-García

    2015-12-01

    Full Text Available In the title compound, C23H16O2S, the thiophene group is rotationally disordered into two fractions almost parallel to each other, with occupation factors of 0.523 (7 and 0.477 (7, and subtending dihedral angles of 10.5 (5 and 9.3 (5°, respectively, to the thiophene group. The molecules are held together by weak C—H...O and C—H...π hydrogen bonds, producing a laminar arrangement, which are further connected in a perpendicular fashion by S...π contacts [S...centroid = 3.539 (8 and 3.497 (8 Å]. In spite of the presence of the entended pyrene group, the structure does not present any parallel π–π stacking interactions. The structure was refined as an inversion twin.

  1. 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.

  2. 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.

  3. Photochemical manipulation of colloidal structures in liquid-crystal colloids

    Science.gov (United States)

    Yamamoto, T.; Tabe, Y.; Yokoyama, H.

    2007-05-01

    We investigated photochemical manipulation of physical properties and colloidal structures in liquid-crystal (LC) colloids containing azobenzene compounds. In a LC suspension where polymeric particles were dispersed in a host LC, we achieved photochemical control of light-scattering properties of the suspension. In a nematic phase, when the suspension was sandwiched with two glass plates, the film became opaque. This would be attributable to an appearance of both multidomain structures of LC alignment and mismatches of refractive indices between the materials. The opaque state turned into a transparent one when a nematic-to-isotropic phase transition was induced by the trans-to-cis photoisomerization of the azo-dye. This will result from a disappearance of both the multidomain structures and the refractive-index mismatches in the isotropic phase. The transparent film went back into the initial opaque film when the nematic phase was obtained by the cis-to-trans photoisomerization. In a LC emulsion in which glycerol or water droplets were dispersed in liquid crystals, we examined photochemical change of defect structures and inter-droplet distances by the photochemical manner. At the initial state, Saturn ring and hedgehog defects were formed around the droplets. For the glycerol droplets, we observed structural transformations between Saturn ring and boojums on irradiation with ultra-violet and visible light. For the water droplets, the inter-droplet distances varied by changing defect size on the irradiation. These phenomena would result from modulation of anchoring conditions of the droplets by the photoisomerization of the azo-dyes.

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

    Directory of Open Access Journals (Sweden)

    Ana María Atria

    2014-11-01

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

  5. Synthesis, Dimeric Crystal Structure, and Biological Activities of N-(4-Methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N-(2-trifluoromethyl-phenyl)-guanidine

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The title compound, N-(4-methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N′-(2-trifluoromethyl-phenyl)-guanidine, was synthesized and its structure was confirmed by using IR, MS, 1H NMR, and elemental analysis. The single crystal structure of the title compound was determined by X-ray diffraction. The preliminary biological test showed that the synthesized compound has a weak herbicidal activity.

  6. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith (UC)

    2008-11-12

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 {angstrom} resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an 'arm' structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

  7. Crystal structure of the petal death protein from carnation flower.

    Science.gov (United States)

    Teplyakov, Alexey; Liu, Sijiu; Lu, Zhibing; Howard, Andrew; Dunaway-Mariano, Debra; Herzberg, Osnat

    2005-12-20

    Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase, the enzyme is actually a C-C bond cleaving lyase exhibiting a broad substrate profile. The crystal structure of PDP has been determined at 2.7 A resolution, revealing a dimer-of-dimers oligomeric association. Consistent with sequence homology, the overall alpha/beta barrel fold of PDP is the same as that of other isocitrate lyase/PEP mutase superfamily members, including a swapped eighth helix within a dimer. Moreover, Mg(2+) binds in the active site of PDP with a coordination pattern similar to that seen in other superfamily members. A compound, covalently bound to the catalytic residue, Cys144, was interpreted as a thiohemiacetal adduct resulting from the reaction of glutaraldehyde used to cross-link the crystals. The Cys144-carrying flexible loop that gates access to the active site is in the closed conformation. Models of bound substrates and comparison with the closed conformation of isocitrate lyase and 2-methylisocitrate lyase revealed the structural basis for the broad substrate profile of PDP.

