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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. Crystal structure and prediction.

    Science.gov (United States)

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

    2015-04-01

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

  3. 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.

  4. 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...

  5. 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.

  6. Frustrated polymer crystal structures

    Science.gov (United States)

    Lotz, B.; Strasbourg, 67083

    1997-03-01

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

  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. 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...

  10. THE CRYSTAL STRUCTURE OF DIPHENYLTELLURIUM DIBROMIDE,

    Science.gov (United States)

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

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

    Science.gov (United States)

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

  12. Demonstration of Crystal Structure.

    Science.gov (United States)

    Neville, Joseph P.

    1985-01-01

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

  13. 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

  14. Artemin, a diapause-specific chaperone, contributes to the stress tolerance of Artemia franciscana cysts and influences their release from females.

    Science.gov (United States)

    King, Allison M; Toxopeus, Jantina; MacRae, Thomas H

    2014-05-15

    Females of the crustacean Artemia franciscana produce either motile nauplii or gastrula stage embryos enclosed in a shell impermeable to nonvolatile compounds and known as cysts. The encysted embryos enter diapause, a state of greatly reduced metabolism and profound stress tolerance. Artemin, a diapause-specific ferritin homolog in cysts has molecular chaperone activity in vitro. Artemin represents 7.2% of soluble protein in cysts, approximately equal to the amount of p26, a small heat shock protein. However, there is almost twice as much artemin mRNA in cysts as compared with p26 mRNA, suggesting that artemin mRNA is translated less efficiently. RNA interference employing the injection of artemin double-stranded RNA into the egg sacs of A. franciscana females substantially reduced artemin mRNA and protein in cysts. Decreasing artemin diminished desiccation and freezing tolerance of cysts, demonstrating a role for this protein in stress resistance. Knockdown of artemin increased the time required for complete discharge of a brood of cysts carried within a female from a few hours up to 4 days, an effect weakened in successive broods. Artemin, an abundant molecular chaperone, contributes to stress tolerance of A. franciscana cysts while influencing their development and/or exit from females.

  15. Crystal structure of cafenstrole

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

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

  16. Crystal structure of nuarimol

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

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

  17. Crystal structure refinement with SHELXL.

    Science.gov (United States)

    Sheldrick, George M

    2015-01-01

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

  18. Crystal structure refinement with SHELXL

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-01

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

  19. 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.

  20. Recombinant expression, purification and dimerization of the neurotrophic growth factor Artemin for in vitro and in vivo use.

    Science.gov (United States)

    Bruinzeel, Wouter; Masure, Stefan

    2012-01-01

    Artemin (ARTN) is a neurotrophic growth factor of the GDNF ligand family that signals through the specific GFRα-3 coreceptor/cRet tyrosine kinase-mediated signaling cascade. Its expression and signaling action in adults are restricted to nociceptive sensory neurons in the dorsal root ganglia. Consequently, Artemin supports survival and growth of sensory neurons and has been studied as a possible treatment for neuropathic pain paradigms. In this paper, we describe the development of an efficient method for the recombinant bacterial production of large quantities of highly pure, biologically active ARTN for in vitro and in vivo studies. Using Escherichia coli expression of an NH(2)-terminal SUMO-Artemin fusion protein and subsequent refolding from inclusion bodies followed by cleavage of the SUMO fusion part, mature Artemin with a native NH(2)-terminal amino acid sequence was obtained at high purity (>99%). Experiments using the reducing agent dithiothreitol (DTT) demonstrated that the intermolecular disulphide bridge in the cysteine knot is dispensable for dimerization of stable ARTN monomers. Our production method could facilitate in vitro and in vivo experimentation for the possible development of Artemin as a therapeutic agent for neuropathic pain.

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

    Science.gov (United States)

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

  2. Pattern information extraction from crystal structures

    OpenAIRE

    Okuyan, Erhan

    2005-01-01

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

  3. 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.

  4. Treatment of transected peripheral nerves with artemin improved motor neuron regeneration, but did not reduce nerve injury-induced pain behaviour.

    Science.gov (United States)

    Widenfalk, Johan; Wu, Weiping; Hao, Jingxia; Person, Jonas K E; Wiesenfeldt-Hallin, Zsuzsanna; Risling, Mårten

    2009-01-01

    Incomplete recovery of function and neuropathic pain are common problems after peripheral nerve injury. To develop new treatment strategies for peripheral nerve injuries we investigated whether the neurotrophic factor artemin could improve outcome after sciatic nerve injuries in rats. Artemin is a member of the glial cell line-derived neurotrophic factor (GDNF) family and exerts neuroprotective effects on sensory neurons as well as influencing behavioural thermal sensitivity. We additionally evaluated if fibrin sealant, which is sometimes used as a nerve glue, had any effects on neuropathic pain-related behaviour. After the sciatic nerve had been transected, 30 animals were randomised to one of three groups: treatment with a fibrin sealant that contained artemin in conjunction with sutures; fibrin sealant with no artemin (sham) in conjunction with sutures; or sutures alone (n=10 in each group). Motor function, sensory function, and autotomy were evaluated from 1 to 12 weeks after injury. Retrograde flourogold tracing 12 weeks after injury showed that the addition of artemin increased the number of regenerating motor neurons. However, it did not improve their performance, as measured by the Sciatic Function Index, compared with sham or suture alone. Animals treated with artemin had a non-significant increase in motor nerve conduction velocity compared with sham. However, artemin did not reverse nerve injury-induced pain behaviour such as cold or heat hypersensitivity. Fibrin sealant in itself did not ameliorate motor performance, or regeneration of motor neurons, or give rise to nerve injury-induced pain behaviour. The results indicate that artemin is of value as a treatment for peripheral nerve injuries, although the effects were limited. As the artemin high-affinity receptor GFRalpha-3 is present in Schwann cells and not in motor neurons, the effect on motor neuron axon regeneration may result from an indirect effect through Schwann cells in the injured nerve.

  5. Crystal structure of fiber structured pentacene thin films

    OpenAIRE

    2007-01-01

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

  6. 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.

  7. 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.

  8. Predicting crystal structures of organic compounds.

    Science.gov (United States)

    Price, Sarah L

    2014-04-07

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

  9. 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.

  10. Crystal structure analysis of intermetallic compounds

    Science.gov (United States)

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

    1968-01-01

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

  11. THE CRYSTAL STRUCTURE OF ALPHA-DIMETHYLTELLURIUM DICHLORIDE,

    Science.gov (United States)

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

  12. 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. 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.

  14. Method of fabricating patterned crystal structures

    KAUST Repository

    Yu, Liyang

    2016-12-15

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

  15. Photonic-crystal fibre: Mapping the structure

    DEFF Research Database (Denmark)

    Markos, Christos

    2015-01-01

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

  16. Pattern information extraction from crystal structures

    Science.gov (United States)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

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

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

    Science.gov (United States)

    Skála, Roman; Císařová, Ivana

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

  18. Structures of cyano-biphenyl liquid crystals

    Science.gov (United States)

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

    1989-01-01

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

  19. 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...

  20. 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.

  1. 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.

  2. Crystal structure of 9-methacryloylanthracene

    Directory of Open Access Journals (Sweden)

    Aditya Agrahari

    2015-04-01

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

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

    Science.gov (United States)

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

    1994-01-01

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

  4. Crystal structure of putrescine aspartic acid complex

    OpenAIRE

    Ramaswamy, S.; Murthy, MRN

    1990-01-01

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

  5. Crystal structure of canagliflozin hemihydrate.

    Science.gov (United States)

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

    2016-05-01

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

  6. Crystal structure of canagliflozin hemihydrate

    Directory of Open Access Journals (Sweden)

    Kai-Hang Liu

    2016-05-01

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

  7. Crystal Structure of 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.

  8. 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.

  9. 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.

  10. Modular crystals as modulated structures

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  11. 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.

  12. 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...

  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. Determining crystal structures through crowdsourcing and coursework

    OpenAIRE

    2016-01-01

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

  15. 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.

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

    Science.gov (United States)

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

  17. 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.

  18. Synthesis and Crystal Structure of Dehydroandrographolide Dipolycyclophosphate

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

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

  19. Crystal structure of low-symmetry rondorfite

    Science.gov (United States)

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

    2008-03-01

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

  20. 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.

  1. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  2. 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.

  3. 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.

  4. Crystal Structures of New Ammonium 5-Aminotetrazolates

    Directory of Open Access Journals (Sweden)

    Martin Lampl

    2014-11-01

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

  5. 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.

  6. 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.

  7. Crystal Structure Refinement of Synthetic Pure Gyrolite

    Directory of Open Access Journals (Sweden)

    Arūnas Baltušnikas

    2015-03-01

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

  8. Lessons from crystal structures of kainate receptors.

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

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

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

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

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

    Science.gov (United States)

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

  12. Crystal structure of natural phaeosphaeride A

    Directory of Open Access Journals (Sweden)

    Victoria V. Abzianidze

    2015-08-01

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

  13. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2014-01-28

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

  15. 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.

  16. 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.

  17. 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.

  18. Crystal structure of a DNA catalyst.

    Science.gov (United States)

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

    2016-01-14

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

  19. Elasticity of some mantle crystal structures. II.

    Science.gov (United States)

    Wang, H.; Simmons, G.

    1973-01-01

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

  20. Crystal Structure of Marburg Virus VP24

    OpenAIRE

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

    2014-01-01

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

  1. Crystal structure of Marburg virus VP24.

    Science.gov (United States)

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

    2014-05-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  3. Crystal structure of (ferrocenylmethyldimethylammonium hydrogen oxalate

    Directory of Open Access Journals (Sweden)

    Mamadou Ndiaye

    2015-08-01

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

  4. Syntheses and Crystal Structures of Pyrazoline Derivants

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  5. 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.

  6. Crystal structure of yeast Sco1

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-05

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

  7. Temperature dependent spin structures in Hexaferrite crystal

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-01

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

  8. 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.

  9. 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.

  10. Crystal structure of human nicotinamide riboside kinase.

    Science.gov (United States)

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

    2007-08-01

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

  11. Crystal Structure of Human Nicotinamide Riboside Kinase

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-01

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

  12. Structural Transitions in Cholesteric Liquid Crystal Droplets

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-01

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

  13. Crystal structures of five 6-mercaptopurine derivatives

    Directory of Open Access Journals (Sweden)

    Lígia R. Gomes

    2016-03-01

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

  14. 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.

  15. 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.

  16. Extraction and Crystal Structure of Karounidiol

    Institute of Scientific and Technical Information of China (English)

    巢志茂; 王诚

    2003-01-01

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

  17. Crystal Structures of Respiratory Pathogen Neuraminidases

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  18. The crystal structure Escherichia coli Spy.

    Science.gov (United States)

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

    2010-11-01

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

  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. Affine structures and a tableau model for E_6 crystals

    CERN Document Server

    Jones, Brant

    2009-01-01

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

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

    Science.gov (United States)

    Marechal, Matthieu; Dijkstra, Marjolein

    2008-06-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  3. 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.

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

    Science.gov (United States)

    Hong, Y. S.; And Others

    1980-01-01

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

  5. 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.

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

    Science.gov (United States)

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

    2015-03-01

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

  7. 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...

  8. 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…

  9. 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.

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

    Science.gov (United States)

    Cady, Susan G.

    1997-01-01

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

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

    Science.gov (United States)

    Obata, Shigeaki; Goto, Hitoshi

    2015-02-01

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

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

    OpenAIRE

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

    2010-01-01

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

  13. PLANAR OPTICAL WAVEGUIDES WITH PHOTONIC CRYSTAL STRUCTURE

    DEFF Research Database (Denmark)

    2003-01-01

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

  14. 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.

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

    Science.gov (United States)

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

    2009-06-01

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

  16. SiBr4 - Prediction and Determination of Crystal Structures

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  17. 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.

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

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

    2017-02-09

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

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

    Science.gov (United States)

    Valle, Mario; Oganov, Artem R

    2010-09-01

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

  1. 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.

  2. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    OpenAIRE

    2013-01-01

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

  3. Crystal structure and characterization of pyrroloquinoline quinone disodium trihydrate

    Directory of Open Access Journals (Sweden)

    Ikemoto Kazuto

    2012-06-01

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

  4. Structure and Properties of Liquid Crystals

    CERN Document Server

    Blinov, Lev M

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ke-Qin Zhang

    2013-03-01

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

  6. 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.

  7. 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)

  8. Missing strings of residues in protein crystal structures.

    Science.gov (United States)

    Djinovic-Carugo, Kristina; Carugo, Oliviero

    2015-01-01

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

  9. 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.

  10. 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.

  11. 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.

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

    Science.gov (United States)

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

    2017-04-26

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

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

    Science.gov (United States)

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

    2017-04-01

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

  14. 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.

  15. 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.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Z. A. Rahima

    2015-09-01

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

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

    Science.gov (United States)

    Marx, Ailie; Adir, Noam

    2013-03-01

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

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

    DEFF Research Database (Denmark)

    Wolny, Janusz; Lebech, Bente

    1986-01-01

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

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

    Science.gov (United States)

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

    2016-01-18

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

  1. Chiral Liquid Crystals: Structures, Phases, Effects

    Directory of Open Access Journals (Sweden)

    Ingo Dierking

    2014-06-01

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

  2. 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.

  3. Structure of initial crystals formed during human amelogenesis

    Science.gov (United States)

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

    1992-02-01

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

  4. 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.

  5. The different conformations and crystal structures of dihydroergocristine

    Science.gov (United States)

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

    2016-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Alberto Cabrera

    2015-12-01

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

  7. 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.

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

    Science.gov (United States)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

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

  9. Protein dynamics derived from clusters of crystal structures.

    OpenAIRE

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

    1997-01-01

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

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

    Science.gov (United States)

    Jungblut, Swetlana; Dellago, Christoph

    2016-09-01

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

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

    Science.gov (United States)

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

    2011-11-21

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  13. Crystal structure of 2-aminopyridinium 6-chloronicotinate

    Directory of Open Access Journals (Sweden)

    N. Jeeva Jasmine

    2015-09-01

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

  14. 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.

  15. 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.

  16. 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-...

  17. 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.

  18. 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.

  19. 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....

  20. 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

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

    Science.gov (United States)

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

    2013-06-10

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

  2. 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.

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

    Science.gov (United States)

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

    2017-01-23

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

  4. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-15

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

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

    Science.gov (United States)

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

    2016-03-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2011-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Hasna Yassine

    2015-10-01

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

  10. Synthesis and Crystal Structure of Isosteviol Derivatives

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  11. CRYSTAL STRUCTURE 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.

