Sample records for abstract crystal structure

  1. ICCG-10: Tenth International Conference on Crystal Growth. Oral presentation abstracts

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Oral presentation abstracts from the tenth International Conference on Crystal Growth (ICCG) (Aug. 16-21, 1992) are provided. Topics discussed at the conference include superconductors, semiconductors, nucleation, crystal growth mechanisms, and laser materials. Organizing committees, ICCG advisory board and officers, and sponsors of the conference are also included.

  2. ICCG-10: Tenth International Conference on Crystal Growth. Poster presentation abstracts

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Poster presentation abstracts from the tenth International Conference on Crystal Growth (ICCG) (Aug. 16-21, 1992) are provided. Topics discussed at the conference include crystal growth mechanisms, superconductors, semiconductors, laser materials, optical materials, and biomaterials. Organizing committees, ICCG advisory board and officers, and sponsors of the conference are also included.

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

    PubMed Central

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

    2017-01-01

    Abstract 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 129Xe NMR spectroscopy. The high sensitivity of the 129Xe 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. PMID:28111848

  4. Synthesis and crystal structure analysis of uranyl triple acetates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com; Department of Chemistry, Samara National Research University, 443086 Samara; Serezhkina, Larisa B.

    2016-12-15

    Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studiedmore » and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.« less

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

    PubMed Central

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

    2016-01-01

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

  6. User-Extensible Graphics Using Abstract Structure,

    DTIC Science & Technology

    1987-08-01

    Flex 6 The Algol68 model of the graphical abstract structure 5 The creation of a PictureDefinition 6 The making of a picture from a PictureDefinition 7...data together with the operations that can be performed on that data. i 7! ś I _ § 4, The Alqol68 model of the graphical abstract structure Every

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rao Popuri, Srinivasa; University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac; National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara

    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 reversiblemore » 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.« less

  8. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

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

  9. A review on the synthesis, crystal growth, structure and physical properties of rare earth based quaternary intermetallic compounds

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

    2016-04-15

    This review highlights the synthesis and crystal growth of quaternary intermetallic compounds based on rare earth metals. In the first part of this review, we highlight briefly about intermetallics and their versatile properties in comparison to the constituent elements. In the next part, we have discussed about various synthesis techniques with more focus on the metal flux technique towards the well shaped crystal growth of novel compounds. In the subsequent parts, several disordered quaternary compounds have been reviewed and then outlined most known ordered quaternary compounds with their complex structure. A special attention has been given to the ordered compoundsmore » with structural description and relation to the parent binary and ternary compounds. The importance of electronic and structural feature is highlighted as the key roles in designing these materials for emerging applications. - Graphical abstract: Rare earth based quaternary intermetallic compounds crystallize in complex novel crystal structures. The diversity in the crystal structure may induce unique properties and can be considered them as future materials. - Highlights: • Crystal growth and crystal structure of quaternary rare earth based intermetallics. • Structural complexity of quaternary compounds in comparison to the parent compounds. • Novel quaternary compounds display unique crystal structure.« less

  10. Synthesis, crystal structure and electronic structure of the binary phase Rh{sub 2}Cd{sub 5}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Koley, Biplab; Chatterjee, S.; Jana, Partha P., E-mail: ppj@chem.iitkgp.ernet.in

    2017-02-15

    A new phase in the Rh-Cd binary system - Rh{sub 2}Cd{sub 5} has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh{sub 2}Cd{sub 5} crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh{sub 2}Cd{sub 5} can be described as a defect form of the In{sub 3}Pd{sub 5} 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 ofmore » (3{sup 5}) (3{sup 7})- 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 Rh{sub 2}Cd{sub 5}. - Graphical abstract: (3.6.3.6)-Kagomé nets of cadmium atoms (top) and (3{sup 5}) (3{sup 7})- nets of both cadmium and rhodium atoms (bottom) in the structure of Rh{sub 2}Cd{sub 5}.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vognsen, Tina, E-mail: tv@farma.ku.dk; Kristensen, Ole, E-mail: ok@farma.ku.dk

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer The crystal structure of the NTF2-like domain of Rasputin protein is presented. Black-Right-Pointing-Pointer Differences to known ligand binding sites of nuclear transport factor 2 are discussed. Black-Right-Pointing-Pointer A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 A resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a {beta}-sheet and three {alpha}-helices forming a cone-like shape. However, known binding sites formore » RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.« less

  12. Potassium and magnesium succinatouranilates – Synthesis and crystal structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Novikov, S.A., E-mail: serg.alex.novikov@gmail.com; Grigoriev, M.S.; Serezhkina, L.B.

    2017-04-15

    Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}] [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), where C{sub 4}H{sub 4}O{sub 4}{sup 2-} is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} with the same A{sub 2}Q{sup 02}{sub 3} crystallochemical formula (A=UO{sub 2}{sup 2+}, Q{sup 02}=C{sub 4}O{sub 4}H{sub 4}{sup 2-}), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ionsmore » is one of the factors, which affects the structure of [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A{sub 2}Q{sup 02}{sub 3} crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality. - Graphical abstract: Crystal structures of two new uranium(VI) coordination polymers with succinate linkers, namely K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), were determined by single-crystal XRD. Crystals of studied compounds are based on 2D or 1D structural units with the same composition and crystallochemical formula. Topological isomerism in A{sub 2}Q{sup 02}{sub 3} crystallochemical group and conformations of succinate anions in uranyl complexes are under discussion. - Highlights: • Two new uranium coordination polymers were synthesized. • Their structural units have the same composition and crystallochemical formula. • In spite the same composition and CCF dimensionality of units is different. • Structural features of

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

    NASA Astrophysics Data System (ADS)

    Ni, Yunxiang

    1995-01-01

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

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

    PubMed

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

    2009-12-24

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

  15. Study of structural and optical properties of YAG and Nd:YAG single crystals

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kostić, S.; Lazarević, Z.Ž., E-mail: lzorica@yahoo.com; Radojević, V.

    2015-03-15

    Highlights: • Transparent YAG and pale pink Nd:YAG single crystals were produced by the Czochralski technique. • Growth mechanisms and shape of the liquid/solid interface and incorporation of Nd{sup 3+} were studied. • The structure of the crystals was investigated by X-ray diffraction, Raman and IR spectroscopy. • The 15 Raman and 17 IR modes were observed. • The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. - Abstract: Yttrium aluminum garnet (YAG, Y{sub 3}Al{sub 5}O{sub 12}) and yttrium aluminum garnet doped with neodymium (Nd:YAG) single crystals were grown by the Czochralski technique. Themore » critical diameter and the critical rate of rotation were calculated. Suitable polishing and etching solutions were determined. As a result of our experiments, the transparent YAG and pale pink Nd:YAG single crystals were produced. The obtained crystals were studied by X-ray diffraction, Raman and IR spectroscopy. The crystal structure was confirmed by XRD. The 15 Raman and 17 IR modes were observed. The Raman and IR spectroscopy results are in accordance with X-ray diffraction analysis. The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. The absence of a core was confirmed by viewing polished crystal slices. Also, it is important to emphasize that the obtained Nd:YAG single crystal has a concentration of 0.8 wt.% Nd{sup 3+} that is characteristic for laser materials.« less

  16. Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

    PubMed

    Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

    2017-10-10

    Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

  17. Typographic Settings for Structured Abstracts.

    ERIC Educational Resources Information Center

    Hartley, James

    2000-01-01

    Lists some of the major typographic variables involved in structured abstracts (containing sub-headings). Illustrates how typography can affect clarity by presenting seven examples that illustrate the effects of these typographic variables in practice. Concludes with a final example of an effective approach. (SR)

  18. Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Eliziario Nunes, Sayonara; Department of Materials Engineering, Federal University of São Carlos, 13565-905 São Carlos, SP; Wang, Chun-Hai

    2015-02-15

    We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, 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. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu;more » A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.« less

  19. Integrative interactive visualization of crystal structure, band structure, and Brillouin zone

    NASA Astrophysics Data System (ADS)

    Hanson, Robert; Hinke, Ben; van Koevering, Matthew; Oses, Corey; Toher, Cormac; Hicks, David; Gossett, Eric; Plata Ramos, Jose; Curtarolo, Stefano; Aflow Collaboration

    The AFLOW library is an open-access database for high throughput ab-initio calculations that serves as a resource for the dissemination of computational results in the area of materials science. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, band structure, and Brillouin zone. Interactivity is obtained using two synchronized JSmol implementations, one for the crystal structure and one for the Brillouin zone, along with a D3-based band-structure diagram produced on the fly from data obtained from the AFLOW database. The current website portal (http://aflowlib.mems.duke.edu/users/jmolers/matt/website) allows interactive access and visualization of crystal structure, Brillouin zone and band structure for more than 55,000 inorganic crystal structures. This work was supported by the US Navy Office of Naval Research through a Broad Area Announcement administered by Duke University.

  20. Structural study of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} single crystals

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ishii, Yuto; Matsushita, Yoshitaka; Oda, Migaku

    Single crystals of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} were synthesized and the crystal structures at 293 K and 113 K were studied using X-ray diffraction experiments. We found a structural phase transition from the room-temperature crystal structure with space group C2/c to a low-temperature structure with space group P2{sub 1}/c, resulting from a rotational displacement of SiO{sub 4} tetrahedra. The temperature dependence of magnetic susceptibility shows a broad maximum around 116 K, suggesting an opening of the Haldane gap expected for one-dimensional antiferromagnets with S=1. However, an antiferromagnetic long-range order was developed below 24 K, probably caused by amore » weak inter-chain magnetic coupling in the compound. - Graphical abstract: Low temperature crystal structure of LiVSi{sub 2}O{sub 6} and an orbital arrangement within the V-O zig-zag chain along the c-axis. - Highlights: • A low temperature structure of LiVSi{sub 2}O{sub 6} was determined by single crystal X-ray diffraction measurements. • The origin of the structural transition is a rotational displacement of SiO{sub 4} tetrahedra. • The uniform orbital overlap in the V-O zigzag chain makes the system a quasi one-dimensional antiferromagnet.« less

  1. Synthesis, crystal structure, and magnetic properties of two-dimensional divalent metal glutarate/dipyridylamine coordination polymers, with a single crystal-to-single crystal transformation in the copper derivative

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Montney, Matthew R.; Supkowski, Ronald M.; Staples, Richard J.

    Hydrothermal reaction of divalent metal chlorides with glutaric acid and 4,4'-dipyridylamine (dpa) has afforded an isostructural family of coordination polymers with formulation [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate). Square pyramidal coordination is seen in 1-3, with semi-ligation of a sixth donor to produce a '5+1' extended coordination sphere. Neighboring metal atoms are linked into 1D [M(glu)]{sub n} neutral chains through chelating/monodentate bridging glutarate moieties with a syn-anti binding mode, and semi-chelation of the pendant carboxylate oxygen. These chains further connect into 2D layers through dipodal dpa ligands. Neighboring layers stack into the pseudo 3D crystal structure ofmore » 1-3 through supramolecular hydrogen bonding between dpa amine units and the semi-chelated glutarate oxygen atoms. The variable temperature magnetic behavior of 1-3 was explored and modeled as infinite 1D Heisenberg chains. Notably, complex 3 undergoes a thermally induced single crystal-to-single crystal transformation between centric and acentric space groups, with a conformationally disordered unilayer structure at 293 K and an ordered bilayer structure at 173 K. All materials were further characterized via infrared spectroscopy and elemental and thermogravimetric analyses. - Graphical abstract: The coordination polymers [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate, dpa=4,4'-dipyridylamine) exhibit 2D layer structures based on 1D [M(glu)]{sub n} chains linked through dpa tethers. Antiferromagnetic coupling is observed for 2 and 3, while ferromagnetism is predominant in 1. Compound 3 undergoes a thermally induced single crystal-to-single crystal transformation from an acentric to a centrosymmetric space group.« less

  2. Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

    PubMed

    Price, Sarah Sally L

    2009-01-20

    The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible

  3. Argument structure and the representation of abstract semantics.

    PubMed

    Rodríguez-Ferreiro, Javier; Andreu, Llorenç; Sanz-Torrent, Mònica

    2014-01-01

    According to the dual coding theory, differences in the ease of retrieval between concrete and abstract words are related to the exclusive dependence of abstract semantics on linguistic information. Argument structure can be considered a measure of the complexity of the linguistic contexts that accompany a verb. If the retrieval of abstract verbs relies more on the linguistic codes they are associated to, we could expect a larger effect of argument structure for the processing of abstract verbs. In this study, sets of length- and frequency-matched verbs including 40 intransitive verbs, 40 transitive verbs taking simple complements, and 40 transitive verbs taking sentential complements were presented in separate lexical and grammatical decision tasks. Half of the verbs were concrete and half were abstract. Similar results were obtained in the two tasks, with significant effects of imageability and transitivity. However, the interaction between these two variables was not significant. These results conflict with hypotheses assuming a stronger reliance of abstract semantics on linguistic codes. In contrast, our data are in line with theories that link the ease of retrieval with availability and robustness of semantic information.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Crystal structure, spectral, thermal and dielectric studies of a new zinc benzoate single crystal

    NASA Astrophysics Data System (ADS)

    Bijini, B. R.; Prasanna, S.; Deepa, M.; Nair, C. M. K.; Rajendra Babu, K.

    2012-11-01

    Single crystals of zinc benzoate with a novel structure were grown in gel media. Sodium metasilicate of gel density 1.04 g/cc at pH 6 was employed to yield transparent single crystals. The crystal structure of the compound was ascertained by single crystal X-ray diffractometry. It was noted that the crystal belongs to monoclinic system with space group P21/c with unit cell parameters a = 10.669(1) Å, b = 12.995(5) Å, c = 19.119(3) Å, and β = 94.926(3)°. The crystal was seen to possess a linear polymeric structure along b-axis; with no presence of coordinated or lattice water. CHN analysis established the stoichiometric composition of the crystal. The existence of functional groups present in the single crystal system was confirmed by FT-IR studies. The thermal characteristic of the sample was analysed by TGA-DTA techniques, and the sample was found to be thermally stable up to 280 °C. The kinetic and thermodynamic parameters were also determined. UV-Vis spectroscopy corroborated the transparency of the crystal and revealed the optical band gap to be 4 eV. Dielectric studies showed decrease in the dielectric constant of the sample with increase in frequency.

  6. Crystal structure, electronic structure, and photoluminescent properties of SrMoO{sub 4}:Tb{sup 3+} phosphors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Park, Sung Wook; Moon, Byung Kee; Jeong, Jung Hyun, E-mail: jhjeong@pknu.ac.kr

    2015-10-15

    Highlights: • SrMoO{sub 4}:Tb{sup 3+} phosphor samples were synthesized at different temperatures. • The crystal and electronic structures, and luminescence properties were studied. • The excitation peak shifts to red with increasing the sintering temperature. • The luminescence mechanism of SrMoO{sub 4}:Tb{sup 3+} was suggested. - Abstract: The experimental and theoretical studies of the optical properties of SrMoO{sub 4}:Tb{sup 3+} phosphors were carried out. The structural, optical, and electronical properties of the phosphors were systematically studied. The phosphor samples were crystallized at different temperatures via a sol–gel method. Excitation spectra of SrMoO{sub 4}:Tb{sup 3+} powder samples exhibited gradual red shiftmore » and luminescent intensity changed with increasing the sintering temperature. Such spectral changes depend strongly on the crystallographic properties such as lattice parameters and crystallinity. The shift of the excitation spectra is mainly ascribed to the covalent bond interaction between Mo−O bonds. An energy band model was demonstrated to describe the luminescence mechanism in the material.« less

  7. Investigating the Abstractness of Children's Early Knowledge of Argument Structure

    ERIC Educational Resources Information Center

    McClure, Kathleen; Pine, Julian M.; Lieven, Elena V. M.

    2006-01-01

    In the current debate about the abstractness of children's early grammatical knowledge, Tomasello & Abbott-Smith (2002) have suggested that children might first develop "weak" or "partial" representations of abstract syntactic structures. This paper attempts to characterize these structures by comparing the development of constructions around…

  8. Crystal structure of NucB, a biofilm-degrading endonuclease

    PubMed Central

    Baslé, Arnaud; Hewitt, Lorraine; Koh, Alan; Lamb, Heather K; Thompson, Paul; Burgess, J Grant; Hall, Michael J; Hawkins, Alastair R; Murray, Heath

    2018-01-01

    Abstract Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent. PMID:29165717

  9. Crystal growth and electronic structure of low-temperature phase SrMgF{sub 4}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Atuchin, Victor V.; Functional Electronics Laboratory, Tomsk State University, Tomsk 634050; Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, Novosibirsk 630090

    2016-04-15

    Using the vertical Bridgman method, the single crystal of low temperature phase SrMgF{sub 4} is obtained. The crystal is in a very good optical quality with the size of 10×7×5 mm{sup 3}. Detailed photoemission spectra of the element core levels are determined by a monochromatic AlKa (1486.6 eV) X-ray source. Moreover, the first-principles calculations are performed to investigate the electronic structure of SrMgF{sub 4}. A good agreement between experimental and calculated results is achieved. It is demonstrated that almost all the electronic orbitals are strongly localized and the hybridization with the others is very small, but the Mg–F bonds covalencymore » is relatively stronger than that of Sr–F bonds. - Graphical abstract: Large size of low-temperature phase SrMgF{sub 4} crystal was obtained (right) and its electronic structure was investigated by X-ray photoelectron spectroscopy and first-principles calculation (left). - Highlights: • Large size single crystal of low-temperature phase SrMgF{sub 4} is obtained. • Electronic structure of SrMgF{sub 4} is measured by X-ray photoelectron spectroscopy. • Partial densities of states are determined by first-principles calculation. • Good agreement between experimental and calculated results is achieved. • Strong ionic characteristics of chemical bonds are exhibited in SrMgF{sub 4}.« less

  10. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  11. Likelihood-based modification of experimental crystal structure electron density maps

    DOEpatents

    Terwilliger, Thomas C [Sante Fe, NM

    2005-04-16

    A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

  12. Band structures in fractal grading porous phononic crystals

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

    2018-05-01

    In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Crystal structure of low-symmetry rondorfite

    NASA Astrophysics Data System (ADS)

    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.

