WorldWideScience

Sample records for artemin crystal structure

  1. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  2. Effects of the neurotrophic factor artemin on sensory afferent development and sensitivity

    Institute of Scientific and Technical Information of China (English)

    Shuying WANG; Christopher M. Elitt; Sacha A. Malin; Kathryn M. Albers

    2008-01-01

    Artemin is a neuronal survival and differentiation factor in the glial cell line-derived neurotrophic factor family. Its receptor GFRα3 is expressed by a subpopulation of nociceptor type sensory neurons in the dorsal root and trigeminal ganglia (DRG and TG). These neurons co-express the heat, capsaicin and proton-sensitive channel TRPV 1 and the cold and chemical-sensitive channel TRPA1. To further investigate the effects of artemin on sensory neurons, we isolated transgenic mice (ARTN-OE mice) that overexpress artemin in keratinocytes of the skin and tongue. Enhanced levels of artemin led to a 20% increase in the total number of DRG neurons and increases in the level of mRNA encoding TRPV1 and TRPAI. Calcium imaging showed that isolated sensory neurons from ARTN-OE mice were hypersensitive to the TRPV 1 agonist capsaicin and the TRPA1 agonist mustard oil. Behavioral testing of ARTN-OE mice also showed an increased sensitivity to heat, cold, capsaicin and mustard oil stimuli applied either to the skin or in the drinking water. Sensory neurons from wildtype mice also exhibited potentiated capsaicin responses following artemin addition to the media. In addition, injection of artemin into hindpaw skin produced transient thermal hyperalgesia. These findings indicate that artemin can modulate sensory function and that this regulation may occur through changes in channel gene expression. Because artemin mRNA expression is up-regulated in inflamed tissue and following nerve injury, it may have a significant role in cellular changes that underlie pain associated with pathological conditions. Manipulation of artemin expression may therefore offer a new pain treatment strategy.

  3. 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...

  4. Incommensurability in crystal structures

    International Nuclear Information System (INIS)

    Incommensurate or modulated crystal structures (TaS2, Srsub(1-p)Cr2Sesub(4-p), etc.) are examined and compared with superstructures (TaSe2, Basub(1-p)Cr2Sesub(4-p)). Observed and calculated structure factors are given for Eusub(1-p)Cr2Sesub(4-p). (C.F.)

  5. Overexpression of artemin in the tongue increases expression of TRPV1 and TRPA1 in trigeminal afferents and causes oral sensitivity to capsaicin and mustard oil

    OpenAIRE

    Elitt, Christopher M.; Malin, Sacha A.; Koerber, H Richard; Davis, Brian M.; Albers, Kathryn M.

    2008-01-01

    Artemin, a member of the glial cell line-derived neurotrophic factor (GDNF) family, supports a subpopulation of trigeminal sensory neurons through activation of the Ret/GFRα3 receptor tyrosine kinase complex. In a previous study we showed that artemin is increased in inflamed skin of wildtype mice and that transgenic overexpression of artemin in skin increases TRPV1 and TRPA1 expression in dorsal root ganglia neurons. In this study we examined how transgenic overexpression of artemin in tongu...

  6. 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.

  7. 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.

  8. 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.

  9. Crystal structure of dimethomorph

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-09-01

    Full Text Available In the title compound, C21H22ClNO4 [systematic name: (E-3-(4-chlorophenyl-3-(3,4-dimethoxyphenyl-1-(morpholin-4-ylprop-2-en-1-one], which is the morpholine fungicide dimethomorph, the dihedral angles between the mean planes of the central chlorophenyl and the terminal benzene and morpholine (r.m.s. deviation = 0.2233 Å rings are 71.74 (6 and 63.65 (7°, respectively. In the crystal, molecules are linked via C—H...O hydrogen bonds and weak Cl...π interactions [3.8539 (11 Å], forming a three-dimensional structure.

  10. 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...

  11. Artemin growth factor increases nicotinic cholinergic receptor subunit expression and activity in nociceptive sensory neurons

    OpenAIRE

    Albers, Kathryn M.; Zhang, Xiu Lin; Diges, Charlotte M.; Schwartz, Erica S.; Yang, Charles I; Davis, Brian M.; Gold, Michael S.

    2014-01-01

    Background Artemin (Artn), a member of the glial cell line-derived growth factor (GDNF) family, supports the development and function of a subpopulation of peptidergic, TRPV1-positive sensory neurons. Artn (enovin, neublastin) is elevated in inflamed tissue and its injection in skin causes transient thermal hyperalgesia. A genome wide expression analysis of trigeminal ganglia of mice that overexpress Artn in the skin (ART-OE mice) showed elevation in nicotinic acetylcholine receptor (nAChR) s...

  12. 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

  13. Crystal structure of triclopyr

    OpenAIRE

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

    2014-01-01

    In the title compound {systematic name: 2-[(3,5,6-trichloropyridin-2-yl)oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent molecules in which the dihedral angles between the mean plane of the carboxylic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of intermolecular O—H...O hydrogen bonds form dimers through an R22(8) ring motif and are extended into chains along [100] by weak π–π interactions [ring ce...

  14. Crystal structure of pencycuron

    OpenAIRE

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

    2015-01-01

    In the title compound [systematic name: 1-(4-chlorobenzyl)-1-cyclopentyl-3-phenylurea], C19H21ClN2O, which is a urea fungicide, the cyclopentyl ring adopts an envelope conformation, with one of the methylene C atoms adjacent to the C atom bonding to the N atom as the flap. The dihedral angles between the mean planes of the central cyclopentyl ring (all atoms) and the chlorobenzyl and phenyl rings are 77.96 (6) and 57.77 (7)°, respectively. In the crystal, N—H...O hydrogen bonds link adjacent ...

  15. Crystal structure of fenclorim

    OpenAIRE

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

    2015-01-01

    In the title compound, C10H6Cl2N2 (systematic name: 4,6-dichloro-2-phenylpyrimidine), which is used commercially as the herbicide safener, fenclorim, the dihedral angle between the dichloropyrimidyl and phenyl rings is 9.45 (10)°. In the crystal, C—H...N hydrogen bonds link adjacent molecules, forming chains along the c-axis direction. In addition, weak intermolecular C—Cl...π [3.6185 (10) Å] and π–π [3.8796 (11) Å] interactions are present, forming a three-dimensional network....

  16. Crystal structure of fenclorim

    Directory of Open Access Journals (Sweden)

    Eunjin Kwon

    2015-10-01

    Full Text Available In the title compound, C10H6Cl2N2 (systematic name: 4,6-dichloro-2-phenylpyrimidine, which is used commercially as the herbicide safener, fenclorim, the dihedral angle between the dichloropyrimidyl and phenyl rings is 9.45 (10°. In the crystal, C—H...N hydrogen bonds link adjacent molecules, forming chains along the c-axis direction. In addition, weak intermolecular C—Cl...π [3.6185 (10 Å] and π–π [3.8796 (11 Å] interactions are present, forming a three-dimensional network.

  17. Crystal structure of metobromuron

    OpenAIRE

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

    2015-01-01

    The title compound [systematic name: 3-(4-bromophenyl)-1-methoxy-1-methylurea], C9H11BrN2O2, is a phenylurea herbicide. The dihedral angle between the plane of the urea group and that of the bromophenyl ring is 39.13 (10)°. In the crystal, N—H...O and C—H...O hydrogen bonds and weak C—H...π interactions link adjacent molecules, forming chains along the a-axis direction. In addition, short intermolecular Br...Br contacts [3.648 (4) Å] are present, resulting in a two-dimensional network extendi...

  18. Crystal structure of azimsulfuron

    OpenAIRE

    Youngeun Jeon; Jineun Kim; Eunjin Kwon; Tae Ho Kim

    2015-01-01

    The title compound {systematic name: 1-(4,6-dimethoxypyrimidin-2-yl)-3-[1-methyl-4-(2-methyl-2H-tetrazol-5-yl)pyrazol-5-ylsulfonyl]urea}, C13H16N10O5S, is a sulfonylurea herbicide. In this compound, the dihedral angles between the planes of the central pyrazole and the terminal dimethoxypyrimidine and tetrazole rings are 79.10 (8) and 17.21 (16)°, respectively. In the crystal, N—H...O hydrogen bonds link adjacent molecules, forming R22(8) inversion dimers. In addition, weak C—H...O and C—H......

  19. Crystal structure of dimethomorph

    OpenAIRE

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

    2015-01-01

    In the title compound, C21H22ClNO4 [systematic name: (E)-3-(4-chlorophenyl)-3-(3,4-dimethoxyphenyl)-1-(morpholin-4-yl)prop-2-en-1-one], which is the morpholine fungicide dimethomorph, the dihedral angles between the mean planes of the central chlorophenyl and the terminal benzene and morpholine (r.m.s. deviation = 0.2233 Å) rings are 71.74 (6) and 63.65 (7)°, respectively. In the crystal, molecules are linked via C—H...O hydrogen bonds and weak Cl...π interactions [3.8539 (11) Å], forming a t...

  20. Crystal structure of triclopyr

    Directory of Open Access Journals (Sweden)

    Seonghwa Cho

    2014-09-01

    Full Text Available In the title compound {systematic name: 2-[(3,5,6-trichloropyridin-2-yloxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent molecules in which the dihedral angles between the mean plane of the carboxylic acid group and the pyridyl ring plane are 79.3 (6 and 83.8 (5°. In the crystal, pairs of intermolecular O—H...O hydrogen bonds form dimers through an R22(8 ring motif and are extended into chains along [100] by weak π–π interactions [ring centroid separations = 3.799 (4 and 3.810 (4 Å]. In addition, short intermolecular Cl...Cl contacts [3.458 (2 Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020. The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4.

  1. Crystal structure of triclopyr.

    Science.gov (United States)

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

    2014-09-01

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

  2. Crystal structure of triclopyr

    OpenAIRE

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

    2014-01-01

    In the title compound {systematic name: 2-[(3,5,6-tri­chloro­pyridin-2-yl)­oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the mean plane of the carb­oxy­lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter­molecular O—H⋯O hydrogen bonds form dimers through an R 2 2(8) ring motif and are extended into chains along [100] by weak π–π inter­actions ...

  3. Crystal structure of flumioxazin

    OpenAIRE

    Hyunjin Park; Jineun Kim; Eunjin Kwon; Tae Ho Kim

    2015-01-01

    The title compound {systematic name: 2-[7-fluoro-3,4-dihydro-3-oxo-4-(prop-2-yn-1-yl)-2H-1,4-benzoxazin-6-yl]-4,5,6,7-tetrahydro-1H-isoindole-1,3(2H)-dione}, C19H15FN2O4, is a dicarboximide herbicide. The dihedral angle between the maleimide and benzene ring planes is 66.13 (5)°. In the crystal, C—H...O and C—H...F hydrogen bonds and weak C—H...π interactions [3.5601 (19) Å] link adjacent molecules, forming two-dimensional networks extending parallel to the (110) plane.

  4. Crystal structure of pyrazoxyfen

    OpenAIRE

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

    2015-01-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di­chloro­benzo­yl)-1,3-di­methyl­pyrazol-5-yl}­oxy}-1-phenyl­ethan-1-one), is the benzoyl­pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol­ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the di­chloro­phenyl and phenyl rings. In the crystal, C—H⋯O and C—H⋯N hydrogen bonds, and C—H⋯π and π–π [3.646 (2)...

  5. Crystal structure of flumioxazin

    Directory of Open Access Journals (Sweden)

    Hyunjin Park

    2015-10-01

    Full Text Available The title compound {systematic name: 2-[7-fluoro-3,4-dihydro-3-oxo-4-(prop-2-yn-1-yl-2H-1,4-benzoxazin-6-yl]-4,5,6,7-tetrahydro-1H-isoindole-1,3(2H-dione}, C19H15FN2O4, is a dicarboximide herbicide. The dihedral angle between the maleimide and benzene ring planes is 66.13 (5°. In the crystal, C—H...O and C—H...F hydrogen bonds and weak C—H...π interactions [3.5601 (19 Å] link adjacent molecules, forming two-dimensional networks extending parallel to the (110 plane.

  6. Crystal structure of fenclorim

    OpenAIRE

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

    2015-01-01

    In the title compound, C10H6Cl2N2 (systematic name: 4,6-di­chloro-2-phenyl­pyrimidine), which is used commercially as the herbicide safener, fenclorim, the dihedral angle between the di­chloro­pyrimidyl and phenyl rings is 9.45 (10)°. In the crystal, C—H⋯N hydrogen bonds link adjacent mol­ecules, forming chains along the c-axis direction. In addition, weak inter­molecular C—Cl⋯π [3.6185 (10) Å] and π–π [3.8796 (11) Å] inter­actions are present, forming a three-dimensional network....

  7. Crystal structure of cyproconazole

    OpenAIRE

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

    2015-01-01

    The title compound [systematic name: 2-(4-chlorophenyl)-3-cyclopropyl-1-(1H-1,2,4-triazol-1-yl)butan-2-ol], C15H18ClN3O, is a conazole fungicide. The asymmetric unit comprises two enantiomeric pairs (molecules A and B) in which the dihedral angles between the chlorophenyl and triazole rings are 46.54 (9) (molecule A) and 67.03 (8)° (molecule B). In the crystal, C—H...O, O—H...N and C—H...Cl hydrogen bonds and weak C—H...π interactions [3.473 (2) Å] link adjacent molecules, forming columns alo...

  8. Crystal structure of pencycuron

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available In the title compound [systematic name: 1-(4-chlorobenzyl-1-cyclopentyl-3-phenylurea], C19H21ClN2O, which is a urea fungicide, the cyclopentyl ring adopts an envelope conformation, with one of the methylene C atoms adjacent to the C atom bonding to the N atom as the flap. The dihedral angles between the mean planes of the central cyclopentyl ring (all atoms and the chlorobenzyl and phenyl rings are 77.96 (6 and 57.77 (7°, respectively. In the crystal, N—H...O hydrogen bonds link adjacent molecules, forming C(4 chains propagating along the b-axis direction. The chains are linked by weak π–π interactions between the chlorobenzene rings [centroid–centroid separation = 3.9942 (9 Å], resulting in two-dimensional networks extending parellel to the (110 plane.

  9. Crystal structure of pyrazoxyfen

    OpenAIRE

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

    2015-01-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-dichlorobenzoyl)-1,3-dimethylpyrazol-5-yl}oxy}-1-phenylethan-1-one), is the benzoylpyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent molecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the dichlorophenyl and phenyl rings. In the crystal, C—H...O and C—H...N hydrogen bonds, and C—H...π and π–π [3.646 (2) Å] i...

  10. Crystal structure of metobromuron

    OpenAIRE

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

    2015-01-01

    The title compound [systematic name: 3-(4-bromo­phen­yl)-1-meth­oxy-1-methyl­urea], C9H11BrN2O2, is a phenyl­urea herbicide. The dihedral angle between the plane of the urea group and that of the bromo­phenyl ring is 39.13 (10)°. In the crystal, N—H⋯O and C—H⋯O hydrogen bonds and weak C—H⋯π inter­actions link adjacent mol­ecules, forming chains along the a-axis direction. In addition, short inter­molecular Br⋯Br contacts [3.648 (4) Å] are present, resulting in a two-dimensional network extend...

  11. Crystal structure of cyproconazole

    OpenAIRE

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

    2015-01-01

    The title compound [systematic name: 2-(4-chloro­phen­yl)-3-cyclo­propyl-1-(1H-1,2,4-triazol-1-yl)butan-2-ol], C15H18ClN3O, is a conazole fungicide. The asymmetric unit comprises two enanti­omeric pairs (mol­ecules A and B) in which the dihedral angles between the chloro­phenyl and triazole rings are 46.54 (9) (mol­ecule A) and 67.03 (8)° (mol­ecule B). In the crystal, C—H⋯O, O—H⋯N and C—H⋯Cl hydrogen bonds and weak C—H⋯π inter­actions [3.473 (2) Å] link adjacent mol­ecules, forming columns a...

  12. Crystal structure of pencycuron

    OpenAIRE

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

    2015-01-01

    In the title compound [systematic name: 1-(4-chloro­benz­yl)-1-cyclo­pentyl-3-phenyl­urea], C19H21ClN2O, which is a urea fungicide, the cyclo­pentyl ring adopts an envelope conformation, with one of the methyl­ene C atoms adjacent to the C atom bonding to the N atom as the flap. The dihedral angles between the mean planes of the central cyclo­pentyl ring (all atoms) and the chloro­benzyl and phenyl rings are 77.96 (6) and 57.77 (7)°, respectively. In the crystal, N—H⋯O hydrogen bonds link adj...

  13. Crystal structure of metobromuron

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available The title compound [systematic name: 3-(4-bromophenyl-1-methoxy-1-methylurea], C9H11BrN2O2, is a phenylurea herbicide. The dihedral angle between the plane of the urea group and that of the bromophenyl ring is 39.13 (10°. In the crystal, N—H...O and C—H...O hydrogen bonds and weak C—H...π interactions link adjacent molecules, forming chains along the a-axis direction. In addition, short intermolecular Br...Br contacts [3.648 (4 Å] are present, resulting in a two-dimensional network extending parallel to (101.

  14. Crystal structure of cyproconazole

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-12-01

    Full Text Available The title compound [systematic name: 2-(4-chlorophenyl-3-cyclopropyl-1-(1H-1,2,4-triazol-1-ylbutan-2-ol], C15H18ClN3O, is a conazole fungicide. The asymmetric unit comprises two enantiomeric pairs (molecules A and B in which the dihedral angles between the chlorophenyl and triazole rings are 46.54 (9 (molecule A and 67.03 (8° (molecule B. In the crystal, C—H...O, O—H...N and C—H...Cl hydrogen bonds and weak C—H...π interactions [3.473 (2 Å] link adjacent molecules, forming columns along the a axis.

  15. Crystal structure of flumioxazin

    OpenAIRE

    Park, Hyunjin; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound {systematic name: 2-[7-fluoro-3,4-di­hydro-3-oxo-4-(prop-2-yn-1-yl)-2H-1,4-benzoxazin-6-yl]-4,5,6,7-tetra­hydro-1H-iso­indole-1,3(2H)-dione}, C19H15FN2O4, is a dicarboximide herbicide. The dihedral angle between the male­imide and benzene ring planes is 66.13 (5)°. In the crystal, C—H⋯O and C—H⋯F hydrogen bonds and weak C—H⋯π inter­actions [3.5601 (19) Å] link adjacent mol­ecules, forming two-dimensional networks extending parallel to the (110) plane....

  16. Crystal structure of azimsulfuron

    OpenAIRE

    Jeon, Youngeun; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound {systematic name: 1-(4,6-di­meth­oxy­pyrimidin-2-yl)-3-[1-methyl-4-(2-methyl-2H-tetra­zol-5-yl)pyrazol-5-ylsulfon­yl]urea}, C13H16N10O5S, is a sulfonyl­urea herbicide. In this compound, the dihedral angles between the planes of the central pyrazole and the terminal di­meth­oxy­pyrimidine and tetra­zole rings are 79.10 (8) and 17.21 (16)°, respectively. In the crystal, N—H⋯O hydrogen bonds link adjacent mol­ecules, forming R 2 2(8) inversion dimers. In addition, weak C—H⋯O a...

  17. Crystal structure of azimsulfuron

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

    Full Text Available The title compound {systematic name: 1-(4,6-dimethoxypyrimidin-2-yl-3-[1-methyl-4-(2-methyl-2H-tetrazol-5-ylpyrazol-5-ylsulfonyl]urea}, C13H16N10O5S, is a sulfonylurea herbicide. In this compound, the dihedral angles between the planes of the central pyrazole and the terminal dimethoxypyrimidine and tetrazole rings are 79.10 (8 and 17.21 (16°, respectively. In the crystal, N—H...O hydrogen bonds link adjacent molecules, forming R22(8 inversion dimers. In addition, weak C—H...O and C—H...N hydrogen bonds and weak π–π interactions [ring centroid separation = 3.8255 (12 Å] are present, resulting in a three-dimensional architecture.

  18. Crystal structure of dimethomorph

    OpenAIRE

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

    2015-01-01

    In the title compound, C21H22ClNO4 [systematic name: (E)-3-(4-chloro­phen­yl)-3-(3,4-di­meth­oxy­phen­yl)-1-(morpholin-4-yl)prop-2-en-1-one], which is the morpholine fungicide dimethomorph, the dihedral angles between the mean planes of the central chloro­phenyl and the terminal benzene and morpholine (r.m.s. deviation = 0.2233 Å) rings are 71.74 (6) and 63.65 (7)°, respectively. In the crystal, molecules are linked via C—H⋯O hydrogen bonds and weak Cl⋯π interactions [3.8539 (11) Å], forming ...

  19. Crystal structure determination of Efavirenz

    Energy Technology Data Exchange (ETDEWEB)

    Popeneciu, Horea, E-mail: horea.popeneciu@itim-cj.ro; Dumitru, Ristoiu [College of Environmental Science on Engineering Babes Bolyai University, 30 Fantanele, 400294 Cluj Napoca (Romania); Tripon, Carmen, E-mail: horea.popeneciu@itim-cj.ro; Borodi, Gheorghe, E-mail: horea.popeneciu@itim-cj.ro; Pop, Mihaela Maria, E-mail: mihaelapop@teracrystal.com

    2015-12-23

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

  20. Crystal structure of pymetrozine

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

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

  1. Crystal structure of cyclosulfamuron

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available The title compound (systematic name: 1-{[2-(cyclopropylcarbonylanilino]sulfonyl}-3-(4,6-dimethoxypyrimidin-2-ylurea, C17H19N5O6S, is a pyrimidinylsulfonylurea herbicide. The dihedral angles between the mean planes of the central benzene ring and the cyclopropyl and pyrimidinyl rings are 75.32 (9 and 88.79 (4°, respectively. The C atoms of the methoxy groups lie almost in the plane of the pyrimidine ring [deviations = 0.043 (2 and 0.028 (2 Å] and intramolecular N—H...N, N—H...O and C—H...O hydrogen bonds all close S(6 rings. In the crystal, N—H...O and C—H...O hydrogen bonds and weak π–π interactions [centroid–centroid distances = 3.6175 (9 and 3.7068 (9 Å] link adjacent molecules, forming a three-dimensional network.

  2. Crystal structure of pyrazoxyfen

    Directory of Open Access Journals (Sweden)

    Eunjin Kwon

    2015-12-01

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

  3. Inhibition of TRPA1 channel activity in sensory neurons by the glial cell line-derived neurotrophic factor family member, artemin

    Directory of Open Access Journals (Sweden)

    Wang Shenglan

    2011-05-01

    Full Text Available Abstract Background The transient receptor potential (TRP channel subtype A1 (TRPA1 is known to be expressed on sensory neurons and respond to changes in temperature, pH and local application of certain noxious chemicals such as allyl isothiocyanate (AITC. Artemin is a neuronal survival and differentiation factor and belongs to the glial cell line-derived neurotrophic factor (GDNF family. Both TRPA1 and artemin have been reported to be involved in pathological pain initiation and maintenance. In the present study, using whole-cell patch clamp recording technique, in situ hybridization and behavioral analyses, we examined the functional interaction between TRPA1 and artemin. Results We found that 85.8 ± 1.9% of TRPA1-expressing neurons also expressed GDNF family receptor alpha 3 (GFR α3, and 87.5 ± 4.1% of GFRα3-expressing neurons were TRPA1-positive. In whole-cell patch clamp analysis, a short-term treatment of 100 ng/ml artemin significantly suppressed the AITC-induced TRPA1 currents. A concentration-response curve of AITC resulting from the effect of artemin showed that this inhibition did not change EC50 but did lower the AITC-induced maximum response. In addition, pre-treatment of artemin significantly suppressed the number of paw lifts induced by intraplantar injection of AITC, as well as the formalin-induced pain behaviors. Conclusions These findings that a short-term application of artemin inhibits the TRPA1 channel's activity and the sequential pain behaviors suggest a role of artemin in regulation of sensory neurons.

  4. Crystal structure of gold hydride

    International Nuclear Information System (INIS)

    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

  5. 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.

  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. 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.

  8. CALYPSO: a method for crystal structure prediction

    OpenAIRE

    Wang, Yanchao; Lv, Jian; Zhu, Li; Ma, Yanming

    2012-01-01

    We have developed a software package CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) to predict the energetically stable/metastable crystal structures of materials at given chemical compositions and external conditions (e.g., pressure). The CALYPSO method is based on several major techniques (e.g. particle-swarm optimization algorithm, symmetry constraints on structural generation, bond characterization matrix on elimination of similar structures, partial random structures...

  9. Photonic crystal laser-driven accelerator structures

    CERN Document Server

    Cowan, Benjamin

    2005-01-01

    We discuss simulated photonic crystal structure designs, including two- and three-dimensional planar structures and fibers. The discussion of 2D structures demonstrates guiding of a speed-of-light accelerating mode by a defect in a photonic crystal lattice and reveals design considerations and trade-offs. With a three-dimensional lattice, we introduce a candidate geometry and discuss beam dynamics, coupling, and manufacturing techniques for that structure. In addition we discuss W-band scale tests of photonic crystal structures. The computational methods are also discussed.

  10. Crystal structure of benzimidazolium salicylate

    Directory of Open Access Journals (Sweden)

    M. Amudha

    2015-10-01

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

  11. 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.

  12. 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.

  13. Theoretical prediction of crystal structures of rubrene

    Science.gov (United States)

    Obata, Shigeaki; Miura, Toshiaki; Shimoi, Yukihiro

    2014-01-01

    We theoretically predict crystal structures and molecular arrangements for rubrene molecule using CONFLEX program and compare them with the experimental ones. The most, second-most, and fourth-most stable predicted crystal structures show good agreement with the triclinic, orthorhombic, and monoclinic polymorphs of rubrene, respectively. The change in molecular conformation is also predicted between crystalline and gas phases: the tetracene backbone takes flat conformation in crystalline phase as in the observed structure. Meanwhile, it is twisted in gas phase. The theoretical prediction method used in this work provides the successful results on the determination of the three kinds of crystal structures and molecular arrangements for rubrene molecule.

  14. Neutron diffraction analysis of crystal magnetic structures

    International Nuclear Information System (INIS)

    An investigation of the state-of-the art of the neutron diffraction analysis of magnetic structures from the point of view of the theory of crystal symmetry is given. Various and numerous structures determined from the neutron diffraction analysis investigations can be classified and described with the theory of space group representations of crystals. The analysis of quite a number of various magnetic structures shows that they arise according to Landau hypothesis. The foundations of a symmetry analysis of magnetic structures and the methods for their determination are given. A physical explanation is given for the existence of magnetic structures. The experimental investigations of the crystal lattice distortions accompanying a magnetic ordering are reviewed. In this review is given a symmetry approach to the description of the magnetic structures of crystals; and a possibility to analyze them by a scattering of nonpolarized and polarized neutrons

  15. Crystal structure of cyclohexylammonium thiocyanate

    OpenAIRE

    Abdulaziz A. Bagabas; Sultan B. Alhoshan; Hazem A. Ghabbour; C S Chidan Kumar; Hoong-Kun Fun

    2015-01-01

    In the title salt, C6H11NH3+·SCN−, the cyclohexylammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial interactions. In the crystal, the components are linked by N—H...N and N—H...S hydrogen-bonding interactions, resulting in a three-dimensional network.

  16. Crystal structure of cyclohexylammonium thiocyanate

    Directory of Open Access Journals (Sweden)

    Abdulaziz A. Bagabas

    2015-01-01

    Full Text Available In the title salt, C6H11NH3+·SCN−, the cyclohexylammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial interactions. In the crystal, the components are linked by N—H...N and N—H...S hydrogen-bonding interactions, resulting in a three-dimensional network.

  17. Pholcodine monohydrate: Crystal structure and polymorphism

    Science.gov (United States)

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

    2013-07-01

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

  18. 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...

  19. Crystal structure of 2-pentyloxybenzamide

    OpenAIRE

    Bernhard Bugenhagen; Yosef Al Jasem; Thies Thiemann

    2014-01-01

    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...

  20. Crystal structure of L-alanine phosphate

    International Nuclear Information System (INIS)

    The crystal structure of L-alanine phosphate (C3O2NH7 · H3PO4) is determined by the single-crystal diffraction technique; a 11.918(1) A, b = 9.117(1) A, c = 7.285(1) A, γ = 104.7(1) deg., space group P21, and Z = 4. The amino group of the alanine is protonated by the hydrogen atom of the phosphoric acid. Pairs of H2PO-4 hydrogen-bonded ions are packed into layers alternating with layers of alanine molecules in the crystal. No hydrogen bonds are formed immediately between the alanine molecules

  1. Crystal and molecular structure of paclitaxel (taxol).

    OpenAIRE

    Mastropaolo, D; Camerman, A; Luo, Y.; Brayer, G. D.; Camerman, N

    1995-01-01

    Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus severa...

  2. 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.