  12. 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.

  13. STRUCTURE FORMATION OF COLLOIDS IN NEMATIC LIQUID CRYSTALS

    Directory of Open Access Journals (Sweden)

    B.I.Lev

    2003-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    周秋生; 李小斌; 彭志宏; 刘桂华

    2004-01-01

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

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

    Science.gov (United States)

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

    2007-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-03-15

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

  17. 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.

  18. 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....

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

    Directory of Open Access Journals (Sweden)

    Mohamed H Abd El-Razek

    2010-01-01

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

  20. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

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

    2012-01-01

    , such as body-centered cubic and face-centered cubic, can be suppressed by a proper choice of the potential depth and periodicity. Furthermore, by varying the harmonic trap parameters and/or the optical potential in time, controlled transitions between crystal structures can be obtained with close to unit...

  1. 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.

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

    Science.gov (United States)

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  3. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.

    NARCIS (Netherlands)

    Sprogoe, D.; Broek, van den L.A.M.; Mirza, O.; Kastrup, J.S.; Voragen, A.G.J.; Gajhede, M.; Skov, L.K.

    2004-01-01

    Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and a-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphoryla

  4. 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...

  5. 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....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-01

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

  7. Band structures in Sierpinski triangle fractal porous phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-01

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

  8. 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.

  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. Microprobe of structure of crystal/liquid interface boundary layers

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The molecular structures and its evolutive regularities within the boundary layers in the crystal growth of KDP and DKDP have been studied in real time by using holography and Raman microprobe. The experiments show that the molecular structure of mother solution within the boundary layers is distinctly different from that of the solutions alone. In this paper, the effects of cations within the boundary layers on the structure of solution are considered. Within the characteristic boundary layers, the effects of cations cause the changes in O-P-O bond angle, electronic density redistribution of the phosphate groups, and significant changes in the bond intensity, thus leading to the breaking of partial hydrogen bonds of the phosphate associations, the readjustment of geometry of anionic phosphate groups and desolvation, and the forming of the smectic ordering structure of the anions_cations. Finally, the crystallization unit of anion_cation should be formed at the proximate interface.

  11. Crystal structure and magnetization of a Co3B2O6 single crystal

    Science.gov (United States)

    Kazak, N. V.; Platunov, M. S.; Ivanova, N. B.; Knyazev, Yu. V.; Bezmaternykh, L. N.; Eremin, E. V.; Vasil'ev, A. D.; Bayukov, O. A.; Ovchinnikov, S. G.; Velikanov, D. A.; Zubavichus, Ya. V.

    2013-07-01

    The crystal structure and magnetic properties of Co3B2O6 single crystals are studied. Orthorhombic symmetry with space group Pnnm is detected at room temperature. The measurements of static magnetization and dynamic magnetic susceptibility reveal two magnetic anomalies at T 1 = 33 K and T 2 = 10 K and an easy-axis magnetic anisotropy. The effective magnetic moment indicates a high-spin state of the Co2+ ion. A spin-flop transition is found at low temperatures and H sf = 23 kOe. EXAFS spectra of the K-edge absorption of Co are recorded at various temperatures, the temperature-induced changes in the parameters of the local environment of cobalt are analyzed, and the effective Co-Co and Co-O distances are determined. The magnetic interactions in the crystal are analyzed in terms of an indirect coupling model.

  12. Crystal structures at high pressures and temperatures

    Science.gov (United States)

    Caldwell, Wendel Alexander

    2000-10-01

    The diamond anvil cell (DAC) is a unique instrument that can generate pressures equivalent to those inside planetary interiors (pressures on the order of 1 million atmospheres) under sustained conditions. When combined with a bright source of collimated x-rays, the DAC can be used to probe the structure of materials in-situ at ultra-high pressures. An understanding of the high-pressure structure of materials is important in determining what types of processes may take place in the Earth at great depths. Motivated by previous studies showing that xenon becomes metallic at pressures above ˜1 megabar (100 GPa), we examined the stable structures and reactivity of xenon at pressures approaching that of the core-mantle boundary in the Earth. Our findings indicate the transformation of xenon from face-centered cubic (fcc) to hexagonal close-packed (hcp) structures is kinetically hindered at room temperature, with the equilibrium fcc--hcp phase boundary at 21 (+/-3) gigapascals, a pressure lower than was previously thought. Additionally, we find no tendency on the part of xenon to form a metal alloy with iron or platinum to at least 100 to 150 gigapascals, making it unlikely that the Earth's core serves as a reservoir for primordial xenon. Measurements of the compressibility of natural (Mg.75,Fe .25)2SiO4 gamma-spinel at pressures of the Earth's transition zone yield a pressure derivative of the bulk modulus K0 ' = 6.3 (+/-0.3). As gamma-spinel is considered to be a dominant mineral phase of the transition-zone of the Earth's mantle (400--670 km depth), the relatively high value of K0' for gamma-spinel may help explain the rapid increase with depth of seismic velocities through the transition zone. The thermodynamics, mechanisms and kinetics of pressure-induced amorphization are not well understood. We report here new studies indicating little or no entropy difference between the crystalline and glassy states of Ca(OH) 2 (portlandite). Additional work on the pressure

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

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Z.A., E-mail: ze.tian@gmail.com [School of Physics and Electronics, Hunan University, Changsha 410082 (China); Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052 (Australia); Dong, K.J.; Yu, A.B. [Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052 (Australia)

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

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

    Science.gov (United States)

    Neumann, Marcus A

    2008-08-14

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

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Gao, Xiu-Gong; Maldonado, Ernesto; Perez-Montfort, Ruy; Garza-Ramos, Georgina; Tuena de Gomez-Puyou, Marietta; Gomez-Puyou, Armando; Rodriguez-Romero, Adela

    1999-08-01

    To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2- angstrom resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 angstrom from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.

  18. Modulation mechanism and disorder structure in hollandite-type crystals

    Energy Technology Data Exchange (ETDEWEB)

    Wu Xiaojing; Fujiki, Yoshiki; Horiuchi, Shigeo (National Inst. for Research in Inorganic Materials, Ibaraki (Japan)); Ishigame, Mareo (Research Inst. for Scientific Measurements, Tohoku Univ., Sendai (Japan))

    1991-07-01

    The structural modulation in some hollandite-type crystals is explained by a vacancy-displacive modulation model. In this model the large cations located in the tetragonal channels along the c axis deviate from the average position to form a modulation wave. Three types of disorder in the initial phase of the modulation wave have been introduced to interpret apparently different diffraction patterns in hollandite-type crystals. A mathematical analysis as well as optical diffraction give results similar to those experimentally observed. High-resolution transmission electron microscope images have been observed to confirm the discussion further. (orig.).

  19. Crystal structure of alpha poly-p-xylylene.

    Science.gov (United States)

    Kubo, S.; Wunderlich, B.

    1971-01-01

    A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

  20. 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.

  1. 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.

  2. 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.

  3. Crystal structure and density of helium to 232 kbar

    Science.gov (United States)

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

    1988-01-01

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

  4. 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.

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2015-07-15

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

  7. 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...

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

    Science.gov (United States)

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

    2016-11-01

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

  9. Crystal structure of hexagonal RE(CO{sub 3})OH

    Energy Technology Data Exchange (ETDEWEB)

    Michiba, Kiyonori; Tahara, Takeshi; Nakai, Izumi [Tokyo Univ. of Science, Shinjuku (Japan). Faculty of Science; Miyawaki, Ritsuro; Matsubara, Satoshi [National Museum of Nature and Science, Tokyo (Japan). Dept. of Geology and Paleontology

    2011-07-01

    Hexagonal rare earth carbonate hydroxides, RE(CO{sub 3})OH, where RE = La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, and Er, were hydrothermally synthesized from formic acid and hydroxide gels of rare earth elements. The crystals exhibited bicephalous hexagonal prisms with lengths of several tens of micrometers. The crystal structures of a series of hexagonal RE(CO{sub 3})OH were solved using the single crystal CCD-XRD intensity data sets. The space groups of the synthetic hexagonal RE(CO{sub 3})OH crystals are all P- anti 6. The present study has cast doubt upon the space group P- anti 62c previously reported for the natural Ce(CO{sub 3})OH, hydroxylbastnaesite-(Ce). The cell parameters decreased linearly with decreases in the ionic radii of the rare earth elements. La(CO{sub 3})OH showed the largest unit cell (a = 12.6752(6), c = 10.0806(10) A), while Er(CO{sub 3})OH showed the smallest (a = 11.8977(4), c = 9.6978(8) A). The rare earth atoms are in ninefold coordination with oxygen atoms to form a tricapped trigonal prism. The structure consists of layers of {sup 2}{infinity}[(OH)RE{sub 3/3}]{sup 2+} ions linked by carbonate ions. Raman spectra indicate the presence of carbonate and hydroxide groups. An evolutionary shift was observed from La to Er towards higher frequency, which was associated with a decreasing RE-O bond length. (orig.)

  10. 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.

  11. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  12. Improved switching using Fano resonances in photonic crystal structures

    DEFF Research Database (Denmark)

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

    2013-01-01

    We present a simple and robust structure for realizing asymmetric Fano transmission characteristics in photonic crystal waveguide-cavity structures. The use of Fano resonances for optical switching is analyzed using temporal coupled mode theory in combination with three-dimensional finite...... difference time domain simulations taking into account the signal bandwidth. The results suggest a significant energy reduction by employing Fano resonances compared to more well established Lorentzian resonance structures. A specific example of a Kerr nonlinearity shows an order of magnitude energy...

  13. Photonic crystal type structure in bivalve ligament of Pinctada maxima

    Institute of Scientific and Technical Information of China (English)

    ZHANG GangSheng

    2007-01-01

    The dry ligament of Pinctada maxima normally appears black; however, it can exhibit striking blue structural colors after being wetted by water. The field-mission SEM investigation shows that the ligament is made of lamellae, which, about 35 μm thick, are made of proteins and aragonite fibers of about 78 nm in diameter. In each single lamella, the fibers are highly aligned characterized by a 2D photonic crystal type structure. According to measured reflective spectra and theoretical simulations, the dry and wet ligaments possess photonic stop band at ultraviolet and blue wavelengths, respectively, which are responsible for structural colorations of ligament.

  14. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao (Hebei); (Toronto); (Huazhong)

    2012-06-28

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

  15. 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.

  16. 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.

  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. '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)

  19. The crystal structure of synthetic kutinaite, Cu14Ag6As7

    DEFF Research Database (Denmark)

    Karanovic, Ljiljana; Poleti, Dejan; Makovicky, Emil;

    2002-01-01

    kutinaite, X-ray diffraction, powder method, crystal structure, icosahedral alloy, arsenide, metal clusters......kutinaite, X-ray diffraction, powder method, crystal structure, icosahedral alloy, arsenide, metal clusters...

  20. 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

  1. Solid State Synthesis and Crystal Structure of K3SI

    Institute of Scientific and Technical Information of China (English)

    ZHAO Zhen-Qian; LIU Xi; CHEN Wen-Tong; LI Yan; WU A-Qing; ZENG Hui-Yi; GUO Guo-Cong; HUANG Jin-Shun

    2006-01-01

    A new ternary alkali metal chalcogenide halide, K3SI, has been synthesized by solid state reaction method and structurally characterized by X-ray crystallography. The crystal belongs to hexagonal, space group P63cm with a = 11.699(1), c = 5.8279(9) (A), Mr = 276.26, V = 690.8(1)(A)3, Z = 6, Dc = 3.985 g/cm3, F(000) = 756, μ= 9.913 mm-1, S = 1.004, R = 0.0719 and wR = 0.2204. The title compound is the first example containing S anion in the ternary alkali metal chalcogenide halides family M3QX (M = alkali metal, Q = chalcogenide, X = halide), which crystallizes in the hexagonal anti-perovskite structure type.

  2. 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.

  3. Crystal structure of Pb3(IO4(OH22

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-07-01

    Full Text Available The structure of the title compound, trilead(II bis[dihydroxidotetraoxidoiodate(VII], was determined from a crystal twinned by non-merohedry with two twin domains present [twin fraction 0.73 (1:0.27 (1]. It contains three Pb2+ cations and two IO4(OH23− anions in the asymmetric unit. Each of the Pb2+ cations is surrounded by eight O atoms (cut-off value = 3.1 Å in the form of a distorted polyhedron. The octahedral IO4(OH23− anions are arranged in rows extending parallel to [021], forming a distorted hexagonal rod packing. The cations and anions are linked into a framework structure. Although H-atom positions could not be located, O...O distances suggest medium-strength hydrogen-bonding interactions between the IO4(OH2 octahedra, further consolidating the crystal packing.

  4. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatezinc

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-03-01

    Full Text Available The ZnII atom in the title complex, [ZnCl2(C4H6N2S22], is coordinated in a distorted tetrahedral manner by two Cl atoms and two terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. In the crystal, the complex molecules are connected through C—H...Cl hydrogen bonds and Cl...S contacts, leading to a two-dimensional structure extending parallel to the ab plane.

  5. Dispersion Based Photonic-Crystal Structures for RF Applications

    Science.gov (United States)

    2006-06-01

    dimensional FDTD simulation. In our experiment, we fabricated the device using a computer numerically controlled ( CNC ) router . A tapered planar structure is...millimeter-wave photonic crystals are fabricated in Rexolite slabs by a computer numerically controlled ( CNC ) micro-milling system. Using the millimeter...loss, and low cost. In particular, it can be fabricated using a CNC micro-milling machine. Also, its low index provides a weaker confinement in the

  6. 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.

  7. Topology optimization for transient response of photonic crystal structures

    DEFF Research Database (Denmark)

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

    2010-01-01

    An optimization scheme based on topology optimization for transient response of photonic crystal structures is developed. The system response is obtained by a finite-element time-domain analysis employing perfectly matched layers as an absorbing boundary condition. As an example a waveguide...... the stored energy inside the microcavity in the decaying regime of the transient response. Manufacturable designs are achieved by filtering techniques capable of controlling minimum length scales of the design features. © 2010 Optical Society of America....

  8. Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.

    Science.gov (United States)

    Han, Qian; Robinson, Howard; Gao, Yi Gui; Vogelaar, Nancy; Wilson, Scott R; Rizzi, Menico; Li, Jianyong

    2006-12-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75A high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1A resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  9. 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.

  10. 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.

  11. Nanoconfinement-induced structures in chiral liquid crystals.

    Science.gov (United States)

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

    2013-08-28

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

  12. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Carol K. Hall

    2013-08-01

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

  13. 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.