  16. Ferroelectric performances and crystal structures of (Pb, La)(Zr, Ti, Nb)O{sub 3}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kitamura, Naoto; Division of Ecosystem Research, Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510; Mizoguchi, Takuma

    2014-02-15

    In this study, we focused on Nb and La substituted Pb(Zr, Ti)O{sub 3}: i.e., (Pb, La)(Zr, Ti, Nb)O{sub 3}. As for the samples, dependences of ferroelectric properties on La and Nb compositions were examined. In addition, the crystal structures were analyzed by the Rietveld method, and then a relationship between the metal compositions and the crystal structures were discussed. From P–E hysteresis loop measurements, it was found that the remanant polarization of Pb(Zr, Ti)O{sub 3} was increased by both the La and Nb substitutions although the heavy substitution of La had an undesirable effect. It was also indicated that themore » Curie temperature decreased with increasing La content. The Rietveld analysis using synchrotron X-ray diffraction patterns demonstrated that the structure distortion was relaxed by the La and Nb substitutions. Such a change in the crystals was well consistent with the harmful effects on the Curie temperature and the remanent polarization by the heavy La substitution. - Graphical abstract: Rietveld refinement pattern of 2 mol% PbSiO{sub 3}-added Pb{sub 0.95}La{sub 0.05}Zr{sub 0.50}Ti{sub 0.45}Nb{sub 0.05}O{sub 3} (synchrotron X-ray diffraction). Display Omitted - Highlights: • (Pb,La)(Zr,Ti,Nb)O{sub 3} were successfully synthesized. • Remanant polarization of Pb(Zr,Ti)O{sub 3} was improved by substitutions of La and Nb. • Crystal structures of (Pb,La)(Zr,Ti,Nb)O{sub 3} were refined and the distortions were estimated.« less

  17. Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

    We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

  18. Structure-property evolution during polymer crystallization

    NASA Astrophysics Data System (ADS)

    Arora, Deepak

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

  19. Crystal structure of minoxidil at low temperature and polymorph prediction.

    PubMed

    Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

    2008-02-01

    An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

  20. From molecule to solid: The prediction of organic crystal structures

    NASA Astrophysics Data System (ADS)

    Dzyabchenko, A. V.

    2008-10-01

    A method for predicting the structure of a molecular crystal based on the systematic search for a global potential energy minimum is considered. The method takes into account unequal occurrences of the structural classes of organic crystals and symmetry of the multidimensional configuration space. The programs of global minimization PMC, comparison of crystal structures CRYCOM, and approximation to the distributions of the electrostatic potentials of molecules FitMEP are presented as tools for numerically solving the problem. Examples of predicted structures substantiated experimentally and the experience of author’s participation in international tests of crystal structure prediction organized by the Cambridge Crystallographic Data Center (Cambridge, UK) are considered.

  1. Synthesis, growth, structure, mechanical and optical properties of a new semi-organic 2-methyl imidazolium dihydrogen phosphate single crystal

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nagapandiselvi, P., E-mail: nagapandiselvip@ssn.edu.in; Baby, C.; Gopalakrishnan, R.

    2016-09-15

    Highlights: • 2MIDP crystals were grown by slow evaporation solution growth technique. • Single crystal XRD revealed self-assembled supramolecular framework. • Z scan technique is employed for third order nonlinear optical susceptibility. • Structure-property correlation is established. - Abstract: A new semi-organic compound, 2-methyl imidazolium dihydrogen phosphate (2MIDP), was prepared and good quality single crystals of 2MIDP were grown by slow evaporation solution growth technique. Crystal structure elucidated using Single crystal XRD showed that 2MIDP crystallizes in monoclinic system with P2{sub 1}/c space group. FT-IR, UV-Vis-NIR, Fluorescence and FT-NMR spectra confirm the molecular structure of 2MIDP. The UV-Vis-NIR spectra establishedmore » the suitability of the compound for NLO applications. TG-DSC showed that 2MIDP is thermally stable up to 200 °C. Mechanical characteristics like hardness number (H{sub v}), stiffness constant (C{sub 11}), yield strength (σ{sub v}), fracture toughness (K{sub c}) and brittleness index (B{sub i}) were assessed using Vicker’s microhardness tester. Third order nonlinear optical properties determined from Z-scan measurement using femto and picosecond lasers showed two photon reverse saturable absorption. The enhancement of nonlinear optical properties in femto second laser, revealed the suitability of 2MIDP for optical limiting applications.« less

  2. Hydrothermal synthesis, crystal structure and properties of 2-D and 3-D lanthanide sulfates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xu Yan; Ding Shaohua; Zheng Xuefang

    2007-07-15

    Two new lanthanum sulfates DySO{sub 4}(OH) 1 and Eu{sub 2}(SO{sub 4}){sub 3}(H{sub 2}O){sub 8} 2 have been hydrothermally synthesized. The colorless crystals were characterized by IR, TGA, ICP and XRD. The structure was determined by single-crystal X-ray diffraction. 1 crystallizes with monoclinic symmetry, space group P2(1)/n [a=7.995(4) A, b=10.945(5) A, c=8.164(4) A, {alpha}=90{sup o}, {beta}=93.619(6){sup o}, {gamma}=90{sup o}, V=713.0(5) A{sup 3}, Z=8]. It displays a three-dimensional framework, based on the novel Dy-O chains connected by the sulfate groups through helical chains. 2 crystallizes with monoclinic symmetry, space group C2/c, [a=13.5605(17) A, b=6.7676(8) A, c=18.318(2) A, {alpha}=90{sup o}, {beta}=102.265(2){sup o}, {gamma}=90{supmore » o}, V=1642.7 (4) A{sup 3}, Z=4]. Its layered framework is attained by the europium atoms connected by the sulfate groups arranged in a helical manner. - Graphical abstract: Two new lanthanum sulfates DySO{sub 4}(OH) 1 and Eu{sub 2} (SO{sub 4}){sub 3} (H{sub 2}O){sub 8} 2 have been hydrothermally synthesized. The colorless crystals were characterized by IR, TGA, ICP and XRD. The structure was determined by single-crystal X-ray diffraction. It displays a three dimensional framework, based on the novel Dy-O chains connected by the sulfate groups through helical chains.« less

  3. Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ito, Tasuku; Saikawa, Kyo; Kim, Seonah

    2014-04-25

    Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - Abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-L-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-L-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system ofmore » hydroxyproline-linked β-L-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-L-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn{sup 2+} coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-L-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.« less

  4. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.

    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, EBOVmore » 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 mechanisms governing VP35's functions and inform the design of therapeutics.« less

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

    PubMed

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

    2017-04-05

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

  6. Crystal Structure Prediction via Deep Learning.

    PubMed

    Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

    2018-06-06

    We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

  7. Crystal Structure of Hydrazinium Iodide by Neutron Diffraction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Campbell, Eric V.; Wang, Xiaoping; Miller, Joel S.

    The structure of hydrazinium iodide, [H 5N 2] +·I -, at 100 K has monoclinic (P2 1/n) symmetry from single crystal neutron diffraction with a = 7.4599(7) Å, b = 5.3185(6) Å, c = 10.1628(11) Å, β = 103.150(10)°, V = 392.64(7) Å 3, Z = 4. The refinement converged to R = 0.0575, wR 2 = 0.1602, S = 1.022. Data for the crystal structure was collected on the SNS TOPAZ single-crystal time-of-flight Laue diffractometer. The compound has a one-dimensional structure which displays N–H···N hydrogen bonding. Finally, accurate intra- and intermolecular N–H distances have been determined.

  8. Crystal Structure of Hydrazinium Iodide by Neutron Diffraction

    DOE PAGES

    Campbell, Eric V.; Wang, Xiaoping; Miller, Joel S.

    2017-10-31

    The structure of hydrazinium iodide, [H 5N 2] +·I -, at 100 K has monoclinic (P2 1/n) symmetry from single crystal neutron diffraction with a = 7.4599(7) Å, b = 5.3185(6) Å, c = 10.1628(11) Å, β = 103.150(10)°, V = 392.64(7) Å 3, Z = 4. The refinement converged to R = 0.0575, wR 2 = 0.1602, S = 1.022. Data for the crystal structure was collected on the SNS TOPAZ single-crystal time-of-flight Laue diffractometer. The compound has a one-dimensional structure which displays N–H···N hydrogen bonding. Finally, accurate intra- and intermolecular N–H distances have been determined.

  9. Crystal structures of carbonates up to Mbar pressures determined by single crystal synchrotron radiation diffraction

    NASA Astrophysics Data System (ADS)

    Merlini, M.

    2013-12-01

    The recent improvements at synchrotron beamlines, currently allow single crystal diffraction experiments at extreme pressures and temperatures [1,2] on very small single crystal domains. We successfully applied such technique to determine the crystal structure adopted by carbonates at mantle pressures. The knowledge of carbon-bearing phases is in fact fundamental for any quantitative modelling of global carbon cycle. The major technical difficulty arises after first order transitions or decomposition reactions, since original crystal (apx. 10x10x5 μm3) is transformed in much smaller crystalline domains often with random orientation. The use of 3D reciprocal space visualization software and the improved resolution of new generation flat panel detectors, however, allow both identification and integration of each single crystal domain, with suitable accuracy for ab-initio structure solution, performed with direct and charge-flipping methods and successive structure refinements. The results obtained on carbonates, indicate two major crystal-chemistry trends established at high pressures. The CO32- units, planar and parallel in ambient pressure calcite and dolomite structures, becomes non parallel in calcite- and dolomite-II and III phases, allowing more flexibility in the structures with possibility to accommodate strain arising from different cation sizes (Ca and Mg in particular). Dolomite-III is therefore also observed to be thermodynamically stable at lower mantle pressures and temperatures, differently from dolomite, which undergoes decomposition into pure end-members in upper mantle. At higher pressure, towards Mbar (lowermost mantle and D'' region) in agreement with theoretical calculations [3,4] and other experimental results [5], carbon coordination transform into 4-fold CO4 units, with different polymerisation in the structure depending on carbonate composition. The second important crystal chemistry feature detected is related to Fe2+ in Fe

  10. Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing

    PubMed Central

    Porter, Joanne L.; Carr, Paul D.; Collyer, Charles A.; Ollis, David L.

    2014-01-01

    Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space group P212121 from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space group C2 with two molecules in the asymmetric unit is reported. When crystallized in space group P212121 DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by side chains from two different molecules. Crystallization in space group C2 from a sodium citrate buffer results in new crystallographic protein–protein interfaces. The protein backbone is highly similar, but new crystal contacts cause changes in side-chain orientations and in loop positioning. In regions not involved in crystal contacts, there is little change in backbone or side-chain configuration. The flexibility of surface loops and the adaptability of side chains are important factors enabling DLH to adapt and form different crystal lattices. PMID:25005082

  11. A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

    NASA Astrophysics Data System (ADS)

    Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

    2017-12-01

    Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

  12. Crystal structure of enolase from Drosophila melanogaster.

    PubMed

    Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

    2017-04-01

    Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

  13. Self-powdering and nonlinear optical domain structures in ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals formed in glass

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tsukada, Y.; Honma, T.; Komatsu, T., E-mail: komatsu@mst.nagaokaut.ac.j

    Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3}, (GMO), crystals are formed through the crystallization of 21.25Gd{sub 2}O{sub 3}-63.75MoO{sub 3}-15B{sub 2}O{sub 3} glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 {mu}m spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called 'self-powdering phenomenon during crystallization' in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and amore » spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO{sub 4}){sup 2-} tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals. - Graphical abstract: This figure shows the polarized optical photograph at room temperature for a particle (piece) obtained by a heat treatment of the glass at 590 deg. C for 2 h in an electric furnace in air. This particle was obtained through the self-powdering behavior in the crystallization of glass. The periodic domain structure is observed. Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals are formed in the particle, and second harmonic generations are detected, depending on the domain structure.« less

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

    NASA Technical Reports Server (NTRS)

    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.

  15. The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

    PubMed Central

    Cole, Jason C.

    2017-01-01

    Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility. PMID:28291759

  16. The Cambridge Structural Database: a quarter of a million crystal structures and rising.

    PubMed

    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.

  17. Single-Crystal Structure of a Covalent Organic Framework

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, YB; Su, J; Furukawa, H

    2013-11-06

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

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

    PubMed

    Neumann, Marcus A

    2008-08-14

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

  19. Crystal structure of cbbF from Zymomonas mobilis and its functional implication

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hwang, Hyo-Jeong; Park, Suk-Youl; Kim, Jeong-Sun, E-mail: jsunkim@chonnam.ac.kr

    2014-02-28

    Highlights: • The crystal structure of one cbbF from Zymomonas mobilis was revealed. • Scores of residues form two secondary structures with a non-polar protruded residue. • It exists as a dimeric form in solution. - Abstract: A phosphate group at the C1-atom of inositol-monophosphate (IMP) and fructose-1,6-bisphosphate (FBP) is hydrolyzed by a phosphatase IMPase and FBPase in a metal-dependent way, respectively. The two enzymes are almost indiscernible from each other because of their highly similar sequences and structures. Metal ions are bound to residues on the β1- and β2-strands and one mobile loop. However, FBP has another phosphate andmore » FBPases exist as a higher oligomeric state, which may discriminate FBPases from IMPases. There are three genes annotated as FBPases in Zymomonas mobilis, termed also cbbF (ZmcbbF). The revealed crystal structure of one ZmcbbF shows a globular structure formed by five stacked layers. Twenty-five residues in the middle of the sequence form an α-helix and a β-strand, which occupy one side of the catalytic site. A non-polar Leu residue among them is protruded to the active site, pointing out unfavorable access of a bulky charged group to this side. In vitro assays have shown its dimeric form in solution. Interestingly, two β-strands of β1 and β2 are disordered in the ZmcbbF structure. These data indicate that ZmcbbF might structurally belong to IMPase, and imply that its active site would be reorganized in a yet unreported way.« less

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

    PubMed

    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.

  1. Crystal Structure of Toxoplasma gondii Porphobilinogen Synthase

    PubMed Central

    Jaffe, Eileen K.; Shanmugam, Dhanasekaran; Gardberg, Anna; Dieterich, Shellie; Sankaran, Banumathi; Stewart, Lance J.; Myler, Peter J.; Roos, David S.

    2011-01-01

    Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors. PMID:21383008

  2. Crystal structure and crystal growth of the polar ferrimagnet CaBaFe4O7

    NASA Astrophysics Data System (ADS)

    Perry, R. S.; Kurebayashi, H.; Gibbs, A.; Gutmann, M. J.

    2018-05-01

    Magnetic materials are a cornerstone for developing spintronic devices for the transport of information via magnetic excitations. To date, relatively few materials have been investigated for the purpose of spin transport, mostly due to the paucity of suitable candidates as these materials are often chemically complex and difficult to synthesize. We present the crystal growth and a structure solution on the high-temperature crystal structure of the layered, polar ferrimagnet CaBaFe4O7 , which is a possible new contender for spintronics research. The space group is identified as P 3 by refinement of single crystal and powder neutron diffraction data. At 400 K, the trigonal lattice parameters are a =11.0114 (11 )Å and c =10.330 (3 )Å . The structure is similar to the low-temperature phase with alternating layers of triangular and Kagome-arranged Fe-O tetrahedra. We also present details of the crystal growth by traveling solvent method.

  3. Crystal structures of sialyltransferase from Photobacterium damselae

    DOE PAGES

    Huynh, Nhung; Li, Yanhong; Yu, Hai; ...

    2014-11-15

    Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae α2–6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of α2–6-linked sialosides. In this paper, we report three crystal structures of this enzyme. Two structures with and without a donor substrate analog CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks themore » Ig-domain. Finally, comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold.« less

  4. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure.