  8. Crystal Structure of 3S-hydroxy-7 Melleine

    Science.gov (United States)

    Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai

    2006-10-01

    A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) Å, b=7.2284(13) Å, c=13.398(2) Å, β=104.217(3)°, C10H10O4·H2O, Mr=212.20, V=1022.2(3) Å3, Z=4, Dc=1.379 mg/m3, F(000)=448, μ=0.112 mm-1, the final R=0.0498, ωR=0.101 for 2407 observed reflections (I>2σ(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 μg/disk in the preliminary test.

  9. Crystal structure of K[Hg(SCN)3] - a redetermination.

    Science.gov (United States)

    Weil, Matthias; Häusler, Thomas

    2014-09-01

    The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ▶). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954 (11), 2.4481 (8) and 2.7653 (6) Å in comparison with values of 2.24, 2.43 and 2.77 Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65 (2) to 154.06 (3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ∞[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926 (2) and 3.051 (3) Å.

  10. Crystal Structure of a Marine Natural Compound, Anhydrofusarubin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  11. Synthesis and Crystal Structure of a New Mononuclear Copper Complex

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new kind of Cu (Ⅱ) complex [Cu(tpmb)2Cl2]@CH3OH@H2O (tpmb = 1,3,5-tri(2- pyrimidinyl)sulfanylmethyl-2,4,6-trimethylbenzene) was synthesized, and its structure has been determined by X-ray single-crystal diffraction. It crystallizes in the triclinic, space group P ī with a = 8.8397(2), b = 13.327(3), c = 13.926(3) (A), ( = 63.27(3), ( = 86.96(3), ( = 80.68(3)°, V = 1445.6(5) (A)3, C49H51Cl2CuN12O2S6, Mr = 1166.82, Z = 1, F(000) = 604, Dc = 1.340 g/cm3, μ = 0.735 mm-1, R = 0.0545 and wR = 0.1575 for 4521 observed reflections (I > 2σ(I)). X-ray analysis reveals that the Cu (Ⅱ) ion is coordinated by two Cl- anions and two nitrogen atoms from different pyrimidine groups, forming a square structure.

  12. Angular Structure of Jet Quenching Within a Hybrid Strong/Weak Coupling Model

    CERN Document Server

    Casalderrey-Solana, Jorge; Milhano, Guilherme; Pablos, Daniel; Rajagopal, Krishna

    2017-01-01

    Within the context of a hybrid strong/weak coupling model of jet quenching, we study the modification of the angular distribution of the energy within jets in heavy ion collisions, as partons within jet showers lose energy and get kicked as they traverse the strongly coupled plasma produced in the collision. To describe the dynamics transverse to the jet axis, we add the effects of transverse momentum broadening into our hybrid construction, introducing a parameter $K\\equiv \\hat q/T^3$ that governs its magnitude. We show that, because of the quenching of the energy of partons within a jet, even when $K\

  13. Nematic Liquids in Weak Capillary Poiseuille Flow: Structure Scaling Laws and Effective Conductivity Implications

    Science.gov (United States)

    2007-01-01

    6ErN) (1 + s0 − 2s20 −B1 Er)ErD 2 , C1 = B3 − 2C3 sinh(Er 1/2D) 2 sinh(Er1/2F ) . This result for Poiseuille flow is qualitatively similar to Couette ...nematic flows ,” Physical Review A 34 (4), 3393-3404 (1986). [3] Cui, Z., Forest, M.G., Wang, Q., and Zhou, H., “On weak plane Couette and Poiseuille ...Zhou, H. and Forest, M. G., “Anchoring distortions coupled with plane Couette & Poiseuille flows of nematic polymers in viscous solvents: morphology

  14. Angular Structure of Jet Quenching Within a Hybrid Strong/Weak Coupling Model

    CERN Document Server

    Casalderrey-Solana, Jorge; Milhano, Guilherme; Pablos, Daniel; Rajagopal, Krishna

    2016-01-01

    Within the context of a hybrid strong/weak coupling model of jet quenching, we study the modification of the angular distribution of the energy within jets in heavy ion collisions, as partons within jet showers lose energy and get kicked as they traverse the strongly coupled plasma produced in the collision. To describe the dynamics transverse to the jet axis, we add the effects of transverse momentum broadening into our hybrid construction, introducing a parameter $K\\equiv \\hat q/T^3$ that governs its magnitude. We show that, because of the quenching of the energy of partons within a jet, even when $K\

  15. Crystal structure of Hg2SO4 – a redetermination

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-09-01

    Full Text Available The crystal structure of mercury(I sulfate (or mercurous sulfate, Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969. Acta Chem. Scand. 23, 1607–1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg—Hg = 2.5031 (7 compared to 2.500 (3Å]. The structure consists of alternating rows along [001] of Hg22+ dumbbells (generated by inversion symmetry and SO42− tetrahedra (symmetry 2. The dumbbells are linked via short O—Hg—Hg—O bonds to the sulfate tetrahedra into chains extending parallel to [20-1]. More remote O—Hg—Hg—O bonds connect these chains into a three-dimensional framework.