  3. Involvement of peripheral artemin signaling in tongue pain: possible mechanism in burning mouth syndrome.

    Science.gov (United States)

    Shinoda, Masamichi; Takeda, Mamoru; Honda, Kuniya; Maruno, Mitsuru; Katagiri, Ayano; Satoh-Kuriwada, Shizuko; Shoji, Noriaki; Tsuchiya, Masahiro; Iwata, Koichi

    2015-12-01

    Burning mouth syndrome is characterized by altered sensory qualities, namely tongue pain hypersensitivity. We found that the mRNA expression of Artemin (Artn) in the tongue mucosa of patients with burning mouth syndrome was significantly higher than that of control subjects, and we developed a mouse model of burning mouth syndrome by application of 2,4,6-trinitrobenzene sulfonic acid (TNBS) diluted with 50% ethanol to the dorsum of the tongue. TNBS treatment to the tongue induced persistent, week-long, noninflammatory tongue pain and a significant increase in Artn expression in the tongue mucosa and marked tongue heat hyperalgesia. Following TNBS treatment, the successive administration of the transient receptor potential vanilloid 1 (TRPV1) antagonist SB366791 or neutralizing anti-Artn antibody completely inhibited the heat hyperalgesia. The number of glial cell line-derived neurotrophic factor family receptor α3 (GFRα3)-positive and TRPV1-positive trigeminal ganglion (TG) neurons innervating the tongue significantly increased following TNBS treatment and was significantly reduced by successive administration of neutralizing anti-Artn antibody. The capsaicin-induced current in TG neurons innervating the tongue was enhanced following TNBS treatment and was inhibited by local administration of neutralizing anti-Artn antibody to the tongue. These results suggest that the overexpression of Artn in the TNBS-treated tongue increases the membrane excitability of TG neurons innervating the tongue by increasing TRPV1 sensitivity, which causes heat hyperalgesia. This model may be useful for the study of tongue pain hypersensitivity associated with burning mouth syndrome. PMID:26270588

  4. Involvement of peripheral artemin signaling in tongue pain: possible mechanism in burning mouth syndrome.

    Science.gov (United States)

    Shinoda, Masamichi; Takeda, Mamoru; Honda, Kuniya; Maruno, Mitsuru; Katagiri, Ayano; Satoh-Kuriwada, Shizuko; Shoji, Noriaki; Tsuchiya, Masahiro; Iwata, Koichi

    2015-12-01

    Burning mouth syndrome is characterized by altered sensory qualities, namely tongue pain hypersensitivity. We found that the mRNA expression of Artemin (Artn) in the tongue mucosa of patients with burning mouth syndrome was significantly higher than that of control subjects, and we developed a mouse model of burning mouth syndrome by application of 2,4,6-trinitrobenzene sulfonic acid (TNBS) diluted with 50% ethanol to the dorsum of the tongue. TNBS treatment to the tongue induced persistent, week-long, noninflammatory tongue pain and a significant increase in Artn expression in the tongue mucosa and marked tongue heat hyperalgesia. Following TNBS treatment, the successive administration of the transient receptor potential vanilloid 1 (TRPV1) antagonist SB366791 or neutralizing anti-Artn antibody completely inhibited the heat hyperalgesia. The number of glial cell line-derived neurotrophic factor family receptor α3 (GFRα3)-positive and TRPV1-positive trigeminal ganglion (TG) neurons innervating the tongue significantly increased following TNBS treatment and was significantly reduced by successive administration of neutralizing anti-Artn antibody. The capsaicin-induced current in TG neurons innervating the tongue was enhanced following TNBS treatment and was inhibited by local administration of neutralizing anti-Artn antibody to the tongue. These results suggest that the overexpression of Artn in the TNBS-treated tongue increases the membrane excitability of TG neurons innervating the tongue by increasing TRPV1 sensitivity, which causes heat hyperalgesia. This model may be useful for the study of tongue pain hypersensitivity associated with burning mouth syndrome.

  5. 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.

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

    Science.gov (United States)

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

    1994-01-01

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

  7. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...

  8. Surface structure of potassium sulphate crystals

    International Nuclear Information System (INIS)

    Full text: It is known, that the surface structure of crystals differs from crystal structure far from a surface. It is connected to that on a surface there is a necessity of indemnification of charges of surface ions. In this connection occurs either a relaxation, or reorganization of surface structure. As many electronic processes, including a luminescence and processes of energy transfer, can be subject to influence of the surface phenomena, the knowledge of structure of a surface can be crucial. Objects of research in the present work are the crystal K2SO4, and also the activated crystal K2SO4-Tl. Potassium sulfate has ionic type of connection between metal ions and oxi-anionic group. Inside oxi-anionic groups four atoms of oxygen and one atom of sulfur are connected by covalent connection. The atom of sulfur is located in the center of tetrahedral pyramids on which tops atoms of oxygen settle down. It agrees to the data of X-ray structural analysis an ion SO4- has correct a tetrahedral structure. The formula of such connection can be written down as AIAIIX4, where AI and AII - potassium ions in positions I and II, and X - SO4- -anion. Monocrystals of researched sulfates were raised from water solutions by a method of slow evaporation. Crystals - the columns extended along one direction have been chosen. Measurements on a scanning electronic microscope were carried out on the natural raw side. For this purpose on this side the corresponding covering was rendered. The surface of crystals has been covered with set of 'tracks' in width about 10 microns. Tracks represented long bent raised roads above a surface of constant width and constant height. In directions of tracks there is no system. They are frequently crossed; some tracks come to an end, being gradually narrowed on distance 10-15 microns. All tracks have in the middle a failure of constant width about 1 micron. Such system of tracks is present as on a surface of a pure crystal, and a crystal an impurity

  9. 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.

  10. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Crystal structure of riboflavin synthase

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-05

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

  17. Crystal structure of low-symmetry rondorfite

    International Nuclear Information System (INIS)

    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 3 bar , 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.

  18. The Surface Structure of Ground Metal Crystals

    Science.gov (United States)

    Boas, W.; Schmid, E.

    1944-01-01

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

  19. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    by the theory, the predicted crystal structures are in accord with experiment in all cases except 79Au. In addition, they have investigated the effect of pressure upon the alkali metals (3Li, 11Na, 37Rb, 55Cs) and selected lanthanide metals (57La, 58Ce, 71Lu) and actinide metals (90Th, 91Pa). In these cases...... the theory gives accurate predictions of the stability of the closed-packed structures but is found to be less accurate for open structures such as α-U...

  20. 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.

  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 Prediction from First Principles: The Crystal Structures of Glycine

    OpenAIRE

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

    2015-01-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the ...

  5. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    2016-09-01

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

  6. Crystal structure of Cryptosporidium parvum pyruvate kinase.

    Directory of Open Access Journals (Sweden)

    William J Cook

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

  7. Synthesis and Crystal Structure of Tetraimidzolium Dinicotinatooctamolybdate

    Institute of Scientific and Technical Information of China (English)

    KANGJie; ZHANGQuan-Zheng; 等

    2003-01-01

    The title compound,[C3H5N2]4(C6H5NO2)2(Mo8O26)]1,was synthesized by the reaction of H2MoO4,nicotinic acid and imidazole in aqueous solution,Single-crystal X-ray analysis has revealed that compound 1 (C24H30Mo8N10O30) crystallizes in the monoclinic system,space group P21/n,Mr=1706,10,a=12.529(1),b=12.796(1),c=14.038(1)°↑A,β=100.2(1)°,V=2215.3(2)°↑A3,Z=2,Dc=2.558 g/cm3,F(000)=1640,μ=2.299mm-1,the final R=0.0527 and wR=0.0964 for 3064 observed reflections with I>2σ(I),X-ray crystal structure analysis suggests that compound 1 consists of centrosymmetric dinicotinatooctamolybdate anion and four protonated imidazole cations ,which are linked into a three-dimensional frmawork through hydrogen bonding.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Crystal structure of mammalian acid sphingomyelinase.

    Science.gov (United States)

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

    2016-01-01

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

  15. Near Surface Structure of Organic Semiconductor Tetracene Single Crystal

    Science.gov (United States)

    Wakabayashi, Yusuke; Morisaki, Hazuki; Kimura, Tsuyoshi; Miwa, Kazumoto; Koretsune, Takashi; Takeya, Jun

    2014-03-01

    Electric conduction in organic crystals is highly anisotropic because of the anisotropic molecular orbitals. Crystal structure governs the transfer through the overlap integral among the highest occupied (or lowest unoccupied) molecular orbitals. In case of organic devices, the place where electrons conduct is the interface. Therefore, the surface structure of organic single crystals is relevant. Surface relaxation of the structure of rubrene single crystal was firstly observed by means of surface x-ray diffraction a few years ago. This time we performed similar measurement on tetracene single crystal, whose molecular shape has large similarity with rubrene while the crystal structure is very different. Tetracene single crystal was grown by the physical vapor transport method, and the surface x-ray diffraction experiments were performed at BL-3A and 4C of the Photon Factory, KEK, Japan. Obtained electron density profile shows a large structural deformation at the surface layer of tetracene.

  16. Prediction of binary hard-sphere crystal structures.

    Science.gov (United States)

    Filion, Laura; Dijkstra, Marjolein

    2009-04-01

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

  17. Crystal structure of strontium dinickel iron orthophosphate

    Directory of Open Access Journals (Sweden)

    Said Ouaatta

    2015-10-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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. PMID:19950907

  3. ARTEMIN promotes de novo angiogenesis in ER negative mammary carcinoma through activation of TWIST1-VEGF-A signalling.

    Directory of Open Access Journals (Sweden)

    Arindam Banerjee

    Full Text Available The neurotrophic factor ARTEMIN (ARTN has been reported to possess a role in mammary carcinoma progression and metastasis. Herein, we report that ARTN modulates endothelial cell behaviour and promotes angiogenesis in ER-mammary carcinoma (ER-MC. Human microvascular endothelial cells (HMEC-1 do not express ARTN but respond to exogenously added, and paracrine ARTN secreted by ER-MC cells. ARTN promoted endothelial cell proliferation, migration, invasion and 3D matrigel tube formation. Angiogenic behaviour promoted by ARTN secreted by ER-MC cells was mediated by AKT with resultant increased TWIST1 and subsequently VEGF-A expression. In a patient cohort of ER-MC, ARTN positively correlated with VEGF-A expression as measured by Spearman's rank correlation analysis. In xenograft experiments, ER-MC cells with forced expression of ARTN produced tumors with increased VEGF-A expression and increased microvessel density (CD31 and CD34 compared to tumors formed by control cells. Functional inhibition of ARTN by siRNA decreased the angiogenic effects of ER-MC cells. Bevacizumab (a humanized monoclonal anti-VEGF-A antibody partially inhibited the ARTN mediated angiogenic effects of ER-MC cells and combined inhibition of ARTN and VEGF-A by the same resulted in further significant decrease in the angiogenic effects of ER-MC cells. Thus, ARTN stimulates de novo tumor angiogenesis mediated in part by VEGF-A. ARTN therefore co-ordinately regulates multiple aspects of tumor growth and metastasis.

  4. 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.

  5. 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.

  6. 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…

  7. Crystal structure of triphenyl(vinylphosphonium tetraphenylborate

    Directory of Open Access Journals (Sweden)

    Joseph L. Bradfield

    2014-10-01

    Full Text Available The title ionic salt, C21H20P+·C24H20B−, crystallized with two independent vinyltriphenylphosphonium cations and two independent tetraphenylborate anions per asymmetric unit. These four independent moieties contain nearly perfect tetrahedral symmetry about their respective central C atoms. In the crystal, there are no π-stacking or other intermolecular interactions present.

  8. 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...

  9. 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.

  10. 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.

  11. 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.

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

    Science.gov (United States)

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

    2012-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-15

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

  14. 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.

  15. Synthesis and peculiarities of the cesium zeolite crystal structure (cesite)

    International Nuclear Information System (INIS)

    An attempt is made to synthesize cesium zeolite by introduction of amorphous seed crystals which correspond by composition with cesium-containing zeolite into the aluminosilicate gel, since this method can produce zeolite with a crystal structure it would not adopt under the usual conditions. It is seen that during crystablization upon introduction of a seed crystal the cesium content in zeolite decreases. A more complete structural elucidation of zeolite obtained by the suggested method was carried out by x0ray and IR spectral analyses. The data of x-ray analysis showed that the structures of synthesized zeolite and binary octagonal pores are similar

  16. A SAPO-11 Silicoaluminophosphate Molecular Sieve with Stable Crystal Structure

    Institute of Scientific and Technical Information of China (English)

    Yue Ming LIU; Feng Mei ZHANG; Hai Hong WU; Hai Jiao ZHANG; Jian Guo YANG; Xing Tian SHU; Ming Yuan HE

    2004-01-01

    A SAPO-11 silicoaluminophosphate molecular sieve with stable crystal structure was synthesized for the first time. After removing template by calcination, its crystal space group still retains Icm2 which the as-synthesized has. The catalyst deriving from the present SAPO-11materials shows higher isomerization selectivity and higher paraffin hydroisomerization yield than those reported elsewhere.

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

    CERN Document Server

    Martirosian, A H; Harurtjunian, V S

    2001-01-01

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

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

    International Nuclear Information System (INIS)

    By means of X-ray structure analysis, the crystal structure of neodymium gallium perovskite (NGP) single crystals (NdGaO3) being used as a substrate for HTSC film epitaxy has been refined and the position of atoms has been determined. The possibility of YBa2Cu3O7-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 LaGaO3 and LaAlO3 substrates. It is intimated that the twinning in the NGP substrates oriented as (001) can result in creation of 90 degrees twin bonds in a film, and in the case of (110)-oriented plates it is possible to ignore the twinning presence in substrate completely. (author)

  19. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    Science.gov (United States)

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

    2012-06-01

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

  20. 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.

  1. Molecular and Crystal Structures of Three Berberine Derivatives

    Directory of Open Access Journals (Sweden)

    Jiří Dostál

    2001-04-01

    Full Text Available 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.

  2. 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.

  3. 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....

  4. 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.

  5. 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 bot...

  6. 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.

  7. Crystal structure of 3-carbamothioylpyridinium thiocyanate

    OpenAIRE

    Hasna Bouchareb; Mhamed Boudraa; Sofiane Bouacida; Hocine Merazig; El Hossain Chtoun

    2015-01-01

    In the cation of the title salt, C6H7N2S+·SCN−, the C=S bond is oriented trans with respect to the C—C=N fragment in the pyridine ring. The planes of the aromatic ring and the thioamide fragment of the cation make a dihedral angle of 38.31 (4)°. In the crystal, the components are linked by N—H...S and N—H...N, hydrogen bonds, forming a two-dimensional network parallel to (10-1).

  8. Crystal structure of 3-carbamothioylpyridinium thiocyanate

    Directory of Open Access Journals (Sweden)

    Hasna Bouchareb

    2015-01-01

    Full Text Available In the cation of the title salt, C6H7N2S+·SCN−, the C=S bond is oriented trans with respect to the C—C=N fragment in the pyridine ring. The planes of the aromatic ring and the thioamide fragment of the cation make a dihedral angle of 38.31 (4°. In the crystal, the components are linked by N—H...S and N—H...N, hydrogen bonds, forming a two-dimensional network parallel to (10-1.

  9. Crystal structure of 4-(4-methoxyphenoxybenzaldehyde

    Directory of Open Access Journals (Sweden)

    Andreas Schäfer

    2015-12-01

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

  10. Optical and thermal control of domain structures in ferroelectric crystals

    OpenAIRE

    Brown, Paul Thomas

    1999-01-01

    This thesis presents the results of investigations into the thermal and optical control of ferroelectric domains within lithium tantalate and strontium barium niobate crystals. The aim of the work was to develop techniques for optically pattering domain inverted structures within ferroelectric crystals. Initial studies involving strontium barium niobate revealed an enhanced temperature sensitivity for transient repoling occurring at room temperatures for this material. This has important...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...... for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization...

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

    Science.gov (United States)

    Clark, J.R.

    1963-01-01

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

  13. 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 con...... fragment in the structures of Cu4Bi4Se9 and of the first cuprobismutite homologue, Cu4Bi5S10....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

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

    Science.gov (United States)

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

    2015-07-01

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

  16. 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.

  17. 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.

  18. Crystal structure of 2-[(dichloromethanesulfonyl]pyridine

    Directory of Open Access Journals (Sweden)

    Zhiqiu Chen

    2014-12-01

    Full Text Available The asymmetric unit of the title compound, C6H5Cl2NO2S, contains two molecules with similar conformations (r.m.s. overlay fit for the non-H atoms = 0.067 Å. Atoms attached to the pendent Csp3—S bond are arranged in a staggered conformation with one of the Cl atoms anti to the C atom in the aromatic ring [C—S—C—Cl torsion angles = 178.41 (11 and −176.70 (13°]. In the crystal, molecules are linked by C—H...N and C—H...O hydrogen bonds, generating a three-dimensional network, and weak aromatic π–π stacking is also observed [centroid–centroid separation = 3.8902 (17 Å].

  19. 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.

  20. Crystal structure of 4-formylpyridine semicarbazone hemihydrate

    Directory of Open Access Journals (Sweden)

    Mayara Hissami Inoue

    2015-05-01

    Full Text Available The molecule of the title compound C7H8N4O·0.5H2O, alternatively called (E-1-(pyridin-4-ylmethylenesemicarbazide hemihydrate, is in the E conformation and is almost planar; the r.m.s. deviation of the positions of the atoms of the pyridine ring from the best-fit plane is 0.0039 Å. The C, N and O atoms of the rest of the molecule sits close on this plane with a largest deviation of 0.115 (4 Å for the O atom of the semicarbazone moiety. There is an intramolecular N—H...N hydrogen bond. In the crystal, molecules are linked into an infinite three-dimensional network by classical N—H...Os (s = semicarbazone and Ow—H...N (w = water hydrogen bonds.

  1. 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....

  2. 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-...

  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. Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures

    International Nuclear Information System (INIS)

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

  5. 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.

  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. Optical loss due to intrinsic structural variations of photonic crystals

    CERN Document Server

    Koenderink, A F; Vos, Willem L.

    2004-01-01

    A bottleneck limiting the widespread application of photonic crystals is scattering of light by unavoidable variations in size and position of the crystals' building blocks. We present a new model for both 2 and 3-dimensional photonic crystals that relates the resulting loss length to the magnitude of the variations. The predicted lengths agree well with our experiments on high-quality opals and inverse opals over a wide frequency range, and with literature data analyzed by us. In state-of-the-art structures, control over photons is limited to distances of 50 lattice parameters (~ 15 micron). Consequently, applications of photonic crystals in optical integrated circuits remain a fata morgana, unless an unprecedented reduction of the random variations is achieved.

  8. 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.

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-15

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

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

    Science.gov (United States)

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

    1964-01-01

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

  12. Utilization of Protein Crystal Structures in Industry

    Science.gov (United States)

    Ishikawa, Kohki

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

  13. 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.

  14. 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.

  15. Photonics of liquid-crystal structures: A review

    International Nuclear Information System (INIS)

    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.

  16. Crystal structure of solid C70

    International Nuclear Information System (INIS)

    Detailed analysis of the room temperature X-ray powder diffraction data of pure solid C70 is reported. C70 prepared by slow evaporation from toluene solution adopts an hcp structure (space group P63/mmc) with a=10.53(1) A and C=17.24(1)A. C70 sublimed on to Si wafer adopts an fcc structure with a=14.89(1) A. The occurrence of both the hcp and fcc phases is rationalized in terms of cohesive energy calculations. Theoretical calculations of the diffraction pattern for the hcp structure, taking into account (a) orientational disorder amongst the molecules (b) presence of stacking faults and (c) a fraction of the sample to be amorphous/microcrystalline is seen to provide very good agreement with the experimental diffraction pattern. (author). 24 refs., 5 figs

  17. 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)

  18. Solving crystal structures with the symmetry minimum function

    International Nuclear Information System (INIS)

    Unravelling the Patterson function (the auto-correlation function of the crystal structure) (A.L. Patterson, Phys. Rev. 46 (1934) 372) can be the only way of solving crystal structures from neutron and incomplete diffraction data (e.g. powder data) when direct methods for phase determination fail. The negative scattering lengths of certain isotopes and the systematic loss of information caused by incomplete diffraction data invalidate the underlying statistical assumptions made in direct methods. In contrast, the Patterson function depends solely on the quality of the available diffraction data. Simpson et al. (P.G. Simpson et al., Acta Crystallogr. 18 (1965) 169) showed that solving a crystal structure with a particular superposition of origin-shifted Patterson functions, the symmetry minimum function, is advantageous over using the Patterson function alone, for single-crystal X-ray data.This paper describes the extension of the Patterson superposition approach to neutron data and powder data by (a) actively using the negative regions in the Patterson map caused by negative scattering lengths and (b) using maximum entropy Patterson maps (W.I.F. David, Nature 346 (1990) 731). Furthermore, prior chemical knowledge such as bond lengths and angles from known fragments have been included. Two successful structure solutions of a known and a previously unknown structure (M. Hofmann, J. Solid State Chem., in press) illustrate the potential of this new development. ((orig.))

  19. 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.

  20. 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.

  1. Crystal structure of clathrates of Hofmann dma-type

    International Nuclear Information System (INIS)

    Seven new clathrates Cd(DMA)2Ni(CN)4·xG (x=1, G=aniline, 2,3-xylidine, 2,4-xylidine, 2,5-xylidine, 2,6-xylidine, 3,5-xylidine, and x=2, G=2,4,6-trimethylaniline) of Hofmann type are synthesized by amine substitution for dimethylamine (DMA). On the base of x-ray diffraction data it is shown that geometry of guest molecule in cage-like hollow determines the structure of the host and crystal structure of clathrates. Two-dimension metallocomplex of the host of studied clathrates is characterized by elastic folded structure appearing as a result of angular deformation of bond between Cd atoms and host cyanide bridge. Guest molecule orientation is fixed by hydrogen bond. Structural elasticity of the host complex directs to differences in crystal structure of clathrates formed and to considerable variety of incorporated guests

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

    Science.gov (United States)

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

    2013-08-01

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

  3. 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...

  4. 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.

  5. 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....

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

    Science.gov (United States)

    1975-01-01

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

  7. 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...

  8. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Vasily F. Shabanov

    2013-08-01

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

  11. Band structures in Sierpinski triangle fractal porous phononic crystals

    Science.gov (United States)

    Wang, Kai; Liu, Ying; 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.

  12. Crystal structure of cerium(4) - dicesium trisulfate

    International Nuclear Information System (INIS)

    Cerium(4) - dicesium trisulfate is investigated by the X-ray diffraction method. Parameters of a monoclinic cell equal: a = 9.772(2), b = 16.797(2), c = 14.812(1)A, β 96.40(1), sp.gr. P21. The structure is formed by interchanging of anion [Ce4(SO4)128-]∞ and cation (Cs+) layers arranged parallel (101). Atoms Ce and Cs are arranged according to the law of a cubic close packing. Coordination polyhedron Ce1 and Ce2 is the two-hat trigonal prism, nine vertices Ce3 and Ce4 are one-hat antiprism

  13. Progress in ALCHEMI analysis of crystal structure

    International Nuclear Information System (INIS)

    The atomic location by channeling-enhanced microanalysis (ALCHEMI) is an effective technique to clarify the atomic configuration in multi-component compounds. Recent development of the theory on the characteristic x-ray emission has made ALCHEMI a more reliable and expansive technique. On this revised ALCHEMI, the characteristic x-ray intensities are measured at various electron-incidence directions in a transmission electron microscope, and are compared with x-ray intensities calculated from dynamical electron diffraction and inelastic scattering theories. On the present work, this technique was applied to thermoelectric materials. The occupation probabilities of Mn atoms on Fe I and Fe II sites in a thermoelectric semiconductor Fe0.97Mn0.03Si2 of a β-FeSi2 structure were 0.434 and 0.574, respectively. As another example, the occupancy of Ce atoms on voids and the coordinates (z1, z2) of Sb atoms in Ce0.5Fe3NiSb12 of a skutterrudite CoSb3 structure was determined to be 0.33 and (z1=0.336, z2=0.147), respectively. (Y.K.)

  14. Surface induced structures in nematic liquid crystal colloids

    OpenAIRE

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

    2014-01-01

    We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyimide surfaces using micron size masks). These bulk structures arise from non-zero boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configura...

  15. 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.

  16. 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.

  17. 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. PMID:18642947

  18. Crystal structure and magnetism of Tb2Ni3Si5 single crystal

    International Nuclear Information System (INIS)

    The structure transition of Tb2Ni3Si5 single crystal and the spin arrangement in the transition structure were studied by the magnetism measurement and neutron diffraction analysis. The powder X-ray diffraction experiment determined the mother sample was U2Co3Si5 type structure. The measurement results of magnetic susceptibility showed Neel temperature at 34.2 K and three magnetic phases depend on the antiferromagnetic transition at 3.8 K and 8.3 K. The magnetization curve showed complex magnetism arrangement and small change of differential magnetization among each magnetic phase. The neutron diffraction experiment of single crystal indicated that Tb atom shifted and constructed the lattice with 12/7a x 1/4b x 1/2c unit and the composite structure consisted of two kinds of lattice nested. The stable composite structure is unusual in the metal lattice. The spin arrangement of single crystal made clear that Tb magnetic moment existed in the plane and it was complex antiferromagnetism with incommensurate period expressed by three wave vectors such as k1, k2 and k3 in the low and middle temperature phase. On the magnetic phase transition in the low and middle temperature phase, the strength ratio of magnetic scattering changed so large, that the phase, which determined the spin direction, changed in the two magnetic phases. In the high temperature, each magnetic phase showed complex antiferromagnetic spin arrangement. (S.Y.)

  19. Coefficient of crystal lattice matching as a parameter of substrate - crystal structure compatibility in silumins

    Directory of Open Access Journals (Sweden)

    J. Piątkowski

    2009-07-01

    Full Text Available Adding high-melting point elements (Mo, Nb, Ni, Ti, W to complex silumins results in hardening of the latter ones, owing to the formation of new intermetallic phases of the AlxMey type, with refinement of dendrites in α solution and crystals in β phase. The hardening is also due to the effect of various inoculants. An addition of the inoculant is expected to form substrates, the crystal lattice of which, or some (privileged lattice planes and interatomic spaces should bear a strong resemblance to the crystal nucleus. To verify this statement, using binary phase equilibria systems, the coefficient of crystal lattice matching, being one of the measures of the crystallographic similarity, was calculated. A compatibility of this parameter (up to 20% may decide about the structure compatibility between the substrate and crystal which, in turn, is responsible for the effectiveness of alloy modification. Investigations have proved that, given the temperature range of their formation, the density, the lattice type, and the lattice parameter, some intermetallic phases of the AlxMey type can act as substrates for the crystallisation of aluminium and silicon, and some of the silumin hardening phases.

  20. 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.

  1. 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.

  2. 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.

  3. Crystal structure and density of helium to 232 kbar

    International Nuclear Information System (INIS)

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

  4. Synthesis and Crystal Structure of Tetranuclear Zinc Benzoate

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  5. 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.

  6. 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.

  7. Alternative models for two crystal structures of bovine rhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    Stenkamp, Ronald E., E-mail: stenkamp@u.washington.edu [Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195 (United States)

    2008-08-01

    Two crystal structures of rhodopsin that were originally described using trigonal symmetry can be interpreted in a hexagonal unit cell with a smaller asymmetric unit. The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P3{sub 1}) can be re-interpreted as hexagonal (space group P6{sub 4}). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y)

  8. Crystal structure of Er26Ge23-x compound

    International Nuclear Information System (INIS)

    Crystal structure of Er26Ge23-x compound (Nicolet R3 autodiffractometer,ω - method) is studied by monocrystal method. Germanide belongs to tetragonal crystal system, space group P4/nmm, a=1.4576(3), c=1.0228(2) nm. Structure is interpreted in anisotropic appoximation up to R=0.036 (for 968 independent reflexes). Er26Ge23-x compound belongs to a new type of binary germanides. Coordination polyhedrons of germanium atoms are tetragonal antiprism, trigonal prism and cube. Coordination numbers 16-17 are characteristic of erbium. Polyhedrons laying in a structure is considered. Intermetallide has no analogues among binary germanides but it is related to the earlier known Ge26Li5Ge22+x compound

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

    Science.gov (United States)

    Zheng, Huirong; Lou, Benyong

    2016-05-01

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

  10. Crystal structure of Brinzolamide: a carbonic anhydrase inhibitor

    Directory of Open Access Journals (Sweden)

    Huirong Zheng

    2016-05-01

    Full Text Available In crystal structure of the title compound, C12H21N3O5S3 [systematic name: (R-4-ethylamino-2-(3-methoxypropyl-3,4-dihydro-2H-thieno[3,2-e][1,2]thiazine-6-sulfonamide 1,1-dioxide], there exist three kinds of hydrogen-bonding interactions. The sulfonamide group is involved in hydrogen bonding with the secondary amine and the methoxy O atom, resulting in the formation of layers parallel to the bc plane. The layers are linked by an N—H...O hydrogen bond involving a sulfonamide O atom as acceptor and the secondary amine H atom as donor, which gives rise to the formation of a unique bilayer structure. The absolute structure of the molecule in the crystal was determined by resonant scattering [Flack parameter = 0.01 (4].

  11. First crystal structure and catalytic mechanism of a bacterial glucuronosyltransferase

    International Nuclear Information System (INIS)

    Xanthomonas campestris GumK (β-1,2-glucuronosyltransferase) is a membrane associated protein involved in the biosynthesis of xanthan, an exo polysaccharide crucial for this bacterium's phyto pathogenicity. Xanthan is also used in many important industrial applications. The x-ray crystal structure of apo-GumK was solved at 1.9 A resolution. The enzyme has two well defined Rossmann domains with a catalytic cleft between them. Recently, the crystal structure of GumK complexed with the donor substrate was also solved. We identified a number of catalytically important residues, including Asp157, which serves as the general base in the transfer reaction. The biological and structural data reported here shed light on the molecular basis for donor and acceptor selectivity in glucuronosyltransferases. (author)

  12. 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...

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

    Science.gov (United States)

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

    2015-09-01

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

  14. 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.

  15. 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.

  16. Crystal structure and magnetic studies of the uranium ternary pnictides

    International Nuclear Information System (INIS)

    Crystallographic and magnetic properties of seven identified phases in the ternary U-Cu(Ni)-P(As) systems are reported. Preliminary studies performed on both polycrystalline and single-crystal samples have indicated a new type of crystal structure for UCuP2, UCuAs2 and UNiAs2. Magnetic susceptibility measurements of these phases have shown that the U-Cu-P(As) ternaries are ferromagnetically ordered with TC being 216, 76, 140 and 131 K for UCu2P2, UCuP2, UCu2As2 and UCuAs2 respectively. The U-NiP(As) ternaries are antiferromagnets with TN=228 K for UNiAs2 and 111 K for UNi2P2. The seventh phase obtained in the form of single crystals with, as yet, uncertain composition denoted as ''U3Cu3P5'' and having a complex tetragonal crystal structure with c/a=9.2, exhibits an antiferromagnetic phase transition below 146 K. Magnetization measurements reveal a strong magnetic anisotropy in all the ferromagnetic compounds examined. (orig.)