  14. 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.

  15. Pressure effects on crystal and electronic structure of bismuth tellurohalides

    Science.gov (United States)

    Rusinov, I. P.; Menshchikova, T. V.; Sklyadneva, I. Yu; Heid, R.; Bohnen, K.-P.; Chulkov, E. V.

    2016-11-01

    We study the possibility of pressure-induced transitions from a normal semiconductor to a topological insulator (TI) in bismuth tellurohalides using density functional theory and tight-binding method. In BiTeI this transition is realized through the formation of an intermediate phase, a Weyl semimetal, that leads to modification of surface state dispersions. In the topologically trivial phase, the surface states exhibit a Bychkov-Rashba type dispersion. The Weyl semimetal phase exists in a narrow pressure interval of 0.2 GPa. After the Weyl semimetal-TI transition occurs, the surface electronic structure is characterized by gapless states with linear dispersion. The peculiarities of the surface states modification under pressure depend on the band-bending effect. We have also calculated the frequencies of Raman active modes for BiTeI in the proposed high-pressure crystal phases in order to compare them with available experimental data. Unlike BiTeI, in BiTeBr and BiTeCl the topological phase transition does not occur. In BiTeBr, the crystal structure changes with pressure but the phase remains a trivial one. However, the transition appears to be possible if the low-pressure crystal structure is retained. In BiTeCl under pressure, the topological phase does not appear up to 18 GPa due to a relatively large band gap width in this compound.

  16. 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.

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

    Science.gov (United States)

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

    2014-09-16

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

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

    Science.gov (United States)

    Thomas, Noel W

    2015-08-01

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

  19. Fourier transform infrared transmission microspectroscopy of photonic crystal structures.

    Science.gov (United States)

    Kilby, Gregory R; Gaylord, Thomas K

    2009-07-01

    The detailed microscopic characterization of photonic crystal (PC) structures is challenging due to their small sizes. Generally, only the gross macroscopic behavior can be determined. This leaves in question the performance at the basic structure level. The single-incident-angle plane-wave transmittances of one-dimensional photonic crystal (PC) structures are extracted from multiple-incident-angle, focused-beam measurements. In the experimental apparatus, an infrared beam is focused by a reflecting microscope objective to produce an incident beam. This beam can be modeled as multiple, variable-intensity plane waves incident on the PC structure. The transmittance of the structure in response to a multiple-incident-angle composite beam is measured. The composite beam measurement is repeated at various incident angle orientations with respect to the sample normal so that, at each angular orientation, the included set of single-angle plane-wave components is unique. A set of measurements recorded over a range of angular orientations results in an underspecified matrix algebra problem. Regularization techniques can be applied to the problem to extract the single-angle plane-wave response of the structure from the composite measurements. Experimental results show very good agreement between the measured and theoretical single-angle plane-wave transmittances.

  20. 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.

  1. Band structures in the nematic elastomers phononic crystals

    Science.gov (United States)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    2017-02-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  2. Crystal structure of seleno-l-cystine dihydrochloride

    OpenAIRE

    Carl Henrik Görbitz; Vladimir Levchenko; Jevgenijs Semjonovs; Mohamed Yusuf Sharif

    2015-01-01

    Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar disulfide bridge. The title compound [systematic name: (R,R)-1,1′-dicarboxy-2,2′-(diselanediyl)diethanaminium dichloride], C6H14N2O4Se22+·2Cl−, is the first example of a small molecule structure of the biologically important analogue with a —CH2—Se—Se—CH2— bridging unit. Bon...

  3. Crystal structure of 3-bromo-2-hydroxybenzoic acid

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2015-05-01

    Full Text Available Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a central R22(8 ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the short a axis observed in the title structure are frequent packing motifs in this set.

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

    Science.gov (United States)

    Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

    1994-01-01

    The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

  5. 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.

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

    Science.gov (United States)

    Smirnov, M; Saint-Grégoire, P

    2014-05-01

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

  7. Crystal Structure of an Ammonia-Permeable Aquaporin

    DEFF Research Database (Denmark)

    Kirscht, Andreas; Kaptan, Shreyas S; Bienert, Gerd Patrick;

    2016-01-01

    the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals...... an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity...

  8. 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.

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

    Science.gov (United States)

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

    1987-01-01

    The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

  10. 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.

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  14. Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes.

    Science.gov (United States)

    Goldenberg, Barbara L; Young, Victor G; Barany, George

    2015-10-01

    The present paper reports crystallographic studies on three related compounds that were of inter-est as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitro-gen-protecting groups: (N-methyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C3H4Cl3NOS2, (1), (N-benzyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (3). Their mol-ecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent mol-ecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [110], which are linked by short Cl⋯Cl and S⋯O contacts forming sheets parallel to (001). In the crystal of (2), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O⋯Cl contacts forming ribbons along the c-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking.

  15. Effect of crystal packing on the structures of polymeric metallocenes.

    Science.gov (United States)

    Dinnebier, R E; van Smaalen, Sander; Olbrich, F; Carlson, S

    2005-02-21

    The pressure dependencies of the crystal structures of the polymeric metallocenes lithium cyclopentadienide (LiCp) and potassium cyclopentadienide (KCp) have been determined by synchrotron X-ray powder diffraction. The decrease of the volume of LiCp by 34% up to a pressure of p = 12.2 GPa and of KCp by 23% at p = 5.3 GPa as well as the bulk moduli of K = 7.7 GPa for LiCp and 4.9 GPa for KCp indicate a high compressibility for these compounds. The crystal structures of KCp have been determined up to p = 3.9 GPa. An increase of the bend angle is found from 45 degrees at p = 0 GPa up to 51 degrees at p = 3.9 GPa. This variation is completely explained by a model invoking attractive K+ Cp- interaction and repulsive nonbonded carbon-carbon interactions. It is proposed that the bend angle in the polymeric alkali metal metallocenes is the result of the optimization of the crystal packing.

  16. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    Science.gov (United States)

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  17. Synthesis and Crystal Structure of a New Adamantane Amide Derivative

    Institute of Scientific and Technical Information of China (English)

    ZHOU Ying-Hua; LV Qi-Chun; ZHANG Qian; CHENG Yong; SHENG En-Hong

    2012-01-01

    A novel adamantane acyl amide derivative containing two phthalimido pendant groups(C31H31N3O5) has been synthesized,and its structure was characterized by elemental analysis,IR,1 H NMR spectra,and single-crystal X-ray diffraction.The crystal belongs to triclinic,space group P1 with a=7.3158(10),b=13.2405(18),c=14.378(2),α=72.419(2),β=84.496(2),γ=81.799(2)o,V=1312.0(3)3,Z=2,Dc=1.330 g/cm 3,μ=0.09 mm-1,Mr=525.59,F(000)=556,S=1.001,R=0.0523 and wR=0.0707 for 5901 unique reflections with 2363 observed ones(I〉2σ(I)).π-π stacking interactions(offset face-to-face) exist between the two rings of phthalimides from the neighboring molecules in the title crystal structure.The intermolecular dihedral angle between the two rings of neighboring phthalic amides is 6.26° and the distance is 4.008.

  18. 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].

  19. 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.

  20. Crystal Structure of Ethanolamine 5-Nitrosalicylic Acid Organic Adduct

    Institute of Scientific and Technical Information of China (English)

    金轶; 车云霞; 魏荣敏; 郑吉民

    2004-01-01

    The title adduct (C18H24N4O12, Mr = 488.41) crystallizes in monoclinic, space group P21/c with a = 4.0514(19), b = 25.193(11), c = 10.751(5)(A), β = 95.070(8)o, V = 1093.0(9)(A)3, Z = 4, Dc = 1.484 g/cm3, F(000) = 512, μ(MoKα) = 1.26 cm-1, T = 293 K, the final R = 0.0593 and wR = 0.0862 for 956 observed reflections with I > 2(I). The compound is a 1:1 adduct of ethanolamine and 5-nitrosalicylic acid. The nitrogen atom of ethanolamine is protonated. In this crystal there exist a number of hydrogen bonds which link the ethanolamine and 5-nitrosalicylic acid molecules to form a three-dimensional infinite network structure.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Bismuth zinc vanadate, BiZn2VO6 : new crystal structure type and electronic structure.

    OpenAIRE

    Nunes, Sayonara Eliziario; Wang, Chun-Hai; So, Karwei; Evans, John S. O.; Evans, Ivana Radosavljevic

    2015-01-01

    We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn2VO6, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn2VO6 adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO4 tetrahedra, ZnO6 octahedra and VO4 tet...

  7. 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.

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

    Science.gov (United States)

    Clark, Noel A.

    2000-01-01

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

  9. The optical Tamm states in a photonic-crystal Structure based on the cholesteric liquid crystal

    CERN Document Server

    Vetrov, Stepan Ya; Timofeev, Ivan V

    2015-01-01

    We investigate the localized surface modes in a structure consisting of the cholesteric liquid crystal layer, a phase plate, and a metal layer. These modes are analogous to the optical Tamm states. The anisotropy of transmission of light propagating the forward and backward directions is established. It is demonstrated that the transmission spectrum can be controlled by external fields acting on the cholesteric and by varying the plane of polarization of the incident light. [The text is presented both in English (pp 1-10) and in Russian (pp 11-20)

  10. Study of crystal structure at high temperature phase in KIO sub 3 crystal by synchrotron powder X-ray diffraction

    CERN Document Server

    Kasatani, H; Kuroiwa, Y; Yagi, K; Katayama, R; Terauchi, H

    2003-01-01

    The accurate crystal structure of the I-phase in KIO sub 3 crystal has been obtained at 530 K, for the first time, by the MEM/Rietveld analysis from high-energy X-ray powder-diffraction data. The crystal structure of the I-phase is the rhombohedral perovskite structure (space group R3m; Z=1). The MEM charge-density distributions reveal that the shorter I-O bond exhibits a covalent bonding character and others (I-K, K-O and longer I-O bonds) an ionic.

  11. In situ proteolysis to generate crystals for structure determination: an update.

    Directory of Open Access Journals (Sweden)

    Amy Wernimont

    Full Text Available For every 100 purified proteins that enter crystallization trials, an average of 30 form crystals, and among these only 13-15 crystallize in a form that enables structure determination. In 2007, Dong et al reported that the addition of trace amounts of protease to crystallization trials--in situ proteolysis--significantly increased the number of proteins in a given set that produce diffraction quality crystals. 69 proteins that had previously resisted structure determination were subjected to crystallization with in situ proteolysis and ten crystallized in a form that led to structure determination (14.5% success rate. Here we apply in situ proteolysis to over 270 new soluble proteins that had failed in the past to produce crystals suitable for structure determination. These proteins had produced no crystals, crystals that diffracted poorly, or produced twinned and/or unmanageable diffraction data. The new set includes yeast and prokaryotic proteins, enzymes essential to protozoan parasites, and human proteins such as GTPases, chromatin remodeling proteins, and tyrosine kinases. 34 proteins yielded deposited crystal structures of 2.8 A resolution or better, for an overall 12.6% success rate, and at least ten more yielded well-diffracting crystals presently in refinement. The success rate among proteins that had previously crystallized was double that of those that had never before yielded crystals. The overall success rate is similar to that observed in the smaller study, and appears to be higher than any other method reported to rescue stalled protein crystallography projects.

  12. Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

    Science.gov (United States)

    Bindel, Thomas H.

    2008-01-01

    A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

  13. Crystal Structure of Borophosphate with 61 Screw Axis Helices

    Institute of Scientific and Technical Information of China (English)

    石恒真; 单永奎; 戴立益; 刘煜炎; 翁林红

    2003-01-01

    A brilliant purple octahedral single crystal is hydrothermally synthesized by the reaction of CoCl2·6H2O, H3BO3 and H3PO4 in NaOH aqueous solution of CH3(CH2)15N(CH3)3Br, and its crystal structure has been characterized by single-crystal X-ray diffraction. The compound, NaCo(H2O)2BP2O8·H2O (Mr = 336.72), belongs to hexagonal, space group P6122 with a = 9.447(5), c = 15.83(1) (A。), V = 1223(1) (A。)3, Dc = 2.742 g/cm3, Z = 6, F(000) = 1002 and β= 2.606 mm-1. The three-dimensional framework in the compound is built up from the linkage tetrahedral ribbons, in which the BO4 and PO4 tetrahedra alternate with CoO6 octahedra. The sodium ions and water molecules are located within the free thread of the helical ribbons.

  14. The crystal structure and superconducting properties of monatomic bromine.

    Science.gov (United States)

    Duan, Defang; Meng, Xing; Tian, Fubo; Chen, Changbo; Wang, Liancheng; Ma, Yanming; Cui, Tian; Liu, Bingbing; He, Zhi; Zou, Guangtian

    2010-01-13

    The crystal structure and superconducting properties of monatomic bromine under high pressure have been studied by first-principles calculations. We have found the following phase transition sequence with increasing pressure: from body-centered orthorhombic (bco, phase II) to body-centered tetragonal structure (bct, phase III) at 126 GPa, then to face-centered cubic structure (fcc, phase IV) at 157 GPa, which is stable at least up to 300 GPa. The calculated superconducting critical temperature T(c) = 1.46 K at 100 GPa is consistent with the experimental value of 1.5 K. In addition, our results of T(c) decrease with increasing pressure in all the monatomic phases of bromine, similar to monatomic iodine. Further calculations show that the decrease of λ with pressure in phase IV is mainly attributed to the weakening of the 'soft' vibrational mode caused by pressure.

  15. Crystal structure of the bacteriophage P2 integrase catalytic domain.

    Science.gov (United States)

    Skaar, Karin; Claesson, Magnus; Odegrip, Richard; Högbom, Martin; Haggård-Ljungquist, Elisabeth; Stenmark, Pål

    2015-11-30

    Bacteriophage P2 is a temperate phage capable of integrating its DNA into the host genome by site-specific recombination upon lysogenization. Integration and excision of the phage genome requires P2 integrase, which performs recognition, cleavage and joining of DNA during these processes. This work presents the high-resolution crystal structure of the catalytic domain of P2 integrase, and analysis of the structure-function relationship of several previously identified non-functional P2 integrase mutants. The DNA binding area is characterized by a large positively charged patch, harboring key residues. The structure reveals potential for large dimer flexibility, likely essential for rearrangement of DNA strands upon integration and excision of the phage DNA.

  16. 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).

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

    Science.gov (United States)

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

    2016-04-05

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

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

    Science.gov (United States)

    Orlando, Benjamin J; Malkowski, Michael G

    2016-10-01

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

  19. 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.