  16. Band structure of absorptive two-dimensional photonic crystals

    Science.gov (United States)

    van der Lem, Han; Tip, Adriaan; Moroz, Alexander

    2003-06-01

    The band structure for an absorptive two-dimensional photonic crystal made from cylinders consisting of a Drude material is calculated. Absorption causes the spectrum to become complex and form islands in the negative complex half-plane. The boundaries of these islands are not always formed by the eigenvalues calculated for Bloch vectors on the characteristic path, and we find a hole in the spectrum. For realistic parameter values, the real part of the spectrum is hardly influenced by absorption, typically less than 0.25%. The employed method uses a Korringa-Kohn-Rostoker procedure together with analytical continuation. This results in an efficient approach that allows these band-structure calculations to be done on a Pentium III personal computer.

  17. Structural noise tolerance of photonic crystal optical properties

    Science.gov (United States)

    Odontsengel, Nyam-Erdene; Cai, DongSheng; Cole, James B.

    2016-12-01

    Using nonstandard (NS) finite difference time domain (FDTD) scheme to perform 2D electromagnetic (EM) simulations, we investigate how the optical properties of 2D photonic crystals (PCs) are affected by various different kinds of structural noises in the PC lattice. While the transmission spectrum is strongly affected by noises, the position and the depth of the band gap in the transmission spectrum are remarkably robust. It is shown that rather coarse numerical grids can be used to evaluate various PC structures in NS-FDTD EM simulations. The combination of noises affects transmission spectrum in the same way as the most influential individual noise. It is shown that reducing the most influential individual noise is a very efficient method to make PC more accurate.

  18. Crystal structure of Li3Ga(BO32

    Directory of Open Access Journals (Sweden)

    Robert W. Smith

    2017-03-01

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

  19. Crystal structure of PvdO from Pseudomonas aeruginosa.

    Science.gov (United States)

    Yuan, Zenglin; Gao, Fei; Bai, Guohui; Xia, Hengchuan; Gu, Lichuan; Xu, Sujuan

    2017-02-26

    Pyoverdine I (PVDI) is a water-soluble fluorescein siderophore with strong iron chelating ability from the gram-negative pathogen Pseudomonas aeruginosa PAO1. Compared to common siderophores, PVDI is a relatively large compound whose synthesis requires a group of enzymes with different catalytic activities. In addition to four nonribosomal peptide synthetases (NRPS) which are responsible for the production of the peptide backbone of PVDI, several additional enzymes are associated with the modification of the side chains. PvdO is one of these enzymes and participates in PVDI precursor maturation in the periplasm. We determined the crystal structure of PvdO at 1.24 Å resolution. The PvdO structure shares a common fold with some FGly-generating enzymes (FGE) and is stabilized by Ca(2+). However, the catalytic residues in FGE are not observed in PvdO, indicating PvdO adopts a unique catalytic mechanism.

  20. Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

    Science.gov (United States)

    Yorinaga, Yutaka; Kumasaka, Takashi; Yamamoto, Masaki; Hamada, Kensaku; Kawamukai, Makoto

    2017-02-01

    Chitosanases belong to glycoside hydrolase families 5, 7, 8, 46, 75 and 80 and hydrolyse glucosamine polymers produced by partial or full deacetylation of chitin. Herein, we determined the crystal structure of chitosanase from the β-proteobacterium, Mitsuaria chitosanitabida, (McChoA) at 1.75 Å resolution; the first structure of a family 80 chitosanase. McChoA is a 34 kDa extracellular protein of 301 amino acids that fold into two (upper and lower) globular domains with an active site cleft between them. Key substrate-binding features are conserved with family 24 lysozymes and family 46 chitosanases. The distance between catalytic residues E41 and E61 (10.8 Å) indicates an inverting type mechanism. Uniquely, three disulphide bridges and the C terminus might contribute to enzyme activity.