  17. 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·.

  18. Crystal structure optimisation using an auxiliary equation of state

    International Nuclear Information System (INIS)

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

  19. 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.

  20. 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.

  1. EVO—Evolutionary algorithm for crystal structure prediction

    Science.gov (United States)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

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

  2. '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)

  3. 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

  4. 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. PMID:26594525

  5. Crystal structure of N′-hydroxypyrimidine-2-carboximidamide

    Directory of Open Access Journals (Sweden)

    Nithianantham Jeeva Jasmine

    2014-10-01

    Full Text Available The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The molecule adopts an E configuration about the C=N double bond. In the crystal, adjacent molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(10 ring motif. The dimers are further linked via N—H...N and O—H...N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N—H...O and weak C—H...O hydrogen bonds and offset π–π stacking interactions between adjacent pyrimidine rings [centroid–centroid distance = 3.622 (1 Å].

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

    Science.gov (United States)

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

    2008-04-01

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

  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 Structures of Cisplatin Bound to a Human Copper Chaperone

    Energy Technology Data Exchange (ETDEWEB)

    Boal, Amie K.; Rosenzweig, Amy C.; (NWU)

    2010-08-16

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

  9. Crystal structure of (ferrocenylmethyl)dimethylammonium hydrogen oxalate

    OpenAIRE

    Mamadou Ndiaye; Abdoulaye Samb; Libasse Diop; Thierry Maris

    2015-01-01

    The crystal structure of the title salt, [Fe(C5H5)(C8H13N)](HC2O4), consists of discrete (ferrocenylmethyl)dimethylammonium 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.

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

    OpenAIRE

    Faber, Felix; Lindmaa, Alexander; 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 ...

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

    NARCIS (Netherlands)

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

    1972-01-01

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

  12. 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.

  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 C-phycocyanin from Cyanidium caldarium provides a new perspective on phycobilisome assembly.

    OpenAIRE

    Stec, B.; Troxler, R F; Teeter, M M

    1999-01-01

    The crystal structure of the light-harvesting protein phycocyanin from the cyanobacterium Cyanidium caldarium with novel crystal packing has been solved at 1.65-A resolution. The structure has been refined to an R value of 18.3% with excellent backbone and side-chain stereochemical parameters. In crystals of phycocyanin used in this study, the hexamers are offset rather than aligned as in other phycocyanins that have been crystallized to date. Analysis of this crystal's unique packing leads t...

  15. Synthesis and Crystal Structure of 3-(Trichloroacetyl) Indole

    Institute of Scientific and Technical Information of China (English)

    ZENG Xiang-Chao; XU Shi-Hai; LIU Po-Run; DENG Qin-Ying

    2005-01-01

    3-(Trichloroacetyl) indole has been synthesized by the reaction of indole with trichloroacetyl chloride in 73% yield, and its crystal structure was determined by X-ray diffraction method. The crystal is of orthorhombic, space group Pnma with a = 20.781(7), b = 6.857(2), c = 7.431(3) (A), V = 1058.8(6) (A)3, Z = 4, Mr = 262.51, Dc = 1.647 g/cm3, λ = 0.71073(A), μ(MoKα) = 0.833 mm(A) 1 and F(000) = 528. The structure was refined to R = 0.0286 and wR = 0.0749 for 1073 observed reflections with I > 2σ(I). It exhibits a characteristic plane structure consisting of all atoms except Cl(2) and Cl(2)A. Two kinds of intermolecular hydrogen bonds are formed: N(1)- H(8A)…O(1) and N(1)H(8A)…Cl(1). There also exist three kinds of π-π stacking in the crystal.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Crystal structure of inactive form of Rab3B

    International Nuclear Information System (INIS)

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

  1. Ionic conductivity in crystal structures with isolated tetragonal anions

    International Nuclear Information System (INIS)

    A unique peculiarity - the presence of complex isolated tetrahedron anions TZK4(4y-Z), where K - oxygen or Hal atom, y - its valency, Z - T element valency, is showh to be characteristic for different groups of superionic conductors including complex oxides of zirconium, scandium and molybdenum. It is possible to integrate and systematize a large number of ionic conductors on the basis of the given peculiarities of the crystal structure. Such an approach allows to consider the structure and electrophysical properties of a great number of cation conductors on the common ground, and to mark the concrete ways for searching new ion conducting materials

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    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.

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    Luca eRonda

    2015-04-01

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

  7. 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.

  8. Crystal structure and vibrational analysis of novel nonlinear optical L-histidinium tetrafluoroborate (L-HFB) single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Gokul Raj, S.; Ramesh Kumar, G.; Mohan, R. [Department of Physics, Presidency College, Chepauk, Chennai 600 005 (India); Jayavel, R. [Crystal Growth Centre, Anna University, Sardar Patel Road, Chennai 600 025 (India); Varghese, Babu [Sophisticated Analytical Instrument Facility, IIT, Chennai 600 025 (India)

    2007-02-15

    Single crystals of L-histidinium tetrafluoroborate (L-HFB) were grown by slow evaporation of an aqueous solution at room temperature. The crystal structure has been elucidated through single crystal X-ray crystallography. The infrared (IR) and Raman spectroscopic measurements fully confirm the X-ray crystal structure. The potential role of hydrogen bonds of the title crystal and its influence on interaction between the L-histidinium cation and tetrafluoroborate anion has been discussed in detail. The crystal is a very good second harmonic generator. Its powder SHG efficiency is calculated as d{sub eff} = 1.70 d{sub eff} (KDP). (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

    Science.gov (United States)

    Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.

  10. 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].

  11. Synthesis and Crystal Structure of a Degraded Dehydroabietylamine Thiophene Imine

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A degraded dehydroabietylamine thiophene imine (C24H30NS, Mr-364.55)has been synthesized from dehydroabietic acid, and its structure was characterized by IR, 1HNMR spectroscopy and single-crystal X-ray diffraction.White crystals of the title compound crystallize in the monoclinic system, space group P21 with a = 5.9490(12), b = 16.337(3), c = 10.780(2)(A), β= 92.21(3)°, V = 1046.9(3)(A)3, Z = 2, Dc = 1.156g/cm3, λ= 0.71073(A),μ= 0.162 mm-1, F(000) = 394, the final R = 0.0443 and wR = 0.0805 for 1325 observed reflections with(I>2σ(I).The imine group was directly attached to the chiral carbon atom of tricyclo hydrophenthenrane structure with a trans configuration.The dihedral angle between two aromatic rings is 88.3°.

  12. 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.

  13. Crystal structure of (1Z,2E)-cinnamaldehyde oxime

    Science.gov (United States)

    Bugenhagen, Bernhard; Al Soom, Nuha; Al Jasem, Yosef; Thiemann, Thies

    2015-01-01

    The title compound, C9H9NO, crystallized with two independent mol­ecules (A and B) in the asymmetric unit. The conformation of the two mol­ecules differs slightly with the phenyl ring in mol­ecule A, forming a dihedral angle of 15.38 (12)° with the oxime group (O—N=C), compared to the corresponding angle of 26.29 (11)° in mol­ecule B. In the crystal, the A and B mol­ecules are linked head-to-head by O—H⋯N hydrogen bonds, forming –A–B–A–B– zigzag chains along [010]. Within the chains and between neighbouring chains there are C—H⋯π inter­actions present, forming a three-dimensional structure. PMID:26870499

  14. Crystal structure of (1Z,2E-cinnamaldehyde oxime

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2015-12-01

    Full Text Available The title compound, C9H9NO, crystallized with two independent molecules (A and B in the asymmetric unit. The conformation of the two molecules differs slightly with the phenyl ring in molecule A, forming a dihedral angle of 15.38 (12° with the oxime group (O—N=C, compared to the corresponding angle of 26.29 (11° in molecule B. In the crystal, the A and B molecules are linked head-to-head by O—H...N hydrogen bonds, forming –A–B–A–B– zigzag chains along [010]. Within the chains and between neighbouring chains there are C—H...π interactions present, forming a three-dimensional structure.

  15. 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.

  16. Crystal structure of jinshajiangite from the Norra Kaerr complex (Sweden)

    International Nuclear Information System (INIS)

    The structure of the mineral jinshajiangite from the Norra Kaerr alkaline complex (Sweden) was determined by single-crystal X-ray diffraction and refined to R = 6.7%. The monoclinic unit-cell parameters are a = 5.350(2) A, b = 6.909(6) A, c = 20.96(1) A, β = 99.83(4)o, sp. gr. P2/m. This mineral is an Fe-rich analogue of surkhobite and perraultite, but it crystallizes in a different space group, and the unit-cell parameters a and b are two times smaller than those of these two minerals. The framework of jinshajiangite from Norra Kaerr contains narrow and wide channels, which are occupied by Ca, Na, Ba, and K atoms in an ordered fashion.

  17. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE OF BIS-(2-HYDROXYBENZALDEHYDEDIAMINOGUANIZONE

    Directory of Open Access Journals (Sweden)

    Diana Dragancea, Vladimir B. Arion, Sergiu Shova

    2008-12-01

    Full Text Available The new ligand, bis(2-hydroxybenzaldehydediaminoguanizone (1 has been synthesized and characterized by elemental analysis, IR and 1H NMR spectroscopies. The crystal structure of the compound was determined by X-ray diffraction. The ligand C15H15N5O2·C2H5OH crystallizes in the monoclinic space group P21/c with unit cell parameters a = 8.9102(3, b = 10.0357(3, c = 19.7618(6 Å, β = 98.385(2°, Z = 4, V = 1748.21(9 Å3, R1 = 0.040. The amino form of the ligand adopts a planar conformation stabilized by two intramolecular hydrogen bonds of the type O–H···N, in which the H atoms of the central amino group are directed to the lone-pair regions of the azomethine nitrogen atoms.

  18. 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.

  19. 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.

  20. Crystal and molecular structure of Np(4) sulfate

    International Nuclear Information System (INIS)

    Monocrystals are prepared and crystal structure of Np(SO4)2·4H2O is detected: a=14.597(4), b=11.036(2), c=5.663(2) A, space group - Pnma. The structure is layered, electroneutral layers of [Np(SO4)2(H2O)4]n are perpendicular to [100] direction, hydrogen bonds combine layers into three-dimensional packing. Coordination Np(4) polyhedron is quadratic prism and is formed by oxygen atoms of bidentate-bridge sulfate ions and four water molecules. Np-O bond lengths and bond angles are determined. Peculiarities of structure of double neptunium sulfates with K, Na, Cs in dependence on ligand number and effect of outer spheric cations and water molecules on structure of coordination spheres of Np atoms are considered

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

    Science.gov (United States)

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

    2006-05-19

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

  2. Crystal growth,structure and properties of bismuth triborate BiB3O6 crystal

    Institute of Scientific and Technical Information of China (English)

    滕冰; 王继扬; 王正平; 江怀东; 刘宏; 胡小波; 董胜明; 刘跃岗; 邵宗书

    2002-01-01

    BiB3O6 (BIBO) single crystals with size of 46 × 23 × 10 mm3 and weight of 26.0 g have been successfully grown by top-seeded method.Problems encountered in the growth process of this crystal have been discussed in detail,and the methods of growing high-quality large crystals have been put forward.The relationship between their structure and properties is studied.The space group of monoclinic BiB3O6 is C2 and 03(7),b=4.9948(7),c=6.5077(7),the cell parameters are a=7.1293(5)3.The density of BIBO is 4.8965 g/cm3.β=105.586(8)″,and V=222. The Mohs's scale of hardness is 5.5-6.There is no cleavage face in the crystal.The transmittance of BIBO is about 80 percent in the range from visible coherent light to near-infrared light.The ultraviolet cutoff wavelength is at 276 nm.BiB3O6 is a biaxial crystal and has two sets of axes,and the relative orientation of (X,Y,Z) with regard to (a,b,c) is: X//b,(Y,c)=47.2°,(Z,a)=31.6°,determined by X-ray analysis combined with polarized microscopy.Second-harmonic-generation (SHG) experiments were carried out for the first time.In type I phase-matching (PM) directions (11.1°,90°) and (168.9°,90°),SHG conversion efficiencies of two directions for 1.064 μm light are up to 67.7 % and 58%,respectively.We have also obtained the third-harmonic-generation (THG) of 1.064 μm.The comparative experiments between BIBO and KTP were carried out on conversion efficiency,transmittance and hardness.All the above results indicate that BiB3O6 is a kind of excellent nonlinear optical (NLO) crystal.

  3. 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.

  4. Crystal and molecular structure of perindopril erbumine salt

    Science.gov (United States)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  5. 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.

  6. Investigation of crystal structure and associated electronic structure of Sr 6BP 5O 20

    Science.gov (United States)

    Ehrenberg, Helmut; Laubach, Sonja; Schmidt, P. C.; McSweeney, R.; Knapp, M.; Mishra, K. C.

    2006-04-01

    Strontium borophosphate phosphate (Sr 6BP 5O 20, SrBP), activated by divalent europium ions is a bluish-green phosphor emitting in a broad band with the emission peak near 480 nm. In this paper, we report the crystal structure of SrBP determined from an analysis of the X-ray diffraction pattern of a prismatic single crystal (size 60 μm×50 μm×40 μm). This crystal was chosen from undoped phosphor powder samples prepared for this purpose by solid-state reaction. SrBP is observed to crystallize in a body-centered tetragonal lattice with the lattice parameters a=9.7895(7) Å and c=19.032(3) Å, the associated space group being I4¯c2 (space group 120). Using the structural data from this study, we have also calculated its electronic structure using the augmented spherical wave method and the local density approximation (LDA). We show the ordering of the electronic states by the density of states (DOS) and the partial DOS plots. The LDA gives a direct optical band gap at the Γ point of about 5 eV. The significance of the crystal structure and associated electronic structure is discussed with respect to maintenance of this phosphor in Hg-discharge lamps.

  7. Low-temperature structure of rubrene single crystals grown by vapor transport

    NARCIS (Netherlands)

    Jurchescu, OD; Meetsma, A; Palstra, TTM; Jurchescu, Oana D.

    2006-01-01

    We report the crystal structure of rubrene, C42H28 (5,6,11,12-tetraphenyltetracene), in the temperature interval 100-300 K. The crystals are grown by physical vapor transport in an open system. The crystal structure is orthorhombic over the entire temperature range.

  8. 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…

  9. The crystal structure of TlFe3Te3

    International Nuclear Information System (INIS)

    TlFe3Te3 is hexagonal, space group P63/m-Csub(2h)6, a = 9.350(2)A, c = 4.2230 (7)A,Z = 2. Iron and tellurium atoms occupy the positions 6(h) with x = 0.170, y = 0,149 and x = 0.046, y = 0.357 respectively. Thallium atoms are situated in 2(d). The structure was determined on the basis of single crystal data obtained from a four circle diffractometer. Refinement yielded an R-value of 4.8% for an asymmetric set of 267 reflections. TlFe3Te3 is a new structure type. The structure and its relations to the Mn5Si3-, the Nb3Te4- and the Tlsub(x)V6S8-type are discussed. (author)

  10. 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).

  11. 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.

  12. Nanocrystalline structure formation at crystallization of Fe-Nd films

    International Nuclear Information System (INIS)

    Fe100-xNdx films (x=33,50,75,83) were prepared by vacuum evaporation technique. The TEM data show that initial films contain amorphous phase. Maximal quantity of amorphous phase was found for x=33. The diffraction of amorphous phase differs from ones of as-quenched alloys. The films were treated by electron beam treatment in-situ at multistage regime. The crystallization process was registered step by step. The different behavior at various intensity of treatment was observed. During the first stage of treatment the nanosize precipitations (7-50 nm) are found to form. Relatively stable nanocrystalline structure at x=33 consists of α-Fe precipitations in amorphous matrix. Fine dispersed nanosize structure appears at first stage of crystallization in films with x=75. During electron beam treatment the last structure transforms in local spherical areas. In films at x=83 the bcc-Nd based solid solution and/or fcc γ-phase appear. (orig.)

  13. 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

    2016-04-01

    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 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.

  14. New halides of neodymium and their crystal structures

    International Nuclear Information System (INIS)

    The crystal structures of the peritectic phases NdClsub(2.27) (t-phase) and NdClsub(2.37) (rh-phase) were determined. The structure of the rh-phase was solved, from the t-phase only the elementary cell could be determined because no single crystals of sufficient quality were obtained. Jutting out feature of the rh-phase which has to be formulated as Nd14Cl32O is a polyeder cluster of 6 quadratic antiprisms the inner cubo octahedric cavity of which is occupied by an oxygen atom. The linkage of these polyeder cluster ensues only under each other along the triple axis of the rhomboedric system over 3 upper and 3 lower common borders each. Therewith for the first time a superlattice of the fluorite-type was found in which this unit exclusively occurs. The type of linkage of polyeder clusters causes the occurrence of an exceptional polyeder around the twovalent Nd ions which can be looked at as a zwitter polyeder of icosahedron and cube and therefore coordinates tenfold the twovalent neodymium. The strict order of chemically and crystallografically clearly differentiated cations is expressed by a hexagonal-rhomboedric superstructure of the fluorite-aristotyp with a doubled c-axis. The phase diagram of the system Nd-NdBr3 was determined and a structure proposition was worked out for the first Vernier phase in there with n=4 of the series Lnsub(n)Xsub(2n+1). (SPI)

  15. Study of the crystal structure of silicon nanoislands on sapphire

    Energy Technology Data Exchange (ETDEWEB)

    Krivulin, N. O., E-mail: krivulin@phys.unn.ru; Pirogov, A. V.; Pavlov, D. A.; Bobrov, A. I. [Lobachevsky State University of Nizhny Novgorod (Russian Federation)

    2015-02-15

    The results of studies of the crystal structure of silicon nanoislands on sapphire are reported. It is shown that the principal defects in silicon nanoislands on sapphire are twinning defects. As a result of the formation of such defects, different crystallographic orientations are formed in silicon nanoislands on sapphire. In the initial stages of the molecular-beam epitaxy of silicon on sapphire, there are two basic orientations: the (001) orientation parallel to the surface and the (001) orientation at an angle of 70° to the surface.

  16. 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.

  17. Crystal structure of tris­(piperidinium) hydrogen sulfate sulfate

    OpenAIRE

    Tamara J. Lukianova; Vasyl Kinzhybalo; Adam Pietraszko

    2015-01-01

    In the title molecular salt, 3C5H12N+·HSO4−·SO42−, each cation adopts a chair conformation. In the crystal, the hydrogen sulfate ion is connected to the sulfate ion by a strong O—H...O hydrogen bond. The packing also features a number of N—H...O hydrogen bonds, which lead to a three-dimensional network structure. The hydrogen sulfate anion accepts four hydrogen bonds from two cations, whereas the sulfate ion, as an acceptor, binds to five separate piperidinium cations, forming seven hydrogen ...

  18. 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.

  19. Crystal structure of S,N-dibenzyl-d-penicillamine monohydrate

    Directory of Open Access Journals (Sweden)

    Nobuto Yoshinari

    2014-11-01

    Full Text Available In the asymmetric unit of the title compound, C19H23NO2S·H2O, there are two independent organic molecules and two water molecules. Both organic molecules exist as the zwitterionic form. The dihedral angles between the planes of the rings in the organic molecules are 86.84 (10 and 88.77 (11°. An intramolecular N—H...S hydrogen bond occurs. In the crystal, organic and water molecules are linked by N—H...O and O—H...O hydrogen bonds, generating a tape structure running along the b-axis direction.

  20. 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.

  1. Inorganic chiral 3-D photonic crystals with bicontinuous gyroid structure replicated from butterfly wing scales

    OpenAIRE

    Mille, Christian; Tyrode, Eric; Corkery, Robert W.

    2011-01-01

    Three dimensional silica photonic crystals with the gyroid minimal surface structure have been synthesized. The butterfly Callophrys rubi was used as a biotemplate. This material represents a significant addition to the small family of synthetic bicontinuous photonic crystals. QC 20110913

  2. Magnetic and Crystal Structure of α-RuCl3

    Science.gov (United States)

    Sears, Jennifer

    The layered honeycomb material α-RuCl3 has been proposed as a candidate material to show significant bond-dependent Kitaev type interactions. This has prompted several recent studies of magnetism in this material that have found evidence for multiple magnetic transitions in the temperature range of 8-14 K. We will present elastic neutron scattering measurements collected using a co-aligned array of α-RuCl3 crystals, identifying zigzag magnetic order within the honeycomb planes with an ordering temperature of ~8 K. It has been reported that the ordering temperature depends on the c axis periodicity of the layered structure, with ordering temperatures of 8 and 14 K for three and two-layer periodicity respectively. While the in-plane magnetic order has been identified, it is clear that a complete understanding of magnetic ordering and interactions will depend on the three dimensional structure of the crystal. Evidence of a structural transition at ~150 K has been reported and questions remain about the structural details, in particular the stacking of the honeycomb layers. We will present x-ray diffraction measurements investigating the low and high temperature structures and stacking disorder in α-RuCl3. Finally, we will present inelastic neutron scattering measurements of magnetic excitations in this material. Work done in collaboration with K. W. Plumb (Johns Hopkins University), J. P. Clancy, Young-June Kim (University of Toronto), J. Britten (McMaster University), Yu-Sheng Chen (Argonne National Laboratory), Y. Qiu, Y. Zhao, D. Parshall, and J. W. Lynn (NCNR).

  3. Can the Low-Resolution Structures of Photointermediates of Bacteriorhodopsin Explain Their Crystal Structures?

    OpenAIRE

    Kamikubo, Hironari; Kataoka, Mikio

    2004-01-01

    To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstra...

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

    Science.gov (United States)

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

    2015-09-01

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

  5. 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.

  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 structures of superconducting sodium intercalates of hafnium nitride chloride

    International Nuclear Information System (INIS)

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

  8. 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.

  9. Crystal structure of pyruvate decarboxylase from Zymobacter palmae.

    Science.gov (United States)

    Buddrus, Lisa; Andrews, Emma S V; Leak, David J; Danson, Michael J; Arcus, Vickery L; Crennell, Susan J

    2016-09-01

    Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and Rr.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were Rwork = 0.186 (0.271 in the highest resolution bin) and Rfree = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions. PMID:27599861

  10. Crystal structure of the superconducting phase of sulfur hydride

    Science.gov (United States)

    Einaga, Mari; Sakata, Masafumi; Ishikawa, Takahiro; Shimizu, Katsuya; Eremets, Mikhail I.; Drozdov, Alexander P.; Troyan, Ivan A.; Hirao, Naohisa; Ohishi, Yasuo

    2016-09-01

    A superconducting critical temperature above 200 K has recently been discovered in H2S (or D2S) under high hydrostatic pressure. These measurements were interpreted in terms of a decomposition of these materials into elemental sulfur and a hydrogen-rich hydride that is responsible for the superconductivity, although direct experimental evidence for this mechanism has so far been lacking. Here we report the crystal structure of the superconducting phase of hydrogen sulfide (and deuterium sulfide) in the normal and superconducting states obtained by means of synchrotron X-ray diffraction measurements, combined with electrical resistance measurements at both room and low temperatures. We find that the superconducting phase is mostly in good agreement with the theoretically predicted body-centred cubic (bcc) structure for H3S. The presence of elemental sulfur is also manifest in the X-ray diffraction patterns, thus proving the decomposition mechanism of H2S to H3S + S under pressure.

  11. 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...... structural results were obtained from full-profile Rietveld refinements of powder data [goodness of fit = 1.38 and 2.54 for (b) and (c), respectively]. The Al2Br6 molecule consists of two edge-sharing, almost regular AlBr4 tetrahedra. The Al-Br bond distances are in the range 2.21-2.42 Angstrom...

  12. Synthesis and crystal structure of PdSnTe

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-22

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

  13. Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome.

    Science.gov (United States)

    Page, Rebecca; Grzechnik, Slawomir K; Canaves, Jaume M; Spraggon, Glen; Kreusch, Andreas; Kuhn, Peter; Stevens, Raymond C; Lesley, Scott A

    2003-06-01

    As the field of structural genomics continues to grow and new technologies are developed, novel strategies are needed to efficiently crystallize large numbers of protein targets, thus increasing output, not just throughput [Chayen & Saridakis (2002). Acta Cryst. D58, 921-927]. One strategy, developed for the high-throughput structure determination of the Thermotoga maritima proteome, is to quickly determine which proteins have a propensity for crystal formation followed by focused SeMet-incorporated protein crystallization attempts. This experimental effort has resulted in over 320 000 individual crystallization experiments. As such, it has provided one of the most extensive systematic data sets of commonly used crystallization conditions against a wide range of proteins to date. Analysis of this data shows that many of the original screening conditions are redundant, as all of the T. maritima proteins that crystallize readily could be identified using just 23% of the original conditions. It also shows that proteins that contain selenomethionine and are more extensively purified often crystallize in distinctly different conditions from those of their native less pure counterparts. Most importantly, it shows that the two-tiered strategy employed here is extremely successful for predicting which proteins will readily crystallize, as greater than 99% of the proteins identified as having a propensity to crystallize under non-optimal native conditions did so again as selenomethionine derivatives during the focused crystallization trials. This crystallization strategy can be adopted for both large-scale genomics programs and individual protein studies with multiple constructs and has the potential to significantly accelerate future crystallographic efforts. PMID:12777766

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

    Science.gov (United States)

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

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

  15. The crystal structures of potassium and cesium trivanadates

    Science.gov (United States)

    Evans, H.T.; Block, S.

    1966-01-01

    Potassium and cesium trivanadates are monoclinic and isomorphous, space group P21/m, with the following dimensions (Z = 2): KV3O8, a = 7.640 A, b = 8.380 A, c = 4.979 A, ??= 96?? 57???; CsV3O8, a = 8.176 A, b = 8.519 A, c = 4.988 A, ?? = 95?? 32???. The crystal structure of KV3O8 has been determined from hk0, 0kl, and h0l Weissenberg data with an R factor of 0.15. The structure of CsV3O8 has been refined with 1273 hkl Weissenberg data to an R factor of 0.089. The structures consist of corrugated sheets based on a linkage of distorted VO6, octahedra. Two of the vanadium atoms lie in double, square-pyramid groups V2O8, which are linked through opposite basal corners into chains along the b axis. The chains are joined laterally along the c axis into sheets by the third vanadium atom in VO groups, also forming part of a square-pyramid coordination. Various aspects of these structures are compared with other known oxovanadate structures.

  16. Colloidal Photonic Crystals Containing Silver Nanoparticles with Tunable Structural Colors

    Directory of Open Access Journals (Sweden)

    Chun-Feng Lai

    2016-05-01

    Full Text Available Polystyrene (PS colloidal photonic crystals (CPhCs containing silver nanoparticles (AgNPs present tunable structural colors. PS CPhC color films containing a high concentration of AgNPs were prepared using self-assembly process through gravitational sedimentation method. High-concentration AgNPs were deposited on the bottom of the substrate and acted as black materials to absorb background and scattering light. Brilliant structural colors were enhanced because of the absorption of incoherent scattering light, and color saturation was increased by the distribution AgNPs on the PS CPhC surfaces. The vivid iridescent structural colors of AgNPs/PS hybrid CPhC films were based on Bragg diffraction and backward scattering absorption using AgNPs. The photonic stop band of PS CPhCs and AgNPs/PS hybrid CPhCs were measured by UV–visible reflection spectrometry and calculated based on the Bragg–Snell law. In addition, the tunable structural colors of AgNPs/PS hybrid CPhC films were evaluated using color measurements according to the Commission International d’Eclairage standard colorimetric system. This paper presents a simple and inexpensive method to produce tunable structural colors for numerous applications, such as textile fabrics, bionic colors, catalysis, and paints.

  17. Crystal structure of the human glucose transporter GLUT1

    Science.gov (United States)

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-01

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  18. Crystal Structure of the Human Cytomegalovirus Glycoprotein B.

    Directory of Open Access Journals (Sweden)

    Heidi G Burke

    2015-10-01

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

  19. Crystal Structures and Antimicrobial Activity of Two Phosphorus Compounds

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    One phosphorus heterocycle compound 1, C13H13N2OPS, was synthesized by the reaction of Lawesson's reagent (LR) with o-phenylene diamine. The crystal belongs to the orthorhombic system, space group P212121 with a = 5.5274(11), b = 8.1603(16), c = 28.830(6) (A), V =1300.4(4) (A)3, Z = 4, Mr= 276.28, Dc = 1.411 g/cm3, F(000) = 576,μ = 0.360 mm-1, R = 0.0259 and wR = 0.0652 for 1414 observed reflections with I > 2σ(I). While compound 2, C14H17N2O2PS, was obtained as a ring-cleavage product of compound 1. This crystal is of monoclinic system, space group P21/c with a = 9.5619(19), b = 21.879(4), c = 7.3618(15) (A), β= 103.03(3)°, V=1500.4(5) (A)3,Z = 4, Mr= 308.33, Dc = 1.365 g/cm3, F(000) = 648, μ = 0.325 mm-1, R = 0.0383 and wR =0.0742for 2283 observed reflections with I > 2σ(I). Phosphorus atom in each compound bonds with sulfur and carbon atoms using sp3 hybrid orbitals, and crystals of these two compounds are formed and stabilized by intermolecular hydrogen bonds and Van der Waals' forces. The special structure of compound 1 leads to its good antimicrobial activity against staphylococcus aureus.