  20. Potassium and magnesium succinatouranilates - Synthesis and crystal structure

    Science.gov (United States)

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

    2017-04-01

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

  1. Crystal structure of Ca5Nb5O17

    Science.gov (United States)

    Guevarra, J.; van Smaalen, S.; Rotiroti, N.; Paulmann, C.; Lichtenberg, F.

    2005-09-01

    The crystal structure of Ca5Nb5O17, an n=5 member of the homologous series AnBnO, at room temperature has been determined by single-crystal X-ray diffraction using synchrotron radiation with a CCD area detector. The structure is monoclinic with spacegroup P21/c ( b unique) and lattice parameters a=7.7494(3) Å, b=5.4928(1) Å, c=32.241(1) Å, and β=96.809(4)∘. It consists of perovskite-like slabs of corner-sharing NbO6 octahedra separated by an interslab region, where the octahedra on opposite sides of the gap do not share oxygen atoms resulting in an extra layer of oxygen atoms with respect to the ideal perovskite structure. The slabs are five octahedra wide. Ca atoms within the slabs occupy 12-fold coordinated sites whereas those at the borders show irregular coordination environments. The distortion of the octahedra increases from the center to the borders of the slabs. The computed valences for the Nb ions are very close to 5 at the borders while smaller values were obtained for sites in the middle of the slabs which suggests that the electrical conduction takes place predominantly in the middle of the slabs.

  2. 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.

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

    Science.gov (United States)

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

    2011-09-26

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

  4. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-09-15

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

  6. Topological Structure of Knotted Vortex Lines in Liquid Crystals

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  7. 9R structure in drawn industrial single crystal copper wires

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian; YAN Wen; FAN Xin-hui

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Brian J. Anderson

    2016-02-01

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

  9. 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.

  10. Structure and Dynamics of Freely Suspended Liquid Crystals

    Science.gov (United States)

    Clark, Noel A.

    2004-01-01

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

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

    Science.gov (United States)

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

    2017-02-01

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

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

    Science.gov (United States)

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

    2015-09-02

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

  13. 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.

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

    Science.gov (United States)

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

    2007-05-01

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

  15. 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.

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

    Science.gov (United States)

    Weil, Matthias; Häusler, Thomas

    2014-09-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

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

    Science.gov (United States)

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

    2006-10-01

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

  19. Crystal Structure of a Marine Natural Compound, Anhydrofusarubin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  20. 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.

  1. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.

    Science.gov (United States)

    Bruhn, Jessica F; Kirchdoerfer, Robert N; Urata, Sarah M; Li, Sheng; Tickle, Ian J; Bricogne, Gérard; Saphire, Erica Ollmann

    2017-01-15

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

  2. 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.

  3. Crystal structure of seleno-l-cystine dihydrochloride

    Directory of Open Access Journals (Sweden)

    Carl Henrik Görbitz

    2015-06-01

    Full Text Available Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar disulfide bridge. The title compound [systematic name: (R,R-1,1′-dicarboxy-2,2′-(diselanediyldiethanaminium dichloride], C6H14N2O4Se22+·2Cl−, is the first example of a small molecule structure of the biologically important analogue with a —CH2—Se—Se—CH2— bridging unit. Bond lengths and angles of seleno-l-cystine dihydrochloride and its isotypic sulfur analogue l-cystine dihydrochloride are compared.

  4. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  5. 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.

  6. Structural noise tolerance of photonic crystal optical properties

    Science.gov (United States)

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

    2016-12-01

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

  7. Crystal structure of Li3Ga(BO32

    Directory of Open Access Journals (Sweden)

    Robert W. Smith

    2017-03-01

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

  8. Crystal structure of PvdO from Pseudomonas aeruginosa.

    Science.gov (United States)

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

    2017-02-26

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

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

    Science.gov (United States)

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

    2017-02-01

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

  10. Crystal structure of Hg2SO4 – a redetermination

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-09-01

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

  11. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    Science.gov (United States)

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  17. 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.

  18. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-08-09

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

  20. Crystal and mol-ecular structure of aflatrem.

    Science.gov (United States)

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

    2015-11-01

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

  1. 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.

  2. Crystal structure of sulfotransferase STF9 from Mycobacterium avium.

    Science.gov (United States)

    Hossain, Md Murad; Moriizumi, Yuuji; Tanaka, Shotaro; Kimura, Makoto; Kakuta, Yoshimitsu

    2012-02-01

    Sulfotransferases catalyze the sulfate conjugation of a wide variety of endogenous and exogenous molecules. Human pathogenic mycobacteria produce numerous sulfated molecules including sulfolipids which are well related to the virulence of several strains. The genome of Mycobacterium avium encodes eight putative sulfotransferases (stf1, stf4-stf10). Among them, STF9 shows higher similarity to human heparan sulfate 3-O-sulfotransferase isoforms than to the bacterial STs. Here, we determined the crystal structure of sulfotransferase STF9 in complex with a sulfate ion and palmitic acid at a resolution of 2.6 Å. STF9 has a spherical structure utilizing the classical sulfotransferase fold. STF9 exclusively possesses three N-terminal α-helices (α1, α2, α3) parallel to the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) binding motif. The sulfate ion binds to the PAPS binding structural motif and the palmitic acid molecule binds in the deep cleft of the predicted substrate binding site suggesting the nature of endogenous acceptor substrate of STF9 resembles palmitic acid. The substrate binding site is covered by a flexible loop which may have involvement in endogenous substrate recognition. Based on the mutational study (Hossain et al., Mol Cell Biochem 350:155-162; 2011) and structural resemblance of STF9-sulfate ion-palmitic acid complex to the hHS3OST3 complex with PAP (3'-phosphoadenosine-5'-phosphate) and an acceptor sugar chain, Glu170 and Arg96 are appeared to be catalytic residues in STF9 sulfuryl transfer mechanism.

  3. REFMAC5 for the refinement of macromolecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Skubák, Pavol [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Lebedev, Andrey A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Pannu, Navraj S. [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Steiner, Roberto A. [Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, London (United Kingdom); Nicholls, Robert A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Winn, Martyn D. [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Long, Fei; Vagin, Alexei A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom)

    2011-04-01

    The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.

  4. Crystal Structure of the Human Cannabinoid Receptor CB1.

    Science.gov (United States)

    Hua, Tian; Vemuri, Kiran; Pu, Mengchen; Qu, Lu; Han, Gye Won; Wu, Yiran; Zhao, Suwen; Shui, Wenqing; Li, Shanshan; Korde, Anisha; Laprairie, Robert B; Stahl, Edward L; Ho, Jo-Hao; Zvonok, Nikolai; Zhou, Han; Kufareva, Irina; Wu, Beili; Zhao, Qiang; Hanson, Michael A; Bohn, Laura M; Makriyannis, Alexandros; Stevens, Raymond C; Liu, Zhi-Jie

    2016-10-20

    Cannabinoid receptor 1 (CB1) is the principal target of Δ(9)-tetrahydrocannabinol (THC), a psychoactive chemical from Cannabis sativa with a wide range of therapeutic applications and a long history of recreational use. CB1 is activated by endocannabinoids and is a promising therapeutic target for pain management, inflammation, obesity, and substance abuse disorders. Here, we present the 2.8 Å crystal structure of human CB1 in complex with AM6538, a stabilizing antagonist, synthesized and characterized for this structural study. The structure of the CB1-AM6538 complex reveals key features of the receptor and critical interactions for antagonist binding. In combination with functional studies and molecular modeling, the structure provides insight into the binding mode of naturally occurring CB1 ligands, such as THC, and synthetic cannabinoids. This enhances our understanding of the molecular basis for the physiological functions of CB1 and provides new opportunities for the design of next-generation CB1-targeting pharmaceuticals.

  5. 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.

  6. Growth, Structural and Microhardness Studies on New Semiorganic Single Crystals of Calcium Para Nitrophenolate Dihydrate

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Good quality crystals of calcium p-nitrophenolate (NPCa) were grown from saturated solution by slow evaporation method. The crystal structure analysis and the molecular arrangement of these crystals were determined using X-ray diffraction (XRD). From single crystal XRD studies, NPCa is found to be crystallized in the monoclinic system with a space group P21/n. The functional groups of the material were confirmed qualitatively by FTIR (Fourier transform infrared spectroscopy) spectral analysis. Optical absorption studies reveal the absorption region and microhardness studies were carried out to confirm the mechanical behaviour of the crystals.

  7. Nanoconfinement crystallization of frustrated alkyl groups: crossover of mesophase to crystalline structure.

    Science.gov (United States)

    Shi, Haifeng; Wang, Haixia; Xin, John H; Zhang, Xingxiang; Wang, Dujin

    2011-04-07

    Crossover of mesophase to crystalline structure in the nanoconfinement crystallization process of frustrated side groups elucidates the critical crystal thickness d(c) or the length scale of side groups, which defines the transition process from mesophase (hexagonal and monoclinic phase) to crystalline phase (orthorhombic phase) of confined CH(2) sequences in a given crystal size restriction.

  8. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-09

    ABSTRACT

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

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

  9. 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.

  10. Systematic conformational bias in small-molecule crystal structures is rare and explicable

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.; Liebeschuetz, J.W.; Allen, F.H.

    2012-01-01

    Analysis of the Cambridge Structural Database, together with DFT and crystal structure prediction calculations, show that the observation of higher-energy planar conformers of biphenyl (BP) and cyclobutane (CB) is possible because of improved intermolecular interactions in their crystal structures.

  11. Preparation and Crystal Structure of Acetyl Hemerocallin and Structural Revision of Hemerocallin

    Institute of Scientific and Technical Information of China (English)

    LIU Yan-ze; WU Jie; ZHU Yu; DU Chen-xia; CHANG Jun-biao; XIE Jing-xi

    2013-01-01

    Objective To revise the structure of hemerocallin,an active and toxic compound isolated from the roots of Hemerocallis fulva,which was first reported in 1974 based on the chemical and spectral data.Methods The structure of acetyl hemerocallin was determined through the acetyl derivative preparing and X-ray diffraction.Results The title compound acetyl hemerocallin (1) has been prepared and structurally characterized by X-ray single-crystal diffraction method.X-ray analysis revealed that the two naphthalene rings in compound 1 were significantly twisted with an average dihedral angle of 44.1°.The two acetate groups in each naphthalene ring adopted anti-parallel conformation.In addition,the π-π stacking interactions were found in the crystal structure,the molecules were linked into a supramolecular network,and the crystal structure was stabilized.Conclusion The structure of hemerocallin is identified as 2,2'-bi(1,8-dihydroxy-6-methyl-7-acetylnaphthalene) (3).

  12. The crystal structure of {gamma}-AlD{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Brinks, H.W. [Institute for Energy Technology, P.O. Box 40, Kjeller N-2027 (Norway); Brown, C. [Department of Chemistry, University of Hawaii, Honolulu, HI 96822 (United States); Jensen, C.M. [Department of Chemistry, University of Hawaii, Honolulu, HI 96822 (United States); Graetz, J. [Department of Energy Sciences and Technologies, Brookhaven National Laboratory, Upton, NY 11973 (United States); Reilly, J.J. [Department of Energy Sciences and Technologies, Brookhaven National Laboratory, Upton, NY 11973 (United States); Hauback, B.C. [Institute for Energy Technology, P.O. Box 40, Kjeller N-2027 (Norway)]. E-mail: bjorn.hauback@ife.no

    2007-08-30

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

  13. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase.

    Science.gov (United States)

    Romero, Elvira; Castellanos, J Rubén Gómez; Mattevi, Andrea; Fraaije, Marco W

    2016-12-19

    Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio-, chemo-, and enantioselectivity. However, the low stability of many Baeyer-Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate-binding cavity explains its preference for small rather than bulky substrates. Small-scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology.

  14. 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)

  15. 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.

  16. Synthesis and Crystal Structure of N-Ferrocenesulfonyl Hexahydropyridine

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The title compound (C15H19FeNO2S, Mr = 333.22) was synthesized by the re- action of ferrocenesulfonyl chloride with hexahydropyridine, and characterized by 1H NMR, IR and elemental analysis. The crystal belongs to monoclinic, space group P21/n with a = 6.0472(5), b = 20.4897(6), c = 11.6584(8)(A), β = 91.3120(10)°, V = 1444.16(16)(A)3, Z = 4, Dc = 1.533 g/cm3, F(000) = 696, μ = 1.188 mm-1, the final R = 0.0309 and wR = 0.0736 for 2057 observed reflection with I > 2σ(I). The structure analysis demonstrates that two cyclopentadienyl rings are almost parallel with a dihedral angle of 1.70o, and hexahydropyridine moiety exists in a chair conformation. Bioassay indicates that the title compound has a good fungicidal activity.

  17. 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.

  18. 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.

  19. Hierarchical structuring of liquid crystal polymer-Laponite hybrid materials.

    Science.gov (United States)

    Tritschler, Ulrich; Zlotnikov, Igor; Zaslansky, Paul; Aichmayer, Barbara; Fratzl, Peter; Schlaad, Helmut; Cölfen, Helmut

    2013-09-03

    Biomimetic organic-inorganic composite materials were fabricated via one-step self-organization on three hierarchical levels. The organic component was a polyoxazoline with pendent cholesteryl and carboxyl (N-Boc-protected amino acid) side chains that was able to form a chiral nematic lyotropic phase and bind to positively charged inorganic faces of Laponite. The Laponite particles formed a mesocrystalline arrangement within the liquid-crystal (LC) polymer phase upon shearing a viscous dispersion of Laponite nanoparticles and LC polymer in DMF. Complementary analytical and mechanical characterization techniques (AUC, POM, TEM, SEM, SAXS, μCT, and nanoindentation) covering the millimeter, micrometer, and nanometer length scales reveal the hierarchical structures and properties of the composite materials consisting of different ratios of Laponite nanoparticles and liquid-crystalline polymer.