    PubMed

    Pellach, Michal; Mondal, Sudipta; Harlos, Karl; Mance, Deni; Baldus, Marc; Gazit, Ehud; Shimon, Linda J W

    2017-03-13

    The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Tailoring the Crystal Structure Toward Optimal Super Conductors

    DTIC Science & Technology

    2016-06-23

    AFRL-AFOSR-VA-TR-2016-0210 TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS Emilia Morosan WILLIAM MARSH RICE UNIV HOUSTON TX Final...TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS 5a. CONTRACT NUMBER FA9550-11-1-0023 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...studied the properties of layered transition metal compounds in search of unconventional superconductors . The aim is to identify ground states competing

  6. Growth, structural, optical, thermal and mechanical properties of cytosinium hydrogen selenite: A novel nonlinear optical single crystal

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jaikumar, P.; Sathiskumar, S.; Balakrishnan, T., E-mail: balacrystalgrowth@gmail.com

    Highlights: • Growth of bulk single crystals of cytosinium hydrogen selenite (CHS) is reported. • Dielectric constant of CHS is measured as a function of Frequency and temperature. • Lower cut off value of UV–vis-NIR spectrum of CHS crystal is observed at 210 nm. • Meyer’s index value of CHS crystal calculated identifies it as a soft material. • Powder SHG efficiency of CHS is about 1.5 times that of KDP crystal. - Abstract: A novel nonlinear optical single crystal of cytosinium hydrogen selenite was grown from aqueous solution of cytosinium hydrogen selenite by slow solvent evaporation method at roommore » temperature. The structural properties of grown crystal have been studied by single crystal and powder X-ray diffraction analysis. Presence of various functional groups was identified from Fourier transform infrared spectroscopy. The optical transmittance and absorbance spectra were recorded by UV–vis-NIR spectrometer and the grown crystal possesses good transparency in the entire visible region. The dielectric constant and dielectric loss of the crystal were calculated as a function of frequency at different temperatures. The mechanical strength of the cytosinium hydrogen selenite crystal was estimated using Vicker’s microhardness tester. Etch patterns of the cytosinium hydrogen selenite crystal were obtained using distilled water as etchant for different etching time. Second harmonic generation efficiency tested using Nd:YAG laser is about 1.5 times that of KDP.« less

  7. How evolutionary crystal structure prediction works--and why.

    PubMed

    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

  8. Nonlinear coherent structures in granular crystals

    NASA Astrophysics Data System (ADS)

    Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

    2017-10-01

    The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

  9. Crystal structure of simple metals at high pressures

    NASA Astrophysics Data System (ADS)

    Degtyareva, Olga

    2010-09-01

    The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

  10. Communication: Hot-atom abstraction dynamics of hydrogen from tungsten surfaces: The role of surface structure

    NASA Astrophysics Data System (ADS)

    Galparsoro, Oihana; Busnengo, Heriberto Fabio; Juaristi, Joseba Iñaki; Crespos, Cédric; Alducin, Maite; Larregaray, Pascal

    2017-09-01

    Adiabatic and non-adiabatic quasiclassical molecular dynamics simulations are performed to investigate the role of the crystal face on hot-atom abstraction of H adsorbates by H scattering from covered W(100) and W(110). On both cases, hyperthermal diffusion is strongly affected by the energy dissipated into electron-hole pair excitations. As a result, the hot-atom abstraction is highly reduced in favor of adsorption at low incidence energy and low coverages, i.e., when the mean free path of the hyperthermal H is typically larger. Qualitatively, this reduction is rather similar on both surfaces, despite at such initial conditions, the abstraction process involves more subsurface penetration on W(100) than on W(110).

  11. How large B-factors can be in protein crystal structures.

    PubMed

    Carugo, Oliviero

    2018-02-23

    Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.

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

    USGS Publications Warehouse

    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.

  13. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  14. Crystal structure, optical and thermal studies of a new organic nonlinear optical material: L-Histidinium maleate 1.5-hydrate

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gonsago, C. Alosious; Albert, Helen Merina; Karthikeyan, J.

    2012-07-15

    Highlights: ► L-Histidinium maleate 1.5-hydrate, a new organic crystal has been grown for the first time. ► The crystal structure is reported for the first time (CCDC 845975). ► The crystal belongs to monoclinic system with space group P2{sub 1}, Z = 4, a = 11.4656(7) Å, b = 8.0530(5) Å, c = 14.9705(9) Å and β = 101.657(2)°. ► The optical absorption study substantiates the complete transparency of the crystal. ► Kurtz powder SHG test confirms the nonlinear property of the crystal. -- Abstract: A new organic nonlinear optical material L-histidinium maleate 1.5-hydrate (LHM) with the molecular formula C{submore » 10}H{sub 16}N{sub 3}O{sub 7.5} has been successfully synthesized from aqueous solution by slow solvent evaporation method. The structural characterization of the grown crystal was carried out by single crystal X-ray diffraction at 293(2) K. In the crystal, molecules are linked through inter and intramolecular N-H⋯O and O-H⋯O hydrogen bonds, generate edge fused ring motif. The hydrogen bonded motifs are linked to each other to form a three dimensional network. The FT-IR spectroscopy was used to identify the functional groups of the synthesized compound. The optical behavior of the grown crystal was examined by UV–visible spectral analysis, which shows that the optical absorption is almost negligible in the wavelength range 280–1300 nm. The nonlinear optical property was confirmed by the powder technique of Kurtz and Perry. The thermal behavior of the grown crystal was analyzed by thermogravimetric analysis.« less

  15. Effects of scandium substitution on the crystal structure and luminescence properties of LuBO{sub 3}: Ce{sup 3+}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wu, Yuntao, E-mail: caswyt@hotmail.com; Ren, Guohao, E-mail: rgh@mail.sic.ac.cn; Ding, Dongzhou

    2012-10-15

    The calcite phase of LuBO{sub 3} and ScBO{sub 3} polycrystalline powders were synthesized by solid state reaction method, and the Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce (x=0.2, 0.5, 0.7) single crystals were grown by the Czochralski method. A large composition deviation between the initial polycrystalline powders and final single crystal was confirmed by electron probe micro-analysis. Raman spectroscopy revealed that moderate lattice disorder was induced by scandium substitution. However, based on the single crystal X-ray study, we finally concluded that the crystal structure of lutetium scandium orthoborate still crystallized in the rhombohedral system belonging to R3{sup -}c. Furthermore, the relationship between themore » energies of the five 5d levels of Ce{sup 3+} and the crystalline environment was revealed. The total redshift, total crystal field splitting, and centroid shift of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce{sup 3+} were calculated based on their VUV excitation spectra. The variations trend of these observed spectroscopic parameters was in accordance with the predicted ones. - Graphical abstract: The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. The relationship between the energies of the five Ce{sup 3+} 5d levels and the crystalline environment is established. Highlights: Black-Right-Pointing-Pointer Moderate lattice disorder is induced by scandium doping. Black-Right-Pointing-Pointer The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. Black-Right-Pointing-Pointer Relationship between energies of Ce{sup 3+} 5d levels and crystalline environment is established. Black-Right-Pointing-Pointer The spectroscopic parameters are experimentally and theoretically calculated.« less

  16. Crystal structure of MboIIA methyltransferase.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Osipiuk, J.; Walsh, M. A.; Joachimiak, A.

    2003-09-15

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

  17. Crystal structure of MboIIA methyltransferase.

    PubMed

    Osipiuk, Jerzy; Walsh, Martin A; Joachimiak, Andrzej

    2003-09-15

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

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

    PubMed

    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.

  19. A unified picture of the crystal structures of metals

    NASA Astrophysics Data System (ADS)

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

    1995-04-01

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

  20. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

    Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

  1. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

    DOE PAGES

    Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

    2017-05-15

    Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

  2. Ordered distribution of I and Cl in the low-temperature crystal structure of mutnovskite, Pb{sub 4}As{sub 2}S{sub 6}ICl: An X-ray single-crystal study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bindi, Luca; Garavelli, Anna; Pinto, Daniela

    2008-02-15

    To study the temperature-dependent structural changes and to analyze the crystal chemical behavior of the halogens as a function of temperature, a crystal of the recently discovered mineral mutnovskite, ideally Pb{sub 2}AsS{sub 3}(I,Cl,Br), has been investigated by X-ray single-crystal diffraction methods at 300 and 110 K. At room temperature (RT) mutnovskite was confirmed to possess a centrosymmetric structure-type, space group Pnma, while at low temperature (110 K) it adopts a non-centrosymmetric orthorhombic structure-type, space group Pnm2{sub 1}, with a=11.5394(9) A, b=6.6732(5) A, c=9.3454(7) A, V=719.64(9) A{sup 3} and Z=2. Mutnovskite reconverts to the centrosymmetric-type upon returning to RT thus indicatingmore » that the phase transition is completely reversible in character. The refinement of the LT-structure leads to a residual factor R=0.0336 for 1827 independent observed reflections [F{sub o}>4{sigma}(F{sub o})] and 80 variables. The crystal structure of cooled mutnovskite is topologically identical to that observed at RT and the slight structural changes occurring during the phase transition Pnma{yields}Pnm2{sub 1} are mainly restricted to the coordination polyhedra around Pb. The structure solution revealed that I and Cl are ordered into two specific sites. Indeed, the unique mixed (I,Cl) position in the RT-structure (Wyckoff position 4c) transforms into two 2a Wyckoff positions in the LT-structure hosting I and Cl, respectively. - Graphical abstract: In the crystal structure of mutnovskite at 110 K the two halogens I and Cl are ordered into two specific sites and only slight changes in the coordination environment around Pb atoms occur during the phase transition Pnma{yields}Pnm2{sub 1} from the RT-structure to the LT-structure. Two kinds of layers alternating along a are present in the LT-structure: Layer I contains Cl atoms and [001] columns of Pb1 and Pb4 prisms, layer II contains I atoms and [001] columns of Pb2 and Pb3 prisms.« less

  3. High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

    DOE PAGES

    Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

    2015-12-03

    Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

  4. High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

    Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

  5. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cornaby, Sterling; CHESS; Szebenyi, Doletha M. E.

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Lauemore » technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.« less

  6. Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

    PubMed

    Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

    2014-02-01

    Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

  7. Multiple solvent crystal structures of ribonuclease A: An assessment of the method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dechene, Michelle; Wink, Glenna; Smith, Mychal

    2010-11-12

    The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

  8. Crystal Structure Variations of Sn Nanoparticles upon Heating

    NASA Astrophysics Data System (ADS)

    Mittal, Jagjiwan; Lin, Kwang-Lung

    2018-04-01

    Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

  9. Structural colored gels for tunable soft photonic crystals.

    PubMed

    Harun-Ur-Rashid, Mohammad; Seki, Takahiro; Takeoka, Yukikazu

    2009-01-01

    A periodically ordered interconnecting porous structure can be embodied in chemical gels by using closest-packed colloidal crystals as templates. The interconnecting porosity not only provides a quick response but also endows the porous gels with structural color arising from coherent Bragg optical diffraction. The structural colors revealed by porous gels can be regulated by several techniques, and thus, it is feasible to obtain desirable, smart, soft materials. A well-known thermosensitive monomer, N-isopropylacrylamide (NIPA), and other minor monomers were used to fabricate various structural colored gels. The selection of minor monomers depended on the targeted properties. This review focuses on the synthesis of templates, structural colored porous gels, and the applications of structural colored gel as smart soft materials for tunable photonic crystals. (c) 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

  10. Crystal structure of simple metals at high pressures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Degtyareva, Olga

    2010-10-22

    The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structuresmore » found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.« less

  11. Structure of initial crystals formed during human amelogenesis

    NASA Astrophysics Data System (ADS)

    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.

  12. Some design constraints required for the assembly of software components: The incorporation of atomic abstract types into generically structured abstract types

    NASA Technical Reports Server (NTRS)

    Johnson, Charles S.

    1986-01-01

    It is nearly axiomatic, that to take the greatest advantage of the useful features available in a development system, and to avoid the negative interactions of those features, requires the exercise of a design methodology which constrains their use. A major design support feature of the Ada language is abstraction: for data, functions processes, resources, and system elements in general. Atomic abstract types can be created in packages defining those private types and all of the overloaded operators, functions, and hidden data required for their use in an application. Generically structured abstract types can be created in generic packages defining those structured private types, as buildups from the user-defined data types which are input as parameters. A study is made of the design constraints required for software incorporating either atomic or generically structured abstract types, if the integration of software components based on them is to be subsequently performed. The impact of these techniques on the reusability of software and the creation of project-specific software support environments is also discussed.

  13. Crystal structure of cathepsin A, a novel target for the treatment of cardiovascular diseases

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schreuder, Herman A., E-mail: herman.schreuder@sanofi.com; Liesum, Alexander, E-mail: alexander.liesum@sanofi.com; Kroll, Katja, E-mail: katja.kroll@sanofi.com

    2014-03-07

    Graphical abstract: - Highlights: • The structures of active cathepsin A and the inactive precursor are very similar. • The only major difference is the absence of a 40 residue activation domain. • The termini of the active catalytic core are held together by a disulfide bond. • Compound 1 reacts with the catalytic Ser150, building a tetrahedral intermediate. • Compound 2 is cleaved by the enzyme and a fragment remained bound. - Abstract: The lysosomal serine carboxypeptidase cathepsin A is involved in the breakdown of peptide hormones like endothelin and bradykinin. Recent pharmacological studies with cathepsin A inhibitors inmore » rodents showed a remarkable reduction in cardiac hypertrophy and atrial fibrillation, making cathepsin A a promising target for the treatment of heart failure. Here we describe the crystal structures of activated cathepsin A without inhibitor and with two compounds that mimic the tetrahedral intermediate and the reaction product, respectively. The structure of activated cathepsin A turned out to be very similar to the structure of the inactive precursor. The only difference was the removal of a 40 residue activation domain, partially due to proteolytic removal of the activation peptide, and partially by an order–disorder transition of the peptides flanking the removed activation peptide. The termini of the catalytic core are held together by the Cys253–Cys303 disulfide bond, just before and after the activation domain. One of the compounds we soaked in our crystals reacted covalently with the catalytic Ser150 and formed a tetrahedral intermediate. The other compound got cleaved by the enzyme and a fragment, resembling one of the natural reaction products, was found in the active site. These studies establish cathepsin A as a classical serine proteinase with a well-defined oxyanion hole. The carboxylate group of the cleavage product is bound by a hydrogen-bonding network involving one aspartate and two glutamate side

  14. The synthesis, single-crystal structure, optical absorption, and resistivity of Th{sub 2}GeSe{sub 5}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Koscielski, Lukasz A.; Malliakas, Christos D.; Sarjeant, Amy A.

    2013-09-15

    The compound Th{sub 2}GeSe{sub 5} has been synthesized by the reaction of the elements at 1273 K. From a single-crystal study Th{sub 2}GeSe{sub 5} crystallizes in the Ba{sub 5}Si{sub 3} structure type with four formula units in the space group D{sup 8}{sub 4h}−P4/ncc of the tetragonal system in a cell with dimensions a=7.4968(4) Å and c=13.6302(9) Å at 100(2) K. From optical absorption measurements Th{sub 2}GeSe{sub 5} is found to have an optical band gap of 1.92 eV (indirect) or 1.98 eV (direct), consistent with its red color. Th{sub 2}GeSe{sub 5} is a wide gap semiconductor, as indicated by itsmore » electrical resistivity at 298 K of 4.37(2)×10{sup 9} Ω cm measured on a single crystal. - Graphical abstract: The structure of Th{sub 2}GeSe{sub 5}. Display Omitted - Highlights: • The new compound Th{sub 2}GeSe{sub 5} was synthesized from the elements and recrystallized from Sb{sub 2}Se{sub 3}. • Th{sub 2}GeSe{sub 5} crystallizes in the Ba{sub 5}Si{sub 3} structure type. • The band gap of Th{sub 2}GeSe{sub 5} is1.92 eV and its resistivity shows it to be a wide gap semiconductor.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in; Perumal, Rajesh Narayana

    2014-04-24

    Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

  16. Synthesis, crystal structure, NLO and Hirshfeld surface analysis of 1,2,3-triazolyl chalcone single crystal

    NASA Astrophysics Data System (ADS)

    Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

    2018-05-01

    Needle shaped brown coloured single crystal of the title compound was grown by slow evaporation technique using methanol as solvent. The grown crystal was characterized using FT-IR, Single crystal XRD, UV-visible and NLO studies. Crystal structure was confirmed by FT-IR study and the functional groups were identified. XRD study reveals that the crystal belongs to orthorhombic crystal system with pnaa space group and the corresponding cell parameters were calculated. UV-visible spectrum shows that the crystal is transparent in the entire visible region and absorption takes place in the UV-range. NLO efficiency of the crystal obtained 0.66 times that of urea was determined by SHG test. The intermolecular interaction and percentage contribution of each individual atom in the crystal lattice was quantized using Hirshfeld surface and 2D finger print analysis.