  20. Preparation, Crystal Structure, and Thermal Analysis of Carbohydrazide Trinitrophloroglucinolate

    Institute of Scientific and Technical Information of China (English)

    LIU Zhen-hua; ZHANG Tong-lai; HU Xiao-chun; ZHANG Jian-guo; YANG Li; QIAO Xiao-jing

    2008-01-01

    A new compound (CHZ)(HTNPG).0.5H2O was synthesized by mixing carbohydrazide(CHZ) and trinitrophloroglucinol(TNPG) and characterized by elemental analysis and Fourier transform infrared (FTIR) spectrum.Its crystal structure was determined by single crystal X-ray diffraction analysis.The crystal belongs to triclinic system,P1 space group,with a=0.45578(9) nm,b=1.0142(2) nm,c=1.3041(3) nm,a=86.53(3)°,β=99.56(3)°,γ=81.94(3)°,V=0.5958(2) nm3,Z=2,Dc=2.008 g/cm3,R1=0.0476,and wR2=O.1139.The compound is a di-substituted salt of TNPG,which consists of a cation (CHZ)2+ and an anion (HTNPG)2-.The thermal analysis of the compound was studied by means of differential scanning calorimetry(DSC) and thermogravimetry-derivative thermogravimetry(TG-DTG).Under nitrogen atmosphere at a heating rate of 10 ℃/min,the thermal decomposition of the compound contained one endothermic process of dehydrating stage and two intense exothermic decomposition processes in a temperature range of 140--232℃ on the DSC trace.The decomposition products of the title compound are nearly gaseous products.The existing complicated hydrogen bond networks and electrostatic attraction between (CHZ)2+ and (HTNPG)2-enhance the thermal stability of the title compound.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fenglei Li

    2006-08-09

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

  2. Crystal Structure and Photoluminescence of a Tetranuclear Cadmium Complex

    Institute of Scientific and Technical Information of China (English)

    史娟; 张尊听

    2012-01-01

    A novel tetranuclear cadmium complex ([{Cd(CIsHsOTS)(H20)(DMSO)}3{Cd(CtsH807S)(H20)2}]. 3DMSO.H20) was obtained by the self-assembly of Cd(II) with 5,7-dihydroxyflavone-6-sulfonate. The complex was characterized by IH NMR, IR, elemental analysis and X-ray single-crystal diffraction studies. It crystallizes in triclinic, space group P]-. In the complex, the chelate atoms of Cd(II) are all from oxygen. Four Cd(II) are con- nected via the carbonyl and 5-hydroxyanion of four ligands and form an approximate square. Four ligands locate at two sides of the square, and two of them at the same side are almost parallel and exist aromatic n-n stacking. Ligands on the opposite side of the square are nearly perpendicular. The result of the luminescent studies indicated that the solid of the complex shwed photoluminescent properties because of a combination of coordination, hydro- gen bonding and n-n stacking interaction in the molecule structure. The complex emits green fluorescence (2em= 496 nrn) when it is excited at the wavelength of 440 nm.

  3. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    Energy Technology Data Exchange (ETDEWEB)

    Polyakova, I. N., E-mail: polyakova@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Saraev, V. V.; Gavrilov, A. S.; Golod, E. L. [St. Petersburg State Technological Institute (Technical University) (Russian Federation)

    2009-05-15

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH{sub 2} groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

  4. Crystal Structure of 7,3'-Dihydroxy-4'-methoxyisoflavone

    Institute of Scientific and Technical Information of China (English)

    丁兰; 王明盛; 郭国聪; 汪汉卿

    2004-01-01

    The title compound 7,3'-dihydroxy-4'-methoxyisoflavone isolated from the stems of Eremosparton songoricum was characterized by IR,1H-NMR,13C-NMR,H1-H1COSY,HMQC,HMBC and EIMS,and its crystal structure was determined by single-crystal X-ray diffraction with the following data: C16H12O5,monoclinic,P21/c,Z = 4,a = 9.926(8),b = 17.091(5),c = 8.001(4)A ',β = 99.07(3)A,V = 1340(1)A3,Mr = 284.26,Dc = 1.409 g/cm3,F(000) = 592,μ = 0.106 mm-1,R = 0.065 and Wr = 0.1337 for 2084 observed reflections (I > 2.0б(I)).The molecular backbone of the compound includes a benzopyrone and a phenyl ring,and the dihedral angle between them is 50.21o.The molecules form extensive networks through the intra-and intermolecular hydrogen bonds.

  5. Tuning the magnetic anisotropy in single-layer crystal structures

    Science.gov (United States)

    Torun, E.; Sahin, H.; Bacaksiz, C.; Senger, R. T.; Peeters, F. M.

    2015-09-01

    The effect of an applied electric field and the effect of charging are investigated on the magnetic anisotropy (MA) of various stable two-dimensional (2D) crystals such as graphene, FeCl2, graphone, fluorographene, and MoTe2 using first-principles calculations. We found that the magnetocrystalline anisotropy energy of Co-on-graphene and Os-doped-MoTe2 systems change linearly with electric field, opening the possibility of electric field tuning MA of these compounds. In addition, charging can rotate the easy-axis direction of Co-on-graphene and Os-doped-MoTe2 systems from the out-of-plane (in-plane) to in-plane (out-of-plane) direction. The tunable MA of the studied materials is crucial for nanoscale electronic technologies such as data storage and spintronics devices. Our results show that controlling the MA of the mentioned 2D crystal structures can be realized in various ways, and this can lead to the emergence of a wide range of potential applications where the tuning and switching of magnetic functionalities are important.

  6. Studies on synthesis, growth, structural, optical properties of organic 8-hydroxyquinolinium succinate single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Thirumurugan, R., E-mail: singlecrystalxrd@gmail.com; Anitha, K., E-mail: singlecrystalxrd@gmail.com [School of Physics, Madurai Kamaraj University, Madurai-625021 (India)

    2014-04-24

    8-hydroxyquinolinium succinate (8HQSU), an organic material has been synthesized and single crystals were grown by employing the technique of slow evaporation. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. 8HQSU crystal belongs to the monoclinic crystallographic system with non-centro symmetric space group of P2{sub 1}. FT-IR spectral investigation has been carried out to identify the various functional groups present in the grown crystal. UV–vis spectral studies reveal that 8HQSU crystals are transparent in the entire visible region and the cut-off wavelength has been found to be 220nm.

  7. Syntheses and Crystal Structures of Some Aryloxy and Alkoxy Substituted Phthalonitriles

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Phthalonitriles substituted with aryloxy and alkoxy groups have been synthesized and characterized by elemental analyses, IR, mass spectra and 1H NMR spectroscopy. And four of such crystal structures have also been determined. In the crystal structures, the major intermolecular interactions between the neighboring molecules are the hydrogen bonds as C≡N…H and C-O…H that lead to similar networks in the crystal structures.

  8. Crystal Structure of iso-propylcyclopentadienylchloro-(bistriphenylphosphine) ruthenium

    Institute of Scientific and Technical Information of China (English)

    金军挺; 黄吉玲; 钱延龙; 朱广宇; 贾一四; 黄其辰

    2000-01-01

    Crystal of the title complex, C44H41ClP2Ru, belongs to monoclinic system, space group P21/n, a=11. 968(2), b=1T. 721(2), c=17. 322(2) A, ββ=97.669(12)°, V=3640.8(9)A3, Mr=768.2, Z=4, Dc=1. 402g. cm-3, μ=5. 217mm-1, F(000)= 1584, the final R=0. 0418 and Rw=0. 0551 for 3734 observed reflections (F>3.9σ(F)). The geometry around the ruthenium can be considered as a distorted tetrahedron. The electronic and steric effects of iso-propyl substituent on the structure of the title complex(I) are discussed.

  9. Structural conditionality of the piezoelectric properties of langasite family crystals

    International Nuclear Information System (INIS)

    The atomic displacements upon isomorphic substitutions in crystals of the langasite family have been analyzed. The thermal parameters are determined and the probability density function of atoms is analyzed. Local potential energy minima are found which can be occupied by atoms under external effects. The contributions of cations in all four independent crystallographic positions and anions in all three such positions to the piezoelectric properties are established. One specific structural feature is the constant (at isomorphic substitutions) or possible (under external effects) but always opposite displacements of two cations along symmetry axis 2. Large cations in eight-vertex polyhedra make the main contribution to the piezoelectric properties. The cations in the tetrahedra on symmetry axis 2 weaken these properties. The cations in the octahedra in the origin of coordinates and in the tetrahedra on symmetry axes 3 only slightly affect the piezoelectricity.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-19

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

  11. Crystal structure of (E-2-hydroxy-4′-methoxyazastilbene

    Directory of Open Access Journals (Sweden)

    Suchada Chantrapromma

    2015-06-01

    Full Text Available The title azastilbene derivative, C14H13NO2 {systematic name: (E-2-[(4-methoxybenzylideneamino]phenol}, is a product of the condensation reaction between 4-methoxybenzaldehyde and 2-aminophenol. The molecule adopts an E conformation with respect to the azomethine C=N bond and is almost planar, the dihedral angle between the two substituted benzene rings being 3.29 (4°. The methoxy group is coplanar with the benzene ring to which it is attached, the Cmethyl—O—C—C torsion angle being −1.14 (12°. There is an intramolecular O—H...N hydrogen bond generating an S(5 ring motif. In the crystal, molecules are linked via C—H...O hydrogen bonds, forming zigzag chains along [10-1]. The chains are linked via C—H...π interactions, forming a three-dimensional structure.

  12. Crystal chemistry and structural design of iron-based superconductors

    Institute of Scientific and Technical Information of China (English)

    Jiang Hao; Sun Yun-Lei; Xu Zhu-An; Cao Guang-Han

    2013-01-01

    The second class of high-temperature superconductors (HTSCs),iron-based pnictides and chalcogenides,necessarily contain Fe2X2 (“X” refers to a pnictogen or a chalcogen element) layers,just like the first class of HTSCs which possess the essential CuO2 sheets.So far,dozens of iron-based HTSCs,classified into nine groups,have been discovered.In this article,the crystal-chemistry aspects of the known iron-based superconductors are reviewed and summarized by employing “hard and soft acids and bases (HSAB)” concept.Based on these understandings,we propose an alternative route to exploring new iron-based superconductors via rational structural design.

  13. Crystal structure of tris(ethylenediammonium hexasulfatopraseodymium(III hexahydrate

    Directory of Open Access Journals (Sweden)

    Peter Held

    2014-10-01

    Full Text Available In the title salt, (C2H10N23[Pr2(SO46]·6H2O, the PrIII cation is surrounded ninefold by five sulfate groups (two monodentate and three chelating and by one water molecule [range of Pr—O bond lengths 2.383 (3 to 2.582 (3 Å]. The [Pr(SO45(H2O] groups are arranged in sheets parallel to (010. Two crystal water molecules and two ethylenediammonium cations (one with point group symmetry -1 connect the sheets via O—H...O and N—H...O hydrogen bonds from weak up to medium strength into a three-dimensional framework structure.

  14. Optical nonreciprocal transmission in an asymmetric silicon photonic crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zheng; Chen, Juguang; Ji, Mengxi; Huang, Qingzhong; Xia, Jinsong; Wang, Yi, E-mail: yingwu2@126.com, E-mail: ywangwnlo@mail.hust.edu.cn [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Wu, Ying, E-mail: yingwu2@126.com, E-mail: ywangwnlo@mail.hust.edu.cn [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)

    2015-11-30

    An optical nonreciprocal transmission (ONT) is realized by employing the nonlinear effects in a compact asymmetric direct-coupled nanocavity-waveguide silicon photonic crystal structure with a high loaded quality factor (Q{sub L}) of 42 360 and large extinction ratio exceeding 30 dB. Applying a single step lithography and successive etching, the device can realize the ONT in an individual nanocavity, alleviating the requirement to accurately control the resonance of the cavities. A maximum nonreciprocal transmission ratio of 21.1 dB as well as a working bandwidth of 280 pm in the telecommunication band are obtained at a low input power of 76.7 μW. The calculated results by employing a nonlinear coupled-mode model are in good agreement with the experiment.

  15. Optical nonreciprocal transmission in an asymmetric silicon photonic crystal structure

    International Nuclear Information System (INIS)

    An optical nonreciprocal transmission (ONT) is realized by employing the nonlinear effects in a compact asymmetric direct-coupled nanocavity-waveguide silicon photonic crystal structure with a high loaded quality factor (QL) of 42 360 and large extinction ratio exceeding 30 dB. Applying a single step lithography and successive etching, the device can realize the ONT in an individual nanocavity, alleviating the requirement to accurately control the resonance of the cavities. A maximum nonreciprocal transmission ratio of 21.1 dB as well as a working bandwidth of 280 pm in the telecommunication band are obtained at a low input power of 76.7 μW. The calculated results by employing a nonlinear coupled-mode model are in good agreement with the experiment

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

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2015-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-15

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

  18. Crystal structure of Brinzolamide: a carbonic anhydrase inhibitor

    OpenAIRE

    Zheng, Huirong; Lou, Benyong

    2016-01-01

    In crystal structure of the title compound, C12H21N3O5S3 [systematic name: (R)-4-ethyl­amino-2-(3-meth­oxy­prop­yl)-3,4-di­hydro-2H-thieno[3,2-e][1,2]thia­zine-6-sulfonamide 1,1-dioxide], there exist three kinds of hydrogen-bonding inter­actions. The sulfonamide group is involved in hydrogen bonding with the secondary amine and the meth­oxy O atom, resulting in the formation of layers parallel to the bc plane. The layers are linked by an N—H⋯O hydrogen bond involving a sulfonamide O atom as a...

  19. 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.

  20. Modulation of defect modes intensity by controlled light scattering in photonic crystal with liquid crystal domain structure

    Science.gov (United States)

    Gunyakov, V. A.; Krakhalev, M. N.; Zyryanov, V. Ya.; Shabanov, V. F.; Loiko, V. A.

    2016-07-01

    A method to modulate the defect modes intensity in a multilayer photonic crystal with a nematic liquid crystal layer arranged midmost has been proposed. The various electrohydrodynamic domain structures (Williams domains, oblique rolls and grid pattern) were formed in the nematic layer under the action of ac electric field. The domains cause a polarization-sensitive light scattering which leads to an anisotropic reduction of the defect modes intensity. Thus by varying the applied voltage, we can tune gradually the transmittance spectrum of photonic crystal. In addition, the spectrum strongly depends on the light polarization direction above threshold voltage.

  1. Manufacturing, structure and properties of recycled polyethylene terephthalate /liquid crystal polymer/montmorillonite clay nanocomposites

    International Nuclear Information System (INIS)

    Polyethylene terephthalate (PET)/liquid crystal polymer (LCP)/monthmorillonite clay (MMT) compositions were obtained by melt mixing. Their mechanical, structural, rheological and thermal properties were investigated

  2. Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1

    Directory of Open Access Journals (Sweden)

    Zhou Cong-Zhao

    2007-06-01

    Full Text Available Abstract Background As the third enzyme of the pentose phosphate pathway, 6-phosphogluconate dehydrogenase (6PGDH is the main generator of cellular NADPH. Both thioredoxin reductase and glutathione reductase require NADPH as the electron donor to reduce oxidized thioredoxin or glutathione (GSSG. Since thioredoxin and GSH are important antioxidants, it is not surprising that 6PGDH plays a critical role in protecting cells from oxidative stress. Furthermore the activity of 6PGDH is associated with several human disorders including cancer and Alzheimer's disease. The 3D structural investigation would be very valuable in designing small molecules that target this enzyme for potential therapeutic applications. Results The crystal structure of 6-phosphogluconate dehydrogenase (6PGDH/Gnd1 from Saccharomyces cerevisiae has been determined at 2.37 Å resolution by molecular replacement. The overall structure of Gnd1 is a homodimer with three domains for each monomer, a Rossmann fold NADP+ binding domain, an all-α helical domain contributing the majority to hydrophobic interaction between the two subunits and a small C-terminal domain penetrating the other subunit. In addition, two citrate molecules occupied the 6PG binding pocket of each monomer. The intact Gnd1 had a Km of 50 ± 9 μM for 6-phosphogluconate and of 35 ± 6 μM for NADP+ at pH 7.5. But the truncated mutants without the C-terminal 35, 39 or 53 residues of Gnd1 completely lost their 6PGDH activity, despite remaining the homodimer in solution. Conclusion The overall tertiary structure of Gnd1 is similar to those of 6PGDH from other species. The substrate and coenzyme binding sites are well conserved, either from the primary sequence alignment, or from the 3D structural superposition. Enzymatic activity assays suggest a sequential mechanism of catalysis, which is in agreement with previous studies. The C-terminal domain of Gnd1 functions as a hook to further tighten the dimer, but it is not

  3. Structures and growth mechanisms of poly-(3-hydroxybutyrate) (PHB) crystallized from solution and thin melt film

    Institute of Scientific and Technical Information of China (English)

    CAO QiKun; QIAO XiaoPing; WANG Hui; LIU JiePing

    2008-01-01

    The spherulitic structures and morphologies of poly-(3-hydroxybutyrate) (PHB) crystallized from a so-lution and a thin melt film were investigated in this study. The formation mechanisms of banded spherulites under different crystallization conditions are proposed. It was found that the formation of banded spherulites was caused by the rhythmic crystal growth of the spherulites and lamellar twisting growth for the polymer crystallization from a thin melt film and a solution, respectively.

  4. Dynamics of the domain structure in non-uniform ferroelectric crystals

    Directory of Open Access Journals (Sweden)

    K.Matyjasek

    2007-01-01

    Full Text Available This work presents a study of the domain reversal characteristics related to the internal bias field in non-uniform telluric acid ammonium phosphate (TAAP crystal. We have shown that there is a direct connection between the defective structure of the crystal and stretched exponential polarization relaxation in ferroelectric crystals. The domain switching was studied by means of the nematic liquid crystal decoration technique.

  5. Structures and growth mechanisms of poly-(3-hydroxybutyrate) (PHB) crystallized from solution and thin melt film

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The spherulitic structures and morphologies of poly-(3-hydroxybutyrate) (PHB) crystallized from a so- lution and a thin melt film were investigated in this study. The formation mechanisms of banded spherulites under different crystallization conditions are proposed. It was found that the formation of banded spherulites was caused by the rhythmic crystal growth of the spherulites and lamellar twisting growth for the polymer crystallization from a thin melt film and a solution, respectively.

  6. Crystal structure of an HIV assembly and maturation switch

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-14

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

  7. Crystal structure of strontium(2) bis[di(hydroxymethyl)phosphinate

    International Nuclear Information System (INIS)

    X-ray diffraction of SrL2 (HL - di(hydroxymethyl)phosphinic acid) is conducted. The crystals have a tetragonal structure: a = 9.929(2), c 5.233(1) A, V = 515.9(2) A3, ρcalc = 2.174 g/cm3, μMo = 55.57 cm-1, F(000) = 1344, M = 337.68 u, Z = 2, sp. gr. P421m. Atom Sr(1) occupies private position mm, atoms P(1), O(1), O(2) disposes on mm plane in the SrL2 structure. Four phosphine oxygen atoms O(1, 2) of four ligands L and four hydroxy atoms O(3) two more ligands are associated with strontium atom. The ligand L is acting as a tetradentate chelate μ3-bridge function. Interval of Sr-O distance is equal to 2.521(3) - 2.683(2) A. Hydrogen bonds O-H-O (O-O 2.723, H-O 1.96 A, angle OHO 170 Deg) provide in the structure. The second phosphinate O(1) atom is inoperative in H-bonds as distinct from O(2) atom involved in two H-bond with hydroxy groups of relative SrO8 polyhedrons

  8. Crystal structure of the epithelial calcium channel TRPV6.

    Science.gov (United States)

    Saotome, Kei; Singh, Appu K; Yelshanskaya, Maria V; Sobolevsky, Alexander I

    2016-06-23

    Precise regulation of calcium homeostasis is essential for many physiological functions. The Ca(2+)-selective transient receptor potential (TRP) channels TRPV5 and TRPV6 play vital roles in calcium homeostasis as Ca(2+) uptake channels in epithelial tissues. Detailed structural bases for their assembly and Ca(2+) permeation remain obscure. Here we report the crystal structure of rat TRPV6 at 3.25 Å resolution. The overall architecture of TRPV6 reveals shared and unique features compared with other TRP channels. Intracellular domains engage in extensive interactions to form an intracellular 'skirt' involved in allosteric modulation. In the K(+) channel-like transmembrane domain, Ca(2+) selectivity is determined by direct coordination of Ca(2+) by a ring of aspartate side chains in the selectivity filter. On the basis of crystallographically identified cation-binding sites at the pore axis and extracellular vestibule, we propose a Ca(2+) permeation mechanism. Our results provide a structural foundation for understanding the regulation of epithelial Ca(2+) uptake and its role in pathophysiology. PMID:27296226

  9. Synthesis and Crystal Structure of Tetra(o-cyanobenzyl)tin

    Institute of Scientific and Technical Information of China (English)

    KUANG Dai-Zhi; JIANG Jiang-Ping; FENG Yong-Lan; ZHANG Fu-Xing; WANG Jian-Qiu; LUO Yi-Ming

    2008-01-01

    The tetra(o-eyanobenzyl)tin compound has been synthesized by the reaction of eyanobenzyl chloride with tin, and its molecular structure was characterized by elemental analysis,IR spectra, 1H NMR and X-ray diffraction. Crystal data for this compound: monoclinie, space group C2/c, M, = 583.24, a = 1.9629(2), b = 1.05967(13), c = 1.41249(18) nm, β = 118.180(2)°, V =2.5898(5) nm3, Z = 4, Dc =1.496 g/cm3, μ(MoKa) = 1.015 cm-1, F(000) = 1176, R = 0.0189, wR =0.0497 (observed reflections with Ⅰ 2σ(Ⅰ)) and R = 0.0218, wR = 0.0513 (all reflections).The molecular structure adopts a distorted tetrahedral geometry around the tin atom. The Sn…N weak interaction between the Sn and N atoms of cyano forms an intermolecular H-bonding, and the bond length is 0.3570 nm; the interaction between hydrogen of methylene and benzene ring of benzyl forms C-H…C with its bond length of 0.2817 nm; and the interaction among hydrogen of benzene ring and carbon of cyano forms Ph-H…C bond (0.2897 nm) of the σ…π interaction. A 3D chain structure is formed by the above weak intermolecular interactions.

  10. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.

    Energy Technology Data Exchange (ETDEWEB)

    Wu, R.; Richter, S.; Zhang, R.; Anderson, V. J.; Missiakas, D.; Joachimiak, A.; Biosciences Division; Univ. of Chicago

    2009-09-04

    Bacillus anthracis elaborates a poly-{gamma}-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the {gamma}-glutamyltranspeptidase CapD with and without {alpha}-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-{gamma}-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-{gamma}-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro{sup 427}, Gly{sup 428}, and Gly{sup 429} activate the catalytic residue of the enzyme, Thr{sup 352}, and stabilize an oxyanion hole via main chain amide hydrogen bonds.

  11. Crystal structure of inhibitor of ;#954;B kinase [beta

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Guozhou; Lo, Yu-Chih; Li, Qiubai; Napolitano, Gennaro; Wu, Xuefeng; Jiang, Xuliang; Dreano, Michel; Karin, Michael; Wu, Hao (Weill-Med); (Merck-Serono); (UCSD); (EMD Serono)

    2011-07-26

    Inhibitor of {kappa}B (I{kappa}B) kinase (IKK) phosphorylates I{kappa}B proteins, leading to their degradation and the liberation of nuclear factor {kappa}B for gene transcription. Here we report the crystal structure of IKK{beta} in complex with an inhibitor, at a resolution of 3.6 {angstrom}. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, {alpha}-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix-loop-helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with I{kappa}B{alpha} that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKK{beta} dimerization, but dimerization per se is not important for maintaining IKK{beta} activity and instead is required for IKK{beta} activation. Other IKK family members, IKK{alpha}, TBK1 and IKK-i, may have a similar trimodular architecture and function.

  12. Crystal Structure of Alcohol Oxidase from Pichia pastoris.

    Directory of Open Access Journals (Sweden)

    Christian Koch

    Full Text Available FAD-dependent alcohol oxidases (AOX are key enzymes of methylotrophic organisms that can utilize lower primary alcohols as sole source of carbon and energy. Here we report the crystal structure analysis of the methanol oxidase AOX1 from Pichia pastoris. The crystallographic phase problem was solved by means of Molecular Replacement in combination with initial structure rebuilding using Rosetta model completion and relaxation against an averaged electron density map. The subunit arrangement of the homo-octameric AOX1 differs from that of octameric vanillyl alcohol oxidase and other dimeric or tetrameric alcohol oxidases, due to the insertion of two large protruding loop regions and an additional C-terminal extension in AOX1. In comparison to other alcohol oxidases, the active site cavity of AOX1 is significantly reduced in size, which could explain the observed preference for methanol as substrate. All AOX1 subunits of the structure reported here harbor a modified flavin adenine dinucleotide, which contains an arabityl chain instead of a ribityl chain attached to the isoalloxazine ring.

  13. Crystal structure of Leishmania tarentolae hypoxanthine-guanine phosphoribosyltransferase

    Directory of Open Access Journals (Sweden)

    Oliva Glaucius

    2007-09-01

    Full Text Available Abstract Background Hypoxanthine-guanine phosphoribosyltransferase (HGPRT (EC 2.4.2.8 is a central enzyme in the purine recycling pathway. Parasitic protozoa of the order Kinetoplastida cannot synthesize purines de novo and use the salvage pathway to synthesize purine bases, making this an attractive target for antiparasitic drug design. Results The glycosomal HGPRT from Leishmania tarentolae in a catalytically active form purified and co-crystallized with a guanosine monophosphate (GMP in the active site. The dimeric structure of HGPRT has been solved by molecular replacement and refined against data extending to 2.1 Å resolution. The structure reveals the contacts of the active site residues with GMP. Conclusion Comparative analysis of the active sites of Leishmania and human HGPRT revealed subtle differences in the position of the ligand and its interaction with the active site residues, which could be responsible for the different reactivities of the enzymes to allopurinol reported in the literature. The solution and analysis of the structure of Leishmania HGPRT may contribute to further investigations leading to a full understanding of this important enzyme family in protozoan parasites.

  14. Crystal structure of unliganded TRAP: implications for dynamic allostery.

    Science.gov (United States)

    Malay, Ali D; Watanabe, Masahiro; Heddle, Jonathan G; Tame, Jeremy R H

    2011-03-15

    Allostery is vital to the function of many proteins. In some cases, rather than a direct steric effect, mutual modulation of ligand binding at spatially separated sites may be achieved through a change in protein dynamics. Thus changes in vibrational modes of the protein, rather than conformational changes, allow different ligand sites to communicate. Evidence for such an effect has been found in TRAP (trp RNA-binding attenuation protein), a regulatory protein found in species of Bacillus. TRAP is part of a feedback system to modulate expression of the trp operon, which carries genes involved in tryptophan synthesis. Negative feedback is thought to depend on binding of tryptophan-bound, but not unbound, TRAP to a specific mRNA leader sequence. We find that, contrary to expectations, at low temperatures TRAP is able to bind RNA in the absence of tryptophan, and that this effect is particularly strong in the case of Bacillus stearothermophilus TRAP. We have solved the crystal structure of this protein with no tryptophan bound, and find that much of the structure shows little deviation from the tryptophan-bound form. These data support the idea that tryptophan may exert its effect on RNA binding by TRAP through dynamic and not structural changes, and that tryptophan binding may be mimicked by low temperature. PMID:21175426

  15. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

    International Nuclear Information System (INIS)

    The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect

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

    Institute of Scientific and Technical Information of China (English)

    LI Wei

    2005-01-01

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

  17. Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-18

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

  18. Crystal structure of lactoperoxidase at 2.4 A resolution.

    Science.gov (United States)

    Singh, Amit Kumar; Singh, Nagendra; Sharma, Sujata; Singh, S Baskar; Kaur, Punit; Bhushan, A; Srinivasan, A; Singh, Tej P

    2008-02-29

    Lactoperoxidase (LPO) is a member of the mammalian peroxidase superfamily. It catalyzes the oxidation of thiocyanate and halides. Freshly isolated and purified samples of caprine LPO were saturated with ammonium iodide and crystallized using 20% polyethylene glycol 3350 in a hanging drop vapor diffusion setup. The structure has been determined using X-ray crystallographic method and refined to R(cryst) and R(free) factors of 0.196 and 0.203, respectively. The structure determination revealed an unexpected phosphorylation of Ser198 in LPO, which is also confirmed by anti-phosphoserine antibody binding studies. The structure is also notable for observing densities for glycan chains at all the four potential glycosylation sites. Caprine LPO consists of a single polypeptide chain of 595 amino acid residues and folds into an oval-shaped structure. The structure contains 20 well-defined alpha-helices of varying lengths including a helix, H(2a), unique to LPO, and two short antiparallel beta-strands. The structure confirms that the heme group is covalently linked to the protein through two ester linkages involving carboxylic groups of Glu258 and Asp108 and modified methyl groups of pyrrole rings A and C, respectively. The heme moiety is slightly distorted from planarity, but pyrrole ring B is distorted considerably. However, an iron atom is displaced only by 0.1 A from the plane of the heme group toward the proximal site. The substrate diffusing channel in LPO is cylindrical in shape with a diameter of approximately 6 A. Two histidine residues and six buried water molecules are connected through a hydrogen-bonded chain from the distal heme cavity to the surface of protein molecule and seemingly form the basis of proton relay for catalytic action. Ten iodide ions have been observed in the structure. Out of these, only one iodide ion is located in the distal heme cavity and is hydrogen bonded to the water molecule W1. W1 is also hydrogen bonded to the heme iron as well as

  19. Crystal and molecular structures of some organophosphorus insecticides and computer methods for structure determination. [Dissertation

    Energy Technology Data Exchange (ETDEWEB)

    Lapp, R.L.

    1979-01-01

    Molecular structure investigations of a set of organophosphorus insecticides have been carried out in order to acquire the data base to develop correlations between such parameters and their toxicities. The crystal and molecular structures of dimethoate (LD/sub 50/ (rats) = 600 mg/kg), IPAT, and leptophos (LD/sub 50/ (rats) = 90 mg/kg) have been determined via three-dimensional x-ray analysis. The crystal and molecular structure of (-)-..cap alpha..-phenylethylammonium (-)-0-methyl-phenylphosphonothioate was solved by conventional Patterson and Fourier techniques to a final R value of 0.057. The crystal and molecular structures of two crystalline forms of calcium formate were determined. A new least-squares refinement program was written which is much more general and efficient than any previous program. In particular, a new block-diagonal approximation has been devised which is much more economical than full-matrix refinement and appears to work much better than previous block-diagonal methods. A Howells, Phillips and Rogers test for a center of symmetry and a Wilson plot have been programmed into the data collection algorithm. Some approximations and special problems are discussed relative to implementing these routines in a real-time mode on a minicomputer. A mathematical background and program description are included for each program.