  20. Crystal structure of 2,5-dimethylanilinium salicylate

    Directory of Open Access Journals (Sweden)

    A. Mani

    2015-09-01

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

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

    Science.gov (United States)

    Japins, Guntis; Berzina, Rita; Zicans, Janis; Merijs Meri, Remo; Ivanova, Tatjana; Kalkis, Valdis; Reinholds, Ingars

    2013-12-01

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-08-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Crystal structure of the RNA component of bacterial ribonuclease P

    Energy Technology Data Exchange (ETDEWEB)

    Torres-Larios, Alfredo; Swinger, Kerren K.; Krasilnikov, Andrey S.; Pan, Tao; Mondragon, Alfonso (NWU); (UC)

    2010-03-08

    Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 {angstrom} resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

  10. Crystal structure of the RNA component of bacterial ribonuclease P.

    Science.gov (United States)

    Torres-Larios, Alfredo; Swinger, Kerren K; Krasilnikov, Andrey S; Pan, Tao; Mondragón, Alfonso

    2005-09-22

    Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 A resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

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

    Directory of Open Access Journals (Sweden)

    Manickam Thairiyaraja

    2015-12-01

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

  12. Crystal structure of iron-oxide nanoparticles synthesized from ferritin

    Energy Technology Data Exchange (ETDEWEB)

    Krispin, Michael, E-mail: michael.krispin@physik.uni-augsburg.de; Ullrich, Aladin, E-mail: aladin.ullrich@physik.uni-augsburg.de; Horn, Siegfried, E-mail: horn@physik.uni-augsburg.de [University of Augsburg, Institute of Physics (Germany)

    2012-02-15

    We have investigated the crystal structure of nanosized iron-oxide by X-ray diffraction (XRD), extended X-ray absorption fine structure measurements at the iron K-edge as well as by transmission electron microscopy (TEM). Iron-oxide nanoparticles were produced by thermal treatment of horse spleen ferritin molecules. The structure of these particles was compared to {alpha}-Fe{sub 2}O{sub 3} and {gamma}-Fe{sub 2}O{sub 3} nanopowder references. The thermal treatment of a submonolayer film of ferritin molecules results in pure {gamma}-Fe{sub 2}O{sub 3} nanoparticles, while for films above a certain thickness {alpha}-Fe{sub 2}O{sub 3} and {gamma}-Fe{sub 2}O{sub 3} coexist, exhibiting two different crystallite sizes. TEM shows a characteristic particle diameter of {approx}7 nm for {gamma}-Fe{sub 2}O{sub 3} resulting from thermal treatment of monolayers, consistent with the crystallite size of the {gamma}-phase as obtained from XRD measurements on multi-layered samples. XRD shows the {alpha}-Fe{sub 2}O{sub 3} phase to be characterized by a crystallite size of {approx}34 nm.

  13. Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism.

    Science.gov (United States)

    Suzuki, Ryuichiro; Katayama, Takane; Kim, Byung-Jun; Wakagi, Takayoshi; Shoun, Hirofumi; Ashida, Hisashi; Yamamoto, Kenji; Fushinobu, Shinya

    2010-10-29

    Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H(2)O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (α,β-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction.

  14. 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.

  15. Crystal structure engineering for improved performance of emerging nanoscale devices

    Science.gov (United States)

    Chimalgi, Vinay Uday

    Recent advances in growth techniques and increasing number of experimental studies have made nanostructures grown along different crystallographic directions a reality. These new structures could not only benefit the electronic devices used in mainstream information technology but also show great promise for applications in lasers, solid-state lighting, near-field photolithography, free-space quantum cryptography, consumer displays, quantum computation, as well as diagnostic medicine and imaging. However, only few theoretical investigations have been performed on these structures due to the complex nature of the interplay of atomicity, structural fields, polarization, and quantum size-quantization, all strong function of the crystallographic direction. The objective of this work is mainly four-fold: (1) Integrate a computational framework employing a combination of fully atomistic valence force-field molecular mechanics and 20-band sp3s*d5-SO tight-binding based electronic band­structure models, and numerically investigate the effects of internal fields on the electronic and optical properties of zincblende InAs/GaAs quantum dots grown on (100), (110), and (111) orientated substrates. (2) Augment/extend the open source NEMO 3-D bandstructure simulator by incorporating a recently proposed first principles based model to gauge the importance of nonlinear piezoelectricity on the single-particle electronic states and interband optical transitions in emerging In(Ga)N/GaN disk-in-wire LED structures having c-plane and m-plane wurtzite crystal symmetry. (3) Coupling the NEMO 3-D software toolkit with a commercial TCAD simulator to determine the terminal electrical and optical characteristics of InGaN/GaN disk-in-wire LEDs; and (4) Finding an optimum crystallographic device for InGaN/GaN disk-in-wire LEDs to achieve improved internal quantum efficiency (IQE).

  16. Crystal structure of nitrogen regulatory protein IIANtr from Neisseria meningitidis

    Directory of Open Access Journals (Sweden)

    Stammers David K

    2005-08-01

    Full Text Available Abstract Background The NMB0736 gene of Neisseria meningitidis serogroup B strain MC58 encodes the putative nitrogen regulatory protein, IIANtr (abbreviated to NM-IIANtr. The homologous protein present in Escherichia coli is implicated in the control of nitrogen assimilation. As part of a structural proteomics approach to the study of pathogenic Neisseria spp., we have selected this protein for structure determination by X-ray crystallography. Results The NM-IIANtr was over-expressed in E. coli and was shown to be partially mono-phosphorylated, as assessed by mass spectrometry of the purified protein. Crystals of un-phosphorylated protein were obtained and diffraction data collected to 2.5 Å resolution. The structure of NM-IIANtr was solved by molecular replacement using the coordinates of the E. coli nitrogen regulatory protein IIAntr [PDB: 1A6J] as the starting model. The overall fold of the Neisseria enzyme shows a high degree of similarity to the IIANtr from E. coli, and the position of the phosphoryl acceptor histidine residue (H67 is conserved. The orientation of an adjacent arginine residue (R69 suggests that it may also be involved in coordinating the phosphate group. Comparison of the structure with that of E. coli IIAmtl complexed with HPr [PDB: 1J6T] indicates that NM-IIANtr binds in a similar way to the HPr-like enzyme in Neisseria. Conclusion The structure of NM-IIANtr confirms its assignment as a homologue of the IIANtr proteins found in a range of other Gram-negative bacteria. We conclude that the NM- IIANtr protein functions as part of a phosphorylation cascade which, in contrast to E. coli, shares the upstream phosphotransfer protein with the sugar uptake phosphoenolpyruvate:sugar phosphotransferase system (PTS, but in common with E. coli has a distinct downstream effector mechanism.

  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. Structure of supersaturated solution and crystal nucleation induced by diffusion

    Science.gov (United States)

    Ooshima, Hiroshi; Igarashi, Koichi; Iwasa, Hideo; Yamamoto, Ren

    2013-06-01

    The effect of a seed crystal on nucleation of L-alanine from a quiescent supersaturated solution was investigated. When a seed crystal was not used, nucleation did not occur at least for 5 h. When a seed crystal was introduced into the supersaturated solution with careful attention to avoid convection of the solution, fine crystals appeared at the place far from the seed crystal. At that time, there was no convection at the place that fine crystals appeared. Namely, there was no possibility that those fine crystals came from the surface of seed crystal. We supposed that nucleation was induced by directional diffusion of solute molecules caused by growth of the seed crystal. In order to prove this hypothesis, we designed an experiment using an apparatus composed of two compartments divided by a dialysis membrane that L-alanine molecules could freely permeate. Two supersaturated solutions having a supersaturation ratio of 1.2 and a smaller ratio were placed in the two compartments in the absence of seed crystals. This apparatus allowed the directional diffusion of solute molecules between two solutions. Nucleation occurred within 30 min. The frequency of nucleation among 7-times repeated experiments was in proportion to the difference of supersaturation ratio between the two solutions. This result poses a new mechanism of the secondary nucleation that the directional diffusion caused by growth of existing crystals induces nucleation.

  19. 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

  20. Steady distribution structure of point defects near crystal-melt interface under pulling stop of CZ Si crystal

    Science.gov (United States)

    Abe, T.; Takahashi, T.; Shirai, K.

    2017-02-01

    In order to reveal a steady distribution structure of point defects of no growing Si on the solid-liquid interface, the crystals were grown at a high pulling rate, which Vs becomes predominant, and the pulling was suddenly stopped. After restoring the variations of the crystal by the pulling-stop, the crystals were then left in prolonged contact with the melt. Finally, the crystals were detached and rapidly cooled to freeze point defects and then a distribution of the point defects of the as-grown crystals was observed. As a result, a dislocation loop (DL) region, which is formed by the aggregation of interstitials (Is), was formed over the solid-liquid interface and was surrounded with a Vs-and-Is-free recombination region (Rc-region), although the entire crystals had been Vs rich in the beginning. It was also revealed that the crystal on the solid-liquid interface after the prolonged contact with the melt can partially have a Rc-region to be directly in contact with the melt, unlike a defect distribution of a solid-liquid interface that has been growing. This experimental result contradicts a hypothesis of Voronkov's diffusion model, which always assumes the equilibrium concentrations of Vs and Is as the boundary condition for distribution of point defects on the growth interface. The results were disscussed from a qualitative point of view of temperature distribution and thermal stress by the pulling-stop.

  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. 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.

  3. Rapid X-ray crystal structure analysis in few second measurements using microstrip gas chamber

    CERN Document Server

    Ochi, A; Tanimori, T; Ohashi, Y; Toyokawa, H; Nishi, Y; Nishi, Y; Nagayoshi, T; Koishi, S

    2001-01-01

    X-ray crystal structure analysis using microstrip gas chamber was successfully carried out in a measurement time within a few seconds. The continuous rotation photograph method, in which most of the diffraction peaks can be obtained within one continuous rotation of the sample crystal (without stopping or oscillation), was applied for this measurement. As an example, the structure of a single crystal of ammonium bitartrate (r=1 mm, spherical) was measured. Diffraction spots from the sample, which were sufficient to obtain crystal structure, were successfully obtained by taking only 2 s measurements with a commercially available laboratory X-ray source.

  4. 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.

  5. 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.

  6. 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.

  7. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    Science.gov (United States)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  8. 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.

  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. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-01

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

  12. 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.

  13. Large scale structures in liquid crystal/clay colloids

    Energy Technology Data Exchange (ETDEWEB)

    Duijneveldt, Jeroen S van [School of Chemistry, Cantock' s Close, University of Bristol, Bristol BS8 1TS (United Kingdom); Klein, Susanne [HP Laboratories, Filton Road, Stoke Gifford, Bristol BS34 8QZ (United Kingdom); Leach, Edward [HP Laboratories, Filton Road, Stoke Gifford, Bristol BS34 8QZ (United Kingdom); Pizzey, Claire [School of Chemistry, Cantock' s Close, University of Bristol, Bristol BS8 1TS (United Kingdom); Richardson, Robert M [H H Wills Physics Laboratory, Tyndall Avenue, University of Bristol, Bristol BS8 1TL (United Kingdom)

    2005-04-20

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

  14. 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.

  15. 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.

  16. 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.

  17. Copper coordination polymers constructed from thiazole-5-carboxylic acid: Synthesis, crystal structures, and structural transformation

    Science.gov (United States)

    Meundaeng, Natthaya; Rujiwatra, Apinpus; Prior, Timothy J.

    2017-01-01

    We have successfully prepared crystals of thiazole-5-carboxylic acid (5-Htza) (L) and three new thiazole-5-carboxylate-based Cu2+ coordination polymers with different dimensionality, namely, 1D [Cu2(5-tza)2(1,10-phenanthroline)2(NO3)2] (1), 2D [Cu(5-tza)2(MeOH)2] (2), and 3D [Cu(5-tza)2]·H2O (3). These have been characterized by single crystal X-ray diffraction and thermogravimetry. Interestingly, the 2D network structure of 2 can directly transform into the 3D framework of 3 upon removal of methanol molecules at room temperature. 2 can also undergo structural transformation to produce the same 2D network present in the known [Cu(5-tza)2]·1.5H2O upon heat treatment for 2 h. This 2D network can adsorb water and convert to 3 upon exposure to air.

  18. 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.

  19. 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....

  20. 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

  1. 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

  2. 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.

  3. Structural study on few co-crystals and a salt of quinoline derivatives having amide bond

    Science.gov (United States)

    Karmakar, Anirban; Kalita, Dipjyoti; Baruah, Jubaraj B.

    2009-10-01

    The N-[2-(4-Methoxy-phenyl)-ethyl]-2-(quinolin-8-yloxy)-acetamide forms 1:1 co-crystals with aromatic diols namely 1,4-dihydroxybenzene, 1,5-dihydroxynaphthalene. In the later case co-crystal is formed in hydrated form. The hydrated form of co-crystal with 1,5-naphthalenediol has two symmetry independent host molecules in its unit cell, whereas such phenomenon in the co-crystal 1,4-dihydroxybenzene is not observed. The crystal structure of perchloric acid salt of (Quinolin-8-ylamino)-acetic acid is determined and this salt also shows two symmetry independent parent molecules in unit cell.

  4. Microscopic Characterization of Defect Structure in RDX Crystals

    Science.gov (United States)

    2013-10-09

    crystals in composition PBXN-109 (Doherty & Watt, 2008), crystal density and impurity content, that is, HMX by HPLC, cyclohexanone and acetone by GC for...kbar) 50.6 38.6 53.3 ρcrystal (g cm−3) 1.795 1.804 1.794 HMX (%) 0.19 8.55 0.02 Cyclohexanone (‰) 0.72/0.87 0.00/0.01 0.58/0.69 Acetone (‰) 0.00/0.049... cyclohexanone and ace- tone are indicative of the solvents used in the crystallization processes. Sample preparation Samples are prepared by embedding

  5. 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.

  6. 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

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

    Science.gov (United States)

    van de Streek, Jacco; Neumann, Marcus A

    2010-10-01

    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 A 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.

  8. 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.

  9. Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution).

    Science.gov (United States)

    Zhang, Weizhe; Zhang, Hongmin; Zhang, Tao; Fan, Haifu; Hao, Quan

    2015-07-01

    Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.

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

    Science.gov (United States)

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

    2014-09-01

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

  11. Boron Arsenide and Boron Phosphide for High Temperature and Luminescent Devices. [semiconductor devices - crystal growth/crystal structure

    Science.gov (United States)

    Chu, T. L.

    1975-01-01

    The crystal growth of boron arsenide and boron phosphide in the form of bulk crystals and epitaxial layers on suitable substrates is discussed. The physical, chemical, and electrical properties of the crystals and epitaxial layers are examined. Bulk crystals of boron arsenide were prepared by the chemical transport technique, and their carrier concentration and Hall mobility were measured. The growth of boron arsenide crystals from high temperature solutions was attempted without success. Bulk crystals of boron phosphide were also prepared by chemical transport and solution growth techniques. Techniques required for the fabrication of boron phosphide devices such as junction shaping, diffusion, and contact formation were investigated. Alloying techniques were developed for the formation of low-resistance ohmic contacts to boron phosphide. Four types of boron phosphide devices were fabricated: (1) metal-insulator-boron phosphide structures, (2) Schottky barriers; (3) boron phosphide-silicon carbide heterojunctions; and (4) p-n homojunctions. Easily visible red electroluminescence was observed from both epitaxial and solution grown p-n junctions.