  17. Physicochemical and crystal structure analyses of the antidiabetic agent troglitazone.

    PubMed

    Kobayashi, Katsuhiro; Fukuhara, Hiroshi; Hata, Tadashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2003-07-01

    The antidiabetic agent troglitazone has two asymmetric carbons located at the chroman ring and the thiazolidine ring and is produced as a mixture of equal amounts of four optical isomers, 2R-5S, 2S-5R, 2R-5R, and 2S-5S. The crystalline powdered drug substance consists of two diastereomer pairs, 2R-5R/2S-5S and 2R-5S/2S-5R. There are many types of crystals obtained from various crystallization conditions. The X-ray structure analysis and the physicochemical analyses of troglitazone were performed. The solvated crystals of the 2R-5R/2S-5S pair were crystallized from several solutions: methanol, ethanol, acetonitrile, and dichloromethane. The ratio of solvent and troglitazone was 1 : 2 (L1/2-form). The monohydrate crystals were obtained from aqueous acetone solution (L1-form). On the other hand, only an anhydrate crystal of the 2R-5S/2S-5R pair was crystallized from various solutions (H0-form). The dihydrous mixed crystal (MA2-form) was obtained from a mixture of the two diastereomer pairs of 2R-5R/2S-5S and 2R-5S/2S-5R in equal amounts by the slow evaporation of aqueous acetone solution. The crystal structure of the MA2-form is similar to the H0-form. When the MA2 crystal was kept under low humidity, it was converted into the dehydrated form (MA0-form) with retention of the single crystal form. The structure of the MA0-form is isomorphous to the H0-form. The MA2-form was converted into the MA0-form and vice versa with retention of the single crystal under low and high humidity, respectively. The crystallization and storage conditions of the drug substances were successfully analyzed.

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

    DOEpatents

    Payne, Stephen A.; Kway, Wayne L.; DeLoach, Laura D.; Krupke, William F.; Chai, Bruce H. T.

    1994-01-01

    Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.

  19. The Crystal Structure of GXGD Membrane Protease FlaK

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    J Hu; Y Xue; S Lee

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices.more » The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.« less

  20. The crystal structure of GXGD membrane protease FlaK

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hu, Jian; Xue, Yi; Lee, Sangwon

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices.more » The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.« less

  1. Crystal structure optimisation using an auxiliary equation of state

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  2. Field-controlled structures in ferromagnetic cholesteric liquid crystals.

    PubMed

    Medle Rupnik, Peter; Lisjak, Darja; Čopič, Martin; Čopar, Simon; Mertelj, Alenka

    2017-10-01

    One of the advantages of anisotropic soft materials is that their structures and, consequently, their properties can be controlled by moderate external fields. Whereas the control of materials with uniform orientational order is straightforward, manipulation of systems with complex orientational order is challenging. We show that a variety of structures of an interesting liquid material, which combine chiral orientational order with ferromagnetic one, can be controlled by a combination of small magnetic and electric fields. In the suspensions of magnetic nanoplatelets in chiral nematic liquid crystals, the platelet's magnetic moments orient along the orientation of the liquid crystal and, consequently, the material exhibits linear response to small magnetic fields. In the absence of external fields, orientations of the liquid crystal and magnetization have wound structure, which can be either homogeneously helical, disordered, or ordered in complex patterns, depending on the boundary condition at the surfaces and the history of the sample. We demonstrate that by using different combinations of small magnetic and electric fields, it is possible to control reversibly the formation of the structures in a layer of the material. In such a way, different periodic structures can be explored and some of them may be suitable for photonic applications. The material is also a convenient model system to study chiral magnetic structures, because it is a unique liquid analog of a solid helimagnet.

  3. [Quality of the structured abstracts presented at a congress].

    PubMed

    dos Santos, Edilson F; Pereira, Maurício G

    2007-01-01

    To assess and compare quality of abstracts presented at a medical congress (XIV Congresso da Sociedade Brasileira de Infectologia, November, 2005). The hypothesis is that material of better quality is chosen for oral presentation. All the 63 abstracts selected for oral presentation were compared with a random sample (n=63) of the 664 abstracts registered as poster presentations. Quality was measured by a structured questionnaire comprised of 33 criteria, distributed in eight categories: purpose, research design, setting, subjects, intervention, measurement, results and conclusions. The questionnaire was applied by one of the authors who were not blind to the objective of the study. The final score could range from 0 (bad) to 1 (excellent). Abstracts quality was considered moderately good. The overall mean quality scores were 0.60 and 0.62 respectively, for poster and oral presentation (p = 0.086). The criteria rated poorly were: subjects, variable measurements, location and conclusion. The tested hypothesis of better quality in abstracts selected for oral presentation has not been confirmed. It is recommended that organizers of the congresses the use of objective quality criteria to select the form of presentation while improving on quality.

  4. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

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

    2004-03-01

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

  5. Fabrication of large binary colloidal crystals with a NaCl structure

    PubMed Central

    Vermolen, E. C. M.; Kuijk, A.; Filion, L. C.; Hermes, M.; Thijssen, J. H. J.; Dijkstra, M.; van Blaaderen, A.

    2009-01-01

    Binary colloidal crystals offer great potential for tuning material properties for applications in, for example, photonics, semiconductors and spintronics, because they allow the positioning of particles with quite different characteristics on one lattice. For micrometer-sized colloids, it is believed that gravity and slow crystallization rates hinder the formation of high-quality binary crystals. Here, we present methods for growing binary colloidal crystals with a NaCl structure from relatively heavy, hard-sphere-like, micrometer-sized silica particles by exploring the following external fields: electric, gravitational, and dielectrophoretic fields and a structured surface (colloidal epitaxy). Our simulations show that the free-energy difference between the NaCl and NiAs structures, which differ in their stacking of the hexagonal planes of the larger spheres, is very small (≈0.002 kBT). However, we demonstrate that the fcc stacking of the large spheres, which is crucial for obtaining the pure NaCl structure, can be favored by using a combination of the above-mentioned external fields. In this way, we have successfully fabricated large, 3D, oriented single crystals having a NaCl structure without stacking disorder. PMID:19805259

  6. Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

    NASA Astrophysics Data System (ADS)

    Marchewka, M. K.; Pietraszko, A.

    2008-02-01

    The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

  7. Crystal structure of κ-Ag2Mg5

    NASA Astrophysics Data System (ADS)

    Castro, Facundo J.; Primo, Gastón A.; Urretavizcaya, Guillermina

    2018-02-01

    The structure of κ-Ag2Mg5 has been refined based on X-ray powder diffraction measurements (Rwp = 0.083). The compound has been prepared by combining mechanical alloying techniques and thermal treatments. The intermetallic presents the prototypical structure of Co2Al5, an hexagonal crystal with the symmetries of space group P63/mmc, and belongs to the family of kappa-phase structure compounds. The unit cell dimensions are a=8.630(1) Å and c=8.914(1) Å. Five crystallographically independent sites are occupied, Wyckoff positions 12k, 6h and 2a are filled with Mg, another 6h site is occupied with Ag, and the 2c site presents mixed Ag/Mg occupancy. The crystal chemistry of the structure and bonding are briefly discussed in the paper.

  8. Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

    PubMed Central

    Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

    2008-01-01

    The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the impact of mutations to the C-terminal domain on the thermal stability of Tb-MscL using circular dichroism and performed molecular dynamics simulations of the original and the revised crystal structures of Tb-MscL. Our results imply that this region is helical and adopts an α-helical bundle conformation similar to that observed in the E. coli MscL model and the revised Tb-MscL crystal structure. PMID:18326638

  9. Effects of thermo-order-mechanical coupling on band structures in liquid crystal nematic elastomer porous phononic crystals.

    PubMed

    Yang, Shuai; Liu, Ying

    2018-08-01

    Liquid crystal nematic elastomers are one kind of smart anisotropic and viscoelastic solids simultaneously combing the properties of rubber and liquid crystals, which is thermal sensitivity. In this paper, the wave dispersion in a liquid crystal nematic elastomer porous phononic crystal subjected to an external thermal stimulus is theoretically investigated. Firstly, an energy function is proposed to determine thermo-induced deformation in NE periodic structures. Based on this function, thermo-induced band variation in liquid crystal nematic elastomer porous phononic crystals is investigated in detail. The results show that when liquid crystal elastomer changes from nematic state to isotropic state due to the variation of the temperature, the absolute band gaps at different bands are opened or closed. There exists a threshold temperature above which the absolute band gaps are opened or closed. Larger porosity benefits the opening of the absolute band gaps. The deviation of director from the structural symmetry axis is advantageous for the absolute band gap opening in nematic state whist constrains the absolute band gap opening in isotropic state. The combination effect of temperature and director orientation provides an added degree of freedom in the intelligent tuning of the absolute band gaps in phononic crystals. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Crystal structure and optical properties of silver nanorings

    NASA Astrophysics Data System (ADS)

    Zhou, Li; Fu, Xiao-Feng; Yu, Liao; Zhang, Xian; Yu, Xue-Feng; Hao, Zhong-Hua

    2009-04-01

    We report the polyol synthesis and crystal structure characterization of silver nanorings, which have perfect circular shape, smooth surface, and elliptical wire cross-section. The characterization results show that the silver nanorings have well-defined crystal of singly twinned along the whole ring. The spatial distribution of the scattering of a silver nanoring with slanted incidence reveals the unique focus effect of the nanoring, and the focus scattering varies with the incident wavelength. The silver nanorings with perfect geometry and well-defined crystal have potential applications in nanoscaled photonics, plasmonic devices, and optical manipulation.

  11. Discovery of a diamond-based photonic crystal structure in beetle scales.

    PubMed

    Galusha, Jeremy W; Richey, Lauren R; Gardner, John S; Cha, Jennifer N; Bartl, Michael H

    2008-05-01

    We investigated the photonic crystal structure inside iridescent scales of the weevil Lamprocyphus augustus. By combining a high-resolution structure analysis technique based on sequential focused ion beam milling and scanning electron microscopy imaging with theoretical modeling and photonic band-structure calculations, we discovered a natural three-dimensional photonic structure with a diamond-based crystal lattice operating at visible wavelengths. Moreover, we found that within individual scales, the diamond-based structure is assembled in the form of differently oriented single-crystalline micrometer-sized pixels with only selected lattice planes facing the scales' top surface. A comparison of results obtained from optical microreflectance measurements with photonic band-structure calculations reveals that it is this sophisticated microassembly of the diamond-based crystal lattice that lends Lamprocyphus augustus its macroscopically near angle-independent green coloration.

  12. Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

    PubMed Central

    Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko

    2014-01-01

    One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077

  13. Structural and optical properties of WTe2 single crystals synthesized by DVT technique

    NASA Astrophysics Data System (ADS)

    Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

    2018-05-01

    Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

  14. A hybrid computational-experimental approach for automated crystal structure solution

    NASA Astrophysics Data System (ADS)

    Meredig, Bryce; Wolverton, C.

    2013-02-01

    Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li-air batteries; and high-pressure silane, SiH4.

  15. Myelin structures formed by thermotropic smectic liquid crystals

    NASA Astrophysics Data System (ADS)

    Peddireddy, Karthik Reddy; Kumar, Pramoda; Thutupalli, Shashi; Herminghaus, Stephan; Bahr, Christian

    2014-03-01

    We report on transient structures, formed by thermotropic smectic-A liquid crystals, resembling the myelin figures of lyotropic lamellar liquid crystals. The thermotropic myelin structures form during the solubilization of a smectic-A droplet in an aqueous phase containing a cationic surfactant at concentrations above the critical micelle concentration. Similar to the lyotropic myelin figures, the thermotropic myelins appear in an optical microscope as flexible tube-like structures growing at the smectic/aqueous interface. Polarizing microscopy and confocal fluorescence microscopy show that the smectic layers are parallel to the tube surface and form a cylindrically bent arrangement around a central line defect in the tube. We study the growth behavior of this new type of myelins and discuss similarities and differences to the classical lyotropic myelin figures.

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

    NASA Technical Reports Server (NTRS)

    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.

  17. Gallium arsenide single crystal solar cell structure and method of making

    NASA Technical Reports Server (NTRS)

    Stirn, Richard J. (Inventor)

    1983-01-01

    A production method and structure for a thin-film GaAs crystal for a solar cell on a single-crystal silicon substrate (10) comprising the steps of growing a single-crystal interlayer (12) of material having a closer match in lattice and thermal expansion with single-crystal GaAs than the single-crystal silicon of the substrate, and epitaxially growing a single-crystal film (14) on the interlayer. The material of the interlayer may be germanium or graded germanium-silicon alloy, with low germanium content at the silicon substrate interface, and high germanium content at the upper surface. The surface of the interface layer (12) is annealed for recrystallization by a pulsed beam of energy (laser or electron) prior to growing the interlayer. The solar cell structure may be grown as a single-crystal n.sup.+ /p shallow homojunction film or as a p/n or n/p junction film. A Ga(Al)AS heteroface film may be grown over the GaAs film.

  18. CMOS-Compatible Fabrication for Photonic Crystal-Based Nanofluidic Structure.

    PubMed

    Peng, Wang; Chen, Youping; Ai, Wu; Zhang, Dailin; Song, Han; Xiong, Hui; Huang, Pengcheng

    2017-12-01

    Photonic crystal (PC)-based devices have been widely used since 1990s, while PC has just stepped into the research area of nanofluidic. In this paper, photonic crystal had been used as a complementary metal oxide semiconductors (CMOS) compatible part to create a nanofluidic structure. A nanofluidic structure prototype had been fabricated with CMOS-compatible techniques. The nanofluidic channels were sealed by direct bonding polydimethylsiloxane (PDMS) and the periodic gratings on photonic crystal structure. The PC was fabricated on a 4-in. Si wafer with Si 3 N 4 as the guided mode layer and SiO 2 film as substrate layer. The higher order mode resonance wavelength of PC-based nanofluidic structure had been selected, which can confine the enhanced electrical field located inside the nanochannel area. A design flow chart was used to guide the fabrication process. By optimizing the fabrication device parameters, the periodic grating of PC-based nanofluidic structure had a high-fidelity profile with fill factor at 0.5. The enhanced electric field was optimized and located within the channel area, and it can be used for PC-based nanofluidic applications with high performance.

  19. Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

    NASA Astrophysics Data System (ADS)

    Wang, Yuan; Liang, Zuozhong

    2017-12-01

    Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

  20. The First Mammalian Aldehyde Oxidase Crystal Structure

    PubMed Central

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

    2012-01-01

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

  1. Synthesis and Crystal Structure Study of 2’-Se-Adenosine-Derivatized DNA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sheng, J.; Salon, J; Gan, J

    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 describemore » 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']{sub 2} was determined at 1.75 {angstrom} 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.« less

  2. Correlation among far-infrared reflection modes, crystal structures and dielectric properties of Ba(Zn{sub 1/3}Nb{sub 2/3})O{sub 3}–CaTiO{sub 3} ceramics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shi, Feng, E-mail: sf751106@sina.com.cn; Sun, Haiqing; Liu, Hongquan

    Highlights: • Crystal symmetry decreases with CT concentration from cubic to hexagonal structure. • Lattice constants as well as the ordered degree change with CT concentration. • Ordered structures turn from 1:1 to 1:2 ordering with change of crystal structures. • There is a correlation between FIR phonon modes and dielectric properties. • There is a correlation between FIR phonon modes and crystal structures. - Abstract: Ba(Zn{sub 1/3}Nb{sub 2/3})O{sub 3} (BZN)–CaTiO{sub 3} (CT) microwave dielectric ceramics were synthesized at 1395 °C for 4 h using conventional solid-state sintering technique with different CT contents. The ceramics were characterized by X-ray diffractionmore » (XRD) and far-infrared reflection (FIR) spectroscopy to evaluate correlations among crystal structures, dielectric properties, and infrared modes. XRD results showed that crystal symmetry decreased with increased CT concentration from cubic to hexagonal structure, and lattice constants and ordered degree changed accordingly. Ordered phases transformed from 1:1 to 1:2 ordered structure with crystal-structure change. FIR results demonstrated that two new IR active modes appeared at 300 cm{sup −1}, and another new mode appeared at 600 cm{sup −1} for the x ≥ 0.60 sample, which agreed with the change in crystal structures as confirmed by XRD results. Correlations between FIR modes and dielectric properties were established.« less

  3. Crystal structure of hexagonal MnAl(4).

    PubMed

    Pauling, L

    1987-06-01

    A structure is proposed for the hexagonal form of MnAl(4), with a(H) = 28.4 A and c(H) = 12.43 A, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-A cubic structure of MnAl(4) and to the 14.19-A cubic structure of Mg(32)(Al,Zn)(49).

  4. Magnetic assembly of nonmagnetic particles into photonic crystal structures.

    PubMed

    He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

    2010-11-10

    We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

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

    ERIC Educational Resources Information Center

    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…

  6. A STUDY OF DISLOCATION STRUCTURE OF SUBBOUNDARIES IN MOLYBDENUM SINGLE CRYSTALS,

    DTIC Science & Technology

    MOLYBDENUM, *DISLOCATIONS), GRAIN STRUCTURES(METALLURGY), SINGLE CRYSTALS, ZONE MELTING, ELECTRON BEAM MELTING, GRAIN BOUNDARIES, MATHEMATICAL ANALYSIS, ETCHED CRYSTALS, ETCHING, ELECTROEROSIVE MACHINING, CHINA

  7. Survey and analysis of crystal polymorphism in organic structures

    PubMed Central

    Kaur, Ramanpreet

    2018-01-01

    With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD) are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components. PMID:29765601

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tian, Z.A., E-mail: ze.tian@gmail.com; Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052; Dong, K.J.

    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 temperaturemore » 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.« less

  9. Crystal structure of spinach plastocyanin at 1.7 A resolution.

    PubMed Central

    Xue, Y.; Okvist, M.; Hansson, O.; Young, S.