  20. Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

    Science.gov (United States)

    Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

    2003-01-01

    Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

  1. Advanced piezoelectric crystal Ca3TaGa3Si2O14: growth, crystal structure perfection, and acoustic properties

    Science.gov (United States)

    Roshchupkin, Dmitry; Ortega, Luc; Plotitcyna, Olga; Erko, Alexei; Zizak, Ivo; Irzhak, Dmitry; Fahrtdinov, Rashid; Buzanov, Oleg

    2014-03-01

    A five-component crystal of the lanthanum-gallium silicate family Ca3TaGa3Si2O14 (CTGS) was grown by the Czochralski method. The CTGS crystal, like the langasite crystal (La3Ga5SiO14, LGS), possesses unique temperature properties and the fewer number of the Ga atoms in the unit cell makes the density much lower and, consequently, increases the velocity of acoustic wave propagation. The unit-cell parameters were determined by the powder diffraction technique. The defects in the CTGS crystal structure were studied by X-ray topography, which enables the visualization of growth banding characteristics of crystals grown by the Czochralski method. Surface acoustic wave (SAW) propagation in the CTGS crystal was investigated by the high-resolution X-ray diffraction method on the BESSY II synchrotron radiation source. The velocities of propagation and power flow angles of SAWs in the Y- and X-cuts of the CTGS crystal were determined from the X-ray diffraction spectra.

  2. Crystal structure of a chimaeric bacterial glutamate dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-23

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

  3. Crystal Structure of an Ammonia-Permeable Aquaporin.

    Science.gov (United States)

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

    2016-03-01

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

  4. Crystal Structure of an Ammonia-Permeable Aquaporin.

    Directory of Open Access Journals (Sweden)

    Andreas Kirscht

    2016-03-01

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

  5. Crystal structure of a chimaeric bacterial glutamate dehydrogenase.

    Science.gov (United States)

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

    2016-06-01

    Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P)(+) as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD(+) versus NADP(+), but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies, as shown by the apo structure of glutamate dehydrogenase from Clostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia coli enzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP(+) cofactor from the parent E. coli domain II, although there are subtle differences in catalytic activity. PMID:27303899

  6. Crystal Structure of a Full-Length [beta]-Catenin

    Energy Technology Data Exchange (ETDEWEB)

    Xing, Yi; Takemaru, Ken-Ichi; Liu, Jing; Berndt, Jason D.; Zheng, Jie J.; Moon, Randall T.; Xu, Wenqing (UW-MED); (SJCH)

    2008-08-19

    {beta}-catenin plays essential roles in cell adhesion and Wnt signaling, while deregulation of {beta}-catenin is associated with multiple diseases including cancers. Here, we report the crystal structures of full-length zebrafish {beta}-catenin and a human {beta}-catenin fragment that contains both the armadillo repeat and the C-terminal domains. Our structures reveal that the N-terminal region of the C-terminal domain, a key component of the C-terminal transactivation domain, forms a long {alpha} helix that packs on the C-terminal end of the armadillo repeat domain, and thus forms part of the {beta}-catenin superhelical core. The existence of this helix redefines our view of interactions of {beta}-catenin with some of its critical partners, including ICAT and Chibby, which may form extensive interactions with this C-terminal domain {alpha} helix. Our crystallographic and NMR studies also suggest that the unstructured N-terminal and C-terminal tails interact with the ordered armadillo repeat domain in a dynamic and variable manner.

  7. Crystal Structure of an Ammonia-Permeable Aquaporin.

    Science.gov (United States)

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

    2016-03-01

    Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants, allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia. Here, we report the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity filter region are sufficient to convert a strictly water-specific human aquaporin into an AtTIP2;1-like ammonia channel. A flexible histidine and a novel water-filled side pore are speculated to deprotonate ammonium ions, thereby possibly increasing permeation of ammonia. The molecular understanding of how aquaporins facilitate ammonia flux across membranes could potentially be used to modulate ammonia losses over the plasma membrane to the atmosphere, e.g., during photorespiration, and thereby to modify the nitrogen use efficiency of plants. PMID:27028365

  8. Crystal structure of ammonium dioxo(2-hydroxynaphthaldehydesemicarbazonato)-vanadate (5)

    Energy Technology Data Exchange (ETDEWEB)

    Kravtsov, V.Kh.; Belyaeva, K.F.; Biyushkin, V.N.; Struchkov, Yu.T.; Bodyu, V.G.; Samus, N.M. (AN Moldavskoj SSR, Kishinev. Inst. Prikladnoj Fiziki; AN SSSR, Moscow. Inst. Ehlementoorganicheskikh Soedinenij; Kishinevskij Gosudarstvennyj Univ. (USSR))

    1981-01-01

    During the interaction of VOSO/sub 4/x3H/sub 2/O with semicarbazone of 2-hydroxynaphthaldehyde (2-Nafsc) the fixation of air oxygen takes place with the formation of diamagnetic compound NH/sub 4/(VO/sub 2/(2-Nafsc-2H) (1). The structure 1 is established using the method of X-ray structural analysis. Crystals 1 are monoclinic: a=13.930(2), b=16.097(3), c=6.267(1)A, ..gamma..=111.12(2)deg, Z=4, sp. gr. B2. In the complex anion V atom has a distorted tetragonal-pyramid coordination. One of two oxo-ligands (V-O 1.609(3)A) is in apical position, four coordination vacancies in the pyramid base are occupied by the other oxo-ligand (V-O 1.654(3)A, by O and N atoms of semicarbazide fragment (V-O and V-N 1.974(2) and 2.127(2)A respectively) and O atom (V-O 1.861(3)A) of aldehyde hydroxy group.

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

    Directory of Open Access Journals (Sweden)

    Manickam Thairiyaraja

    2015-12-01

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

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

    Indian Academy of Sciences (India)

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

    2016-06-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

  12. Raman scattering spectra and crystal structure of acid potassium-lithium sulfate

    International Nuclear Information System (INIS)

    Paper presents the results of the comprehensive investigation into Raman scattering in potassium-lithium acid sulfate crystal. A model of crystal structure is suggested on the basis of the study data. The suggested consistent model of the crystalline structure of potassium-lithium acid sulfate crystal describes well both spectrum high-frequency and low-frequency sections and may be used to analyze models of phase transformation

  13. Synthesis, single crystal structure and energy optimization of a multicomponent salt of imidazole and tetrabromoterepthalic acid

    Energy Technology Data Exchange (ETDEWEB)

    Singha, S.; Kumar, S., E-mail: skndey@gmail.com [Department of Physics, Jadavpur University, Kolkata-700032 (India); Dey, S. K., E-mail: skndey@gmail.com [Department of Physics, Jadavpur University, Kolkata-700032 (India); Department of Physics, NITMAS, 24 Paragana(S)-743368 (India)

    2015-06-24

    Single crystal of a multicomponent salt (IMTBTP) of imidazole with tetrabromoterepthalic acid has been synthesized by slow evaporation method at room temperature. The crystal structure of the salt has been determined by single crystal x-ray diffraction technique. The supramolecular structure analysis reveals that the multicomponent salt is formed by noncovalent hydrogen bonding interaction and Br···π interaction. The energy optimization and HOMO-LUMO energy gap calculation have been carried out by Density Functional Theory.

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

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  15. Effect of local structures on crystallization in deeply undercooled metallic glass-forming liquids

    Science.gov (United States)

    Jiang, S. Q.; Wu, Z. W.; Li, M. Z.

    2016-04-01

    The crystallization mechanism in deeply undercooled ZrCu metallic glass-forming liquids was investigated via molecular dynamics simulations. It was found that the crystallization process is mainly controlled by the growth of crystal nuclei formed by the BCC-like atomic clusters, consistent with experimental speculations. The crystallization rate is found to relate to the number of growing crystal nuclei in the crystallization process. The crystallization rate in systems with more crystal nuclei is significantly hindered by the larger surface fractions of crystal nuclei and their different crystalline orientations. It is further revealed that in the crystallization in deeply undercooled regions, the BCC-like crystal nuclei are formed from the inside of the precursors formed by the FCC-like atomic clusters, and growing at the expense of the precursors. Meanwhile, the precursors are expanding at the expense of the outside atomic clusters. This process is consistent with the so-called Ostwald step rule. The atomic structures of metallic glasses are found to have significant impact on the subsequent crystallization process. In the Zr85Cu15 system, the stronger spatial correlation of Cu atoms could hinder the crystallization processes in deeply undercooled regions.

  16. Structural, thermal and optical studies on 2-naphthol crystals

    Energy Technology Data Exchange (ETDEWEB)

    Guru Prasad, L.; Shanmugam, G. [Department of Physics, Periyar University, Salem - 636 011 (India); Nagalakshmi, R. [Department of Physics, National Institute of Technology, Tiruchirappalli-620 015 (India); Krishnakumar, V.

    2010-10-15

    Single crystals of 2-naphthol was grown in slow evaporation solution growth technique. Grown crystals were characterized by various characterization techniques. Powder X- ray diffraction studies reveal that the grown crystal belongs to monoclinic system with noncentrosymmetric space group. Vibrational bands of the various functional groups and their significance were investigated by analyzing the vibrational spectra. Melting point and the decomposition temperature of the grown crystal was premeditated from the thermal analysis. From the UV-VIS-NIR spectrum the electronic excitation mechanism and the transmittance abilities of the crystal was studied. Theoretical value of first static hyperpolarizability was calculated and compared with urea. Second harmonic generation efficiency of the crystal is 0.6 times that of KDP. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  17. Topology optimization and fabrication of photonic crystal structures

    DEFF Research Database (Denmark)

    Borel, Peter Ingo; Harpøth, Anders; Frandsen, Lars Hagedorn;

    2004-01-01

    Topology optimization is used to design a planar photonic crystal waveguide component resulting in significantly enhanced functionality. Exceptional transmission through a photonic crystal waveguide Z-bend is obtained using this inverse design strategy. The design has been realized in a silicon......-on-insulator based photonic crystal waveguide. A large low loss bandwidth of more than 200 nm for the TE polarization is experimentally confirmed....

  18. Crystal Structure of the Human Astrovirus Capsid Protein

    Science.gov (United States)

    Toh, Yukimatsu; Harper, Justin; Dryden, Kelly A.; Yeager, Mark; Méndez, Ernesto

    2016-01-01

    ABSTRACT Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominant protein species with molecular masses of ∼34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP9071–415 (amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP9071–415 encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP9071–415 is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP9071–415 structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation. IMPORTANCE Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. As a nonenveloped virus

  19. Crystal structure determination by powder neutron diffraction at the spallation neutron source, ISIS

    International Nuclear Information System (INIS)

    The paper concerns the determination of crystal structure by powder neutron diffraction at the spallation neutron source, ISIS. The practicability of the technique is illustrated by a study of the crystal structure of ferric arsenate, FeAsO4. (U.K.)

  20. Lateral-Structure Single-Crystal Hybrid Perovskite Solar Cells via Piezoelectric Poling.

    Science.gov (United States)

    Dong, Qingfeng; Song, Jingfeng; Fang, Yanjun; Shao, Yuchuan; Ducharme, Stephen; Huang, Jinsong

    2016-04-13

    Single-crystal perovskite solar cells with a lateral structure yield an efficiency enhancement 44-fold that of polycrystalline thin films, due to the much longer carrier diffusion length. A piezoelectric effect observed in perovskite single-crystal and the strain-generated grain-boundaries enable ion migration to form a p-i-n structure.

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

    Institute of Scientific and Technical Information of China (English)

    包素锦; 张季平; 常文瑞; 梁栋材

    1999-01-01

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

  2. The Crystal Structure of Toxoplasma gondii Pyruvate Kinase 1

    Energy Technology Data Exchange (ETDEWEB)

    Bakszt, R.; Wernimont, A; Allali-Hassani, A; Mok, M; Hills, T; Hui, R; Pizarro, J

    2010-01-01

    Pyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population. We have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers. We hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two {alpha}-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.

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

    Institute of Scientific and Technical Information of China (English)

    Yu Ma; Mao Xu

    2000-01-01

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

  4. Nanoscale resolved infrared probing of crystal structure and of plasmon-phonon coupling.

    Science.gov (United States)

    Huber, A; Ocelic, N; Taubner, T; Hillenbrand, R

    2006-04-01

    We show that slight variations of a crystal lattice cause significant spectral modifications of phonon-polariton resonant near-field interaction between polar semiconductor crystals and a scanning metal tip. Exploiting the effect for near-field imaging a SiC polytype boundary, we establish infrared mapping of crystal structure and crystal defects at 20 nm spatial resolution (lambda/500). By spectroscopic probing of doped SiC polytypes, we find that phonon-polariton resonant near-field interaction is also sensitive to electronic properties due to plasmon-phonon coupling in the crystals. PMID:16608282

  5. Synthesis, growth, structural, thermal and optical studies of pyrrolidinium-2-carboxylate-4-nitrophenol single crystals

    Science.gov (United States)

    Swarna Sowmya, N.; Sampathkrishnan, S.; Vidyalakshmi, Y.; Sudhahar, S.; Mohan Kumar, R.

    2015-06-01

    Organic nonlinear optical material, pyrrolidinium-2-carboxylate-4-nitrophenol (PCN) was synthesized and single crystals were grown by slow evaporation solution growth method. Single crystal X-ray diffraction analysis confirmed the structure and lattice parameters of PCN crystals. Infrared, Raman and NMR spectral analyses were used to elucidate the functional groups present in the compound. The thermal behavior of synthesized compound was studied by thermogravimetric and differential scanning calorimetry (TG-DSC) analyses. The photoluminescence property was studied by exciting the crystal at 360 nm. The relative second harmonic generation (SHG) efficiency of grown crystal was estimated by using Nd:YAG laser with fundamental wavelength of 1064 nm.

  6. Study of the photonic crystal waveguide based on 2D compound lattice structure

    Institute of Scientific and Technical Information of China (English)

    WU Chao-jun; LI Yan-ping; WANG Zi-u

    2009-01-01

    group velocity dispersion compensation can be realized by the structure optimization. The results provide a reference for the study and application of photonic crystal waveguide based on the compound lattice structure.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-27

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

  8. INVESTIGATION ON VARIOUS DESIGN PARAMETERS WHICH AFFECT THE BANDGAP OF TWO DIMENSIONAL PHOTONIC CRYSTAL STRUCTURE

    OpenAIRE

    Anila Dhingra*, K. C. Roy, Govind Kumar

    2016-01-01

    An emerging element in optical fiber communication, 2D Photonic Crystal is an artificial periodic structure having a bandgap which shows a prohibition of a range of wavelengths to pass away through it. Various design parameters which affect the bandgap of 2D photonic crystal structure such as lattice structure, shape of rods, r/a ratio, dielectric constant etc. are studied in this paper. The Plane Wave Expansion (PWE) method is used to calculate the bandgap structure of two dimensional photon...

  9. CARS polarized microscopy of three-dimensional director structures in liquid crystals

    CERN Document Server

    Kachynski, A V; Prasad, P N; Smalyukh, I I

    2007-01-01

    We demonstrate three-dimensional vibrational imaging of director structures in liquid crystals using coherent anti-Stokes Raman scattering (CARS) polarized microscopy. Spatial mapping of the structures is based on sensitivity of a polarized CARS signal to orientation of anisotropic molecules in liquid crystals. As an example, we study structures in a smectic material and demonstrate that single-scan CARS and two-photon fluorescence images of molecular orientation patterns are consistent with each other and with the structure model.

  10. Effect of crystal anisotropy on mechanical properties of refractory metals and alloys with cph type crystal structure

    International Nuclear Information System (INIS)

    Refractory metals like zirconium (Zr) and titanium (Ti) have the excellent corrosion resistance in highly oxidizing environments like reprocessing nitric acid. However, there are few experiences for practical use as structural materials of these materials. Mechanical properties of these materials, so the tensile test and the impact test of zirconium, titanium, and their alloys were examined with a function of testing temperature. Both 0.2% proof stress and ultimate tensile strength of zirconium decrease with testing temperature, it is suggested to play an important role of the low temperature creep on the mechanical deformation. The crystallographic anisotropy appears clearly in the impact value of zirconium, it has a very low impact value along the crystal orientation of the cph slip planes like (1010). This property is not seen in titanium which has the same crystal structure. It is necessary to consider zirconium showing a remarkable decrease in the deformation resistance along such specific crystal planes. (author)

  11. Microscopic characterization of defect structure in RDX crystals

    NARCIS (Netherlands)

    Bouma, R.H.B.; Duvalois, W.; Heijden, A.E.D.M. van der

    2013-01-01

    Three batches of the commercial energetic material RDX, as received from various production locations and differing in sensitivity towards shock initiation, have been characterized with different microscopic techniques in order to visualize the defect content in these crystals. The RDX crystals are

  12. Crystal structure of 2-pentyl­oxybenzamide

    Science.gov (United States)

    Bugenhagen, Bernhard; Al Jasem, Yosef; Thiemann, Thies

    2014-01-01

    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. PMID:25484660

  13. Crystal structure and phase transition of thermoelectric SnSe.

    Science.gov (United States)

    Sist, Mattia; Zhang, Jiawei; Brummerstedt Iversen, Bo

    2016-06-01

    Tin selenide-based functional materials are extensively studied in the field of optoelectronic, photovoltaic and thermoelectric devices. Specifically, SnSe has been reported to have an ultrahigh thermoelectric figure of merit of 2.6 ± 0.3 in the high-temperature phase. Here we report the evolution of lattice constants, fractional coordinates, site occupancy factors and atomic displacement factors with temperature by means of high-resolution synchrotron powder X-ray diffraction measured from 100 to 855 K. The structure is shown to be cation defective with a Sn content of 0.982 (4). The anisotropy of the thermal parameters of Sn becomes more pronounced approaching the high-temperature phase transition (∼ 810 K). Anharmonic Gram-Charlier parameters have been refined, but data from single-crystal diffraction appear to be needed to firmly quantify anharmonic features. Based on modelling of the atomic displacement parameters the Debye temperature is found to be 175 (4) K. Conflicting reports concerning the different coordinate system settings in the low-temperature and high-temperature phases are discussed. It is also shown that the high-temperature Cmcm phase is not pseudo-tetragonal as commonly assumed.

  14. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar

    2015-09-01

    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  15. Synthesis, single crystal structure and characterization of pentanitromonoformylhexaazaisowurtzitane.

    Science.gov (United States)

    Chen, Huaxiong; Chen, Shusen; Li, Lijie; Jiao, Qingze; Wei, Tianyu; Jin, Shaohua

    2010-03-15

    Pentanitromonoformylhexaazaisowurtzitane (PNMFIW) was synthesized by the nitrolysis of tetraacetyldiformylhexaazaisowurtzitane (TADFIW) in mixed nitric and sulfuric acids and structurally characterized by element analysis, FT-IR, MS and (1)H NMR. Single crystals of PNMFIW were grown from aqueous solution employing the technique of controlled evaporation. PNMFIW belongs to the orthorhombic system having four molecules in the unit cell, with space group P2(1)2(1)2(1) and the lattice parameters a=8.8000(18)A, b=12.534(2)A, and c=12.829(3)A. The calculated density reaches 1.977 g/cm(3) at 93 K, while the experimental density is 1.946 g/cm(3) at 20 degrees C. The calculated detonation velocity and pressure of PNMFIW according to the experimental density are 9195.76 m/s and 39.68G Pa, respectively. PNMFIW is insensitive compared with epsilon-HNIW through drop hammer impact sensitivity test. PMID:19913358

  16. Crystal structure of advanced lithium titanate with lithium oxide additives

    Energy Technology Data Exchange (ETDEWEB)

    Hoshino, Tsuyoshi [Blanket Irradiation and Analysis Group, Fusion Research and Development Directorate, Japan Atomic Energy Agency, 4002, Narita-cho, Oarai-machi, Higashi Ibaraki-gun, Ibaraki, 311-1393 (Japan)], E-mail: hoshino.tsuyoshi@jaea.go.jp; Sasaki, Kazuya [Department of Nuclear Engineering and Management, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656 (Japan); Tsuchiya, Kunihiko; Hayashi, Kimio [Blanket Irradiation and Analysis Group, Fusion Research and Development Directorate, Japan Atomic Energy Agency, 4002, Narita-cho, Oarai-machi, Higashi Ibaraki-gun, Ibaraki, 311-1393 (Japan); Suzuki, Akihiro [Nuclear Professional School, The University of Tokyo, 2-22 Shirakata-Shirane, Ibaraki, 319-1188 (Japan); Hashimoto, Takuya [Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University, 3-8-1 Sakurajousui, Setagaya-ku, Tokyo, 156-8550 (Japan); Terai, Takayuki [Department of Nuclear Engineering and Management, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656 (Japan)

    2009-04-30

    Li{sub 2}TiO{sub 3} is one of the most promising candidates among solid breeder materials proposed for fusion reactors. However, the mass of Li{sub 2}TiO{sub 3} was found to decrease with time in the sweep gas mixed with hydrogen. This mass change indicates that the oxygen content of the sample decreased, suggesting the change from Ti{sup 4+} to Ti{sup 3+}. In the present paper, the crystal structure and the non-stoichiometry of Li{sub 2}TiO{sub 3} added with Li{sub 2}O have been extensively investigated by means of X-ray diffraction (XRD) and thermogravimetry. In the case of the Li{sub 2}TiO{sub 3} samples used in the present study, LiO-C{sub 2}H{sub 5} or LiO-i-C{sub 3}H{sub 7} and Ti(O-i-C{sub 3}H{sub 7}){sub 4} were mixed in the proportion corresponding to the molar ratio Li{sub 2}O/TiO{sub 2} of either 2.00 or 1.00. In thermogravimetry, the mass of this sample decreased with time due to lithium deficiency, where no presence of oxygen deficiency was indicated.

  17. Crystal structure of advanced lithium titanate with lithium oxide additives

    International Nuclear Information System (INIS)

    Li2TiO3 is one of the most promising candidates among solid breeder materials proposed for fusion reactors. However, the mass of Li2TiO3 was found to decrease with time in the sweep gas mixed with hydrogen. This mass change indicates that the oxygen content of the sample decreased, suggesting the change from Ti4+ to Ti3+. In the present paper, the crystal structure and the non-stoichiometry of Li2TiO3 added with Li2O have been extensively investigated by means of X-ray diffraction (XRD) and thermogravimetry. In the case of the Li2TiO3 samples used in the present study, LiO-C2H5 or LiO-i-C3H7 and Ti(O-i-C3H7)4 were mixed in the proportion corresponding to the molar ratio Li2O/TiO2 of either 2.00 or 1.00. In thermogravimetry, the mass of this sample decreased with time due to lithium deficiency, where no presence of oxygen deficiency was indicated.

  18. Influence of Gravity on Structure of Colloidal Crystal Using Simulated Microgravity

    Institute of Scientific and Technical Information of China (English)

    Lei Liu; Jie Wang; Sheng-hua Xu; Zhi-wei Sun; Jing-tong Wang

    2009-01-01

    Liquid mixtures of water and deuterium oxide as the liquid phase, were used to match the density of charged colloidal particles. Kossel diffraction method was used to detect the crystal structures. The experiments under the density-matched (g=0) and unmatched (g=1) conditions are compared to examine the influence of gravity on the crystal structures formed by self-assembly of 110 nm (in diameter) polystyrene microspheres. The result shows that the gravity tends to make the lattice constants of colloidal crystals smaller at lower positions, which indicates that the effect of gravity should be taken into account in the study of the colloidal crystals.

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

    Science.gov (United States)

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

    2016-05-16

    The high-pressure crystal structure, lattice-vibrations, and electronic band structure of BiSbO4 were studied by ab initio simulations. We also performed Raman spectroscopy, infrared spectroscopy, and diffuse-reflectance measurements, as well as synchrotron powder X-ray diffraction. High-pressure X-ray diffraction measurements show that the crystal structure of BiSbO4 remains stable up to at least 70 GPa, unlike other known MTO4-type ternary oxides. These experiments also give information on the pressure dependence of the unit-cell parameters. Calculations properly describe the crystal structure of BiSbO4 and the changes induced by pressure on it. They also predict a possible high-pressure phase. A room-temperature pressure-volume equation of state is determined, and the effect of pressure on the coordination polyhedron of Bi and Sb is discussed. Raman- and infrared-active phonons were measured and calculated. In particular, calculations provide assignments for all the vibrational modes as well as their pressure dependence. In addition, the band structure and electronic density of states under pressure were also calculated. The calculations combined with the optical measurements allow us to conclude that BiSbO4 is an indirect-gap semiconductor, with an electronic band gap of 2.9(1) eV. Finally, the isothermal compressibility tensor for BiSbO4 is given at 1.8 GPa. The experimental (theoretical) data revealed that the direction of maximum compressibility is in the (0 1 0) plane at ∼33° (38°) to the c-axis and 47° (42°) to the a-axis. The reliability of the reported results is supported by the consistency between experiments and calculations. PMID:27128858

  20. Sixty years from discovery to solution: crystal structure of bovine liver catalase form III

    Energy Technology Data Exchange (ETDEWEB)

    Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J. (Michigan)

    2012-03-27

    The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 {angstrom}. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedron motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies.

  1. Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals.

    Science.gov (United States)

    Olson, Isabel A; Shtukenberg, Alexander G; Hakobyan, Gagik; Rohl, Andrew L; Raiteri, Paolo; Ward, Michael D; Kahr, Bart

    2016-08-18

    Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals. PMID:27478906

  2. Is the methanation reaction over Ru single crystals structure dependent?

    DEFF Research Database (Denmark)

    Vendelbo, Søren Bastholm; Johansson, Martin; Nielsen, Jane Hvolbæk;

    2011-01-01

    The influence of monoatomic steps and defects on the methanation reaction over ruthenium has been investigated. The experiments are performed on a Ru(0 1 54) ruthenium single crystal, which contains one monoatomic step atom for each 27 terrace atoms. The methanation activity is measured at one ba...... front-side of the crystal is poisoned faster than the entire crystal containing more defects. We also observe that additional sputtering of the well-defined front-side increases the reactivity measured on the surface. Based on this, we conclude that the methanation reaction takes place...

  3. New bismuth borophosphate Bi4BPO10: Synthesis, crystal structure, optical and band structure analysis

    International Nuclear Information System (INIS)

    New bismuth borophosphate Bi4BPO10 was obtained by spontaneous crystallization from the melt of correspondent composition at 804 °C. Crystal structure with orthorhombic lattice parameters: a = 22.5731(3) Å, b = 14.0523(2) Å, c = 5.5149(1) Å, V = 1749.34(4), Z = 8, SG Pcab was determined by X-ray powder diffraction technique. The [Bi2O2]2+ -layers, which are typical for bismuth oxide compounds, transform into cationic endless strips of 4 bismuth atoms width directed along the c-axis in Bi4BPO10. The strips combining stacks are separated by flat triangle [BO3]3− -anions within stacks. Neighboring stacks are separated by tetrahedral [PO4]3−-anions and shifted relatively to each other. Bismuth atoms are placed in 5–7 vertex oxygen irregular polyhedra. Bi4BPO10 is stable up to 812 °C, then melts according to the peritectic law. The absorption spectrum in the range 350–700 nm was obtained and the width of the forbidden band was estimated as 3.46 eV. The band electronic structure of Bi4BPO10 was modeled using DFT approach. The calculated band gap (3.56 eV) is in good agreement with the experimentally obtained data. - Graphical abstract: Display Omitted - Highlights: • New bismuth borophosphate with composition Bi4BPO10 was synthesized. • The crystal structure was determined by X-ray powder diffraction technique. • Bismuth-oxygen part [Bi4O3]6+ forms endless strips of 4 bismuth atoms width. • Electronic structure was modeled by DFT method. • The calculated band gap (3.56 eV) is very close to the experimental one (3.46 eV)

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

    Science.gov (United States)

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

    2016-08-01

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

  5. Trimorphism of N-methylurea: crystal structures, phase transitions and thermodynamic stabilities

    OpenAIRE

    Baaklini, G.; Gbabode, G.; Clevers, S.; Négrier, P.; Mondieig, D.; Coquerel, G.

    2016-01-01

    International audience a Melt crystallization of N-methylurea (NMU) was investigated by X-ray and differential scanning calorimetry (DSC) techniques. In addition to the known orthorhombic stable Form I, two new polymorphic forms (II and III) crystallizing in the centrosymmetric space group P2 1 /c were obtained at different quenching temperatures. The crystal structures of Forms II and III were determined from X-ray powder diffraction data. The crystallographic results for the monoclinic f...

  6. Draft Crystal Structure of the Vault Shell at 9-Å Resolution

    OpenAIRE

    Anderson, Daniel H; Kickhoefer, Valerie A.; Stuart A Sievers; Rome, Leonard H.; David Eisenberg

    2007-01-01

    Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMV...

  7. Crystal Structure and Characterization of Pd(Ⅱ) Bis(diisopropyldithiocarbamate) Complex

    Institute of Scientific and Technical Information of China (English)

    XU, Liang-Zhong; ZHAO, Pu-Su; ZHANG, Shu-Sheng

    2001-01-01

    The crystal and molecular structure of [Pd(iPr2 dtc)2] (dtc=dithiocarbamate) have been determined by X-ray crystallography. The unit cell of the crystal structure consists of two discrete monomeric molecules of [Pd(iPr2dtc)2]. The Pd(Ⅱ)ion has an square-planar. The electronic and IR spectral data are in agreement with the X-ray structure. The TG data indicate slight degradation of a few percent.