  12. Growth, structure, spectral properties and crystal-field analysis of monoclinic Nd:YNbO4 single crystal

    Science.gov (United States)

    Ding, Shoujun; Zhang, Qingli; Gao, Jinyun; Liu, Wenpeng; Luo, Jianqiao; Sun, Dunlu; Sun, Guihua; Wang, Xiaofei

    2016-12-01

    A Nd:YNbO4 single crystal was successfully grown by Czochralski (Cz) method, its structural and spectroscopic properties were investigated. The X-ray rocking curve of the (010) diffraction face of Nd:YNbO4 crystal was measured, the full width at half maximum (FWHM) of this diffraction peak is 0.05°, which indicates a high crystalline quality of the as-grown crystal. Its lattice parameters, atomic coordinates and so on were obtained by Rietvield refinement to X-ray diffraction data. According to the Archimedes drainage method, the crystal density of Nd:YNbO4 is calculated to be 5.4 g/cm3. The Mohr‧s hardness value along (010) face was determined to be 6.0. The transmission spectrum along (010) face at room temperature was recorded and the excitation and emission spectra at 8 K were measured. Photoluminescence peaks of Nd:YNbO4 were assigned, and the crystal-field splitting of Nd3+ in YNbO4 was obtained. The fluorescence lifetime of the 4F3/2→4I11/2 transition of Nd3+ in YNbO4 is fitted to be 152 μs These spectroscopic and energy splitting data give an important reference for the research of laser property of Nd:YNbO4 crystal.

  13. Crystal Structure of a Potassium Ion Transporter TrkH

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; H Huang; M Getahun Derebe; E Levin; V Kabaleeswaran; Y Pan; M Punta; J Love; et al.

    2011-12-31

    The TrkH/TrkG/KtrB proteins mediate K{sup +} uptake in bacteria and probably evolved from simple K{sup +} channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K{sup +} channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K{sup +} and Rb{sup +} over smaller ions such as Na{sup +} or Li{sup +}. Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K{sup +} flux. These results reveal the molecular basis of K{sup +} selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.

  14. 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.

  15. 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.

  16. Synthesis, Crystal Structure and Electrical Properties of the Molybdenum Oxide

    Directory of Open Access Journals (Sweden)

    Ennajeh Ines

    2013-01-01

    Full Text Available New molybdenum oxide Na1.92Mg2.04Mo3O12 has been synthesized by the solid state method. The title compound crystallizes in the triclinic system (space group P-1. The unit cell parameters are a = 6.9660(7 Å, b = 8.6352(8 Å, c = 10.2501(8 Å, α = 106.938(1°, β = 104.825(1°, γ = 103.206(1°, V = 538.72(9 Å3, and Z = 2. The compound is isotypical to Ag2M2(MoO43 (M = Zn, Mg, Co, Mn. The structure can be described as a three-dimensional anionic mixed framework of MoO4 tetrahedra and pairs of Mg2O10 octahedra sharing common edges. The Na+ ions are disordered and located in the voids forming infinite channels running along the direction [100]. The electrical conductivity investigated from 693 K to 793 K by AC impedance spectroscopy is low ( S cm−1 at 683 K.

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

    Science.gov (United States)

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

    2015-02-01

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

  18. Radiation effect on domain and defect structure of BaTiO3 crystals

    Science.gov (United States)

    Fesenko, Evgeni G.; Lisinska-Czekaj, Agata; Czekaj, Dionizy; Surowiak, Zygmunt

    2003-10-01

    BaTiO3 single crystals were obtained by Remeika-method from solutions of melted salts and oxides. Radioactive Co60 isotope was employed as a source of γ-radiation. Three different radiation doses were applied: 1.2 x 107 rad, 3.0 x 108 rad, and 1.3 x 107 rad. Temperature of single crystals during irradiation did not exceed 313 K. A few batches of crystals were subjected to irradiation, namely: single crystals with natural surface (after the crystal was grown), single crystals with the etched surface layer and single crystals which had been subjected to an influence of the strong direct and alternating electric fields before exposure. Both domain and defect structure of single crystals was investigated by the etching method, decorating method, optical microscopy and scanning electron microscopy. It has been found that irradiation causes destabilization of the domain walls of the head-to-head-type with a negative charge screening spontaneous polarization (Ps). The negative domains in a positive matrix, which did not grow through the whole crystal body, were found to decay under the influence of radiation. In a place previously occupied by decaying negative domains, defect clusters are observed. The investigations have shown that there is a close correlation between the domain structure and the defect structure of BaTiO3 crystals.

  19. First-Principles Study on Electronic Structures and Optical Properties of Doped Ag Crystal

    Institute of Scientific and Technical Information of China (English)

    CAO Can; CHEN Ling-Na; JIA Shu-Ting; ZHANG Dan; XU Hui

    2012-01-01

    By using the first-principles calculation based on density functional theory,we investigate the electronic structures and optical properties of Cl-doped Ag crystal. The results show that the electronic structure of Cl-doped Ag crystal depends on the doped concentration and the site of impurity defect.Interestingly,the calculated adsorption spectra of Cl-doped Ag crystal show isotropy or anisotropy coincide with the symmetry of Ag crystal. These features are discussed to provide guidance to experimental efforts for Ag-based nanoeletronic devices.

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

    Science.gov (United States)

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

    2010-10-01

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

  1. Scaffold mining of kinase hinge binders in crystal structure database

    Science.gov (United States)

    Xing, Li; Rai, Brajesh; Lunney, Elizabeth A.

    2014-01-01

    Protein kinases are the second most prominent group of drug targets, after G-protein-coupled receptors. Despite their distinct inhibition mechanisms, the majority of kinase inhibitors engage the conserved hydrogen bond interactions with the backbone of hinge residues. We mined Pfizer internal crystal structure database (CSDb) comprising of several thousand of public as well as internal X-ray binary complexes to compile an inclusive list of hinge binding scaffolds. The minimum ring scaffolds with directly attached hetero-atoms and functional groups were extracted from the full compounds by applying a rule-based filtering procedure employing a comprehensive annotation of ATP-binding site of the human kinase complements. The results indicated large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds, which serve as the critical recognition elements for protein kinase interaction. Out of the nearly 4,000 kinase-inhibitor complexes in the CSDb we identified approximately 600 unique scaffolds. Hinge scaffolds are overwhelmingly flat with very little sp3 characteristics, and are less lipophilic than their corresponding parent compounds. Examples of the most common as well as the uncommon hinge scaffolds are presented. Although the most common scaffolds are found in complex with multiple kinase targets, a large number of them are uniquely bound to a specific kinase, suggesting certain scaffolds could be more promiscuous than the others. The compiled collection of hinge scaffolds along with their three-dimensional binding coordinates could serve as basis set for hinge hopping, a practice frequently employed to generate novel invention as well as to optimize existing leads in medicinal chemistry.

  2. 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.

  3. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules.

    Science.gov (United States)

    Janjić, Goran V; Ninković, Dragan B; Zarić, Snezana D

    2013-08-01

    Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

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

    Science.gov (United States)

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

    2011-04-01

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

  5. Crystal Structure of a Model Spider Silk Peptide

    Science.gov (United States)

    Chen, Shujun; Gido, Samuel; Valluzzi, Regina; Kaplan, David

    2001-03-01

    Crystallization study on a novel model silk peptide has been carried out using optical microscopy, AFM, TEM and electron diffraction. The sequence of the peptide, (E)5(GDVGGAGATGGS)2(E)5, is based on the GXYGGZ motif in the less repetitive amorphous blocks of Nephila clavipes spider dragline silk. When the peptide was crystallized out of aqueous solution, spherulites as well as dendritic crystals on the order of several to tens of microns in diameter were observed under polarizing optical microscope, depending on drying speed, volume of the droplet and concentration. The same crystals were collected and sonicated in methanol, a non-solvent, to yield individual crystals that were later examined in the electron microscope. Regular-shaped lamellar crystals of micron size were observed in the TEM. The lamellar thickness as determined by Pt/Pd shadowing and AFM is 50 Å. Selected area electron diffraction showed single crystal diffraction patterns indicating a possible orthorhombic unit cell of 9.91 x 5.57 x 20.40 Å.

  6. 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...

  7. Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines.

    Science.gov (United States)

    Bertolani, Arianna; Pizzi, Andrea; Pirrie, Lisa; Gazzera, Lara; Morra, Giulia; Meli, Massimiliano; Colombo, Giorgio; Genoni, Alessandro; Cavallo, Gabriella; Terraneo, Giancarlo; Metrangolo, Pierangelo

    2017-02-10

    Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report how the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure of a DFNKF derivative. Computational studies suggest that both the iodinated and the wild-type peptides populate very similar conformations. Furthermore, the conformer found in the solid-state structure is one of the most populated in solution, making the crystal structure a reliable model for the peptide in solution. The crystal structure of DFNKF(I) confirms the overall features of the amyloid cross-β spine and highlights how aromatic-aromatic interactions are important structural factors in the self-assembly of this peptide. A detailed analysis of such interactions is reported.

  8. 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...

  9. 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.

  10. 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.

  11. 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().

  12. 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.

  13. 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.

  14. The crystal structure of Kirkiite, Pb10Bi3As3S19

    DEFF Research Database (Denmark)

    Makovicky, Emil; Balic Zunic, Tonci; Karanovic, Ljiljana;

    2006-01-01

    The crystal structure of kirkiite has been solved using single-crystal data (MoKa X-ray diffraction, CCD area detector) to the conventional R-factor R1 = 0.069. It crystallizes in space group P21/m, with a 8.621(4), b 26.03(1), c 8.810(4) Å, ß 119.21(1)° and Z = 2. A crystal-structure determination....... The crystal structure of kirkiite can be described as (010) slabs of octahedra, three octahedra thick and related mutually by a refl ection plane situated in the intervening prismatic layer. In another interpretation, it is composed of slabs based on a transitional PbS-SnS archetype, with tightly bonded...

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

    Science.gov (United States)

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

    2015-11-19

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

  16. 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.

  17. Magnetic and structural transitions in crystals with a structure of the NaCl type

    Science.gov (United States)

    Kassan-Ogly, F. A.; Filippov, B. N.

    2009-04-01

    A model of simultaneous magnetic and structural first-order transitions in antiferromagnets with a strong cubic magnetic anisotropy has been constructed on the basis of a synthesis of magnetic modified 6-state and 8-state Potts models and the theoretical model of structural phase transitions in cubic crystals. A revised scheme has been suggested for the derivation of possible magnetic structures in the fcc lattice with allowance for competing interactions between the nearest and next-nearest neighbors. A calculation of the temperature evolution of high-temperature diffuse magnetic scattering of neutrons has been carried out to show that the mechanism of a magnetic transition at the Néel point is caused by the transformation of diffuse magnetic scattering into magnetic Bragg peaks.

  18. Crystal structure of the covalent intermediate of amylosucrase from Neisseria polysaccharea

    DEFF Research Database (Denmark)

    Jensen, Malene H; Mirza, Osman Asghar; Albenne, Cecile;

    2004-01-01

    be used for trapping the reaction intermediate for crystallographic studies. In this paper, the crystal structure of the acid/base catalyst mutant, E328Q, with a covalently bound glucopyranosyl moiety is presented. Sucrose cocrystallized crystals were soaked with alpha-D-glucopyranosyl fluoride, which...

  19. 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

  20. 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.

  1. Crystal structure and stability of Tl2CO3 at high pressures

    OpenAIRE

    Grzechnik, A.; Friese, K

    2010-01-01

    The crystal structure of dithallium carbonate, Tl2CO3 (C2/m, Z = 4), is stable to 5.82 GPa and does not undergo any phase transitions at lower pressures as reported previously. At higher pressures, the material undergoes a phase transition that destroys the single crystal.

  2. 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.

  3. The Crystal Structure and Behavior of Fenamic Acid-Acridine Complex Under High Pressure.

    Science.gov (United States)

    Jerzykiewicz, Lucjan; Sroka, Adam; Majerz, Irena

    2016-12-01

    The crystal structure of fenamic acid-acridine complex is determined by X-ray diffraction. The strong OHN hydrogen bond linking the complex components and other interactions responsible for packing of the molecules into a crystal are investigated within the Quantum Theory of Atom in Molecule theory. The crystal structure is compared with the structure optimized at B3LYP/6-311++G** level and with the theoretical structures optimized under systematically changed pressure. Analysis of the lattice constants, hydrogen bond lengths, and angles of the inter- and intramolecular hydrogen bond under compression is performed. The structural transformation observed at 5 GPa is connected with a change in the intermolecular OHN hydrogen bond. The proton shifts to acceptor and a new interaction in the crystal appears.

  4. The new piezoelectric single crystal obtained by the Ge doping in the α-quartz structure

    Science.gov (United States)

    Miclau, M.; Grozescu, A.; Bucur, R.; Poienar, M.; Vlazan, P.; Grozescu, I.; Miclau, N.; Muscutariu, I.

    2009-03-01

    The most interesting properties of the quartz-like crystals are its piezoelectric properties, which are strongly influenced by the intrinsic structural distortions of the material and the crystal growth conditions. Thus, physical properties such as coupling coefficient, the αβ transition can be directly related to structural distortions in terms of the bridging angle. We propose a new way to increase the structural distortion, using Ge to dope the SiO2 structure with respect to α-quartz structure type. Growth of α -SixGe1-xO2 crystal was realized hydrothermally using a temperature gradient method. Single crystals were investigated by electron microprobe analysis, X-ray diffraction and atomic force microscopy. The results open the possibility to tune the piezoelectric properties of these materials by varying the chemical composition.

  5. Co-crystals of the antiretroviral nevirapine: crystal structures, thermal analysis and dissolution behaviour

    OpenAIRE

    Aucamp, Marique Elizabeth; Engel, Emile; Liebenberg, Wilna; Stieger, Nicole; Caira, Mino R.; Susan A. Bourne

    2012-01-01

    Synthesis and physicochemical characterization of co-crystals of the antiretroviral drug nevirapine (NV) with the pharmaceutically acceptable co-formers saccharin, rac-tartaric acid, maleic acid, glutaric acid and salicylic acid are reported for the first time. The respective stoichiometric NV : co-former ratios are 2 : 1, 1 : 1, 1 : 1, 1 : 1 and 2 : 1. In the 1 : 1 co-crystals, the predicted R22(8) NV(amide)–carboxylic acid supramolecular synthon occurs, whereas in the 2 : 1 species, the co-...