    1998-01-01

    The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins. PMID:9792096

  10. Crystal Structures of the β2-Adrenergic Receptor

    NASA Astrophysics Data System (ADS)

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

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

  11. The Crystal Structure of Oxaliplatin: A Case of Overlooked Pseudo Symmetry.

    PubMed

    Johnstone, Timothy C

    2014-01-08

    The crystal structure of the anticancer drug oxaliplatin, [Pt( R,R- DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P2 1 , confirming the sole presence of the R , R enantiomer of the DACH ligand [M. A. Bruck et al. , Inorg. Chim. Acta , 92 (1984) 279-284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P2 1 /m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al. , Polyhedron , 22 (2003) 1529-1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt( R , R -DACH)I 2 , and a platinum(IV) derivative, trans -[Pt( R , R -DACH)(oxalate)(OH) 2 ], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R , R . A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P2 1 /m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained.

  12. The Crystal Structure of Oxaliplatin: A Case of Overlooked Pseudo Symmetry

    PubMed Central

    Johnstone, Timothy C.

    2013-01-01

    The crystal structure of the anticancer drug oxaliplatin, [Pt(R,R-DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P21, confirming the sole presence of the R,R enantiomer of the DACH ligand [M. A. Bruck et al., Inorg. Chim. Acta, 92 (1984) 279–284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P21/m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al., Polyhedron, 22 (2003) 1529–1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt(R,R-DACH)I2, and a platinum(IV) derivative, trans-[Pt(R,R-DACH)(oxalate)(OH)2], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R,R. A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P21/m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained. PMID:24415827

  13. The Surface Structure of Ground Metal Crystals

    NASA Technical Reports Server (NTRS)

    Boas, W.; Schmid, E.

    1944-01-01

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

  14. Synthesis and structural characterization of bulk Sb2Te3 single crystal

    NASA Astrophysics Data System (ADS)

    Sultana, Rabia; Gahtori, Bhasker; Meena, R. S.; Awana, V. P. S.

    2018-05-01

    We report the growth and characterization of bulk Sb2Te3 single crystal synthesized by the self flux method via solid state reaction route from high temperature melt (850˚C) and slow cooling (2˚C/hour) of constituent elements. The single crystal X-ray diffraction pattern showed the 00l alignment and the high crystalline nature of the resultant sample. The rietveld fitted room temperature powder XRD revealed the phase purity and rhombohedral structure of the synthesized crystal. The formation and analysis of unit cell structure further verified the rhombohedral structure composed of three quintuple layers stacked one over the other. The SEM image showed the layered directional growth of the synthesized crystal carried out using the ZEISS-EVOMA-10 scanning electron microscope The electrical resistivity measurement was carried out using the conventional four-probe method on a quantum design Physical Property Measurement System (PPMS). The temperature dependent electrical resistivity plot for studied Sb2Te3 single crystal depicts metallic behaviour in the absence of any applied magnetic field. The synthesis as well as the structural characterization of as grown Sb2Te3 single crystal is reported and discussed in the present letter.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Dry-growth of silver single-crystal nanowires from porous Ag structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chen, Chuantong, E-mail: chenchuantong@sanken.osaka-u.ac.jp; Nagao, Shijo; Jiu, Jinting

    A fabrication method of single crystal Ag nanowires in large scale is introduced without any chemical synthesis in wet processes, which usually generates fivefold twinned nanowires of fcc metals. Dense single-crystal nanowires grow on a mechanically polished surface of micro-porous Ag structure, which is created from Ag micro-particles. The diameter and the length of the nanowires can be controlled simply by changing the temperature and the time of the heating during the nanowire growth in air. Unique growth mechanism is described in detail, based on stress-induced migration accelerated by the micro-porous structure where the origin of Ag nanowires growth ismore » incubated. Transmission electron microscopy analysis on the single crystal nanowires is also presented. This simple method offered an alternative preparation for metallic nanowires, especially with the single crystal structure in numerous applications.« less

  17. Crystal structure of zwitterionic bisimidazolium sulfonates

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  18. Synthesis and crystal structures of three new benzotriazolylpropanamides

    PubMed Central

    Amenta, Donna S.; Liebing, Phil; Biero, Julia E.; Sherman, Robert J.; Gilje, John W.

    2017-01-01

    The base-catalyzed Michael addition of 2-methyl­acryl­amide to benzotriazole afforded 3-(1H-benzotriazol-1-yl)-2-methyl­propanamide, C10H12N4O (1), in 32% yield in addition to small amounts of isomeric 3-(2H-benzotriazol-2-yl)-2-methyl­propanamide, C10H12N4O (2). In a similar manner, 3-(1H-benzotriazol-1-yl)-N,N-di­methyl­propanamide, C11H14N4O (3), was prepared from benzotriazole and N,N-di­methyl­acryl­amide. All three products have been structurally characterized by single-crystal X-ray diffraction. The crystal structures of 1 and 2 comprise infinite arrays formed by N—H⋯O and N—H⋯N bridges, as well as π–π inter­actions, while the mol­ecules of 3 are aggregated to simple π-dimers in the crystal. PMID:28638650

  19. Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

    PubMed

    Boerneke, Mark A; Dibrov, Sergey M; Hermann, Thomas

    2016-03-14

    RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Crystal structure of hexagonal MnAl4

    PubMed Central

    Pauling, Linus

    1987-01-01

    A structure is proposed for the hexagonal form of MnAl4, with aH = 28.4 Å and cH = 12.43 Å, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-Å cubic structure of MnAl4 and to the 14.19-Å cubic structure of Mg32(Al,Zn)49. Images PMID:16593837

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

    PubMed Central

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

    2015-01-01

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

  2. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han,Q.; Robinson, H.; Gao, Y.

    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 themore » 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.« less

  3. Low-temperature crystal and magnetic structure of α – RuCl 3

    DOE PAGES

    Cao, Huibo B.; Yan, Jiaqiang; Bridges, Craig A.; ...

    2016-04-19

    Here, single crystals of the Kitaev spin-liquid candidate α – RuCl 3 have been studied to determine the low-temperature bulk properties, the structure, and the magnetic ground state. Refinements of x-ray diffraction data show that the low-temperature crystal structure is described by space group C2/m with a nearly perfect honeycomb lattice exhibiting less than 0.2% in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at T N = 7 K. The magnetic order below this temperature exhibits a propagation vector of k=(0,1,1/3), which coincides with a three-layer stacking of the C2/m unit cells. Magnetic transitions at highermore » temperatures up to 14 K can be introduced by deformations of the crystal that result in regions in the crystal with a two-layer stacking sequence. The best-fit symmetry-allowed magnetic structure of the as-grown crystals shows that the spins lie in the ac plane, with a zigzag configuration in each honeycomb layer. The three-layer repeat out-of-plane structure can be refined as a 120° spiral order or a collinear structure with a spin direction of 35° away from the a axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) μB per Ru 3+ ion.« less

  4. Crystal Structure of Two V-shaped Ligands with N-Heterocycles

    NASA Astrophysics Data System (ADS)

    Wang, Gao-Feng; Sun, Shu-Wen; Zhang, Xiao; Sun, Shu-Gang

    2017-12-01

    Two V-shaped ligands with N-heterocycles, bis(4-(1 H-imidazol-1-yl) phenyl)methanone ( 1), and bis(4-(1 H-benzo[d]imidazol-1-yl)phenyl)methanone ( 2) have been synthesized and characterized by elemental analyses, IR and 1 H NMR spectroscopy. Crystal structures of 1 and 2 have been determined by X-ray diffraction. The crystal of 1 is monoclinic, sp. gr. P21/ c, Z = 4. The crystal of 2 is orthorhombic, sp. gr. Fdd2, Z = 8. X-ray diffraction analyses show that the V-shaped angles of 1 and 2 are 122.72(15)° and 120.7(4)°, respectively. Intermolecular C-H···O, C-H···N, C-H···π, and π···π interactions link the components into three-dimensional networks in the crystal structures.

  5. Synthesis, crystal structure, thermal and nonlinear optical properties of new metal-organic single crystal: Tetrabromo (piperazinium) zincate (II) (TBPZ)

    NASA Astrophysics Data System (ADS)

    Boopathi, K.; Babu, S. Moorthy; Ramasamy, P.

    2018-04-01

    Tetrabromo (piperazinium) zincate, a new metal-organic crystal has been synthesized and its single crystal grown by slow evaporation method. The grown crystal has characterized by structural, spectral, thermal, linear and nonlinear optical properties. Single crystal X-ray diffractions study reveals that grown crystal belongs to orthorhombic crystal system with space group P212121. The presence of functional groups is identified by FT-IR spectral analysis. Thermal stability of the crystal was ascertained by TG-DTA measurement. The second order harmonic generation efficiency was measured using Kurtz and Perry technique and it was found to be 1.5 times that of KDP.

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

    ERIC Educational Resources Information Center

    Cady, Susan G.

    1997-01-01

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

  7. Crystal structure and low-energy Einstein mode in ErV{sub 2}Al{sub 20} intermetallic cage compound

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Winiarski, Michał J., E-mail: mwiniarski@mif.pg.gda.pl; Klimczuk, Tomasz

    Single crystals of a new ternary aluminide ErV{sub 2}Al{sub 20} were grown using a self-flux method. The crystal structure was determined by powder X-ray diffraction measurements and Rietveld refinement, and physical properties were studied by means of electrical resistivity, magnetic susceptibility and specific heat measurements. These measurements reveal that ErV{sub 2}Al{sub 20} is a Curie-Weiss paramagnet down to 1.95 K with an effective magnetic moment μ{sub eff} =9.27(1) μ{sub B} and Curie-Weiss temperature Θ{sub CW} =−0.55(4) K. The heat capacity measurements show a broad anomaly at low temperatures that is attributed to the presence of a low-energy Einstein mode withmore » characteristic temperature Θ{sub E} =44 K, approximately twice as high as in the isostructural ‘Einstein solid’ VAl{sub 10.1}. - Graphical abstract: A low-energy Einstein mode is observed in a novel intermetallic cage compound ErV{sub 2}Al{sub 20} by specific heat and resistivity measurements. - Highlights: • Single crystals of a new compound ErV{sub 2}Al{sub 20} were grown by self-flux method. • Crystal structure is reported, based on powder x-ray diffraction. • ErV{sub 2}Al{sub 20} is a Curie-Weiss paramagnet. • Low-energy ‘rattling’ phonon mode (Θ{sub E}=44 K) is found in specific heat measurements.« less

  8. The different conformations and crystal structures of dihydroergocristine

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  9. Theoretical exploration of various lithium peroxide crystal structures in a Li-air battery

    DOE PAGES

    Lau, Kah; Qiu, Dantong; Luo, Xiangyi; ...

    2015-01-14

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

  10. Structural investigation of cooperite (PtS) crystals

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rozhdestvina, V. I., E-mail: veronika@ascnet.ru; Udovenko, A. A.; Rubanov, S. V.

    2016-03-15

    The single-crystal structure of cooperite, a natural platinum sulfide PtS, is studied by X-ray diffraction supported by high-resolution scanning transmission electron microscopy and X-ray spectrum microanalysis. It is found that, in addition to the main reflections corresponding to the known tetragonal cell (a = 3.47 and c = 6.11 Å; space group P4{sub 2}/mmc), many weak reflections with intensities I ≤ 60σ(I) are clearly observed. These reflections fit the tetragonal cell (space group I4/mmm) with doubled parameters. In structures with small (P4{sub 2}/mmc) and large (I4/mmm) cells, the S atoms occupy statistically two special positions. It is shown that themore » chemical composition of the cooperite crystals deviates from the stoichiometric composition: sulfur-deficient specimens predominate.« less

  11. Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

    2015-03-01

    Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

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

    PubMed

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

    2014-09-16

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

  13. Structure, dielectric and electric properties of diisobutylammonium hydrogen sulfate crystal

    NASA Astrophysics Data System (ADS)

    Bednarchuk, Tamara J.; Kinzhybalo, Vasyl; Markiewicz, Ewa; Hilczer, Bożena; Pietraszko, Adam

    2018-02-01

    Diisobutylammonium hydrogen sulfate, a new organic-inorganic hybrid compound, was successfully synthesized and three structural phases in 298-433 K temperature range were revealed by differential scanning calorimetry and X-ray powder diffraction studies. Single crystal X-ray diffraction data were used to describe the crystal structures in each particular case. In phase III (below 336/319 K on heating/cooling) the crystal arrangement appears to be within the triclinic symmetry with P-1 space group. During heating in the 336-339 K region (and 319-337 K on cooling) the crystal exists in the phase II, characterized by monoclinic symmetry with P21/c space group. Consequently, above 339 K (during heating, and 337 K during cooling temperature sequences), i.e. in phase I the crystal exhibits orthorhombic symmetry (Cmce space group). Ferroelastic domain structure was observed in phase III. These phase boundaries (III→II and II→I) were accompanied by the presence of small anomalies, apparent in the dielectric permittivity and electric conductivity experimental data. Fast proton transport with activation energy of 0.23 eV was observed in the high temperature phase I and related to phonon assisted proton diffusion conditioned by disorder of diisobutylammonium (diba) cations, as well as by high thermal displacements of oxygen and sulfur atoms of hydrogen sulfate anion (hs).

  14. Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

    PubMed

    Lemieux, M Joanne

    2007-01-01

    The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

  15. Atomic resolution of structural changes in elastic crystals of copper(II) acetylacetonate

    NASA Astrophysics Data System (ADS)

    Worthy, Anna; Grosjean, Arnaud; Pfrunder, Michael C.; Xu, Yanan; Yan, Cheng; Edwards, Grant; Clegg, Jack K.; McMurtrie, John C.

    2018-01-01

    Single crystals are typically brittle, inelastic materials. Such mechanical responses limit their use in practical applications, particularly in flexible electronics and optical devices. Here we describe single crystals of a well-known coordination compound—copper(II) acetylacetonate—that are flexible enough to be reversibly tied into a knot. Mechanical measurements indicate that the crystals exhibit an elasticity similar to that of soft materials such as nylon, and thus display properties normally associated with both hard and soft matter. Using microfocused synchrotron radiation, we mapped the changes in crystal structure that occur on bending, and determined the mechanism that allows this flexibility with atomic precision. We show that, under strain, the molecules in the crystal reversibly rotate, and thus reorganize to allow the mechanical compression and expansion required for elasticity and still maintain the integrity of the crystal structure.

  16. Machine learning for autonomous crystal structure identification.

    PubMed

    Reinhart, Wesley F; Long, Andrew W; Howard, Michael P; Ferguson, Andrew L; Panagiotopoulos, Athanassios Z

    2017-07-21

    We present a machine learning technique to discover and distinguish relevant ordered structures from molecular simulation snapshots or particle tracking data. Unlike other popular methods for structural identification, our technique requires no a priori description of the target structures. Instead, we use nonlinear manifold learning to infer structural relationships between particles according to the topology of their local environment. This graph-based approach yields unbiased structural information which allows us to quantify the crystalline character of particles near defects, grain boundaries, and interfaces. We demonstrate the method by classifying particles in a simulation of colloidal crystallization, and show that our method identifies structural features that are missed by standard techniques.

  17. USSR and Eastern Europe Scientific Abstracts, Physics and Mathematics, Number 39

    DTIC Science & Technology

    1978-01-17

    examination of a monoclinic single crystal has revealed a U022+ iön, and helical polyphosphate chains with six PO4 tetrahedra per link. Corrugated uranyl...mean mass temperature and local Nusselt number. Figures 5; references 13: 3 Russian, 10 Western. USSR UDC 535.334 DETERMINATION OF THE PARAMETERS...Nuclear Research [Abstract] The theory of pion condensation predicts the existence of super- dense nuclei, on the basis of the structure of the

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

    NASA Astrophysics Data System (ADS)

    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.

  19. Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

    PubMed

    Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

    2017-09-25

    Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

  20. Crystal structure of TBC1D15 GTPase‐activating protein (GAP) domain and its activity on Rab GTPases

    PubMed Central

    Chen, Yan‐Na; Gu, Xin; Zhou, X. Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei

    2017-01-01

    Abstract TBC1D15 belongs to the TBC (Tre‐2/Bub2/Cdc16) domain family and functions as a GTPase‐activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark‐TBC1D15 and Sus‐TBC1D15 belong to the same subfamily of TBC domain‐containing proteins, and their GAP‐domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost. PMID:28168758

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    2012-03-27

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

  2. Crystal growth, structural, low temperature thermoluminescence and mechanical properties of cubic fluoroperovskite single crystal (LiBaF3)

    NASA Astrophysics Data System (ADS)

    Daniel, D. Joseph; Ramasamy, P.; Ramaseshan, R.; Kim, H. J.; Kim, Sunghwan; Bhagavannarayana, G.; Cheon, Jong-Kyu

    2017-10-01

    Polycrystalline compounds of LiBaF3 were synthesized using conventional solid state reaction route and the phase purity was confirmed using powder X-ray diffraction technique. Using vertical Bridgman technique single crystal was grown from melt. Rocking curve measurements have been carried out to study the structural perfection of the grown crystal. The single peak of diffraction curve clearly reveals that the grown crystal was free from the structural grain boundaries. The low temperature thermoluminescence of the X-ray irradiated sample has been analyzed and found four distinguishable peaks having maximum temperatures at 18, 115, 133 and 216 K. Activation energy (E) and frequency factor (s) for the individual peaks have been studied using Peak shape method and the computerized curve fitting method combining with the Tmax- TStop procedure. Nanoindentation technique was employed to study the mechanical behaviour of the crystal. The indentation modulus and Vickers hardness of the grown crystal have values of 135.15 GPa and 680.81 respectively, under the maximum indentation load of 10 mN.