  8. Crystal Structure Prediction could have helped the Experimentalists with Polymorphism in Benzamide!

    OpenAIRE

    2008-01-01

    Abstract Benzamide was the first molecular material for which polymorphism was reported as long as 176 years ago. Unfortunately, due to very similar cell metrics leading to massive peak overlap, the metastable form reported by Liebig escaped structural characterization by XRD until recently. With the help of crystal structure prediction this old riddle of ?Liebig's? polymorph of benzamide could have been solved many years earlier. Performing state of the art crystal structure predi...

  9. Synthesis and structural characterization of CsNiP crystal

    Indian Academy of Sciences (India)

    G S Gopalakrishna; B H Doreswamy; M J Mahesh; M Mahendra; M A Sridhar; J Shashidhara Prasad; K G Ashamanjari

    2004-02-01

    CsNiP crystals were synthesized by hydrothermal technique and characterized by the X-ray diffraction method. This alkaline transition metal phosphide crystallizes in the hexagonal system with space group P6$_3/mmc$ and cell parameters, = 7.173(2) Å, = 5.944(9) Å, = 264.87(7) Å3 and = 2. The final residual factor is 1 = 0.0362 for 206 reflections with > 2().

  10. Crystal structure and magnetization of a Co{sub 3}B{sub 2}O{sub 6} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Kazak, N. V.; Platunov, M. S., E-mail: platunov@iph.krasn.ru [Russian Academy of Sciences, Kirensky Institute of Physics, Siberian Branch (Russian Federation); Ivanova, N. B. [Siberian Federal University (Russian Federation); Knyazev, Yu. V.; Bezmaternykh, L. N.; Eremin, E. V.; Vasil' ev, A. D.; Bayukov, O. A.; Ovchinnikov, S. G.; Velikanov, D. A. [Russian Academy of Sciences, Kirensky Institute of Physics, Siberian Branch (Russian Federation); Zubavichus, Ya. V. [Russian Research Centre Kurchatov Institute (Russian Federation)

    2013-07-15

    The crystal structure and magnetic properties of Co{sub 3}B{sub 2}O{sub 6} 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{sub 1} = 33 K and T{sub 2} = 10 K and an easy-axis magnetic anisotropy. The effective magnetic moment indicates a high-spin state of the Co{sup 2+} ion. A spin-flop transition is found at low temperatures and H{sub 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.

  11. Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure

    Science.gov (United States)

    Campo, Matteo; Speck, Thomas

    2016-08-01

    We study numerically the crystallization of a hard-sphere mixture with 8% polydispersity. Although often used as a model glass former, for small system sizes we observe crystallization in molecular dynamics simulations. This opens the possibility to study the competition between crystallization and structural relaxation of the melt, which typically is out of reach due to the disparate timescales. We quantify the dependence of relaxation and crystallization times on density and system size. For one density and system size we perform a detailed committor analysis to investigate the suitability of local structures as order parameters to describe the crystallization process. We find that local structures are strongly correlated with generic bond order and add little information to the reaction coordinate.

  12. The diminishing of crystal structure of Sn9Zn alloy due to electrical current stressing

    Energy Technology Data Exchange (ETDEWEB)

    He, Jian-Yang [Department of Material Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC (China); Lin, Kwang-Lung, E-mail: matkllin@mail.ncku.edu.tw [Department of Material Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC (China); Wu, Albert T. [Department of Chemical and Material Engineering, National Central University, Jhongli 32001, Taiwan, ROC (China)

    2015-01-15

    Highlights: • Electrical current stressing will diminish the XRD diffraction peaks of Sn9Zn alloy rapidly. • The kinetics of the diminishing of the crystalline peak follows a logarithmic law with respect to current density. • The diminishing of the XRD diffraction is believed to be a result of disruption of the crystal structure. - Abstract: The variations in the crystal structure of Sn9Zn alloy due to electrical current stressing were investigated with in situ synchrotron XRD analysis. The XRD (X-ray Diffraction) orientation peaks of both Sn and Zn crystals diminished rapidly upon current stressing. The behavior of peak diminishing indicated the electrodisruption of the crystal structure. The electrodisruption was correlated logarithmically to the strain, estimated from the XRD peak shift, as induced by current stressing. The peak diminishing of the Zn crystal was also ascribed to the electrodissolution of Zn in the Sn matrix as revealed by SEM image.

  13. π-Stacked structure of thiadiazolo-fused benzotriazinyl radical: Crystal structure and magnetic properties

    Science.gov (United States)

    Miura, Youhei; Yoshioka, Naoki

    2015-04-01

    A novel benzotriazinyl radical with a 2,1,3-thiadiazolo fused ring (1,3-diphenyl-1,2-dihydro-[1,2,5]thiadiazolo[3‧,4‧:3,4]benzo[1,2-e]-1,2,4-triazine-2-yl; NSNBT) was prepared and characterized by ESR measurement, cyclic voltammetry, and X-ray crystallographic analysis. By a detailed study of bond lengths and angles, it was found that the molecular structure of NSNBT borrows characteristics both from 2,1,3-benzothiadiazole and from the unsubstituted benzotriazinyl radical, and the central phenyl ring presents a phenanthrene-type bond alternation. Molecules were shown to be arranged in a π-stacked columnar structure, with columns connected to each other through sulfur-sulfur interactions in the crystal. It exhibited strong antiferromagnetic interactions (J/kB = -434 K) derived from its dimer structure.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination...... with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice...... in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib....

  15. Crystal structure, thermal and optical properties of Benzimidazole benzimidazolium picrate crystal

    Science.gov (United States)

    Jagadesan, A.; Peramaiyan, G.; Srinivasan, T.; Kumar, R. Mohan; Arjunan, S.

    2016-02-01

    A new organic framework of benzimidazole with picric acid has been synthesized. A single crystal with a size of 38×10×4 mm3 was grown by a slow evaporation solution growth technique. X-ray diffraction study revealed that the BZP crystal belongs to triclinic system with space group P-1. High resolution X-ray diffraction study shows the absence of grain boundaries without any defects. The thermal stability and specific heat capacity of BZP were investigated by TG/DT and TG/DSC analyses. From the UV-vis-NIR spectral study, optical transmission window and band gap of BZP were found out. The nonlinear refractive index (n2) and third order susceptibility Re(χ(3)) values of BZP crystal are estimated to be 1.73×10-7 cm2/W and 1.26×10-5 esu, respectively using a Z-scan technique.

  16. Crystal structure and phase transitions in perovskite-like C(NH2)(3)SnCl3

    DEFF Research Database (Denmark)

    Szafranski, M.; Ståhl, Kenny

    2007-01-01

    X-ray single-crystal diffraction, high-temperature powder diffraction and differential thermal analysis at ambient and high pressure have been employed to study the crystal structure and phase transitions of guanidinium trichlorostannate, C(NH2)(3)SnCl3. At 295 K the crystal structure is orthorho......X-ray single-crystal diffraction, high-temperature powder diffraction and differential thermal analysis at ambient and high pressure have been employed to study the crystal structure and phase transitions of guanidinium trichlorostannate, C(NH2)(3)SnCl3. At 295 K the crystal structure...

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

    Institute of Scientific and Technical Information of China (English)

    岳淑美; 苏忠民; 马建方; 廖奕; 阚玉和; 张恒君

    2003-01-01

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

  18. Electrical investigation of the interface band structure in rubrene single-crystal/nickel junction

    NARCIS (Netherlands)

    Kitamura, Yuta; Shikoh, Eiji; Bisri, Satria Zulkarnaen; Takenobu, Taishi; Shiraishi, Masashi

    2011-01-01

    The electronic structure of the interface between rubrene (C42H28) single crystal and ferromagnetic Ni is studied using an electrical method from a viewpoint of spintronics applications of organic single crystals. The Schottky barrier height at the interface is estimated to be 0.56 eV, and our findi

  19. Crystal Structure and Magnetic Studies of a New Nitronyl Nitroxide Compound

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Compound 1 was first synthesized and characterized. Its crystal structure and magnetic property were determined and investigated. Discussion about the molecule packing in crystal and the macroscopic magnetism was also presented, in combination with computing study of the spatial distribution over the molecule.

  20. Shear effects on crystallization behaviors and structure transitions of isotactic poly-1-butene

    DEFF Research Database (Denmark)

    Li, Jingqing; Guan, Peipei; Zhang, Yao;

    2014-01-01

    Different melt pre-shear conditions were applied to isotactic poly-1-butene (iP-1-B) and the effect on the crystallization behaviors and the crystalline structure transitions of iP-1-B were investigated. The polarized optical microscope observations during isothermal crystallization process revea...

  1. A neutron diffraction refinement of the crystal structure of tetragonal nickel sulfate hexahydrate

    International Nuclear Information System (INIS)

    The crystal structure of NiSO4.6H2O,tetragonal,P41212,a=6.787(3), c=18.299(4)A, was refined from 484 independent reflections collected by neutron diffraction on a single crystal. The hydrogen positions have been located. (author)

  2. Synthesis and crystal structure of a cyano-substituted oligo(p-phenylenevinylene)

    NARCIS (Netherlands)

    Gill, RE; vanHutten, PF; Meetsma, A; Hadziioannou, G

    1996-01-01

    Described is the synthesis and the single-crystal structure of an all-trans dicyano-substituted five-ring PPV oligomer having two 12-octyloxy side chains attached onto the central phenyl ring. The crystal density (D-calc = 1.210 g cm(-3)) appears to be almost 10% higher than that of the crystalline

  3. Integrable Structure of $5d$ $\\mathcal{N}=1$ Supersymmetric Yang-Mills and Melting Crystal

    CERN Document Server

    Nakatsu, Toshio; Takasaki, Kanehisa

    2008-01-01

    We study loop operators of $5d$ $\\mathcal{N}=1$ SYM in $\\Omega$ background. For the case of U(1) theory, the generating function of correlation functions of the loop operators reproduces the partition function of melting crystal model with external potential. We argue the common integrable structure of $5d$ $\\mathcal{N}=1$ SYM and melting crystal model.

  4. Fractal structures of dendrites in GaSe crystals

    Science.gov (United States)

    Kolesnikov, N. N.; Borisenko, E. B.; Borisenko, D. N.; Bozhko, S. I.

    2008-07-01

    Solidification of melts at substantial supercooling is associated with instability on the growth front. This causes growth of dendrites, which form as a branched tree in a crystal. In the layered melt-grown GaSe crystals dendrites are observed, if growth rates are rather high [N.N. Kolesnikov, E.B. Borisenko, D.N. Borisenko, V.K. Gartman, Influence of growth conditions on microstructure and properties of GaSe crystals, J. Crystal Growth 300 (2) (2007) 294-298]. Models based on solution of the thermal diffusion problem are traditionally used to describe dendrite growth. Solution of this problem requires information about several physical parameters, such as diffusion coefficient, heat conductivity coefficient and supercooling at the solid/liquid interface. The study of scale invariance of dendrites formed in a crystal provides a new approach to solution of the dynamic growth problem. The calculated fractal dimensionality of the experimentally observed dendrites in GaSe crystals is D=1.7. It coincides with dimensionality of the clusters obtained through computer simulation in terms of the model of diffusion-limited aggregation (DLA). This result provides a new approach to description of the dynamics of dendrite growth. We have shown that the dendrite growth mechanism in the layered semiconductor crystals can be described by a two-dimensional DLA model. It is shown that probabilistic simulation can be used to show the development of a dendrite in any material. In contrast to the classical theories of dendrite growth, this approach does not require information on physical parameters.

  5. Crystal structure of Mg3Pd from first-principles calculations

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  6. Synthesis and crystal structure determination of Br2SeIBr polyhalogen–chalcogen

    Indian Academy of Sciences (India)

    A A Alemi; E Solaimani

    2004-06-01

    In this paper polyhalogen–chalcogen Br2SeIBr was synthesized and the crystal structure was determined by single crystal X-ray diffraction method. This compound was prepared in the temperature range 150–50°C which was brownish-red in colour and crystallized in monoclinic crystal system and space group 21/c with four molecules per unit cell. Lattice parameters were: = 6.3711(1), = 6.7522(2), = 16.8850(5) Å, = = 90°, = 95·96°, = 722·45 Å3.

  7. Effects of tellurium concentration on the structure of melt-grown ZnSe crystals

    International Nuclear Information System (INIS)

    It has been shown that isovalent doping by tellurium positively affects the structural perfection of ZnSe crystals related to the completeness of the wurtzite-sphalerite phase transition. The optimum concentration range of tellurium in ZnSe crystals is 0.3-0.6 mass %. X-ray diffraction studies have shown that in ZnSe1-xTex crystals at tellurium concentrations below 0.3 mass % twinning and packing defects occur, while tellurium concentrations above 0.6 mass % lead to formation of tetragonal crystal lattice

  8. EFFECT OF PAN-MILLING STRESS ON CRYSTAL STRUCTURES OF HIGH DENSITY POLYETHYLENE

    Institute of Scientific and Technical Information of China (English)

    Hua Huang

    2000-01-01

    A detailed study was performed on the crystal structures of pan-milled high-density polyethylene (HDPE) using differential scanning calorimetry (DSC) and X-ray diffraction. The crystallinity of HDPE first decreased slightly, followed by a gradual increase with increasing milling times. Monoclinic crystals appeared after 4 cycles of milling. With increasing times of milling, the proportion of monoclinic crystals increased significantly while the proportion of orthorhombic crystals decreased gradually. With increasing times of milling, the crystallite size of orthorhombic form decreased greatly, while the size of monoclinic crystallites kept almost constant during milling.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-25

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

  10. Fabrication of colloidal crystals with defined and complex structures via layer-by-layer transfer.

    Science.gov (United States)

    Li, Wei; Yang, Bai; Wang, Dayang

    2008-12-01

    A new and versatile way--using poly(dimethylsiloxane) (PDMS) sheets to layer-by-layer (LbL) transfer hexagonal-close-packed particle monolayers from preformed colloidal crystals and stack them on substrates-has been demonstrated to create colloidal crystals. This approach allows LbL control of the thickness of the resulting crystals and especially of the size and the packing structure of the particles in each layer. Furthermore, it also allows fabrication of binary colloidal crystals over large areas by deformation of the PDMS sheets during LbL transfer. Two new binary crystals-one composed of identically sized particles but in different densities and the other of a nonclose-packed monolayer of large particles and a close-packed monolayer of small particles-were created, which are hard grown by other colloidal crystallization techniques developed thus far. PMID:18986179

  11. Viscoplastic Deformation of Crystal-like Dusty Plasma Structures

    International Nuclear Information System (INIS)

    The experimental investigation of a dusty plasma liquid without shearing forces is presented. The boundary value of coupling parameter was determinated, at which clusters began to form. The possible explanation of non-Newtonian behavior of dusty plasma liquid was suggested. The second part of the present work is devoted to the experimental study of viscoplastic flow in the dusty plasma crystal. It was for the first time the viscoplastic flow of dusty plasma crystal was obtained. The threshold type of this viscoplastic flow was demonstrated.

  12. Crystal structure of (1Z,2E)-cinnamaldehyde oxime

    OpenAIRE

    Bernhard Bugenhagen; Nuha Al Soom; Yosef Al Jasem; Thies Thiemann

    2015-01-01

    The title compound, C9H9NO, crystallized with two independent molecules (A and B) in the asymmetric unit. The conformation of the two molecules differs slightly with the phenyl ring in molecule A, forming a dihedral angle of 15.38 (12)° with the oxime group (O—N=C), compared to the corresponding angle of 26.29 (11)° in molecule B. In the crystal, the A and B molecules are linked head-to-head by O—H...N hydrogen bonds, forming –A–B–A–B– zigzag chains along [010]. Within the chains and between ...

  13. Crystal structure of (S-2-amino-2-methylsuccinic acid

    Directory of Open Access Journals (Sweden)

    Isao Fujii

    2015-10-01

    Full Text Available The title compound, C5H9NO4, crystallized as a zwitterion. There is an intramolecular N—H...O hydrogen bond involving the trans-succinic acid and the ammonium group, forming an S(6 ring motif. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming C(7 chains along the c-axis direction. The chains are linked by N—H...O and C—H...O hydrogen bonds, forming sheets parallel to the bc plane. Further N—H...O hydrogen bonds link the sheets to form a three-dimensional framework.

  14. Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus.

    Science.gov (United States)

    Manjula, M; Pampa, K J; Kumar, S M; Mukherjee, S; Kunishima, N; Rangappa, K S; Lokanath, N K

    2015-03-27

    The ATP binding cassette (ABC) transporters, represent one of the largest superfamilies of primary transporters, which are very essential for various biological functions. The crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus has been determined at 1.77 Å resolution. The crystal structure revealed that the protomer has two thick arms, (arm I and II), which resemble 'L' shape. The ATP-binding pocket is located close to the end of arm I. ATP molecule is docked into the active site of the protein. The dimeric crystal structure of ATP-binding subunit of ABC transporter from G. kaustophilus has been compared with the previously reported crystal structure of ATP-binding subunit of ABC transporter from Salmonella typhimurium.

  15. Single crystal particles of a mesoporous mixed transition metal oxide with a wormhole structure.

    Science.gov (United States)

    Lee, B; Lu, D; Kondo, J N; Domen, K

    2001-10-21

    A new type of mesoporous mixed transition metal oxide of Nb and Ta (NbTa-TIT-1) has been prepared through a two-step calcination, which consists of single crystal particles with wormhole mesoporous structure. PMID:12240191

  16. Crystal and electronic structure study of Mn doped wurtzite ZnO nanoparticles

    Directory of Open Access Journals (Sweden)

    O.M. Ozkendir

    2016-08-01

    Full Text Available The change in the crystal and electronic structure properties of wurtzite ZnO nanoparticles was studied according to Mn doping in the powder samples. The investigations were conducted by X-ray Absorption Fine Structure Spectroscopy (XAFS technique for the samples prepared with different heating and doping processes. Electronic analysis was carried out by the collected data from the X-ray Absorption Near-Edge Structure Spectroscopy (XANES measurements. Additional crystal structure properties were studied by Extended-XAFS (EXAFS analysis. Longer heating periods for the undoped wurtzite ZnO samples were determined to own stable crystal geometries. However, for some doped samples, the distortions in the crystal were observed as a result of the low doping amounts of Mn which was treated as an impurity. Besides, the changes in oxygen locations were determined to create defects and distortions in the samples.

  17. Synthesis and X-ray Crystal Structure of a New Molecular Clip

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The synthesis and X-ray crystal structure of a new molecular clip 2 was reported.It (C24H24N4O2, Mr = 400.47) crystallizes in the space group C2/c with a = 15.587(2), b =8.5805(12), c = 15.259(2)(A),β= 102.448(3)°, V = 1992.9 (5)(A)3, Z= 4, Dc = 1.335 g/cm3,μ= 0.087mm-1 and F(000) = 848.It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip.The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C(9)-C(9a).

  18. Nonreciprocal transmission in a nonlinear photonic-crystal Fano structure with broken symmetry

    DEFF Research Database (Denmark)

    Yu, Yi; Chen, Yaohui; Hu, Hao;

    2015-01-01

    Nanostructures that feature nonreciprocal light trans- mission are highly desirable building blocks for realizing photonic integrated circuits. Here, a simple and ultracompact photonic-crystal structure, where a waveguide is coupled to a single nanocavity, is proposed and experimentally demon...

  19. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

    Directory of Open Access Journals (Sweden)

    Monica Totir

    Full Text Available Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.

  20. Space-Filling Curves as a Novel Crystal Structure Representation for Machine Learning Models

    CERN Document Server

    Jasrasaria, Dipti; Rappoport, Dmitrij; Aspuru-Guzik, Alan

    2016-01-01

    A fundamental problem in applying machine learning techniques for chemical problems is to find suitable representations for molecular and crystal structures. While the structure representations based on atom connectivities are prevalent for molecules, two-dimensional descriptors are not suitable for describing molecular crystals. In this work, we introduce the SFC-M family of feature representations, which are based on Morton space-filling curves, as an alternative means of representing crystal structures. Latent Semantic Indexing (LSI) was employed in a novel setting to reduce sparsity of feature representations. The quality of the SFC-M representations were assessed by using them in combination with artificial neural networks to predict Density Functional Theory (DFT) single point, Ewald summed, lattice, and many-body dispersion energies of 839 organic molecular crystal unit cells from the Cambridge Structural Database that consist of the elements C, H, N, and O. Promising initial results suggest that the S...

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

    Directory of Open Access Journals (Sweden)

    Piero Morales

    2010-05-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  3. Optical and structural properties of Zn1-xBexSe mixed crystals

    International Nuclear Information System (INIS)

    Optical and structural properties of Zn1-xBexSe bulk crystals in the range of composition 0 ≤ x ≤ 0.41 have been studied. These crystals were grown by Bridgman method under an argon overpressure. Transmission, absorption, photoluminescence and photoacoustic spectra as a function of composition were investigated. It has been found that the crystal structure is of sphalerite type. The crystal quality increases when the crystallization process of the same boule is performed more than once. In the investigated composition range the lattice constant decreases and the energy gap increases with increasing beryllium content. From photoluminescence measurements the excitonic energy gap about 3.64 eV at 40 K was estimated for the highest obtained beryllium concentration (x =0.41). (author)

  4. Synthesis and Crystal Structure of a Novel Calix [8] arene Ester Derivative

    Institute of Scientific and Technical Information of China (English)

    DaQiangYUAN; RuJiWANG; 等

    2002-01-01

    The synthesis and crystal structure of a novel calix[8] arene ester are reported herein. The calix [8] arene ester derivative has been characterized by IR,NMR and X-ray crystal analysis. The X-ray structure analysis revealed that the 8 phenolic hydroxy groups of the calix [8] arene have been substituted by 4 diethyl dibromomalonate molecules with each two adjacent hydroxy oxygen atoms attached to a bridge diethyl malonate.

  5. Circular dichroism spectra of langasite family crystals in the range of electronic transitions of structure defects

    International Nuclear Information System (INIS)

    The absorption and circular dichroism spectra of langasite family crystals are studied. Wide bands in the range of 285-500 nm that are related to the structure lattice defects are found. For all the crystals, these bands are in approximately the same spectral region, have identical structures, and can be attributed to one type of defects formed by cation vacancies and excess oxygen atoms in the optically active positions.

  6. Defects in GaN single crystals and homoepitaxial structures

    NARCIS (Netherlands)

    Weyher, J.L.; Kamler, G.; Nowak, G.; Borysiuk, J.; Lucznik, B.; Krysko, M.; Grzegory, I.; Porowski, S.

    2005-01-01

    In this communication crystallographic and chemical inhomogeneities occurring in GaN single crystals, homoepitaxial layers and quasi-bulk thick epitaxial layers are described. Practical classification of defects as (i) growth-related and (ii) processing-induced is given. On the basis of numerous stu

  7. Crystal structure of (E-pent-2-enoic acid

    Directory of Open Access Journals (Sweden)

    Tim Peppel

    2015-05-01

    Full Text Available The molecule of the title compound, C5H8O2, a low-melting α,β-unsaturated carboxylic acid, is essentially planar [maximum displacement = 0.0239 (13 Å]. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...O hydrogen bonds.

  8. Low-temperature crystal and magnetic structure of α -RuCl3

    Science.gov (United States)

    Cao, H. B.; Banerjee, A.; Yan, J.-Q.; Bridges, C. A.; Lumsden, M. D.; Mandrus, D. G.; Tennant, D. A.; Chakoumakos, B. C.; Nagler, S. E.

    2016-04-01

    Single crystals of the Kitaev spin-liquid candidate α -RuCl3 have been studied to determine the low-temperature bulk properties, the structure, and the magnetic ground state. Refinements of x-ray diffraction data show that the low-temperature crystal structure is described by space group C 2 /m with a nearly perfect honeycomb lattice exhibiting less than 0.2% in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at TN=7 K. The magnetic order below this temperature exhibits a propagation vector of k =(0 ,1 ,1 /3 ) , which coincides with a three-layer stacking of the C 2 /m unit cells. Magnetic transitions at higher temperatures up to 14 K can be introduced by deformations of the crystal that result in regions in the crystal with a two-layer stacking sequence. The best-fit symmetry-allowed magnetic structure of the as-grown crystals shows that the spins lie in the a c plane, with a zigzag configuration in each honeycomb layer. The three-layer repeat out-of-plane structure can be refined as a 120∘ spiral order or a collinear structure with a spin direction of 35∘ away from the a axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) μB per Ru3 + ion.

  9. Theoretical Exploration of Various Lithium Peroxide Crystal Structures in a Li-Air Battery

    Directory of Open Access Journals (Sweden)

    Kah Chun Lau

    2015-01-01

    Full Text Available We describe a series of metastable Li2O2 crystal structures involving different orientations and displacements of the O22− peroxy ions based on the known Li2O2 crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li2O2 crystal structure (i.e., Föppl structure, all of these newly found metastable Li2O2 crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O22− O-O vibration mode (ω ~ 799–865 cm−1, which is in the range of that commonly observed in Li-air battery experiments, regardless of the random O22− orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li2O2 powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li2O2 compounds that are grown electrochemically under the environment of Li-O2 cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li2O2 crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O22− vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li2O2 crystal structures, as all of them similarly share the similar O22− vibration mode. However considering that the discharge voltage in most Li-O2 cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li2O2 crystal structures appears to be thermodynamically feasible.

  10. Fabrication and optical transmission characteristics of polymers woodpile photonic crystal structures with different crystal planes

    Science.gov (United States)

    Chen, Ling-Jing; Dong, Xian-Zi; Zhao, Yuan-Yuan; Zhang, Yong-Liang; Liu, Jie; Zheng, Mei-Ling; Duan, Xuan-Ming; Zhao, Zhen-Sheng

    2015-10-01

    The photonic band gap effect which originates from the translational invariance of the periodic lattice of dielectrics has been widely applied in the technical applications of microwave, telecommunication and visible wavelengths. Among the various examples, polymers based three dimensional (3D) photonic crystals (PhCs) have attracted considerable interest because they can be easily fabricated by femo-second (fs) ultrafast laser direct writing (DLW) method. However, it is difficult to realize complete band gap in polymers PhCs due to the low index contrast between polymers and air. Here, we report the design and experimental realization of light's nonreciprocal propagation in woodpile PhCs fabricated with DLW method. Firstly, we fabricated several polymers woodpile PhCs on glass substrate with different crystal planes. The Fourier transform infrared spectroscopy (FTIR) measurements are in agreement with the theoretical predictions, which proves the validity and the accuracy of our DLW method. Further measurements of the transmission spectra with respect to the incident angle reveal that the surface crystal planes and incident wave vectors play important roles in the optical response. Furthermore, we designed and fabricated a 30° PhC wedge. And we find nonreciprocal transmission effect between the forward and backward waves, resulting from the nonsymmetrical refraction of the light in different planes. Our results may find potential applications in future 3D photonic integrated circuits and pave the way for the fabrication of other photonic and optical devices with DLW method.

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

    DEFF Research Database (Denmark)

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

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

  12. Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor

    DEFF Research Database (Denmark)

    Svensson, L Anders; Bondensgaard, Kent; Nørskov-Lauritsen, Leif;

    2008-01-01

    The crystal structure of the complex between an N-terminally truncated G129R human prolactin (PRL) variant and the extracellular domain of the human prolactin receptor (PRLR) was determined at 2.5A resolution by x-ray crystallography. This structure represents the first experimental structure...

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

    DEFF Research Database (Denmark)

    Johansson, Kristoffer E.; van de Streek, Jacco

    2016-01-01

    Despite being the earliest reported case of polymorphism in a molecular crystal, the unstable form II of benzamide has thus far evaded thorough structural characterization because collection of experimental data at atomic resolution has proven extremely challenging. Using a highly validated...... computational crystal structure prediction (CSP) method based on dispersion-corrected density functional theory, we correctly predict the stable form I with the lowest energy among all sampled structures and its polytypic form III with slightly higher energy. From Rietveld refinement of selected CSP models...... against synchrotron X-ray powder diffraction data of the historical polymorph, we are able to identify a subtle weakness in the available experimental data and arrive at a revised structure of form II. The revised crystal structure is the first benzamide structure to form catemers rather than dimers...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-02-15

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

  15. Characterization of dislocation structures in silicon carbide single crystals

    Science.gov (United States)

    Vetter, William M.

    1999-07-01

    Two types of defects in PVT-grown 6H and 4H-SiC crystals were studied: screw dislocations that follow the axial direction of the crystal and dislocations that follow directions in the crystal's basal plane. The screw dislocations possessed a range of Burgers vector magnitudes, multiples of the axial parameter c, that could be determined by x-ray topographic image analysis. Hollow cores termed "micropipes" were observed when Burgers, vectors were larger than 3c. The micropipes were studied by a variety of methods: optical microscopy, laser scanning confocal microscopy, scanning electron microscopy, transmission electron microscopy and atomic force microscopy. The micropipes were tubes 0.1 to 10mum in diameter. They were faceted, primarily along the {101¯0} planes, but also had {112¯0} facets. When encountering the growth surface of a crystal, they flared out into a trumpet-shape. Growth spirals sometimes occurred, originating from the trumpets' rims. The screw dislocations are visible in back-reflection synchrotron white beam x-ray topographs of basal-cut SiC wafers in striking contrast as black rings surrounding white circles, though such topographs are contaminated by a series of harmonic reflections, g = (0006n), where n = 3 to 16. By calculating and considering their intensities, and comparison with a g = 00018 Lang topograph taken with CuKalpha1 radiation, the g = 00024 harmonic was shown to be the most important contributor. Basal plane dislocations were seen in x-ray topographs of SiC looping from the points where screw dislocations occurred. Their extinction behavior showed they belonged to the set b = 13 . In some transmission electron micrographs, perfect dislocations with similar extinction behavior, along with partial dislocations with b = 13 , were seen originating from the micropipes' walls, curving out into the crystal a distance of 1 to 3mum, then back to terminate at the micropipe. Others led out of the field of view. Contrast is associated with

  16. Obtaining the band structure of a complicated photonic crystal by linear operations

    Institute of Scientific and Technical Information of China (English)

    吴良; 叶卓; 何赛灵

    2003-01-01

    Absolute band gaps can be created by lifting the degeneracy in the bands of a photonic crystal.To calculate the band structure of a complicated photonic crystal generated by e.g.symmetry breaking,general forms of all possible linear operations are presented in terms of matrices and a procedure to combine these operations is given.Other forms of linear operations(such as the addition,subtraction,and translation transforms) are also presented to obtain an explicit expression for the Fourier coefficient of the dielectric function in the plane-wave expansion method.With the present method,band structures for various complicated photonic crystals(related through these linear operations) can be obtained easily and quickly.As a numerical example,a large absolute band gap for a complicated photonic crystal structure of GaAs is found in the high region of normalized frequency.