  6. 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.

  7. 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.

  8. Photonic crystal alloys: a new twist in controlling photonic band structure properties.

    Science.gov (United States)

    Kim, Hee Jin; Kim, Dong-Uk; Roh, Young-Geun; Yu, Jaejun; Jeon, Heonsu; Park, Q-Han

    2008-04-28

    We identified new photonic structures and phenomenon that are analogous to alloy crystals and the associated electronic bandgap engineering. From a set of diamond-lattice microwave photonic crystals of randomly mixed silica and alumina spheres but with a well defined mixing composition, we observed that both bandedges of the L-point bandgap monotonically shifted with very little bowing as the composition was varied. The observed results were in excellent agreement with the virtual crystal approximation theory originally developed for electronic properties of alloy crystals. This result signifies the similarity and correspondence between photonics and electronics.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. Crystal structure and physical properties of a dithiolene complex crystal with adamantane supramolecular rotator

    OpenAIRE

    Yan, Yin-Nan; Kubo, Kazuya; Noro, Shin-ichiro; Akutagawa, Tomoyuki; Nakamura, Takayoshi

    2014-01-01

    Supramolecular cation salt of adamantane rotator with a dithiolene complex, (fluoroadamantylammonium(+))([18]-crown-6)[Ni(dmit)(2)](-) (1) was synthesized. The fluorine atom of the adamantane unit showed a large thermal factor elongated latitudinally, suggesting molecular rotation in the solid state. Crystal 1 exhibited a large dielectric response by applying an AC field along the a axis.

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

    Directory of Open Access Journals (Sweden)

    Olfa Mtioui-Sghaier

    2015-07-01

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

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

    Science.gov (United States)

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

    2015-07-01

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

  16. Crystal structure of 4-amino-1-(4-methylbenzylpyridinium bromide

    Directory of Open Access Journals (Sweden)

    N. Sharmila

    2014-12-01

    Full Text Available The title molecular salt, C13H15N2+·Br−, crystallized with two independent ion pairs (A and B in the asymmetric unit. In the cations, the planes of the pyridine and benzene rings are inclined to one another by 79.32 (8 and 82.30 (10° in ion pairs A and B, respectively. In the crystal, the anions and cations are connected by N—H...Br hydrogen bonds, forming a centrosymmetric tetramer-like unit enclosing an R84(16 ring motif. These units are linked via C—H...Br hydrogen bonds, forming a three-dimensional network.

  17. 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.

  18. Solving the Phase Problem in Crystal Structure Determination: A Simple Introduction to Direct Methods.

    Science.gov (United States)

    Schenk, H.

    1979-01-01

    Presents a simple way to introduce Direct Methods program systems to solve phase problems in x-ray crystal structure determination. It is intended for the undergraduate chemistry student laboratory. (Author/SA)

  19. 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).

  20. 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.

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

    Institute of Scientific and Technical Information of China (English)

    O.M. Ozkendir; S. Yildirimcan; A. Yuzer; K. Ocakoglu

    2016-01-01

    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 distor-tions in the samples.

  2. 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...

  3. 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.

  4. Synthesis, Character and Crystal Structure of the Complex {Er(DMSO)7} PW12O40

    Institute of Scientific and Technical Information of China (English)

    HAN Qiu-Xia; ZHANG Da-Li; MA Jian-Ru; WANG Jing-Ping; NIU Jing-Yang

    2007-01-01

    The synthesis, X-ray crystal structure, thermal properties and electrochemistry of the new complex formulated as {Er(DMSO)7}PW12O40 are reported. The single-crystal X-ray analysis reveals that the crystal crystallizes in the monoclinic system, space group P21/c with a=11.767(2), b=14.909(3), c=34.905(7)(A), β=98.97(3)°, Mr=3591.33, V=6049(2) (A)3, Dc=3.944g/em3, Z=4, GOOF=1.098, F(000)=6340, R=0.0490 and wR=0.1202. Crystal structure analysis indicates that the Er(Ⅲ) is seven-coordinate with a distorted pentagonal bipyramid and combines to the anion [PW12O40]3- via static electric force.

  5. 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.

  6. 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.

  7. Enhancement of Available Conversion Efficiency of Optical Parametric Amplifier in a Cascaded Photonic Crystal Structure

    Institute of Scientific and Technical Information of China (English)

    LI Wen-Hui; CHEN Li-Xue; TANG Dong-Hua; DING Wei-Qiang; LIU Shu-Tian

    2005-01-01

    @@ Using the cascaded structure of a linear and a second-order nonlinear photonic crystals, we realize a high-efficiency optical parametric amplifier in the case of exact phase matching. This proposal is verified using the slow-envelope nonlinear finite difference time domain numerical method. Compared with the case of the individual nonlinear photonic crystal structure, the oscillation threshold is decreased obviously, and the peak power amplification factor of the transmitted signal is enhanced more than 20 times.

  8. Prediction of inorganic superconductors with quasi-one-dimensional crystal structure

    OpenAIRE

    Volkova, L. M.; Marinin, D. V.

    2012-01-01

    Models of superconductors having a quasi-one-dimensional crystal structure based on the convoluted into a tube Ginzburg sandwich, which comprises a layered dielectric-metal-dielectric structure, have been suggested. The critical crystal chemistry parameters of the Ginzburg sandwich determining the possibility of the emergence of superconductivity and the Tc value in layered high-Tc cuprates, which could have the same functions in quasi-one-dimensional fragments (sandwich-type tubes), have bee...

  9. Crystal Structure of the Geobacillus stearothermophilus Carboxylesterase Est55 and Its Activation of Prodrug CPT-11

    OpenAIRE

    Liu, Ping; Ewis, Hosam E.; Tai, Phang C.; Lu, Chung-Dar; Weber, Irene T.

    2006-01-01

    Several mammalian carboxylesterases were shown to activate the prodrug irinotecan (CPT-11) to produce SN-38, a topoisomerase inhibitor used in cancer therapy. However, the potential use of bacterial carboxylesterases, which have the advantage of high stability, has not been explored. We present the crystal structure of the carboxyesterase Est55 from Geobacillus stearothermophilus and evaluation of its enzyme activity on CPT-11. Crystal structures were determined at pH 6.2 and 6.8 and resoluti...

  10. Crystal Structure of the Urokinase Receptor in a Ligand-Free Form

    DEFF Research Database (Denmark)

    Xu, Xiang; Gårdsvoll, Henrik; Yuan, Cai;

    2012-01-01

    . The crystal structure of human uPAR in its ligand-free state would clarify this issue, but such information remains unfortunately elusive. We now report the crystal structures of a stabilized, human uPAR (H47C/N259C) in its ligand-free form to 2.4 Å and in complex with amino-terminal fragment (ATF) to 3.2 Å...

  11. 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.

  12. 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

  13. Crystal Structure-Ionic Conductivity Relationships in Doped Ceria Systems

    DEFF Research Database (Denmark)

    Omar, Shobit; Wachsman, Eric D.; Jones, Jacob L.;

    2009-01-01

    In the past, it has been suggested that the maximum ionic conductivity is achieved in ceria, when doped with an acceptor cation that causes minimum distortion in the cubic fluorite crystal lattice. In the present work, this hypothesis is tested by measuring both the ionic conductivity and elastic...

  14. Re-investigation of the crystal structure of enstatite under high-pressure conditions

    DEFF Research Database (Denmark)

    Periotto, Benedetta; Balic Zunic, Tonci; Nestola, Fabrizio;

    2012-01-01

    A synthetic single crystal of pure orthoenstatite (MgSiO3, space group Pbca) has been investigated at high pressure for structural determinations by in situ single-crystal X‑ray diffraction using a diamond-anvil cell. Ten complete intensity data collections were performed up to 9.36 GPa. This study...... in the pressure range investigated. Using the data on the pure orthoenstatite as reference, we can confirm the basic influences of element substitutions on the evolution of the crystal structure with pressure....

  15. 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...

  16. 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.

  17. 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.

  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. Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine.

    Science.gov (United States)

    Noble, Christian G; Li, Shi-Hua; Dong, Hongping; Chew, Sock Hui; Shi, Pei-Yong

    2014-11-01

    Flavivirus methyltransferase is a genetically-validated antiviral target. Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. This raises a possibility that SAM is an integral structural component required for the folding of dengue virus (DENV) methyltransferase. Here we exclude this possibility by solving the crystal structure of DENV methyltransferase without SAM. The SAM ligand was removed from the enzyme through a urea-mediated denaturation-and-renaturation protocol. The crystal structure of the SAM-depleted enzyme exhibits a vacant SAM-binding pocket, with a conformation identical to that of the SAM-enzyme co-crystal structure. Functionally, equivalent enzymatic activities (N-7 methylation, 2'-O methylation, and GMP-enzyme complex formation) were detected for the SAM-depleted and SAM-containing recombinant proteins. These results clearly indicate that the SAM molecule is not an essential component for the correct folding of DENV methyltransferase. Furthermore, the results imply a potential antiviral approach to search for inhibitors that can bind to the SAM-binding pocket and compete against SAM binding. To demonstrate this potential, we have soaked crystals of DENV methyltransferase without a bound SAM with the natural product Sinefungin and show that preformed crystals are capable of binding ligands in this pocket.

  20. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures.

    Science.gov (United States)

    Mao, Binchen; Tejero, Roberto; Baker, David; Montelione, Gaetano T

    2014-02-05

    We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10-25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function.

  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. 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.

  3. Crystal structure and Raman spectra of rubidium hydrogen squarate

    Science.gov (United States)

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

    2005-05-01

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

  4. Crystal structure of Cs2[Th(NO36

    Directory of Open Access Journals (Sweden)

    Patrick Woidy

    2014-08-01

    Full Text Available Dicaesium hexanitratothorate(IV, Cs2[Th(NO36], was synthesized in the form of colourless crystals by reaction of thorium nitrate and caesium nitrate in aqueous solution. The Th atom is located on an inversion centre and is coordinated by six chelating nitrate anions. The resulting ThO12 coordination polyhedron is best described as a slightly distorted icosahedron. The Cs atom also has a coordination number of 12, but its coordination polyhedron is considerably more distorted. The crystal packing can be derived from an hexagonal dense packing (hcp of idealized spherical CsO12 and ThO12 units. The CsO12 units form a distorted hcp arrangement and half of the octahedral sites are occupied by the ThO12 units.

  5. Crystal structure of β-d,l-fructose

    Directory of Open Access Journals (Sweden)

    Tomohiko Ishii

    2015-10-01

    Full Text Available The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of d- and l-fructose (1,3,4,5,6-pentahydroxyhexan-2-one, arabino-hexulose or levulose, and it was confirmed that d-fructose (or l-fructose formed β-pyranose with a 2C5 (or 5C2 conformation. In the crystal, two O—H...O hydrogen bonds between the hydroxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral molecules into a column along the a axis. The columns are linked by other O—H...O hydrogen bonds between d- and l-fructose molecules, forming a three-dimensional network.

  6. Crystal structure of human prion protein fragment reveals a motif for oligomer formation

    Science.gov (United States)

    Apostol, Marcin I.; Perry, Kay; Surewicz, Witold K.

    2013-01-01

    The structural transition of the prion protein from α-helical to β-sheet rich underlies its conversion into infectious and disease-associated isoforms. Here we describe the crystal structure of a fragment from human prion protein consisting of the disulfide bond linked portions of helices 2 and 3. Instead of forming a pair-of-sheets steric zipper structure characteristic of amyloid fibers, this fragment crystallized into an β-sheet rich assembly of hexameric oligomers. This study reveals a never before observed structural motif for ordered protein aggregates, and suggests a possible mechanism for self-propagation of misfolded conformations by such non-amyloid oligomers. PMID:23808589

  7. Crystal structure of a human prion protein fragment reveals a motif for oligomer formation.

    Science.gov (United States)

    Apostol, Marcin I; Perry, Kay; Surewicz, Witold K

    2013-07-17

    The structural transition of the prion protein from α-helical- to β-sheet-rich underlies its conversion into infectious and disease-associated isoforms. Here we describe the crystal structure of a fragment from human prion protein consisting of the disulfide-bond-linked portions of helices 2 and 3. Instead of forming a pair-of-sheets steric zipper structure characteristic of amyloid fibers, this fragment crystallized into a β-sheet-rich assembly of hexameric oligomers. This study reveals a never before observed structural motif for ordered protein aggregates and suggests a possible mechanism for self-propagation of misfolded conformations by such nonamyloid oligomers.

  8. Crystal structure of 3-[(2-acetylphenoxycarbonyl]benzoic acid

    Directory of Open Access Journals (Sweden)

    Mohammad Shoaib

    2014-11-01

    Full Text Available In the title compound, C16H12O5, synthesized from isopthaloyl chloride and 2′-hydroxyacetophenone, the dihedral angle between the planes of the aromatic rings is 71.37 (9°. In the crystal, carboxylic acid inversion dimers generate R22(8 loops. The dimers are linked by C—H...O interactions, generating (101 sheets.

  9. Crystal structure of tin(II perchlorate trihydrate

    Directory of Open Access Journals (Sweden)

    Erik Hennings

    2014-12-01

    Full Text Available The title compound, [Sn(H2O3](ClO42, was synthesized by the redox reaction of copper(II perchlorate hexahydrate and metallic tin in perchloric acid. Both the trigonal–pyramidal [Sn(H2O3]2+ cations and tetrahedral perchlorate anions lie on crystallographic threefold axes. In the crystal, the cations are linked to the anions by O—H...O hydrogen bonds, generating (001 sheets.

  10. New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.

    Science.gov (United States)

    Thach, Trung Thanh; Lee, Sangho

    2014-11-01

    Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a=73.5, b=54.3, c=62.7 Å, β=118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cα atoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate (Ap5A) belonged to space group P1, with unit-cell parameters a=53.9, b=62.3, c=63.0 Å, α=101.9, β=112.6, γ=89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

  11. 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.