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

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

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

  4. Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

    PubMed

    Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

    2014-05-05

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Crystal and molecular structure of 2,6-dibromo-3-chloro-4-fluoroaniline

    NASA Astrophysics Data System (ADS)

    Betz, R.

    2015-12-01

    The crystal and molecular structure of 2,6-dibromo-3-chloro-4-fluoroaniline is determined. The crystals are monoclinic, a = 3.8380(3), b = 13.1010(12), c = 8.0980(8) Å, β = 96.010(4)°, V = 404.94(6) Å3, Z = 2, sp. gr. P21. Classical intra- and intermolecular hydrogen bonds of the N-H··· Hal type are observed next to a series of dispersive halogen···halogen interactions in the crystal structure.

  6. Highly sensitive quartz crystal microbalance based biosensor using Au dendrite structure

    NASA Astrophysics Data System (ADS)

    Asai, Naoto; Terasawa, Hideaki; Shimizu, Tomohiro; Shingubara, Shoso; Ito, Takeshi

    2018-02-01

    A Au dendrite structure was obtained by only electroplating under a suitable potential. A blanch like nanostructure was formed along the crystal orientation. In this study, we attempted to fabricate a Au dendrite structure on the electrode of a quartz crystal by electroplating to increase the specific surface area. We estimated the effective surface area by cyclic voltammetry (CV) and monitored the frequency shift induced by antigen-antibody interaction by the quartz crystal microbalance (QCM) method. The dendrite structure with the largest surface area was formed under -0.95 V for 5 min. In the measurement of the antigen-antibody interaction, the frequency shifts of 40, 80, and 110 Hz were obtained with the dendrite structured QCM chips formed at the above potential for 1, 1.5, and 2.0 min, respectively. The sensitivity was improved compared with that QCM chip having a flat surface electrode.

  7. Crystal Structure Prediction and its Application in Earth and Materials Sciences

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang

    discuss if these oxides might exist at earth and planetary conditions. If the target properties are set as the global fitness functions while structure relaxations are energy/enthalpy minimization, such hybrid optimization technique could effectively explore the landscape of properties for the given systems. Here we illustrate this function by the case of searching for superdense carbon allotropes. We find three structures (hP3, tI12, and tP12) that have significantly greater density. Furthermore, we find a collection of other superdense structures based on different ways of packing carbon tetrahedral. Superdense carbon allotropes are predicted to have remarkably high refractive indices and strong dispersion of light. Apart from evolutionary approach, there also exist some other methods for structural prediction. One can also combine the features from different methods. We develop a novel method for crystal structure prediction, based on metadynamics and evolutionary algorithms. This technique can be used to produce efficiently both the ground state and metastable states easily reachable from a reasonable initial structure. We use the cell shape as collective variable and evolutionary variation operators developed in the context of the USPEX method to equilibrate the system as a function of the collective variables. We illustrate how this approach helps one to find stable and metastable states for Al2SiO5, SiO2, MgSiO3. Apart from predicting crystal structures, the new method can also provide insight into mechanisms of phase transitions. This method is especially powerful in sampling the metastable structures from a given configuration. Experiments on cold compression indicated the existence of a new superhard carbon allotrope. Numerous metastable candidate structures featuring different topologies have been proposed for this allotrope. We use evolutionary metadynamics to systematically search for possible candidates which could be accessible from graphite. (Abstract

  8. Growth and structural, optical, and electrical properties of zincite crystals

    NASA Astrophysics Data System (ADS)

    Kaurova, I. A.; Kuz'micheva, G. M.; Rybakov, V. B.

    2013-03-01

    An X-ray diffraction study of ZnO crystals grown by the hydrothermal method has revealed reflections that give grounds to assign them to the sp. gr. P3 rather than to P63 mc. The distribution of Zn1, Zn2, O1, and O2 over structural positions, along with vacancies and incorporated zinc atoms, explains the dissymmetrization observed in terms of the kinetic (growth) phase transition of the order-disorder type, which is caused by ordering Zn and O atoms over structural positions. The color of crystals of refined compositions (Zn0.975□0.025)Zn i(0.015)(O0.990□0.010) (green) and (Zn0.965□0.035)Zn i(0.035)O (bright green) is related to different oxygen contents, which is confirmed by the results of electron probe X-ray microanalysis and absorption spectroscopy. The degree of the structural quality of crystals, their resistivity, and activation energy are also related to oxygen vacancies.

  9. Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

    PubMed

    Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

    2016-01-01

    Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

  10. Solution‐crystallization and related phenomena in 9,9‐dialkyl‐fluorene polymers. II. Influence of side‐chain structure

    PubMed Central

    Perevedentsev, Aleksandr; Stavrinou, Paul N.; Smith, Paul

    2015-01-01

    ABSTRACT Solution‐crystallization is studied for two polyfluorene polymers possessing different side‐chain structures. Thermal analysis and temperature‐dependent optical spectroscopy are used to clarify the nature of the crystallization process, while X‐ray diffraction and scanning electron microscopy reveal important differences in the resulting microstructures. It is shown that the planar‐zigzag chain conformation termed the β‐phase, which is observed for certain linear‐side‐chain polyfluorenes, is necessary for the formation of so‐called polymer‐solvent compounds for these polymers. Introduction of alternating fluorene repeat units with branched side‐chains prevents formation of the β‐phase conformation and results in non‐solvated, i.e. melt‐crystallization‐type, polymer crystals. Unlike non‐solvated polymer crystals, for which the chain conformation is stabilized by its incorporation into a crystalline lattice, the β‐phase conformation is stabilized by complexation with solvent molecules and, therefore, its formation does not require specific inter‐chain interactions. The presented results clarify the fundamental differences between the β‐phase and other conformational/crystalline forms of polyfluorenes. © 2015 The Authors. Journal of Polymer Science Part B: Polymer Physics published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015, 53, 1492–1506 PMID:27546983

  11. Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal.

    PubMed

    Sudhahar, S; Krishna Kumar, M; Sornamurthy, B M; Mohan Kumar, R

    2014-01-24

    Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Synthesis of rhenium nitride crystals with MoS2 structure

    NASA Astrophysics Data System (ADS)

    Kawamura, Fumio; Yusa, Hitoshi; Taniguchi, Takashi

    2012-06-01

    Rhenium nitride (ReN2) crystals were synthesized from a metathesis reaction between ReCl5 and Li3N under high pressure. The reaction was well controlled by the addition of a large amount of NaCl as reaction inhibitor to prevent a violent exothermic reaction. The largest rhenium nitride crystals obtained had a millimeter-order size with a platelet shape. X-ray diffraction analysis revealed that rhenium nitride has MoS2 structure similar to hexagonal rhenium diboride (ReB2) which has recently been investigated as an ultra-hard material. The structure was different from any structures previously predicted for ReN2 by theoretical calculations.

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

    PubMed

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

    2016-08-18

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

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

    USGS Publications Warehouse

    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

  15. Synthesis and Crystal Structure of a Chalcone Derivative

    NASA Astrophysics Data System (ADS)

    Singh, Vikram D.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; Kamni; Anthal, Sumati; Kant, Rajni

    2017-12-01

    (2E)-3-(anthrance-9-yl)-1-(3,4-dichlorophenyl)prop-2-en-1-one [C23H14OCl2] is synthesized and its crystal structure is determined by single X-ray diffraction. There exist two molecules in the asymmetric unit. The dihedral angle between the benzene and anthracene moiety of the molecule A and B is 86.51(12)° and 76.42(13)°, respectively. No classical hydrogen bonds are observed and only van der Waals forces stabilize the crystal packing.

  16. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

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

    2009-02-01

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

  17. Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy.

    PubMed

    Kekilli, Demet; Dworkowski, Florian S N; Pompidor, Guillaume; Fuchs, Martin R; Andrew, Colin R; Antonyuk, Svetlana; Strange, Richard W; Eady, Robert R; Hasnain, S Samar; Hough, Michael A

    2014-05-01

    It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

  18. Crystal structure of bile salt hydrolase from Lactobacillus salivarius.

    PubMed

    Xu, Fuzhou; Guo, Fangfang; Hu, Xiao Jian; Lin, Jun

    2016-05-01

    Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of BSH function, which has hampered the development of BSH-based strategies for improving human and animal health. As an initial step towards the structure-function analysis of BSH, C-terminally His-tagged BSH from Lactobacillus salivarius NRRL B-30514 was crystallized in this study. The 1.90 Å resolution crystal structure of L. salivarius BSH was determined by molecular replacement using the structure of Clostridium perfringens BSH as a starting model. It revealed this BSH to be a member of the N-terminal nucleophile hydrolase superfamily. Crystals of apo BSH belonged to space group P21212, with unit-cell parameters a = 90.79, b = 87.35, c = 86.76 Å (PDB entry 5hke). Two BSH molecules packed perfectly as a dimer in one asymmetric unit. Comparative structural analysis of L. salivarius BSH also identified potential residues that contribute to catalysis and substrate specificity.

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

    PubMed

    Fu, Qianqian; Zhu, Biting; Ge, Jianping

    2017-02-16

    A SiO 2 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 SiO 2 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ankudinov, V. E., E-mail: vladimir@ankudinov.org; Galenko, P. K.; Kropotin, N. V.

    2016-02-15

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

  1. Crystal orientation dependence of femtosecond laser-induced periodic surface structure on (100) silicon.

    PubMed

    Jiang, Lan; Han, Weina; Li, Xiaowei; Wang, Qingsong; Meng, Fantong; Lu, Yongfeng

    2014-06-01

    It is widely believed that laser-induced periodic surface structures (LIPSS) are independent of material crystal structures. This Letter reports an abnormal phenomenon of strong dependence of the anisotropic formation of periodic ripples on crystal orientation, when Si (100) is processed by a linearly polarized femtosecond laser (800 nm, 50 fs, 1 kHz). LIPSS formation sensitivity with a π/2 modulation is found along different crystal orientations with a quasi-cosinusoid function when the angle between the crystal orientation and polarization direction is changed from 0° to 180°. Our experiments indicate that it is much easier (or more difficult) to form ripple structures when the polarization direction is aligned with the lattice axis [011]/[011¯] (or [001]). The modulated nonlinear ionization rate along different crystal orientations, which arises from the direction dependence of the effective mass of the electron is proposed to interpret the unexpected anisotropic LIPSS formation phenomenon. Also, we demonstrate that the abnormal phenomenon can be applied to control the continuity of scanned ripple lines along different crystal orientations.

  2. Crystal growth, structure and morphology of hydrocortisone methanol solvate

    NASA Astrophysics Data System (ADS)

    Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

    2004-04-01

    Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

  3. Atomically-thick two-dimensional crystals: electronic structure regulation and energy device construction.

    PubMed

    Sun, Yongfu; Gao, Shan; Xie, Yi

    2014-01-21

    Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices.

  4. Tl{sub 10}Hg{sub 3}Cl{sub 16}: Single crystal growth, electronic structure and piezoelectric properties

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Khyzhun, O.Y., E-mail: khyzhun@ipms.kiev.ua; Piasecki, M.; Kityk, I.V.

    Single crystal of the ternary halide Tl{sub 10}Hg{sub 3}Cl{sub 16} was grown using Bridgman-Stockbarger method. For the Tl{sub 10}Hg{sub 3}Cl{sub 16} crystal, we have measured X-ray photoelectron spectra for both pristine and Ar{sup +} ion-bombarded surfaces and additionally investigated photoinduced piezoelectricity. Our data indicate that the Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal surface is very sensitive with respect to Ar{sup +} ion-bombardment. In particular, Ar{sup +} ion-bombardment with energy of 3.0 keV over 5 min at an ion current density of 14 μA/cm{sup 2} causes significant changes of the elemental stoichiometry of the Tl{sub 10}Hg{sub 3}Cl{sub 16} surface resulting inmore » an abrupt decrease of the mercury content in the top surface layers of the studied single crystal. As a result of the treatment, the mercury content becomes nil in the top surface layers. In addition, the present XPS measurements allow for concluding about very low hygroscopicity of the Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal surface. The property is extremely important for the crystal handling in optoelectronic or nano-electronic devices working at ambient conditions. The photoinduced piezoelectricity has been explored for Tl{sub 10}Hg{sub 3}Cl{sub 16} depending on nitrogen (λ=371 nm) laser power density and temperature. - Graphical abstract: As-grown single crystal boule of Tl{sub 10}Hg{sub 3}Cl{sub 16}; dependence of the effective piezoelecric coefficient d{sub 33} versus the photoinducing nitrogen laser power density, I, at different temperatures, T; and packing of the polyhedra of halide atoms around Hg atoms in the Tl{sub 10}Hg{sub 3}Cl{sub 16} structure. - Highlights: • High-quality Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal has been grown by Bridgman-Stockbarger method. • Electronic structure of Tl{sub 10}Hg{sub 3}Cl{sub 16} is studied by the XPS method. • Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal surface is sensitive with respect to Ar{sup +} ion

  5. Crystal structure and properties of tetragonal EuAg{sub 4}In{sub 8} grown by metal flux technique

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Subbarao, Udumula; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

    The compound EuAg{sub 4}In{sub 8} has been obtained as single crystals in high yield from reactions run in liquid indium. X-ray diffraction on single crystals suggests that EuAg{sub 4}In{sub 8} crystallizes in the CeMn{sub 4}Al{sub 8} structure type, tetragonal space group I4/mmm with lattice constants a=b=9.7937(2) Å and c=5.7492(2) Å. Crystal structure of EuAg{sub 4}In{sub 8} is composed of pseudo Frank–Kasper cages occupied by one europium atom in each ring, which are shared through the corner along the ab plane resulting in a three dimensional network. The magnetic susceptibility of EuAg{sub 4}In{sub 8} was measured in the temperature range 2–300more » K, which obeyed Curie–Weiss law above 50 K. Magnetic moment value calculated from the fitting indicates the presence of divalent europium, which was confirmed by X-ray absorption near edge spectroscopy. Electrical resistivity measurements suggest that EuAg{sub 4}In{sub 8} is metallic in nature with a probable Fermi liquid behavior at low temperature. - Graphical abstract: The tetragonal EuAg{sub 4}In{sub 8} has been grown as single crystals from reactions run in liquid indium. Magnetic and XANES measurements suggest divalent nature of Eu and resistivity measurements suggest metallic nature. - Highlights: • EuAg{sub 4}In{sub 8} phase having tetragonal phase is grown by metal flux technique. • Magnetic and XANES measurements exhibit divalent nature of Eu in EuAg{sub 4}In{sub 8}. • Resistivity measurement suggests metallic nature and probable Fermi liquid behavior.« less

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

    USGS Publications Warehouse

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

    1964-01-01

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

  7. Crystal structure and hydrogen-bonding patterns in 5-fluoro-cytosinium picrate.

    PubMed

    Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

    2017-03-01

    In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C 4 H 5 FN 3 O + ·C 6 H 2 N 3 O 7 - , one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA - ) anion. In the crystal, the 5FC + cation inter-acts with the PA - anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R 2 1 (6) and R 1 2 (6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.

  8. Free-standing nanomechanical and nanophotonic structures in single-crystal diamond

    NASA Astrophysics Data System (ADS)

    Burek, Michael John

    Realizing complex three-dimensional structures in a range of material systems is critical to a variety of emerging nanotechnologies. This is particularly true of nanomechanical and nanophotonic systems, both relying on free-standing small-scale components. In the case of nanomechanics, necessary mechanical degrees of freedom require physically isolated structures, such as suspended beams, cantilevers, and membranes. For nanophotonics, elements like waveguides and photonic crystal cavities rely on light confinement provided by total internal reflection or distributed Bragg reflection, both of which require refractive index contrast between the device and surrounding medium (often air). Such suspended nanostructures are typically fabricated in a heterolayer structure, comprising of device (top) and sacrificial (middle) layers supported by a substrate (bottom), using standard surface nanomachining techniques. A selective, isotropic etch is then used to remove the sacrificial layer, resulting in free-standing devices. While high-quality, crystalline, thin film heterolayer structures are readily available for silicon (as silicon-on-insulator (SOI)) or III-V semiconductors (i.e. GaAs/AlGaAs), there remains an extensive list of materials with attractive electro-optic, piezoelectric, quantum optical, and other properties for which high quality single-crystal thin film heterolayer structures are not available. These include complex metal oxides like lithium niobate (LiNbO3), silicon-based compounds such as silicon carbide (SiC), III-V nitrides including gallium nitride (GaN), and inert single-crystals such as diamond. Diamond is especially attractive for a variety of nanoscale technologies due to its exceptional physical and chemical properties, including high mechanical hardness, stiffness, and thermal conductivity. Optically, it is transparent over a wide wavelength range (from 220 nm to the far infrared), has a high refractive index (n ~ 2.4), and is host to a vast

  9. Crystal structure, electronic structure, temperature-dependent optical and scintillation properties of CsCe 2Br 7

    DOE PAGES

    Wu, Yuntao; Shi, Hongliang; Chakoumakos, Bryan C.; ...