  17. Crystal Structure and Characterization of a New Eight Coordinated Cadmium Complex

    Energy Technology Data Exchange (ETDEWEB)

    Hakimi, Mohammad; Moeini, Keyvan; Mardani, Zahra; Khorrami, Farzaneh [Payame Noor Univ., Tehran (Iran, Islamic Republic of)

    2013-06-15

    In this work, a new cadmium complex [Cd(L)(CH{sub 3}COO){sub 2}]-2H{sub 2}O (1) with the ligand L, N,N'-bis(2-pyridinecar-boxalidene)-1,2-cyclohexanediamine was prepared and identified by elemental analysis, FT-IR, Raman, {sup 1}H NMR spectroscopy and single-crystal X-ray diffraction. The cadmium atom in the crystal structure of 1 has distorted triangular dodecahedral geometry by coordination of the four nitrogen atoms of L and four oxygen atoms of the two acetate ions. Two water molecules are also incorporated in the crystal network. The O-H···O hydrogen bonds present in the crystal structure of 1. In this work, three structural surveys including coordination numbers of the cadmium atom, coordination modes of L and resonance in pyridine-2-ylmethanimine-based compounds are presented.

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

    Science.gov (United States)

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

    2016-06-01

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

  19. Structural phase transitions and topological defects in ion Coulomb crystals

    International Nuclear Information System (INIS)

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed nonadiabatically. For a second order phase transition, the Kibble–Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation

  20. Structural phase transitions and topological defects in ion Coulomb crystals

    Energy Technology Data Exchange (ETDEWEB)

    Partner, Heather L. [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Nigmatullin, Ramil [Institute of Quantum Physics, Ulm Univ., Ulm (Germany); Burgermeister, Tobias [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Keller, Jonas [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Pyka, Karsten [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Plenio, Martin B. [Center for Integrated Quantum Science and Technology, Ulm Univ., Ulm, (Germany):Institute for Theoretical Physics, Ulm Univ.,Ulm, (Germany); Retzker, Alex [Racah Institute of Physics, The Hebrew University of Jerusalem, Givat Ram (Israel); Zurek, Wojciech Hubert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); del Campo, Adolfo [Univ. of Massachusetts, Amherst, MA (United States). Dept. of Physics; Mehlstaubler, Tanja E. [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany)

    2014-11-19

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed non-adiabatically. For a second order phase transition, the Kibble-Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation.

  1. Structural phase transitions and topological defects in ion Coulomb crystals

    Energy Technology Data Exchange (ETDEWEB)

    Partner, Heather L. [Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig (Germany); Nigmatullin, Ramil [Institute of Quantum Physics, Albert-Einstein Allee-11, Ulm University, 89069 Ulm (Germany); Burgermeister, Tobias; Keller, Jonas; Pyka, Karsten [Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig (Germany); Plenio, Martin B. [Center for Integrated Quantum Science and Technology, Albert-Einstein-Allee 11, Ulm University, 89069 Ulm (Germany); Institute for Theoretical Physics, Albert-Einstein-Allee 11, Ulm University, 89069 Ulm (Germany); Retzker, Alex [Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Givat Ram (Israel); Zurek, Wojciech H. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544 (United States); Campo, Adolfo del [Department of Physics, University of Massachusetts Boston, Boston, MA 02125 (United States); Mehlstäubler, Tanja E., E-mail: tanja.mehlstaeubler@ptb.de [Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig (Germany)

    2015-03-01

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed nonadiabatically. For a second order phase transition, the Kibble–Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation.

  2. Crystal structure of (1Z,2E)-cinnamaldehyde oxime

    OpenAIRE

    Bugenhagen, Bernhard; Al Soom, Nuha; Al Jasem, Yosef; Thiemann, Thies

    2015-01-01

    The title compound, C9H9NO, crystallized with two independent mol­ecules (A and B) in the asymmetric unit. The conformation of the two mol­ecules differs slightly with the phenyl ring in mol­ecule A, forming a dihedral angle of 15.38 (12)° with the oxime group (O—N=C), compared to the corresponding angle of 26.29 (11)° in mol­ecule B. In the crystal, the A and B mol­ecules are linked head-to-head by O—H⋯N hydrogen bonds, forming –A–B–A–B– zigzag chains along [010]. Within the chains and betwe...

  3. Crystal structure of 4,6-dichloro-5-methylpyrimidine

    Directory of Open Access Journals (Sweden)

    Meriem Medjani

    2015-12-01

    Full Text Available The title compound, C5H4Cl2N2, is essentially planar with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4 Å for an N atom. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers, enclosing an R22(6 ring motif.

  4. Supercoiled DNA; plectonemic structure and liquid crystal formation

    CERN Document Server

    Maarel, J R C; Jesse, W; Backendorf, C; Egelhaaf, S U; Lapp, A

    2003-01-01

    We have investigated the phase behaviour of pUC18 plasmid solutions with phase separation experiments and polarized light microscopy. Furthermore, the configuration of the superhelix is monitored with small-angle neutron scattering. The phase diagram is interpreted with liquid crystal theory including the effects of charge, orientation entropy, excluded volume, as well as the elastic, entropic and electrostatic contributions to the molecular free energy.

  5. Crystal structure of 2-methylsulfanyl-1-(thiomorpholin-4-ylethanone

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-09-01

    Full Text Available In the title compound, C7H13NOS2, the thiomorpholine ring adopts a chair conformation and the bond-angle sum at the N atom is 360°. The dihedral angle between the amide group and the thiomorpholine ring (all atoms is 36.48 (12°. In the crystal, C—H...O and C—H...S hydrogen bonds link adjacent molecules, forming two-dimensional networks extending parellel to the (011 plane.

  6. Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets

    Science.gov (United States)

    Rozenberg, Haim; Rabinovich, Dov; Frolow, Felix; Hegde, Rashmi S.; Shakked, Zippora

    1998-12-01

    Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein-DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.

  7. Structural peculiarities of single crystal diamond needles of nanometer thickness

    Science.gov (United States)

    Orekhov, Andrey S.; Tuyakova, Feruza T.; Obraztsova, Ekaterina A.; Loginov, Artem B.; Chuvilin, Andrey L.; Obraztsov, Alexander N.

    2016-11-01

    Diamond is attractive for various applications due to its unique mechanical and optical properties. In particular, single crystal diamond needles with high aspect ratios and sharp apexes of nanometer size are demanded for different types of optical sensors including optically sensing tip probes for scanning microscopy. This paper reports on electron microscopy and Raman spectroscopy characterization of the diamond needles having geometrically perfect pyramidal shapes with rectangular atomically flat bases with (001) crystallography orientation, 2–200 nm sharp apexes, and with lengths from about 10–160 μm. The needles were produced by selective oxidation of (001) textured polycrystalline diamond films grown by chemical vapor deposition. Here we study the types and distribution of defects inside and on the surface of the single crystal diamond needles. We show that sp3 type point defects are incorporated into the volume of the diamond crystal during growth, while the surface of the lateral facets is enriched by multiple extended defects. Nitrogen addition to the reaction mixture results in increase of the growth rate on {001} facets correlated with the rise in the concentration of sp3 type defects.

  8. Inorganic Crystal Structure Data to be Presented in a Form More Useful for Further Studies

    Institute of Scientific and Technical Information of China (English)

    HU Sheng-Zhi(胡盛志); Erwin PARTHé

    2004-01-01

    To make inorganic structure data more useful for further studies a five-point list of simple procedures to be followed by authors of crystal structure papers is proposed. 1. A crystal structure should be described with the space group corresponding to its true symmetry. 2. A new structure proposal should be tested, if it is realistic in principle. 3. A structure should be described with a space group in a setting given in the International Tables. 4. For a comparison with other structures the structure data should be standardized with the program STRUCTURE TIDY. 5. "New" structure data should be checked in the databases, Chemical Abstracts or on-line internet resources, if they are really new. The list is supplemented with many explanations, commentaries, examples and references.

  9. Fast motif-network scheme for extensive exploration of complex crystal structures in silicate cathodes

    CERN Document Server

    Zhao, Xin; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong; Ho, Kai-Ming

    2015-01-01

    A motif-network search scheme is proposed to study the crystal structures of the dilithium/disodium transition metal orthosilicates A2MSiO4. Using this fast and efficient method, the structures of all six combinations with A = Li or Na and M = Mn, Fe or Co were extensively explored. In addition to finding all previously reported structures, we discovered many other different crystal structures which are highly degenerate in energy. These tetrahedral-network-based structures can be classified into 1D, 2D and 3D types based on M-Si-O frames. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.

  10. Fast motif-network scheme for extensive exploration of complex crystal structures in silicate cathodes

    Science.gov (United States)

    Ho, Kai-Ming; Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong

    2015-03-01

    A motif-network search scheme is proposed to study the crystal structures of the dilithium/disodium transition metal orthosilicates A2MSiO4. Using this fast and efficient method, the structures of all six combinations with A = Li or Na and M = Mn, Fe or Co were extensively explored in this work. In addition to finding all previously reported experimental structures, we discover many other different crystal structures which are highly degenerate in energy. These tetrahedral-network-based structures can be classified into 1D, 2D and 3D types. A clear trend of the structural preference in different systems is revealed and possible indicators that affect the structure stabilities are introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.

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

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

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

  12. Synthesis, growth, structure determination and optical properties of chalcone derivative single crystal

    Science.gov (United States)

    Karthi, S.; Girija, E. K.

    2014-04-01

    Acquiring large nonlinear optical (NLO) efficient organic material is essential for the development of optoelectronics and photonic devices. Chalcone is the donor - Π - acceptor - Π - donor (D-Π-A-Π-D) type conjugated molecule with appreciable hyperpolarizability of potential interest in NLO applications. The addition of vinyl and electron donor groups in the chalcone molecule may enhance the second harmonic generation (SHG) efficiency. Here we report the synthesis, crystal growth and characterization of a chalcone derivative 1-(4-methylphenyl)-5-(4-methoxyphenyl)-penta-2,4-dien-1-one (MPMPP). The MPMPP crystal was grown by slow evaporation solution growth technique from acetone. The grown crystal structure was studied by single crystal X-ray diffraction. The SHG efficiency of the grown crystal was determined by Kurtz and Perry method.

  13. Synthesis, growth, structure determination and optical properties of chalcone derivative single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Karthi, S., E-mail: girijaeaswaradas@gmail.com; Girija, E. K., E-mail: girijaeaswaradas@gmail.com [Department of Physics, Periyar University, Salem - 636011 (India)

    2014-04-24

    Acquiring large nonlinear optical (NLO) efficient organic material is essential for the development of optoelectronics and photonic devices. Chalcone is the donor - Π - acceptor - Π - donor (D-Π-A-Π-D) type conjugated molecule with appreciable hyperpolarizability of potential interest in NLO applications. The addition of vinyl and electron donor groups in the chalcone molecule may enhance the second harmonic generation (SHG) efficiency. Here we report the synthesis, crystal growth and characterization of a chalcone derivative 1-(4-methylphenyl)-5-(4-methoxyphenyl)-penta-2,4-dien-1-one (MPMPP). The MPMPP crystal was grown by slow evaporation solution growth technique from acetone. The grown crystal structure was studied by single crystal X-ray diffraction. The SHG efficiency of the grown crystal was determined by Kurtz and Perry method.

  14. Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA

    Institute of Scientific and Technical Information of China (English)

    SALON; Jozef

    2010-01-01

    The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids.Selenium can serve as an excellent anomalous scattering center to solve the phase problem,which is one of the two major bottlenecks in macromolecule X-ray crystallography.The other major bottleneck is crystallization.It has been demonstrated that the incorporated selenium functionality at the 2′-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation.Furthermore,it was observed that the 2′-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality.Herein,we describe a convenient synthesis of the 2′-Se-adenosine phosphoramidite,and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2′-Se-A derivatization.The 3D structure of 2′-Se-A-DNA decamer 5′-GTACGCGT(2′-Se-A)C-3′2 was determined at 1.75 ? resolution,the 2′-Se-functionality points to the minor groove,and the Se-modified and native structures are virtually identical.Moreover,we have observed that the 2′-Se-A modification can greatly facilitate the crystal growth with high diffraction quality.In conjunction with the crystallization facilitation by the 2′-Se-U and 2′-Se-T,this novel observation on the 2′-Se-A functionality suggests that the 2′-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.

  15. Crystal Structure of Human Senescence Marker Protein 30: Insights Linking Structural, Enzymatic, and Physiological Functions

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborti, Subhendu; Bahnson, Brian J. (Delaware)

    2010-05-25

    Human senescence marker protein 30 (SMP30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. The penultimate step in vitamin-C biosynthesis is catalyzed by this enzyme in nonprimate mammals. It has also been implicated as an organophosphate hydrolase, with the ability to hydrolyze diisopropyl phosphofluoridate and other nerve agents. SMP30 was originally identified as an aging marker protein, whose expression decreased androgen independently in aging cells. SMP30 is also referred to as regucalcin and has been suggested to have functions in calcium homeostasis. The crystal structure of the human enzyme has been solved from X-ray diffraction data collected to a resolution of 1.4 {angstrom}. The protein has a 6-bladed {beta}-propeller fold, and it contains a single metal ion. Crystal structures have been solved with the metal site bound with either a Ca{sup 2+} or a Zn{sup 2+} atom. The catalytic role of the metal ion has been confirmed by mutagenesis of the metal coordinating residues. Kinetic studies using the substrate gluconolactone showed a k{sub cat} preference of divalent cations in the order Zn{sup 2+} > Mn{sup 2+} > Ca{sup 2+} > Mg{sup 2+}. Notably, the Ca{sup 2+} had a significantly higher value of K{sub d} compared to those of the other metal ions tested (566, 82, 7, and 0.6 {micro}m for Ca{sup 2+}, Mg{sup 2+}, Zn{sup 2+}, and Mn{sup 2+}, respectively), suggesting that the Ca{sup 2+}-bound form may be physiologically relevant for stressed cells with an elevated free calcium level.

  16. The absence of tertiary interactions in a self-assembled DNA crystal structure.

    Science.gov (United States)

    Nguyen, Nam; Birktoft, Jens J; Sha, Ruojie; Wang, Tong; Zheng, Jianping; Constantinou, Pamela E; Ginell, Stephan L; Chen, Yi; Mao, Chengde; Seeman, Nadrian C

    2012-04-01

    DNA is a highly effective molecule for controlling nanometer-scale structure. The convenience of using DNA lies in the programmability of Watson-Crick base-paired secondary interactions, useful both to design branched molecular motifs and to connect them through sticky-ended cohesion. Recently, the tensegrity triangle motif has been used to self-assemble three-dimensional crystals whose structures have been determined; sticky ends were reported to be the only intermolecular cohesive elements in those crystals. A recent communication in this journal suggested that tertiary interactions between phosphates and cytosine N(4) groups are responsible for intermolecular cohesion in these crystals, in addition to the secondary and covalent interactions programmed into the motif. To resolve this issue, we report experiments challenging this contention. Gel electrophoresis demonstrates that the tensegrity triangle exists in conditions where cytosine-PO(4) tertiary interactions seem ineffective. Furthermore, we have crystallized a tensegrity triangle using a junction lacking the cytosine suggested for involvement in tertiary interactions. The unit cell is isomorphous with that of a tensegrity triangle crystal reported earlier. This structure has been solved by molecular replacement and refined. The data presented here leave no doubt that the tensegrity triangle crystal structures reported earlier depend only on base pairing and covalent interactions for their formation. PMID:22434713

  17. Structure of the manganese superoxide dismutase from Deinococcus radiodurans in two crystal forms

    Energy Technology Data Exchange (ETDEWEB)

    Dennis, Rebecca J.; Micossi, Elena; McCarthy, Joanne [Macromolecular Crystallography Group, European Synchrotron Radiation Facility, 38043 Grenoble CEDEX 9 (France); Moe, Elin [The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø (Norway); Gordon, Elspeth J.; Kozielski-Stuhrmann, Sigrid; Leonard, Gordon A.; McSweeney, Sean, E-mail: mcsweeney@esrf.fr [Macromolecular Crystallography Group, European Synchrotron Radiation Facility, 38043 Grenoble CEDEX 9 (France)

    2006-04-01

    The crystal structures of two crystal forms of manganese superoxide dismutase (Mn-SOD) from the radiation-resistant bacterium D. radiodurans are reported and compared with the crystal structure of Mn-SOD from E. coli. The structure of the manganese superoxide dismutase (Mn-SOD; DR1279) from Deinococcus radiodurans has been determined in two different crystal forms. Both crystal forms are monoclinic with space group P2{sub 1}. Form I has unit-cell parameters a = 44.28, b = 83.21, c = 59.52 Å, β = 110.18° and contains a homodimer in the asymmetric unit, with structure refinement (R = 16.8%, R{sub free} = 23.6%) carried out using data to d{sub min} = 2.2 Å. Form II has unit-cell parameters a = 43.57, b = 87.10, c = 116.42 Å, β = 92.1° and an asymmetric unit containing two Mn-SOD homodimers; structure refinement was effected to a resolution of 2.0 Å (R = 17.2%, R{sub free} = 22.3%). The resulting structures are compared with that of Mn-SOD from Escherichia coli, with which they are shown to be essentially isostructural.

  18. Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity.

    Science.gov (United States)

    Mikulecký, Pavel; Zahradník, Jirí; Kolenko, Petr; Černý, Jiří; Charnavets, Tatsiana; Kolářová, Lucie; Nečasová, Iva; Pham, Phuong Ngoc; Schneider, Bohdan

    2016-09-01

    Interferon-γ receptor 2 is a cell-surface receptor that is required for interferon-γ signalling and therefore plays a critical immunoregulatory role in innate and adaptive immunity against viral and also bacterial and protozoal infections. A crystal structure of the extracellular part of human interferon-γ receptor 2 (IFNγR2) was solved by molecular replacement at 1.8 Å resolution. Similar to other class 2 receptors, IFNγR2 has two fibronectin type III domains. The characteristic structural features of IFNγR2 are concentrated in its N-terminal domain: an extensive π-cation motif of stacked residues KWRWRH, a NAG-W-NAG sandwich (where NAG stands for N-acetyl-D-glucosamine) and finally a helix formed by residues 78-85, which is unique among class 2 receptors. Mass spectrometry and mutational analyses showed the importance of N-linked glycosylation to the stability of the protein and confirmed the presence of two disulfide bonds. Structure-based bioinformatic analysis revealed independent evolutionary behaviour of both receptor domains and, together with multiple sequence alignment, identified putative binding sites for interferon-γ and receptor 1, the ligands of IFNγR2. PMID:27599734

  19. Crystal structure of 2-bromo-4,6-dinitroaniline

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-11-01

    Full Text Available In the title compound, C6H4BrN3O4, the dihedral angles between the nitro groups and the aniline ring are 2.04 (3 and 1.18 (4°, respectively. In the crystal, N—H...O and C—H...O hydrogen bonds and weak side-on C—Br...π interactions [3.5024 (12 Å] link adjacent molecules, forming a three-dimensional network. A close O...Br contact [3.259 (2 Å] may also add additional stability.

  20. Crystal structure of 3-ethynyl-benzoic acid.

    Science.gov (United States)

    Venturini, Chiara; Ratel-Ramond, Nicolas; Gourdon, Andre

    2015-10-01

    In the title compound, C9H6O2, the carb-oxy-lic acid group is almost in the plane of the benzene ring, making a dihedral angle of 2.49 (18)°. In the crystal, mol-ecules are linked by pairs of O-H⋯O hydrogen bonds, forming classical acid-acid inversion dimers, with an R 2 (2)(8) ring motif. The dimers are linked by pairs of C-H⋯O hydrogen bonds forming chains, enclosing R 2 (2)(16) ring motifs, propagating along the c-axis direction. PMID:26594457

  1. Crystal structure of 4-benzamido-2-hydroxybenzoic acid

    OpenAIRE

    Muhammad Shahid; Muhammad Aziz Choudhary; Arshad Farooq Butt; Muhammad Nawaz Tahir; Muhammad Salim

    2015-01-01

    In the title compound, C14H11NO4, the dihedral angle between the mean planes of the aromatic rings is 3.96 (12)° and an intramolecular O—H...O hydrogen bond closes an S(6) ring. A short intramolecular C—H...O contact is also seen. In the crystal, carboxylic acid inversion dimers linked by pairs of O—H...O hydrogen bonds generate R22(8) loops. Conversely, the N—H group does not form a hydrogen bond. Aromatic π–π interactions exist at a centroid–centroid distance of 3.8423 (15) Å between the be...

  2. The structural stability in nano-sized crystals of metals

    Institute of Scientific and Technical Information of China (English)

    MENG; Qingping; (孟庆平); RONG; Yonghua; (戎咏华); HSU; T.; Y.; (XU; Zuyao徐祖耀)

    2002-01-01

    The equation of phase equilibria in nano-sized crystal of metals has been established in terms of thermodynamic equilibrium. The thermodynamic parameters are calculated and the critical grain size for the stable high-temperature phase at room temperature is obtained. As an example, the critical grain size of β-Co at room temperature is determined at 35nm when the excess volume is 10%. The result agrees well with the experiment of Katakimi et al. The factors affecting the stability of β-Co are also discussed.

  3. Crystal structure of 2-chloro-N-(3-fluorophenylacetamide

    Directory of Open Access Journals (Sweden)

    S. Sreenivasa

    2015-05-01

    Full Text Available In the title compound, C8H7ClFNO, the F atom is disordred over the meta positions of the benzene ring in a 0.574 (4:0.426 (4 ratio and the Cl atom is syn to the O atom [O—C—C—Cl = 5.6 (3°]. A short intramolecular C—H...O contact occurs. In the crystal, molecules are linked into amide C(4 chains propagating in [101] by N—H...O hydrogen bonds.

  4. Crystal structure of tetrakis(1-oxidopyridin-2-ylmethane methanol tetrasolvate

    Directory of Open Access Journals (Sweden)

    Kouzou Matsumoto

    2015-10-01

    Full Text Available The asymmetric unit of the title compound, C21H16N4O4·4CH3OH, consists of a quarter molecule of tetrakis(1-oxidopyridin-2-ylmethane and one methanol solvent molecule. In the crystal, the pyridine N-oxide derivative is located about a fourfold rotoinversion axis and exhibits S4 symmetry along the c axis. An intermolecular O—H...O hydrogen bond is observed between the O atom of the pyridine N-oxide and the OH group of the methanol. An intermolecular C—H...O bond is also observed between adjacent pyridine N-oxide rings.

  5. Crystal structure of 5-[(4-carboxybenzyloxy]isophthalic acid

    Directory of Open Access Journals (Sweden)

    Md. Serajul Haque Faizi

    2016-08-01

    Full Text Available The molecular shape of the title compound, C16H12O7, is bent around the central CH2—O bond. The two benzene rings are almost perpendicular to one another, making a dihedral angle of 87.78 (7°. In the crystal, each molecule is linked to three others by three pairs of O—H...O hydrogen bonds, forming undulating sheets parallel to the bc plane and enclosing R22(8 ring motifs. The sheets are linked by C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional network.

  6. Structural features of Ge(Ga) single crystals grown under conditions simulating the microgravity perturbation factors

    Energy Technology Data Exchange (ETDEWEB)

    Prokhorov, I.A.; Strelov, V.I.; Zakharov, B.G. [Space Materials Science Research Centre of the Crystallography Institute, RAS, Akademicheskaya 8, 248640 Kaluga (Russian Federation); Shul' pina, I.L.; Ratnikov, V.V. [Ioffe Physico-Technical Institute, RAS, Politekhnicheskaya 26, 194021 St. Petersburg (Russian Federation)

    2005-04-01

    Peculiarities of the real structure of Ge(Ga) single crystals grown under external mechanical perturbations of the crystallization process simulating actual microgravity environment aboard spacecrafts were investigated by X-ray topography and diffractometry methods, etching analysis and spreading resistance measurements. The applied perturbations included vibrations and variations of growth facility orientation with respect to the direction of gravity force. It has been shown that microinhomogeneity of the crystals grown is defined not only by formation of dopant growth striations at peculiar vibrational perturbations of a melt, but also by specific features of dislocation structure of crystals related with the formation of small angle boundaries, slip bands and other inhomogeneities in dislocation distribution. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  7. Molecular and crystal structure of n-hexyloxybenzoic anhydride at low and room temperatures

    International Nuclear Information System (INIS)

    The crystal and molecular structures of n-hexyloxybenzoic anhydride, C6H13-O-C6H4-C(O)-O-C(O)-C6H4-C6H13, at low (120 K) and room (296 K) temperatures have been investigated. The molecule has an asymmetric bent structure. The dihedral angle between the benzene ring planes is 48.5 deg. The aliphatic chain on one side of the molecule has a transoid orientation with respect to the 'internal' C4 atom of the closest benzene ring, whereas the aliphatic chain on the other side has a cissoid orientation with respect to the analogous C(4A) atom. The crystal packing does not exhibit any pronounced separation of the crystal space into closely packed aromatic or loosely packed aliphatic regions. No weak directional interactions are observed in the packing; this fact explains the absence of liquid-crystal properties for this compound.

  8. Crystallization and X-ray structure determination of a thermoalkalophilic lipase from Geobacillus SBS-4S

    International Nuclear Information System (INIS)

    Crystallization and the structure determination at 1.6 Å resolution of LIPSBS, a thermoalkalophilic lipase from Geobacillus strain SBS-4S, are described. The crystals belonged to orthorhombic space group P212121. A thermoalkalophilic lipase (LIPSBS) from the newly isolated Geobacillus strain SBS-4S which hydrolyzes a wide range of fatty acids has been characterized. In the present study, the crystallization of purified LIPSBS using the sitting-drop vapour-diffusion method and its X-ray diffraction studies are described. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 55.13, b = 71.75, c = 126.26 Å. The structure was determined at 1.6 Å resolution by the molecular-replacement method using the lipase from G. stearothermophilus L1 as a model

  9. The crystal structure of the molybdenum cementite Mo12Fe22C10 (xi-phase)

    International Nuclear Information System (INIS)

    The crystal structure of molybdenum cementite Mo12Fe22C10 (xi-phase) has been determined by means of a single crystal x-ray diffraction study of crystal fragments. The lattice parameters were found to be: a=10.865(3), b=7.767(2), c=6.559(2) A and β=120.13(2)0, space group C2/m; Z=1. From the analysis of Patterson maps and difference Fourier analysis the atomic parameters were derived, yielding a residual of R=0.059. The crystal structure contains octahedral and triangular prismatic groups which accommodate the carbon atoms in their voids, as is usually found in interstitial compounds. The octahedral building group consists of four Mo- and two Fe-atoms, the triangular prism is built up by four Fe- and two Mo-atoms. The mode of filling of the metal polyhedra is discussed. (Author)

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

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  11. Crystal Structure, Energy Band and Optical Properties of Phosphate In(PO3)3

    Institute of Scientific and Technical Information of China (English)

    KAN Zi-Gui; CHENG Wen-Dan; WU Dong-Sheng; ZHANG Hao; GONG Ya-Jing; ZHU Jing; TONG Hua-Nan

    2005-01-01

    The crystal of the title compound (InP3O9, Mr = 351.73) has been prepared and structurally determined by X-ray single-crystal diffraction. It crystallizes in the monoclinic system, space group Cc with a = 13.545(6), b = 19.603(7), c = 9.672(4)(A), β = 127.196(4)°, V = 2045.6(14)(A)3 and Z = 12. The compound, with a three-fold superstructure, has two kinds of infinite chains of PO4 tetrahedra along the c axis. The absorption and luminescence spectra of In(PO3)3 powder have been measured. The calculated results of crystal energy band structure by DFT indicate that the solid state is kind of insulator. What is more, the bonding and optical properties were also investigated with the CASTEP code.

  12. Synthesis and Properties of Triphenylgermanium Heteroaromatic Carboxylates and Crystal Structure of Triphenylgermanium 2-Furoate

    Institute of Scientific and Technical Information of China (English)

    YIN,Han-Dong(尹汉东); WANG,Chuan-Hua(王传华); WANG,Yong(王勇); ZHANG,Ru-Fen(张如芬); MA,Chun-Lin(马春林); TAO,Xu-Quan(陶绪全)

    2001-01-01

    Ten triphenylgermaanium heteroaromatic carboxylates Ph3GeO2CR ( where R = 2-furanyl, 2-furanvinyl, 2-(5-tert-butyl) furonyl, 2-thiophenyl, 2-pyridinyl, 3-pyridinyl, 4-pyridinyl, 3-indolyl, 3-indolyhnethyl, 3-indolylpropyl) were synthesized by the reaction of sodium heteroaromatic carboxylates with the triphenylgermanium chloride. All compounds were characterized by elemental analysis, 1H NMR and MS spectra. The empounds were tested against two human tumour cell lines: MCF-7 and WiDr. The results showed that they had high activities. The crystal structure of triphenyler-mananium 2-furoate was determined by X-ray single crystal diffration. The crystal belongs to monoclinic with space grop P 21/c, a=1.1945(4), t=0.9934(3), c=1.6284(5)nm, β=91.59(5), Z=4. In this crystal, the structure consists of discrete molecule containing four-cnordinate germanimm atom in a distored tetrahedron.