  12. Theory of the crystal structures of the actinide metals; Theorie des structures cristallines des metaux actinides

    Energy Technology Data Exchange (ETDEWEB)

    Penicaud, M. [CEA Bruyeres-le-Chatel, 91 (France)

    2005-07-01

    We describe, by bands calculation methods, the delocalized-localized transition of 5f electrons in the series of actinide metals, at ambient conditions, which happens between {alpha}-Pu and Am, and which is characterized by the change from the open and complex monoclinic crystal structure to the double hexagonal close-packed structure, and by the density collapse from 19.86 g.cm{sup -3} to 13.67 g.cm{sup -3}. The case of the alloy stabilized Pu in the high temperature {delta} phase (face centered cubic) is treated. Its ambient experimental density (15.92 g.cm{sup -3}) is obtained with a localization of the only 5f5/2 electrons. We find a 5f5/2 density of states peak pinned at the Fermi level, in agreement with photoelectron spectroscopy, and the high value of the electronic specific heat coefficient. The crystalline stability under pressure of U, Np, Pu and Am is examined. We find theoretically, at high pressure in Am, the stability of the recently discovered experimentally Am IV structure which is primitive-orthorhombic with four atoms in the unit cell. We calculate this structure also stable for Pu, for which it is proposed that the sequence is: {alpha}-Pu {yields} Am IV {yields} body-centered cubic. (author)

  13. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.

    Science.gov (United States)

    Peach, Megan L; Cachau, Raul E; Nicklaus, Marc C

    2017-02-24

    In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.

  14. 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.

  15. Luminescence labeling and dynamics of growth active crystal surface structures

    Science.gov (United States)

    Bullard, Theresa Vivian

    One aspect of the multifaceted proposal by A. G. Cairns-Smith (CS), that imperfect crystals have the capacity to act as primitive genes by transferring the disposition of their imperfections from one crystal to another, is investigated. An experiment was designed in a model crystalline system unrelated to the composition of the pre-biotic earth but suited to a well-defined test. Plates of potassium hydrogen phthalate were studied in order to ascertain whether, according to CS, parallel screw dislocations could serve as an information store with cores akin to punches in an old computer card. Evidence of screw dislocations was obtained from their associated growth hillocks through differential interference contrast microscopy, atomic force microscopy, and luminescence labeling of hillocks in conjunction with confocal laser scanning microscopy. Inheritance was evaluated by the corresponding patterns of luminescence developed in 'daughter' crystals grown from seed in the presence of fluorophores. The dispositions and evolution of growth active hillock patterns were quantified by fractal correlation analysis and statistical analysis. Along the way, we came to realize that transferring information encoded in the disposition of screw dislocations is complicated by several factors that lead to 'mutations' in the information stored in the pattern of defects. These observations forced us to confront the fundamental mechanisms that give rise to screw dislocations. It became clear that inter-hillock correlations play a significant role in the appearance of new dislocations through growth, and cause the overall pattern of hillocks to be non-random. Tendencies for clustering and correlations along various crystallographic directions were observed. Investigations into the dye-crystal surface chemistries and interactions with hillock steps also ensued through a combination of experimental techniques and force-field calculations. It was established that certain dye molecules not

  16. 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.

  17. 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.

  18. Template Synthesis of Noble Metal Nanocrystals with Unusual Crystal Structures and Their Catalytic Applications.

    Science.gov (United States)

    Fan, Zhanxi; Zhang, Hua

    2016-12-20

    Noble metal nanocrystals own high chemical stability, unique plasmonic and distinctive catalytic properties, making them outstanding in many applications. However, their practical applications are limited by their high cost and scarcity on the earth. One promising strategy to solve these problems is to boost their catalytic performance in order to reduce their usage amount. To realize this target, great research efforts have been devoted to the size-, composition-, shape- and/or architecture-controlled syntheses of noble metal nanocrystals during the past two decades. Impressively, recent experimental studies have revealed that the crystal structure of noble metal nanocrystals can also significantly affect their physicochemical properties, such as optical, magnetic, catalytic, mechanical, electrical and electronic properties. Therefore, besides the well-established size, composition, shape, and architecture control, the rise of crystal structure-controlled synthesis of noble metal nanocrystals will open up new opportunities to further improve their functional properties, and thus promote their potential applications in energy conversion, catalysis, biosensing, information storage, surface enhanced Raman scattering, waveguide, near-infrared photothermal therapy, controlled release, bioimaging, biomedicine, and so on. In this Account, we review the recent research progress on the crystal structure control of noble metal nanocrystals with a template synthetic approach and their crystal structure-dependent catalytic properties. We first describe the template synthetic methods, such as epitaxial growth and galvanic replacement reaction methods, in which a presynthesized noble metal nanocrystal with either new or common crystal structure is used as the template to direct the growth of unusual crystal structures of other noble metals. Significantly, the template synthetic strategy described here provides an efficient, simple and straightforward way to synthesize unusual

  19. 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.

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

    Science.gov (United States)

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

    2010-08-14

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

  1. Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution.

    Science.gov (United States)

    Broser, Matthias; Gabdulkhakov, Azat; Kern, Jan; Guskov, Albert; Müh, Frank; Saenger, Wolfram; Zouni, Athina

    2010-08-20

    The membrane-embedded photosystem II core complex (PSIIcc) uses light energy to oxidize water in photosynthesis. Information about the spatial structure of PSIIcc obtained from x-ray crystallography was so far derived from homodimeric PSIIcc of thermophilic cyanobacteria. Here, we report the first crystallization and structural analysis of the monomeric form of PSIIcc with high oxygen evolution capacity, isolated from Thermosynechococcus elongatus. The crystals belong to the space group C222(1), contain one monomer per asymmetric unit, and diffract to a resolution of 3.6 A. The x-ray diffraction pattern of the PSIIcc-monomer crystals exhibit less anisotropy (dependence of resolution on crystal orientation) compared with crystals of dimeric PSIIcc, and the packing of the molecules within the unit cell is different. In the monomer, 19 protein subunits, 35 chlorophylls, two pheophytins, the non-heme iron, the primary plastoquinone Q(A), two heme groups, 11 beta-carotenes, 22 lipids, seven detergent molecules, and the Mn(4)Ca cluster of the water oxidizing complex could be assigned analogous to the dimer. Based on the new structural information, the roles of lipids and protein subunits in dimer formation of PSIIcc are discussed. Due to the lack of non-crystallographic symmetry and the orientation of the membrane normal of PSIIcc perpendicular ( approximately 87 degrees ) to the crystallographic b-axis, further information about the structure of the Mn(4)Ca cluster is expected to become available from orientation-dependent spectroscopy on this new crystal form.

  2. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    Science.gov (United States)

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  3. 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.

  4. 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.

  5. 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.

  6. Crystal structure and vibrational properties of KMg 4(PO 4) 3

    Science.gov (United States)

    Tomaszewski, Paweł Edward; Mączka, Mirosław; Majchrowski, Andrzej; Waśkowska, Alicja; Hanuza, Jerzy

    2005-10-01

    Single crystals of potassium magnesium phosphate KMg 4(PO 4) 3 have been obtained from flux and characterized by means of single-crystal X-ray diffraction method and IR and Raman spectroscopy. This compound crystallizes in the Pnnm space group with a=16.361(3), b=9.562(19), c=6.171(12) Å and Z=4. The structure is built up of PO 4 tetrahedra, MgO 6 octahedra and MgO 5 polyhedra connected via P sbnd O sbnd Mg bridges to form a three-dimensional framework enclosing tunnels along b-axis occupied by K + ions. IR and Raman spectra are consistent with the crystal structure. The internal and external modes are observed in the 350-1210 cm -1 range and below 330 cm -1, respectively.

  7. Synthesis and Crystal Structure of 1-(2,6-Dichloro-4-nitrophenyl)-5-amino-4-cyanopyrazole

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The crystal structure of 1-(2,6-dichloro-4-nitrophenyl)-5-amino-4-cyanopyrazole (C10H10CI2N5O2, Mr = 298.09) has been determined by single-crystal X-ray diffraction.It crystallizes in the triclinic system, space group P1- with a = 8.1258(10), b = 8.6460(10), c = 10.0214(12) (A),α= 68.986(2), β= 71.598(2), γ= 85.181(2)°, V= 623.26(13) (A)3, Z = 2, Dc = 1.588g/cm3,μ= 0.525 mm-1, F(000) = 300, R = 0.0613 and wR = 0.1524 for 1890 observed reflections, and the extinction coefficient = 0.010(5).The crystal structure is stabilized by N-H…N hydrogenbonds.

  8. Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

    Science.gov (United States)

    Fu, Qianqian; Zhu, Biting; Ge, Jianping

    2017-02-16

    A SiO2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

  9. Crystal structure and electron density distribution in niobium carbide

    Energy Technology Data Exchange (ETDEWEB)

    Will, G.; Platzbecker, R. [Bonn Univ. (Germany). Abt. fuer Mineralogie und Kristallographie

    2001-09-01

    In this paper the bonding properties, e. g. the charge distribution between the atoms and the deformation of niobium carbide densities have been studied. The crystal studied had the composition NbC{sub 0.98}. Careful and redundant data collection (74 unique reflections out of 2087 reflections measured) gave the basis for a detailed study. IAM models (independent atom model), high order and multipole refinements were made resulting in R values of R=0.4% and R=0.07%. In the corresponding deformation density maps electron accumulations between the niobium atoms were detected, but no bonding to the carbon atoms. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Assane Toure

    2016-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Roman Doroschuk

    2015-08-01

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

  12. Defect structures in liquid crystals bounded by microwrinkles

    Science.gov (United States)

    Ohzono, Takuya

    2013-09-01

    Spatially confined liquid crystals (LCs) exhibit non-uniform alignment, often accompanied by self-organized topological defects of non-trivial shape in response to imposed boundary conditions and geometry. Here we show that a nematic LC, when confined in a sinusoidal microwrinkle groove, exhibits a new periodic arrangement of twist deformations and a zigzag line defect. This periodic ordering results from the inherent LC elastic anisotropy and the antagonistic boundary conditions at the top flat LC and the curved LC-groove interfaces. The effect of the LC thickness on the stability of the line defect is also shown.

  13. Parent and trisubstituted triazacoronenes: synthesis, crystal structure and physicochemical properties.

    Science.gov (United States)

    Tan, Qitao; Chen, Huanhuan; Xia, Huaida; Liu, Bingxin; Xu, Bin

    2016-01-11

    A four-step synthesis of the C3-symmetric parent 1,5,9-triazacoronene (TAC) and its derivatives was achieved using a three-fold Bischler-Napieralski cyclization as the key step. The single-crystal X-ray diffraction of 1b (R = n-Bu) demonstrates that the azacoronene core is perfectly co-planar and the molecules adopt a favorable 2-D "brick-wall" arrangement with strong π-π interactions. The unique stacking, tunable photophysical and electronic properties, and high thermal stability should make them promising candidates for emissive and electron-transport materials.

  14. 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.

  15. Crystal structure of 4-meth-oxy-quinazoline.

    Science.gov (United States)

    El-Hiti, Gamal A; Smith, Keith; Hegazy, Amany S; Alshammari, Mohammed B; Kariuki, Benson M

    2014-12-01

    The title compound, C9H8N2O, is almost planar, with the C atom of the meth-oxy group deviating from the mean plane of the quinazoline ring system (r.m.s. deviation = 0.011 Å) by 0.068 (4) Å. In the crystal, mol-ecules form π-π stacks parallel to the b-axis direction [centroid-centroid separation = 3.5140 (18) Å], leading to a herringbone packing arrangement.

  16. Crystal structure of ethyl 2-chloro-6-methylquinoline-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Hasna Hayour

    2014-09-01

    Full Text Available In the title compound, C13H12ClNO2, the dihedral angle between the planes of the quinoline ring system (r.m.s. deviation = 0.029 Å and the ester group is 54.97 (6°. The C—O—C—Cm (m = methyl torsion angle is −140.62 (16°. In the crystal, molecules interact via aromatic π–π stacking [shortest centroid–centroid separation = 3.6774 (9 Å] generating (010 sheets.

  17. Crystal structures of 2,3,6,7,10,11-oxytriphenylenes. Implications for columnar discotic mesophases

    DEFF Research Database (Denmark)

    Andresen, T.L.; Krebs, Frederik C; Thorup, Niels;

    2000-01-01

    in the aim that a detailed structural knowledge of the discotic premesogens could be used to infer detailed structural knowledge with respect to known liquid crystal mesogens where little detailed structural knowledge is available. It was found that the crystal structures of the discotic premesogens were......The structures of the oxysubstituted triphenylene premesogens, 2,3,6,7,10,11-hexahydroxy-triphenylene (4), 2,3,6,7,10,11-hexamethoxytriphenylene (5), 2,3,6,7,10,11-hexaethoxytriphenylene (6), and 2,3,6,7,10,11-hexapropoxytriphenylene (7) were determined, and the structural results were investigated...... very different from the structures expected for discotic columnar behavior. These differences allowed us to shed some light on the structural forces that gives rise to the mesophasic behavior observed in such systems as being not due to stacking of the planar aromatic core as inferred hitherto...

  18. SYNTHESIS AND CRYSTAL STRUCTURE OF A NEW COMPOUND Sr6Sn2Nb8O30

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A new compound Sr6Sn2Nb8O30 was found in th e ternary system of SrO-SnO2-Nb2O5.The transparent colorless crystal wit h n eedle-like shape can be grown by flux method.The crystal structure of new compo un d was determined by X-ray diffraction, and its belongs to tungsten bronze struc ture.Sr6Sn2Nb8O30 crystallizes in orthorhombic system with unit cell parameters a=17.579(1),b=17.509(1),c=7.7880(5),Z=4 and space group Cmm2.

  19. A fast selenium derivatization strategy for crystallization and phasing of RNA structures

    OpenAIRE

    Olieric, Vincent; Rieder, Ulrike; Lang, Kathrin; Serganov, Alexander; Schulze-Briese, Clemens; Micura, Ronald; Dumas, Philippe; Ennifar, Eric

    2009-01-01

    Site-specific 2′-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 2′-OCH3-modified RNA sequences, prior to the replacement of 2′-OCH3 groups with their 2′-SeCH3 counterparts. The method exploits the similar crystallization properties of 2′-OCH3- and 2′-SeCH3-modified RNAs a...

  20. Quality assessment of layer-structured semiconductor single crystals by nuclear quadruple resonance method

    Science.gov (United States)

    Samila, Andriy; Khandozhko, Alexander; Lastivka, Galina; Politansky, Leonid; Khandozhko, Victor

    2015-11-01

    A method for quality assessment of layer-structured semiconductor single crystals (InSe, GaSe, GaS) grown in evacuated ampoules by the Bridgman technique is proposed. For this purpose, nuclear quadruple resonance method with a consecutive scanning of the entire sample volume and evaluation of crystal perfection by the resulting spectra is used. Effective interaction between high-frequency field and crystal and, accordingly, restriction of scanning area of sample under study is provided with the use of a two-way saddle-shaped coil for a nuclear quadruple resonance spectrometer.