    2015-10-05

    CsCe 2Br 7 is a self-activated inorganic scintillator that shows promising performance, but the understanding of the important structure-property relationships is lacking. In this work, we conduct a comprehensive study on CCsCe 2Br 7. The crystal structure of CsCe 2Br 7 is refined using single crystal X-ray study for the first time. It crystallizes into the orthorhombic crystal system with Pmnb space group. Its electronic structure is revealed by Density Functional Theory (DFT) calculations. Two cerium emission centers are identified and the energy barriers related to the thermal quenching to 4f ground states of Ce 3+ for these two Cemore » centers are evaluated. CsCe 2Br 7 single crystal has better light yield and energy resolution than CsCe 2Cl 7, but with an additional slow decay component of 1.7 s. The existence of a deep trap with a depth of 0.9 eV in CsCe 2Cl 7 contributes to its higher afterglow level in comparison to that of CsCe 2Br 7. The most possible point defects in CsCe 2Cl 7 and CsCe 2Br 7 are proposed by considering the vapour pressure in the growth atmosphere upon melting point.« less

  10. Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

    NASA Astrophysics Data System (ADS)

    Karthigha, S.; Krishnamoorthi, C.

    2018-03-01

    An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

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

    NASA Technical Reports Server (NTRS)

    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. Synthesis, crystal structure and optical properties of a novel sodium lead pentaborate, NaPbB{sub 5}O{sub 9}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Min; Graduate University of Chinese Academy of Sciences, Beijing 100049; Pan, Shilie, E-mail: slpan@ms.xjb.ac.c

    A novel sodium lead pentaborate, NaPbB{sub 5}O{sub 9}, has been successfully synthesized by standard solid-state reaction. The single-crystal X-ray structural analysis showed that NaPbB{sub 5}O{sub 9} crystallizes in the monoclinic space group P2{sub 1}/c with a=6.5324(10) A, b=13.0234(2) A, c=8.5838(10) A, {beta}=104.971(10){sup o}, and Z=4. The crystal structure is composed of double ring [B{sub 5}O{sub 9}]{sup 3-} units, [PbO{sub 7}] and [NaO{sub 7}] polyhedra. [B{sub 5}O{sub 9}]{sup 3-} groups connect with each other forming two-dimensional infinite {sub {infinity}}[B{sub 5}O{sub 9}]{sup 3-} layers, while [PbO{sub 7}] and [NaO{sub 7}] polyhedra are located between the layers. [PbO{sub 7}] polyhedra linked together viamore » corner-sharing O atom forming novel infinite {sub {infinity}}[PbO{sub 6}] chains along the c axis. The thermal behavior, IR spectrum and the optical diffuse reflectance spectrum of NaPbB{sub 5}O{sub 9} were reported. -- Graphical abstract: A new phase, NaPbB{sub 5}O{sub 9}, has been discovered in the ternary M{sub 2}O-PbO-B{sub 2}O{sub 3} (M=alkali-metal) system. The crystal structure consists of a novel infinite {sub {infinity}}[PbO{sub 6}] chains. Display Omitted Research highlights: NaPbB{sub 5}O{sub 9} is the first borate discovered in the ternary M{sub 2}O-PbO-B{sub 2}O{sub 3} (M=alkali-metal) system. NaPbB{sub 5}O{sub 9} crystal structure includes a two-dimensional infinite {sub {infinity}}[B{sub 5}O{sub 9}]{sup 3-} layers and a novel one-dimensional infinite {sub {infinity}}[PbO{sub 6}] chains. [PbO{sub 7}] polyhedron has a highly asymmetric bonding configuration.« less

  13. Band gap structures for 2D phononic crystals with composite scatterer

    NASA Astrophysics Data System (ADS)

    Qi, Xiao-qiao; Li, Tuan-jie; Zhang, Jia-long; Zhang, Zhen; Tang, Ya-qiong

    2018-05-01

    We investigated the band gap structures in two-dimensional phononic crystals with composite scatterer. The composite scatterers are composed of two materials (Bragg scattering type) or three materials (locally resonance type). The finite element method is used to calculate the band gap structure, eigenmodes and transmission spectrum. The variation of the location and width of band gap are also investigated as a function of material ratio in the scatterer. We have found that the change trends the widest band gap of the two phononic crystals are different as the material ratio changing. In addition to this, there are three complete band gaps at most for the Bragg-scattering-type phononic crystals in the first six bands; however, the locally resonance-type phononic crystals exist only two complete band gap at most in the first six bands. The gap-tuning effect can be controlled by the material ratio in the scatterer.

  14. Machine learning for the structure-energy-property landscapes of molecular crystals.

    PubMed

    Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

    2018-02-07

    Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

  15. High-brightness tapered laser diodes with photonic crystal structures

    NASA Astrophysics Data System (ADS)

    Li, Yi; Du, Weichuan; Kun, Zhou; Gao, Songxin; Ma, Yi; Tang, Chun

    2018-02-01

    Beam quality of tapered laser diodes is limited by higher order lateral mode. On purpose of optimizing the brightness of tapered laser diodes, we developed a novel design of tapered diodes. This devices based on InGaAs/AlGaAs asymmetry epitaxial structure, containing higher order lateral mode filtering schemes especially photonic crystal structures, which fabricated cost effectively by using standard photolithography and dry etch processes. Meanwhile, the effects of photonic crystal structures on mode control are also investigated theoretically by FDBPM (Finite-Difference Beam Propagation Method) calculation. We achieved a CW optical output power of 6.9W at 940nm for a single emitter with 4 mm cavity length. A nearly diffraction limited beam of M2 ≍1.9 @ 0.5W has been demonstrated, and a highest brightness of β =75MW/(cm2 ·sr) was reached.

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

    PubMed

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

    2010-05-20

    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.

  17. “Skin-Core-Skin” Structure of Polymer Crystallization Investigated by Multiscale Simulation

    PubMed Central

    Ruan, Chunlei

    2018-01-01

    “Skin-core-skin” structure is a typical crystal morphology in injection products. Previous numerical works have rarely focused on crystal evolution; rather, they have mostly been based on the prediction of temperature distribution or crystallization kinetics. The aim of this work was to achieve the “skin-core-skin” structure and investigate the role of external flow and temperature fields on crystal morphology. Therefore, the multiscale algorithm was extended to the simulation of polymer crystallization in a pipe flow. The multiscale algorithm contains two parts: a collocated finite volume method at the macroscopic level and a morphological Monte Carlo method at the microscopic level. The SIMPLE (semi-implicit method for pressure linked equations) algorithm was used to calculate the polymeric model at the macroscopic level, while the Monte Carlo method with stochastic birth-growth process of spherulites and shish-kebabs was used at the microscopic level. Results show that our algorithm is valid to predict “skin-core-skin” structure, and the initial melt temperature and the maximum velocity of melt at the inlet mainly affects the morphology of shish-kebabs. PMID:29659516

  18. Structure and functionality of nanostructured triacylglycerol crystal networks.

    PubMed

    Ramel, Pere R; Co, Edmund D; Acevedo, Nuria C; Marangoni, Alejandro G

    2016-10-01

    In this review, recent advances in the characterization of the nanoscale structure of fat crystal networks are outlined. The effect of different factors on the properties of crystalline nanoplatelets (CNPs) is comprehensively described. These are discussed together with the observed changes in polymorphism and micro- or mesostructural properties so as to have a complete understanding of the influence of different internal and external factors on the material properties of fats. The relationship between the nanostructure and the material properties of fats (i.e., oil binding capacity and rheology) is also described. Characterization of the nanostructure of fats has provided a new dimension to the analysis of fat crystal networks and opportunities for nanoengineering that could result in innovations in the food industry with regards to processing and structuring fatty materials. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Surface modes and reconstruction of diamond structure crystals

    NASA Astrophysics Data System (ADS)

    Goldammer, W.; Ludwig, W.; Zierau, W.

    1986-08-01

    Applying our recently proposed Green function method we calculate the surface phonon spectra for the (111) surfaces of the diamond structure crystals C, Si, Ge and α-Sn on the basis of a phenomenological force constant model. Allowing for changes in the surface force constants we investigate the possibility of a surface phonon softening. Relating these soft modes to surface reconstructions we find evidence for a Si (7 × 7), Ge (8 × 8) and α-Sn (3 × 3) reconstruction, while diamond does not exhibit a soft mode behavior at all. We can thus explain the occurrence of different surface structures in these geometrically identical crystals as being determined to a great extent already by bulk properties. Finally, we derive models of the reconstructed surfaces and discuss our model for the Si (7 × 7) surface with respect to experimental TED patterns.

  20. Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera).

    PubMed

    Jin, Tengchuan; Wang, Cheng; Zhang, Caiying; Wang, Yang; Chen, Yu-Wei; Guo, Feng; Howard, Andrew; Cao, Min-Jie; Fu, Tong-Jen; McHugh, Tara H; Zhang, Yuzhu

    2017-08-30

    Coconut (Cocos nucifera) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. The structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

  1. Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model.

    PubMed

    Gabriëlse, Alexander; Löwen, Hartmut; Smallenburg, Frank

    2017-11-07

    In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO) lattices not previously considered for the square shoulder model.

  2. Synthesis, crystal structure and electrical properties of the tetrahedral quaternary chalcogenides CuM{sub 2}InTe{sub 4} (M=Zn, Cd)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nolas, George S., E-mail: gnolas@usf.edu; Hassan, M. Shafiq; Dong, Yongkwan

    Quaternary chalcogenides form a large class of materials that continue to be of interest for energy-related applications. Certain compositions have recently been identified as possessing good thermoelectric properties however these materials typically have the kesterite structure type with limited variation in composition. In this study we report on the structural, optical and electrical properties of the quaternary chalcogenides CuZn{sub 2}InTe{sub 4} and CuCd{sub 2}InTe{sub 4} which crystallize in the modified zinc-blende crystal structure, and compare their properties with that of CuZn{sub 2}InSe{sub 4}. These p-type semiconductors have direct band gaps of about 1 eV resulting in relatively high Seebeck coefficientmore » and resistivity values. This work expands on the research into quaternary chalcogenides with new compositions and structure types in order to further the fundamental investigation of multinary chalcogenides for potential thermoelectrics applications. - Graphical abstract: The structural, optical and electrical properties of the quaternary chalcogenides CuZn{sub 2}InTe{sub 4} and CuCd{sub 2}InTe{sub 4} are reported for the first time. The unique crystal structure allows for relatively good electrical transports and therefore potential for thermoelectric applications. - Highlights: • The physical properties of CuZn{sub 2}InTe{sub 4} and CuCd{sub 2}InTe{sub 4} are reported for the first time. • These materials have potential for thermoelectric applications. • Their direct band gaps also suggest potential for photovoltaics applications.« less

  3. Effects of cyclic structure inhibitors on the morphology and growth of tetrahydrofuran hydrate crystals

    NASA Astrophysics Data System (ADS)

    Li, Sijia; Wang, Yanhong; Lang, Xuemei; Fan, Shuanshi

    2013-08-01

    Morphology and growth of hydrate crystals with cyclic structure inhibitors at a hydrate-liquid interface were directly observed through a microscopic manipulating apparatus. Tetrahydrofuran (THF) hydrate was employed as an objective. The effects of four kind of cyclic structure inhibitors, polyvinylpyrrolidone (PVP), poly(N-vinyl-2-pyrrolidone-co-2-vinyl pyridine) (PVPP), poly(2-vinyl pyridine-co-N-vinylcaprolactam) (PVPC) and poly(N-vinylcaprolactam) (PVCap), were investigated. Morphological patterns between each hydrate crystal growth from hydrate-liquid interface into droplet were found differ significantly. Lamellar structure growth of hydrate crystal was observed without inhibitor, while with PVP was featheriness-like, PVPP was like long dendritic crystal, PVPC was Mimosa pudica leaf-like and PVCap was like weeds. The growth rate of hydrate crystal without inhibitor was 0.00498 mm3/s, while with PVPP, PVPC and PVCap, were 0.00339 mm3/s, 0.00350 mm3/s, 0.00386 mm3/s and 0.00426 mm3/s, respectively. Cyclic structure inhibitors can decrease the growth rate, degree of reduction in growth rate of hydrate crystals decrease with the increase of cylinder number.

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

    PubMed

    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.

  5. Crystal Structure Predictions Using Adaptive Genetic Algorithm and Motif Search methods

    NASA Astrophysics Data System (ADS)

    Ho, K. M.; Wang, C. Z.; Zhao, X.; Wu, S.; Lyu, X.; Zhu, Z.; Nguyen, M. C.; Umemoto, K.; Wentzcovitch, R. M. M.

    2017-12-01

    Material informatics is a new initiative which has attracted a lot of attention in recent scientific research. The basic strategy is to construct comprehensive data sets and use machine learning to solve a wide variety of problems in material design and discovery. In pursuit of this goal, a key element is the quality and completeness of the databases used. Recent advance in the development of crystal structure prediction algorithms has made it a complementary and more efficient approach to explore the structure/phase space in materials using computers. In this talk, we discuss the importance of the structural motifs and motif-networks in crystal structure predictions. Correspondingly, powerful methods are developed to improve the sampling of the low-energy structure landscape.

  6. Abstraction and Concreteness in the Everyday Mathematics of Structural Engineers.

    ERIC Educational Resources Information Center

    Gainsburg, Julie

    The everyday mathematics processes of structural engineers were studied and analyzed in terms of abstraction. A main purpose of the study was to explore the degree to which the notion of a gap between school and everyday mathematics holds when the scope of practices considered "everyday" is extended. J. Lave (1988) promoted a methodology…

  7. Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

    One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin

  8. Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fischmann, Thierry O.; Smith, Catherine K.; Mayhood, Todd W.

    MEK1 is a member of the MAPK signal transduction pathway that responds to growth factors and cytokines. We have determined that the kinase domain spans residues 35-382 by proteolytic cleavage. The complete kinase domain has been crystallized and its X-ray crystal structure as a complex with magnesium and ATP-{gamma}S determined at 2.1 {angstrom}. Unlike crystals of a truncated kinase domain previously published, the crystals of the intact domain can be grown either as a binary complex with a nucleotide or as a ternary complex with a nucleotide and one of a multitude of allosteric inhibitors. Further, the crystals allow formore » the determination of costructures with ATP competitive inhibitors. We describe the structures of nonphosphorylated MEK1 (npMEK1) binary complexes with ADP and K252a, an ATP-competitive inhibitor (see Table 1), at 1.9 and 2.7 {angstrom} resolution, respectively. Ternary complexes have also been solved between npMEK1, a nucleotide, and an allosteric non-ATP competitive inhibitor: ATP-{gamma}S with compound 1 and ADP with either U0126 or the MEK1 clinical candidate PD325089 at 1.8, 2.0, and 2.5 {angstrom}, respectively. Compound 1 is structurally similar to PD325901. These structures illustrate fundamental differences among various mechanisms of inhibition at the molecular level. Residues 44-51 have previously been shown to play a negative regulatory role in MEK1 activity. The crystal structure of the integral kinase domain provides a structural rationale for the role of these residues. They form helix A and repress enzymatic activity by stabilizing an inactive conformation in which helix C is displaced from its active state position. Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome.« less

  9. Probing the crystal structure landscape by doping: 4-bromo, 4-chloro and 4-methylcinnamic acids.

    PubMed

    Desiraju, Gautam R; Chakraborty, Shaunak; Joseph, Sumy

    2018-06-11

    Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br-atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii and others, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of pi...pi interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Photonic guiding structures in lithium niobate crystals produced by energetic ion beams

    NASA Astrophysics Data System (ADS)

    Chen, Feng

    2009-10-01

    A range of ion beam techniques have been used to fabricate a variety of photonic guiding structures in the well-known lithium niobate (LiNbO3 or LN) crystals that are of great importance in integrated photonics/optics. This paper reviews the up-to-date research progress of ion-beam-processed LiNbO3 photonic structures and reports on their fabrication, characterization, and applications. Ion beams are being used with this material in a wide range of techniques, as exemplified by the following examples. Ion beam milling/etching can remove the selected surface regions of LiNbO3 crystals via the sputtering effects. Ion implantation and swift ion irradiation can form optical waveguide structures by modifying the surface refractive indices of the LiNbO3 wafers. Crystal ion slicing has been used to obtain bulk-quality LiNbO3 single-crystalline thin films or membranes by exfoliating the implanted layer from the original substrate. Focused ion beams can either generate small structures of micron or submicron dimensions, to realize photonic bandgap crystals in LiNbO3, or directly write surface waveguides or other guiding devices in the crystal. Ion beam-enhanced etching has been extensively applied for micro- or nanostructuring of LiNbO3 surfaces. Methods developed to fabricate a range of photonic guiding structures in LiNbO3 are introduced. Modifications of LiNbO3 through the use of various energetic ion beams, including changes in refractive index and properties related to the photonic guiding structures as well as to the materials (i.e., electro-optic, nonlinear optic, luminescent, and photorefractive features), are overviewed in detail. The application of these LiNbO3 photonic guiding structures in both micro- and nanophotonics are briefly summarized.

  11. Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane

    PubMed Central

    Gao, Xiu-Gong; Maldonado, Ernesto; Pérez-Montfort, Ruy; Garza-Ramos, Georgina; de Gómez-Puyou, Marietta Tuena; Gómez-Puyou, Armando; Rodríguez-Romero, Adela

    1999-01-01

    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-Å 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 Å 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. PMID:10468562

  12. Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.