  13. Change in crystal structure and strength of Sen dust alloys under the influence of corona discharge

    International Nuclear Information System (INIS)

    The influence of corona discharge treatment on crystal structure and strength of Sen dust alloy (Fe - 9.4 % Si - 5.2 % Al) is investigated. Using X-ray diffraction analysis and nuclear gamma-resonance spectroscopy it is shown that the treatment in corona discharge induces the redistribution of atoms and vacancies between a surface layer and a bulk portion of crystals as well as between a crystal sublattices. The corona discharge treatment is found to promote an increase of strength properties, electromagnetic parameters and cracking resistance of the alloy

  14. Refined crystal structure of cubic skeletov zinc borate Zn4O[B6O12

    International Nuclear Information System (INIS)

    Cubic crystals of the Zn4O[B6O12] composition obtained from the ZnO-B2O3-Li2O(Na2O,K2O)-H2O system with the NnO addition are studied in the temperature range of 250-450 deg C and at the pressure of 1000 atm. It is established that stable crystallization zones are characteristic for the above compound. The crystals are colourless and possess luminescent properties. Interplane distances, cubic lattice parameters and interatomic distances in the Zn4O[B6O12] structure are determined

  15. Study of BCC and FCC crystal atomic structure under instant plastic deformation

    International Nuclear Information System (INIS)

    Evolution of atomic structure of BCC and FCC crystals under conditions of pulsed external loads and great plastic deformations on the basis of computerized experiments is studied. Deformation of crystals was carried out stage-by-stage up to 32%. The results of computerized experiments showed that by instantaneous external loads plastic deformation, depending on its stage, may proceed either on the account of partial dislocations motion, or on account of twinning , or by means of atomic planes turn and shift. Regularities of the system potential energy turn angle of atomic planes change in dependence on the value of the crystal plastic deformation are determined

  16. A silicon photonic quasi-crystal structure obtained by interference lithography

    Science.gov (United States)

    Lis, S.; Zakrzewski, A.; Gryglewicz, J.; Oleszkiewicz, W.; Patela, S.

    2012-06-01

    Photonic quasi-crystal structures have been prepared and investigated. Symmetrical patterns were fabricated by interference lithography in negative tone photoresist and transferred to silicon by reactive ion etching. Theoretical influences of pattern detail (radius of hole) on the photonic band gap have been studied. Three types of 2D photonic quasi-crystals have been prepared: 8-fold, 10-fold and 12-fold pattern. Finally, finite-difference time-domain method was used for theoretically prediction of transmission spectrum for fabricated 12-fold quasi-crystal.

  17. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    Science.gov (United States)

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  18. Structural Evolution of Colloidal Crystal Films in the Process of Melting Revealed by Bragg Peak Analysis

    OpenAIRE

    Sulyanova, Elena; Shabalin, Anatoly; Yefanov, Oleksandr; Zaluzhnyy, Ivan; Besedin, Ilya; Sprung, Michael; Petukhov, Andrei; Vartaniants, Ivan; Zozulya, Alexey; Meijer, Janne-Mieke; Dzhigaev, Dmitry; Gorobtsov, Oleg; Kurta, Ruslan; Lazarev, Sergey; Lorenz, Ulf

    2015-01-01

    In situ X-ray diffraction studies of structural evolution of colloidal crystal films formed by polystyrene spherical particles upon incremental heating are reported. The Bragg peak parameters, such as peak position, integrated intensity, and radial and azimuthal widths were analyzed as a function of temperature. A quantitative study of colloidal crystal lattice distortions and mosaic spread as a function of temperature was carried out using Williamson–Hall plots based on mosaic block model. T...

  19. Band structure and Bloch states in birefringent 1D magnetophotonic crystals: An analytical approach

    CERN Document Server

    Lévy, M; Levy, Miguel; Jalali, Amir A

    2007-01-01

    An analytical formulation for the band structure and Bloch modes in elliptically birefringent magnetophotonic crystals is presented. The model incorporates both the effects of gyrotropy and linear birefringence generally present in magneto-optic thin film devices. Full analytical expressions are obtained for the dispersion relation and Bloch modes in a layered stack photonic crystal and their properties are analyzed. It is shown that other models recently discussed in the literature are contained as special limiting cases of the formulation presented herein.

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

    Indian Academy of Sciences (India)

    A Duarte Moller

    2014-10-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  2. Molecular and crystal structure of liquid crystalline p-octyloxyphenyl p′-pentyloxybenzoate

    International Nuclear Information System (INIS)

    The crystal and molecular structure of p-octyloxyphenyl p′-pentyloxybenzoate C5H11-O-C6H4-C(O)-O-C6H4-O-C8H17, which forms a nematic mesophase upon melting, was determined by X-ray diffraction. There is one system of weak directional intermolecular C-H…π interactions responsible for the formation of the nematic phase in these crystals.

  3. Rheological study of structural transitions in triblock copolymers in a liquid crystal solvent

    OpenAIRE

    Kempe, Michael D.; Verduzco, Rafael; Scruggs, Neal R.; Kornfield, Julia A.

    2006-01-01

    Rheological properties of triblock copolymers dissolved in a nematic liquid crystal (LC) solvent demonstrate that their microphase separated structure is heavily influenced by changes in LC order. Nematic gels were created by swelling a well-defined, high molecular weight ABA block copolymer with the small-molecule nematic LC solvent 4-pentyl-4-cyanobiphenyl (5CB). The B midblock is a side-group liquid crystal polymer (SGLCP) designed to be soluble in 5CB and the A endblocks are polystyrene, ...

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

    OpenAIRE

    Piero Morales; Jan Lagerwall; Paolo Vacca; Sabine Laschat; Giusy Scalia

    2010-01-01

    Thin films of the discotic liquid crystal hexapentyloxytriphenylene (HAT5), prepared from solution via casting or spin-coating, were investigated by atomic force microscopy and polarizing optical microscopy, revealing large-scale ordered structures substantially different from those typically observed in standard samples of the same material. Thin and very long fibrils of planar-aligned liquid crystal were found, possibly formed as a result of an intermediate lyotropic nematic state arising d...

  5. Crystal structures of Lymnaea stagnalis AChBP in complex with neonicotinoid insecticides imidacloprid and clothianidin

    OpenAIRE

    Ihara, Makoto; Okajima, Toshihide; Yamashita, Atsuko; Oda, Takuma; Hirata, Koichi; Nishiwaki, Hisashi; Morimoto, Takako; Akamatsu, Miki; Ashikawa, Yuji; Kuroda, Shun’ichi; Mega, Ryosuke; Kuramitsu, Seiki; Sattelle, David B; Matsuda, Kazuhiko

    2008-01-01

    Neonicotinoid insecticides, which act on nicotinic acetylcholine receptors (nAChRs) in a variety of ways, have extremely low mammalian toxicity, yet the molecular basis of such actions is poorly understood. To elucidate the molecular basis for nAChR–neonicotinoid interactions, a surrogate protein, acetylcholine binding protein from Lymnaea stagnalis (Ls-AChBP) was crystallized in complex with neonicotinoid insecticides imidacloprid (IMI) or clothianidin (CTD). The crystal structures suggested...

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

    OpenAIRE

    Cooper, R; others

    2016-01-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecu...

  7. Crystal structures of the solvates of diethylaminogossypol with ethyl acetate and pyridine

    Science.gov (United States)

    The crystal structures of diethylaminogossypol with ethyl acetate (DEAG-EA) and pyridine (DEAG-P) were studied by room-temperature X-ray diffraction. The host-to-guest molecule ratio in these complexes is 2:1 for DEAG-EA and 2:5 for DEAG-P. The crystal and cell parameters for DEAG-EA are C34H40N2O6...

  8. A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction

    OpenAIRE

    Boudes, Marion; Garriga, Damià; Fryga, Andrew; Caradoc-Davies, Tom; Coulibaly, Fasséli

    2016-01-01

    While structure determination from micrometre-sized crystals used to represent a challenge, serial X-ray crystallography on microfocus beamlines at synchrotron and free-electron laser facilities greatly facilitates this process today for microcrystals and nanocrystals. In addition to typical microcrystals of purified recombinant protein, these advances have enabled the analysis of microcrystals produced inside living cells. Here, a pipeline where crystals are grown in insect cells, sorted by ...

  9. NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

    CERN Document Server

    Ladik, János

    1975-01-01

    The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

  10. Isolation and extraction of lucidin primeveroside from Rubia tinctorum L. and crystal structure elucidation.

    Science.gov (United States)

    Henderson, Robert L; Rayner, Christopher M; Blackburn, Richard S

    2013-11-01

    Madder (Rubia tinctorum L.) has been used as a dye for over 2000 years with alizarin and purpurin the major natural dyes analysed from extractions undertaken. The use of ethanol as the solvent in the extraction process produced an extract that yielded four anthraquinone compounds lucidin primeveroside, ruberythric acid, alizarin and lucidin-ω-ethyl ether. Gravitational separation of the extract was used to record the first crystal structure of lucidin primeveroside, which is also the first ever known crystal structure of a glycoside containing anthraquinone moiety. The crystal structure along with (1)H and (13)C NMR helped elucidate and confirm the structure of this overlooked natural dye which has been shown to be a major compound in R. tinctorum L. PMID:23891215

  11. Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus

    OpenAIRE

    Shin, Dong Hae; Yokota, Hisao; Kim, Rosalind; Kim, Sung-Hou

    2002-01-01

    The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined by using x-ray crystallography. The protein belongs to the domain of unknown function DUF28 in the Pfam and PALI databases for which there was no structural information available until now. A structural homology search with the DALI algorithm indicates that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protei...

  12. Crystal structure and magnetic properties of Ce{sub 3}CuSnSe{sub 7}

    Energy Technology Data Exchange (ETDEWEB)

    Gulay, L.D. [Department of General and Inorganic Chemistry, Volyn State University, Voli Ave 13, 43009 Lutsk (Ukraine); Kaczorowski, D. [Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 WrocIaw (Poland)]. E-mail: D.Kaczorowski@int.pan.wroc.pl; Pietraszko, A. [Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 WrocIaw (Poland)

    2005-11-10

    The crystal structure of a quaternary compound Ce{sub 3}CuSnSe{sub 7} was determined by means of X-ray single crystal diffraction: La{sub 3}CuSiS{sub 7} structure type, space group P6{sub 3}, Pearson symbol hP24, a=1.0637(1)nm, c=0.6254(1)nm, R1=0.0297, wR2=0.0368. Magnetic studies revealed the presence of magnetic moments localized on Ce{sup 3+} ions that order at T{sub N}=5K with a complex antiferromagnetic-like spin structure.

  13. Research on the large band gaps in multilayer radial phononic crystal structure

    Science.gov (United States)

    Gao, Nansha; Wu, Jiu Hui; Guan, Dong

    2016-04-01

    In this paper, we study the band gaps (BGs) of new proposed radial phononic crystal (RPC) structure composed of multilayer sections. The band structure, transmission spectra and eigenmode displacement fields of the multilayer RPC are calculated by using finite element method (FEM). Due to the vibration coupling effects between thin circular plate and intermediate mass, the RPC structure can exhibit large BGs, which can be effectively shifted by changing the different geometry values. This study shows that multilayer RPC can unfold larger and lower BGs than traditional phononic crystals (PCs) and RPC can be composed of single material.

  14. Crystal structure of 3-(2,5-dimethoxyphenylpropionic acid

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2015-05-01

    Full Text Available In the crystal of the title compound, C11H14O4, the aromatic ring is almost coplanar with the 2-position methoxy group with which it subtends a dihedral of 0.54 (2°, while the 5-position methoxy group makes a corresponding dihedral angle of just 5.30 (2°. The angle between the mean planes of the aromatic ring and the propionic acid group is 78.56 (2°. The fully extended propionic side chain is in a trans configuration with a C—C—C—C torsion angle of −172.25 (7°. In the crystal, hydrogen bonding is limited to dimer formation via R22(8 rings. The hydrogen-bonded dimers are stacked along the b axis. The average planes of the two benzene rings in a dimer are parallel to each other, but at an offset of 4.31 (2 Å. Within neighbouring dimers along the [101] direction, the average molecular benzene planes are almost perpendicular to each other, with a dihedral angle of 85.33 (2°.

  15. Crystal structure of β-d,l-psicose

    Directory of Open Access Journals (Sweden)

    Tomohiko Ishii

    2015-05-01

    Full Text Available The title compound, C6H12O6, a C-3 position epimer of fructose, was crystallized from an aqueous solution of equimolar mixture of d- and l-psicose (1,3,4,5,6-pentahydroxyhexan-2-one, ribo-2-hexulose, allulose, and it was confirmed that d-psicose (or l-psicose formed β-pyranose with a 2C5 (or 5C2 conformation. In the crystal, an O—H...O hydrogen bond between the hydroxy groups at the C-3 and C-2 positions connects homochiral molecules into a column along the b axis. The columns are linked by other O—H...O hydrogen bonds between d- and l-psicose molecules, forming a three-dimensional network. An intramolecular O—H...O hydrogen bond is also observed. The cell volume of racemic β-d,l-psicose [763.21 (6 Å3] is almost the same as that of chiral β-d-psicose [753.06 Å3].

  16. Single crystal growth, structural characterization, thermal and optical properties of a novel organometallic nonlinear optical crystal: MnHg(SCN) 4(C 2H 5NO) 2

    Science.gov (United States)

    Wang, X. Q.; Cheng, X. F.; Zhang, S. J.; Xu, D.; Zhang, G. H.; Sun, Z. H.; Yu, F. P.; Liu, X. J.; Liu, W. L.; Chen, C. L.

    2010-02-01

    A novel potentially useful organometallic nonlinear optical crystal, manganese mercury thiocyanate-bis(N-methylformamide), MnHg(SCN) 4(C 2H 5NO) 2 (MMTN) has been prepared, and large highly-optical quality single crystals with dimensions up to 29×28×14 mm 3 have been grown. The structural characterization, thermal and optical properties of the grown crystals are investigated. The growth morphology was obtained by indexing the X-ray powder diffraction data and compared with that deducing from the single crystal structure data using the Bravais-Friedel-Donnay-Harker model. The thermal analysis reveals that MMTN crystal possesses good physicochemical stability. The specific heat of the crystal is 635.1 J mol -1 K -1 at 300 K. The thermal expansion coefficient along the a, b, and c axis is α1=6.18×10 -5 K -1, α2=3.91×10 -5 K -1 and α3=9.53×10 -6 K -1, respectively. The laser damage threshold of MMTN crystal is about 225.7 MW/cm 2 with pulse width of 18 ns at 1064 nm. The powder second harmonic efficiency of the crystal is about 1.1 pm/V and the UV transparency cutoff is 354 nm, which are interpreted on the basis of the crystal structure with the Molecular Orbital theory using a GAUSSIAN03 program.

  17. METHODS OF RECEIVING OF FINE-GRAINED STRUCTURE OF CASTINGS AT CRYSTALLIZATION

    Directory of Open Access Journals (Sweden)

    N. K. Tolochko

    2012-01-01

    Full Text Available The article deals with methods for fine-grained structure of ingots during crystallization depending on the used foundry technologies. It is shown that by using modern scientific and technological advances may improve the traditional and the development of new casting processes, providing production of cast parts with over fine-grained structure and enhanced properties.

  18. Experimental demonstration of non-reciprocal transmission in a nonlinear photonic-crystal Fano structure

    DEFF Research Database (Denmark)

    Yu, Yi; Chen, Yaohui; Hu, Hao;

    2015-01-01

    We suggest and experimentally demonstrate a photonic-crystal structure with more than 30 dB difference between forward and backward transmission levels. The non-reciprocity relies on the combination of ultrafast carrier nonlinearities and spatial symmetry breaking in a Fano structure employing...

  19. Crystal-Structure Contribution to the Solid Solubility in Transition Metal Alloys

    DEFF Research Database (Denmark)

    Ruban, Andrei; Skriver, Hans Lomholt; Nørskov, Jens Kehlet

    1998-01-01

    The solution energies of 4d metals in other 4d metals as well as the bcc-hcp structural energy differences in random 4d alloys are calculated by density functional theory. It is shown that the crystal structure of the host plays a crucial role in the solid solubility. A local virtual bond...

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

    Science.gov (United States)

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

    2016-03-21

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

  1. Diode-pumped garnet crystal waveguide structures fabricated by pulsed laser deposition

    OpenAIRE

    May-Smith, T.C.; Wang, J.; Mackenzie, J.I.; Shepherd, D.P.; EASON, R. W.

    2006-01-01

    We report progress with diode-pumping of garnet crystal waveguide structures fabricated by PLD. Lasing has been achieved in a single-layer Nd:GGG film, and a four-layer structure with a Nd:GSGG core is currently undergoing laser trials.

  2. The crystal structure of human dopamine  β-hydroxylase at 2.9 Å resolution

    DEFF Research Database (Denmark)

    Vendelboe, Trine Vammen; Harris, Pernille; Zhao, Y.;

    2016-01-01

    , Alzheimer’s disease, attention deficit hyperactivity disorder, and cocaine dependence. We report the crystal structure of human dopamine β-hydroxylase, which is the enzyme converting dopamine to norepinephrine. The structure of the DOMON (dopamine β-monooxygenase N-terminal) domain, also found in >1600...

  3. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Kristensen, Ole

    2012-01-01

    The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a ß-sheet and three a-helices forming...

  4. Development of photonic crystal structures for on-board optical communication

    NARCIS (Netherlands)

    Khan, M.U.; Justice, J.; Boersma, A.; Mourad, M.; Ee, R.J. van; Blaaderen, A. van; Wijnhoven, J.; Corbett, B.

    2014-01-01

    We present designs for sharp bends in polymer waveguides using colloidal photonic crystal (PhC) structures. Both silica (SiO2) sphere based colloidal PhC and core-shell colloidal PhC structures having a titania (TiO 2) core inside silica (SiO2) shells are simulated. The simulation results show that

  5. Fano resonance control in a photonic crystal structure and its application to ultrafast switching

    DEFF Research Database (Denmark)

    Yu, Yi; Heuck, Mikkel; Hu, Hao;

    2014-01-01

    We experimentally demonstrate a photonic crystal structure that allows easy and robust control of the Fano spectrum. Its operation relies on controlling the amplitude of light propagating along one of the light paths in the structure from which the Fano resonance is obtained. Short-pulse dynamic...

  6. Tuning the Colloidal Crystal Structure of Magnetic Particles by External Field

    NARCIS (Netherlands)

    Pal, Antara; Malik, Vikash; He, Le; Erne, Ben H.; Yin, Yadong; Kegel, Willem K.; Petukhov, A. V.

    2015-01-01

    Manipulation of the self-assembly of magnetic colloidal particles by an externally applied magnetic field paves a way toward developing novel stimuli responsive photonic structures. Using microradian X-ray scattering technique we have investigated the different crystal structures exhibited by self-a

  7. Crystal structure and elementary electronic properties of Bi-stabilized α-In2Se3

    International Nuclear Information System (INIS)

    Highlights: • The introduction of Bi stabilizes α-In2Se3 and facilitates the crystal growth. • Optical measurements show an indirect band gap. • Transport measurements show semiconducting temperature dependence. - Abstract: The introduction of Bi as a substitution for In at ∼12% in In2Se3 stabilizes the α-polymorph and facilitates the crystal growth by the modified Bridgeman method. The crystal structure (R−3m, Z = 3, a = 3.9978(8) Å, c = 28.276(6) Å) and composition, (In0.88Bi0.12)2Se3, of the crystals were determined by single crystal X-ray diffraction. The structure, of the tetradymite type, displays positional disorder within the middle Se layer. Optical measurements indicate that (In0.88Bi0.12)2Se3 has an indirect band gap of about 1.19 eV, shown by electronic structure calculations to be from valence band states near the Γ point to conduction band states at the L point. Resistivity and Hall effect measurements on Sn-doped crystals of composition (In0.88Bi0.115Sn0.005)2Se3 show it to have a relatively high semiconducting resistivity, about 6 × 104 Ω cm at 300 K, with an n-type carrier concentration varying from 1012/cm3 at 300 K to 1015/cm3 at 400 K

  8. Crystal orientation dependence of femtosecond laser-induced periodic surface structure on (100) silicon.

    Science.gov (United States)

    Jiang, Lan; Han, Weina; Li, Xiaowei; Wang, Qingsong; Meng, Fantong; Lu, Yongfeng

    2014-06-01

    It is widely believed that laser-induced periodic surface structures (LIPSS) are independent of material crystal structures. This Letter reports an abnormal phenomenon of strong dependence of the anisotropic formation of periodic ripples on crystal orientation, when Si (100) is processed by a linearly polarized femtosecond laser (800 nm, 50 fs, 1 kHz). LIPSS formation sensitivity with a π/2 modulation is found along different crystal orientations with a quasi-cosinusoid function when the angle between the crystal orientation and polarization direction is changed from 0° to 180°. Our experiments indicate that it is much easier (or more difficult) to form ripple structures when the polarization direction is aligned with the lattice axis [011]/[011¯] (or [001]). The modulated nonlinear ionization rate along different crystal orientations, which arises from the direction dependence of the effective mass of the electron is proposed to interpret the unexpected anisotropic LIPSS formation phenomenon. Also, we demonstrate that the abnormal phenomenon can be applied to control the continuity of scanned ripple lines along different crystal orientations.

  9. High-pressure studies on molecular crystals-relations between structure and high-pressure behavior

    Energy Technology Data Exchange (ETDEWEB)

    Orgzall, Ingo [Institut fuer Duennschichttechnologie und Mikrosensorik e.V., Kantstrasse 55, D-14513 Teltow (Germany); Emmerling, Franziska [Bundesanstalt fuer Materialforschung und -pruefung, Richard-Willstaetter-Strasse 11, D-12489 Berlin (Germany); Schulz, Burkhard [Institut fuer Physik, Universitaet Potsdam, Am Neuen Palais 10, D-14469 Potsdam (Germany); Franco, Olga [Heinrich-Heine-Universitaet Duesseldorf, Institut fuer Physikalische Chemie II, Universitaetsstrasse 1, Gebaeude 26.42.02, D-40225 Duesseldorf (Germany)], E-mail: orgzall@uni-potsdam.de, E-mail: franziska.emmerling@bam.de, E-mail: buschu@uni-potsdam.de, E-mail: olga.franco@uni-duesseldorf.de

    2008-07-23

    This paper summarizes attempts to understand structure-property relationships for a large class of aromatic diphenyl-1,3,4-oxadiazole molecules. Starting from the investigation of the crystal structure several common packing motifs as well as characteristic differences are derived. Many different molecules show a rather planar conformation in the solid state. A stronger intermolecular twist is only observed for compounds with substituents occupying the ortho-positions of the phenyl rings. Most crystal structures are characterized by the formation of stacks leading to intense {pi}-{pi} acceptor-donor interactions between oxadiazole and phenyl rings. High-pressure investigations result in a soft compression behavior typical for organic molecular crystals. The bulk behavior may be described by the Murnaghan equation of state with similar coefficients (bulk modulus and its pressure derivative) for nearly all investigated compounds but also for related substances. The compression shows a strong anisotropy resulting from the specific features and packing motifs of the crystal structure. This is clearly indicated by a corresponding strain analysis. Additionally to the crystal structure the Raman spectrum was also investigated under increasing pressure. The different pressure behavior of external and internal modes reflects the difference between intra- and intermolecular interactions.

  10. High-pressure studies on molecular crystals-relations between structure and high-pressure behavior

    International Nuclear Information System (INIS)

    This paper summarizes attempts to understand structure-property relationships for a large class of aromatic diphenyl-1,3,4-oxadiazole molecules. Starting from the investigation of the crystal structure several common packing motifs as well as characteristic differences are derived. Many different molecules show a rather planar conformation in the solid state. A stronger intermolecular twist is only observed for compounds with substituents occupying the ortho-positions of the phenyl rings. Most crystal structures are characterized by the formation of stacks leading to intense π-π acceptor-donor interactions between oxadiazole and phenyl rings. High-pressure investigations result in a soft compression behavior typical for organic molecular crystals. The bulk behavior may be described by the Murnaghan equation of state with similar coefficients (bulk modulus and its pressure derivative) for nearly all investigated compounds but also for related substances. The compression shows a strong anisotropy resulting from the specific features and packing motifs of the crystal structure. This is clearly indicated by a corresponding strain analysis. Additionally to the crystal structure the Raman spectrum was also investigated under increasing pressure. The different pressure behavior of external and internal modes reflects the difference between intra- and intermolecular interactions

  11. Membrane Protein Crystallization in Lipidic Mesophases. Hosting Lipid Effects on the Crystallization and Structure of a Transmembrane Peptide

    Energy Technology Data Exchange (ETDEWEB)

    Hfer, Nicole; Aragao, David; Lyons, Joseph A.; Caffrey, Martin (Trinity)

    2011-09-28

    Gramicidin is an apolar pentadecapeptide antibiotic consisting of alternating d- and l-amino acids. It functions, in part, by creating pores in membranes of susceptible cells rendering them leaky to monovalent cations. The peptide should be able to traverse the host membrane either as a double-stranded, intertwined double helix (DSDH) or as a head-to-head single-stranded helix (HHSH). Current structure models are based on macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR). However, the HHSH form has only been observed by NMR. The shape and size of the different gramicidin conformations differ. We speculated therefore that reconstituting it into a lipidic mesophase with bilayers of different microstructures would preferentially stabilize one form over the other. By using such mesophases for in meso crystallogenesis, the expectation was that at least one would generate crystals of gramicidin in the HHSH form for structure determination by MX. This was tested using commercial and in-house synthesized lipids that support in meso crystallogenesis. Lipid acyl chain lengths were varied from 14 to 18 carbons to provide mesophases with a range of bilayer thicknesses. Unexpectedly, all lipids produced high-quality, structure-grade crystals with gramicidin only in the DSDH conformation.

  12. Crystal structure of a bioactive sesquiterpene isolated from Artemisia reticulata

    Directory of Open Access Journals (Sweden)

    A. K. Bauri

    2016-04-01

    Full Text Available The title compound, C15H24O2 {systematic name: 1-[6-hydroxy-7-(propan-2-yl-4-methylidene-2,3,3a,4,5,6,7,7a-octahydro-1H-inden-1-yl]ethanone} was isolated from A. reticulata by column chromatography over silica gel by gradient solvent elution. The molecule comprises a bicyclo[4.3.0]nonane ring bearing acetoxy, hydroxy and isopropyl substituents, and an exocyclic double bond on the cyclohexane ring. In the bicyclic skeleton, the cyclohexane ring adopts a chair conformation ring and the cyclopentane ring is in an envelope conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains along [010]. These chains are cross-linked by C—H...O hydrogen bonds.

  13. Crystal structure of the product of an anomalous Robinson annulation

    Energy Technology Data Exchange (ETDEWEB)

    Carter, B.; Laing, M.; Sommerville, P. (Natal Univ., Durban (South Africa). Dept. of Chemistry)

    1984-01-01

    Robinson annulation of 2-methylcyclohexane-1,3-dione with methyl 4-oxohex-5-enoate in the presence of (-)-phenyl-alanine gave a highly crystalline, optically active, product. This was identified, with the aid of X-ray crystallography, as (-)-2,6-dioxo-6..beta..-hydroxy-1..beta..-methylbicyclo(3.3.1)nonyl-6-3'-propionic acid lactone, formed by lactonization of the expected intermediate aldol. The crystals were orthorhombic, space group P2/sub 1/2/sub 1/2/sub 1/, a = 7,702(4), b = 11,190(5), c = 13,593(7), Z = 4. The two six-membered rings are distorted chairs.

  14. 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.

  15. 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.

  16. 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.

  17. Crystal structure of 2-pentyl­oxybenzamide

    OpenAIRE

    Bugenhagen, Bernhard; Al Jasem, Yosef; Thiemann, Thies

    2014-01-01

    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 ot...

  18. Crystal structure of 4-benzamido-2-hydroxybenzoic acid

    Directory of Open Access Journals (Sweden)

    Muhammad Shahid

    2015-06-01

    Full Text Available In the title compound, C14H11NO4, the dihedral angle between the mean planes of the aromatic rings is 3.96 (12° and an intramolecular O—H...O hydrogen bond closes an S(6 ring. A short intramolecular C—H...O contact is also seen. In the crystal, carboxylic acid inversion dimers linked by pairs of O—H...O hydrogen bonds generate R22(8 loops. Conversely, the N—H group does not form a hydrogen bond. Aromatic π–π interactions exist at a centroid–centroid distance of 3.8423 (15 Å between the benzene rings. An extremely weak C—H...π interaction also is present.

  19. Crystal structure of 4-(dimethylaminopyridinium 4-aminobenzoate dihydrate

    Directory of Open Access Journals (Sweden)

    A. Thirunavukkarasu

    2015-01-01

    Full Text Available In the title hydrated molecular salt, C7H11N2+·C7H6NO2−·2H2O, the cation is protonated at the pyridine N atom and the dihedral angle between the benzene ring and the CO2− group in the anion is 8.5 (2°. In the crystal, the cation forms an N—H...O hydrogen bond to the anion and the anion forms two N—H...O hydrogen bonds to adjacent water molecules. Both water molecules form two O—H...O hydrogen bonds to carboxylate O atoms. In combination, these hydrogen bonds generate a three-dimensional network and two weak C—H...π interactions are also observed.

  20. Crystal structure of 4-[(E-(2-carbamothioylhydrazinylidenemethyl]benzoic acid

    Directory of Open Access Journals (Sweden)

    Muhammad Nawaz Tahir

    2015-10-01

    Full Text Available The title compound, C9H9N3O2S, is close to planar with an r.m.s. deviation of 0.032 Å. An intramolecular N—H...N hydrogen bond closes an S(5 ring. In the crystal, molecules are connected into inversion dimers of the R22(8 type by pairs of O—H...O interactions. The dimers are further connected by pairs of N—H...S interactions, which also complete R22(8 ring motifs. The chains of dimers are cross-linked by N—H...O bonds and hence R42(28 rings are completed. Taken together, these interactions lead to infinite sheets propagating in the (122 plane.