    PubMed

    Gao, X G; Maldonado, E; Pérez-Montfort, R; Garza-Ramos, G; de Gómez-Puyou, M T; Gómez-Puyou, A; Rodríguez-Romero, A

    1999-08-31

    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-A 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 A 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.

  13. Structure and Dynamics of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    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

  14. The effect of ultrasonic intensity on the crystal structure of palm oil.

    PubMed

    Patrick, Maria; Blindt, Renoo; Janssen, Jo

    2004-05-01

    It has been known for a long time that both the crystal structure and kinetics of crystallisation can be affected by ultrasound. In the past systems used have relied on high power ultrasonic probes to produce crystals. The majority of these probes produce cavitation in the system and it has been difficult to differentiate between effects caused by the ultrasound alone or by the cavitation produced by ultrasound on the crystal structure. Some materials, such as fats, are very susceptible to the production of free radicals that lead to "off-flavours" being obtained. These "off-flavours" are easily produced when the standard high power probes are used. This has meant that, although the crystal structure of the final product might be improved, the presence of 'off' flavours has prevented ultrasound being considered as a commercial technique for the crystallisation of edible fats. At Unilever R&D a system has been developed which can investigate the effect of ultrasound on the crystallisation of fats under controlled conditions covering a range of intensities and cooling rates. The intensity levels used were both below and above the cavitational threshold. By keeping the cooling regime constant it has been possible to show that the structure of the final product can vary from a material looking similar to cottage cheese through to a fine cream simply by varying the ultrasonic intensity. This paper describes the effect of ultrasound on both the crystal structure and kinetics of palm oil crystallisation at intensities below and above the cavitational threshold.

  15. Stochastic generation of complex crystal structures combining group and graph theory with application to carbon

    NASA Astrophysics Data System (ADS)

    Shi, Xizhi; He, Chaoyu; Pickard, Chris J.; Tang, Chao; Zhong, Jianxin

    2018-01-01

    A method is introduced to stochastically generate crystal structures with defined structural characteristics. Reasonable quotient graphs for symmetric crystals are constructed using a random strategy combined with space group and graph theory. Our algorithm enables the search for large-size and complex crystal structures with a specified connectivity, such as threefold sp2 carbons, fourfold sp3 carbons, as well as mixed sp2-sp3 carbons. To demonstrate the method, we randomly construct initial structures adhering to space groups from 75 to 230 and a range of lattice constants, and we identify 281 new sp3 carbon crystals. First-principles optimization of these structures show that most of them are dynamically and mechanically stable and are energetically comparable to those previously proposed. Some of the new structures can be considered as candidates to explain the experimental cold compression of graphite.

  16. Rare-earth metal gallium silicides via the gallium self-flux method. Synthesis, crystal structures, and magnetic properties of RE(Ga 1–xSi x)₂ (RE=Y, La–Nd, Sm, Gd–Yb, Lu)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Darone, Gregory M.; Hmiel, Benjamin; Zhang, Jiliang

    Fifteen ternary rare-earth metal gallium silicides have been synthesized using molten Ga as a molten flux. They have been structurally characterized by single-crystal and powder X-ray diffraction to form with three different structures—the early to mid-late rare-earth metals RE=La–Nd, Sm, Gd–Ho, Yb and Y form compounds with empirical formulae RE(Ga xSi 1–x)₂ (0.38≤x≤0.63), which crystallize with the tetragonal α-ThSi₂ structure type (space group I4₁/amd, No. 141; Pearson symbol tI12). The compounds of the late rare-earth crystallize with the orthorhombic α-GdSi₂ structure type (space group Imma, No. 74; Pearson symbol oI12), with refined empirical formula REGa xSi 2–x–y (RE=Ho, Er, Tm;more » 0.33≤x≤0.40, 0.10≤y≤0.18). LuGa₀.₃₂₍₁₎Si₁.₄₃₍₁₎ crystallizes with the orthorhombic YbMn₀.₁₇Si₁.₈₃ structure type (space group Cmcm, No. 63; Pearson symbol oC24). Structural trends are reviewed and analyzed; the magnetic susceptibilities of the grown single-crystals are presented. - Graphical abstract: This article details the exploration of the RE–Ga–Si ternary system with the aim to systematically investigate the structural “boundaries” between the α-ThSi₂ and α-GdSi₂-type structures, and studies of the magnetic properties of the newly synthesized single-crystalline materials. Highlights: • Light rare-earth gallium silicides crystallize in α-ThSi₂ structure type. • Heavy rare-earth gallium silicides crystallize in α-GdSi₂ structure type. • LuGaSi crystallizes in a defect variant of the YbMn₀.₁₇Si₁.₈₃ structure type.« less

  17. Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

    PubMed

    Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

    1981-08-04

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  19. The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

    PubMed Central

    Gilliland, Gary L.; Tung, Michael; Ladner, Jane

    1996-01-01

    The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

  20. Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

    PubMed

    Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

    2017-05-05

    A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  1. Band structure and optical properties of opal photonic crystals

    NASA Astrophysics Data System (ADS)

    Pavarini, E.; Andreani, L. C.; Soci, C.; Galli, M.; Marabelli, F.; Comoretto, D.

    2005-07-01

    A theoretical approach for the interpretation of reflectance spectra of opal photonic crystals with fcc structure and (111) surface orientation is presented. It is based on the calculation of photonic bands and density of states corresponding to a specified angle of incidence in air. The results yield a clear distinction between diffraction in the direction of light propagation by (111) family planes (leading to the formation of a stop band) and diffraction in other directions by higher-order planes (corresponding to the excitation of photonic modes in the crystal). Reflectance measurements on artificial opals made of self-assembled polystyrene spheres are analyzed according to the theoretical scheme and give evidence of diffraction by higher-order crystalline planes in the photonic structure.

  2. Research Article Abstracts in Two Subdisciplines of Business--Move Structure and Hedging between Management and Marketing

    ERIC Educational Resources Information Center

    Li, Qian; Pramoolsook, Issra

    2015-01-01

    The importance of RA abstracts lies in their influence on the readers' decision about whether the accompanying article is worth reading. A number of studies have investigated the move structure of abstracts and have generated several influential models. However, little research has been conducted on subdisciplinary variations in move structure of…

  3. Writing a Structured Abstract for the Thesis

    ERIC Educational Resources Information Center

    Hartley, James

    2010-01-01

    This article presents the author's suggestions on how to improve thesis abstracts. The author describes two books on writing abstracts: (1) "Creating Effective Conference Abstracts and Posters in Biomedicine: 500 tips for Success" (Fraser, Fuller & Hutber, 2009), a compendium of clear advice--a must book to have in one's hand as one prepares a…

  4. Crystal structure, vibrational and DFT simulation studies of melaminium dihydrogen phosphite monohydrate

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

    2013-08-01

    The crystal structure investigations of melamine with phosphorous acid, namely melaminium dihydrogenphosphite monohydrate (C3N6H7·H2PO3·H2O) have been investigated by means of single crystal X-ray diffraction method. The title compound crystallizes in monoclinic crystal system, and the space group is P21/c with a = 10.069 Å, b = 21.592 Å, c = 12.409 Å and Z = 12. The vibrational assignments and analysis of melaminium dihydrogen phosphite monohydrate have also been performed by FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical simulations were performed with DFT (B3LYP) method using 6-31G**, cc-pVTZ, and 6-311++G** basis sets to determine the energy, structural, thermodynamic parameters and vibrational frequencies of melaminium dihydrogen phosphite monohydrate. The hydrogen atom from phosphorous acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H···O and Nsbnd H···O hydrogen bonds shows notable vibrational effects.

  5. In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Michalska, Karolina; Tan, Kemin; Chang, Changsoo

    A prototype of a 96-well plate scanner forin situdata collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection atT= 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-coolingmore » can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software,in situdata collection will become available for the SBC user program including remote access.« less

  6. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Heroux, A.; Bozinovski, D; Valley, M

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. Themore » oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.« less

  7. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    DOE PAGES

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; ...

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

  8. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAPmore » β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

  9. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

  10. Inorganic Crystal Structure Database (ICSD) and Standardized Data and Crystal Chemical Characterization of Inorganic Structure Types (TYPIX)—Two Tools for Inorganic Chemists and Crystallographers

    PubMed Central

    Fluck, Ekkehard

    1996-01-01

    The two databases ICSD and TYPIX are described. ICSD is a comprehensive compilation of crystal structure data of inorganic compounds (about 39 000 entries). TYPIX contains 3600 critically evaluated data sets representative of structure types formed by inorganic compounds. PMID:27805158

  11. The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

    NASA Astrophysics Data System (ADS)

    Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

    2017-10-01

    A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.

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

    PubMed Central

    Harlow, Richard L.

    1996-01-01

    A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures. PMID:27805169

  13. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

    PubMed

    Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

    2005-06-01

    Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

  14. The crystal structure of human GDP-L-fucose synthase.

    PubMed

    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.

  15. Tunable alumina 2D photonic-crystal structures via biomineralization of peacock tail feathers

    NASA Astrophysics Data System (ADS)

    Jiang, Yonggang; Wang, Rui; Feng, Lin; Li, Jian; An, Zhonglie; Zhang, Deyuan

    2018-04-01

    Peacock tail feathers with subtle periodic nanostructures exhibit diverse striking brilliancy, which can be applied as natural templates to fabricate artificial photonic crystals (PhCs) via a biomineralization method. Alumina photonic-crystal structures are successfully synthesized via an immersion and two-step calcination process. The lattice constants of the artificial PhCs are greatly reduced compared to their natural matrices. The lattice constants are tunable by modifying the final annealing conditions in the biomineralization process. The reflection spectra of the alumina photonic-crystal structures are measured, which is related to their material and structural parameters. This work suggests a facile fabrication process to construct alumina PhCs with a high-temperature resistance.

  16. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  17. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    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; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    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.

  18. Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

    PubMed

    Horrell, Sam; Kekilli, Demet; Sen, Kakali; Owen, Robin L; Dworkowski, Florian S N; Antonyuk, Svetlana V; Keal, Thomas W; Yong, Chin W; Eady, Robert R; Hasnain, S Samar; Strange, Richard W; Hough, Michael A

    2018-05-01

    High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  20. Crystal structure of the ternary silicide Gd2Re3Si5.

    PubMed

    Fedyna, Vitaliia; Kozak, Roksolana; Gladyshevskii, Roman

    2014-12-01

    A single crystal of the title compound, the ternary silicide digadolinium trirhenium penta-silicide, Gd2Re3Si5, was isolated from an alloy of nominal composition Gd20Re30Si50 synthesized by arc melting and investigated by X-ray single-crystal diffraction. Its crystal structure belongs to the U2Mn3Si5 structure type. All atoms in the asymmetric lie on special positions. The Gd site has site symmetry m..; the two Mn atoms have site symmetries m.. and 2.22; the three Si atoms have site symmetries m.., ..2 and 4.. . The coordination polyhedra of the Gd atoms have 21 vertices, while those of the Re atoms are cubo-octa-hedra and 13-vertex polyhedra. The Si atoms are arranged as tricapped trigonal prisms, bicapped square anti-prisms, or 11-vertex polyhedra. The crystal structure of the title compound is also related to the structure types CaBe2Ge2 and W5Si3. It can be represented as a stacking of Gd-centred polyhedra of composition [GdSi9]. The Re atoms form infinite chains with an Re-Re distance of 2.78163 (5) Å and isolated squares with an Re-Re distance of 2.9683 (6) Å.

  1. Synthesis and Crystal Structure of 2’-Se-modified guanosine Containing DNA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Salon, J.; Sheng, J; Gan, J

    Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2{prime}-SeMe-modified guanosine (G{sub Se}) phosphoramidite, and report the first incorporation of the 2{prime}-Se-G moiety into DNA. The X-ray crystal structure of the 2{prime}-Se-modified octamer DNA (5{prime}-GTG{sub Se}TACAC-3{prime}) was determined at a resolution of 1.20 {angstrom}. We also found that the 2{prime}-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2{prime}-Se-G modification can significantly facilitate themore » crystal growth with respect to the corresponding native DNA.« less

  2. Crystal structure of tin(IV) chloride octa­hydrate

    PubMed Central

    Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

    2014-01-01

    The title compound, [SnCl4(H2O)2]·6H2O, was crystallized according to the solid–liquid phase diagram at lower temperatures. It is built-up of SnCl4(H2O)2 octa­hedral units (point group symmetry 2) and lattice water mol­ecules. An intricate three-dimensional network of O—H⋯O and O—H⋯Cl hydrogen bonds between the complex molecules and the lattice water molecules is formed in the crystal structure. PMID:25552971

  3. Photonic-magnonic crystals: Multifunctional periodic structures for magnonic and photonic applications

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kłos, J. W., E-mail: klos@amu.edu.pl; Krawczyk, M.; Dadoenkova, Yu. S.

    2014-05-07

    We investigate the properties of a photonic-magnonic crystal, a complex multifunctional one-dimensional structure with magnonic and photonic band gaps in the GHz and PHz frequency ranges for spin waves and light, respectively. The system consists of periodically distributed dielectric magnetic slabs of yttrium iron garnet and nonmagnetic spacers with an internal structure of alternating TiO{sub 2} and SiO{sub 2} layers which form finite-size dielectric photonic crystals. We show that the spin-wave coupling between the magnetic layers, and thus the formation of the magnonic band structure, necessitates a nonzero in-plane component of the spin-wave wave vector. A more complex structure perceivedmore » by light is evidenced by the photonic miniband structure and the transmission spectra in which we have observed transmission peaks related to the repetition of the magnetic slabs in the frequency ranges corresponding to the photonic band gaps of the TiO{sub 2}/SiO{sub 2} stack. Moreover, we show that these modes split to very high sharp (a few THz wide) subpeaks in the transmittance spectra. The proposed novel multifunctional artificial crystals can have interesting applications and be used for creating common resonant cavities for spin waves and light to enhance the mutual influence between them.« less

  4. Identification of surface domain structure on enamel crystals using polyamidoamine dendrimer

    NASA Astrophysics Data System (ADS)

    Chen, Haifeng; Clarkson, Brian H.; Orr, Bradford; Majoros, Istvan; Banaszak Holl, Mark M.

    2002-03-01

    The control of hydroxyapatite crystal nucleation and crystal growth is central to the mineralization and remineralization of enamel and dentin of teeth. However, the precise biomolecular mechanisms involved remain obscure. The intimate association between the crystal's surface and extracellular protein components implies a modulating role for organic crystal interactions probably mediated via specific crystal surface domains. These include lattice defects and specific stereochemical arrays on associated organic molecules. The nature of protein-crystal interaction depends upon the physical forces of attraction / repulsion between specific biomolecular groups and crystal surface domains. The proposed study is to utilize specific polyamidoamine (PAMAM) dendrimers, also known as “artificial proteins”, acting as nanoprobe. These will be used to probe specific surface domain on the surface of the naturally derived crystals of hydroxyapatite and to determine how control of growth and dissolution may be affected at the biomolecular level. The hydroxyapatite crystals are extracted from the maturation stage enamel of rats. Three types of PAMAM dendrimers, respectively with amine-, carboxylic acid and methyl-capped surface, will be applied in the study. The dendrimer binding on the surface of the hydoxyapatite crystals will be characterized using atomic force microscopy (AFM). The different dendrimer binding on the crystals will disclose the specific surface domain structure on the crystals, which is assumed to be important in binding the extracellular protein.

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

    NASA Astrophysics Data System (ADS)

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

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

  6. The crystal structure of calcite III

    NASA Astrophysics Data System (ADS)

    Smyth, Joseph R.; Ahrens, Thomas J.

    The crystal structure of calcite III has been deduced from existing high pressure powder X-ray diffraction patterns, based on the assumption that it is a displacive modification of the calcite I structure. The structure is monoclinic with space group C2 and a Z of 6. There are two Ca and two C positions, and five O positions, and atom coordinates have been refined by distance-least-squares methods to give reasonable octahedral coordination for Ca and parallel, planar CO3 groups. Unit cell parameters refined from a published powder diffraction pattern at 4.1 GPa are: a = 8.746(8)Å b = 4.685(5)Å c = 8.275(8)Å and β= 94.4°. The structure has a calculated density of 2.949 Mg/m³ at 4.1 GPa which is less than that of aragonite at this pressure and consistent with early piston cylinder studies. This implies that calcite III is indeed a metastable intermediary between calcite I and aragonite.

  7. Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

    PubMed

    Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

    2018-01-18

    Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

  8. The 20,000 Article Problem: How a Structured Abstract Can Help Practitioners Sort out Educational Research

    ERIC Educational Resources Information Center

    Miech, Edward J.; Nave, Bill; Mosteller, Frederick

    2005-01-01

    This article describes what a structured abstract is and how a structured abstract can help researchers sort out information. Today over 1,000 education journals publish more than 20,000 articles in the English language each year. No systematic tool is available at present to get the research findings from these tens of thousands of articles to…

  9. Synthesis, crystal and electronic structure of the quaternary sulfides Ln{sub 2}CuMS{sub 5} (Ln=La, Ce; M=Sb, Bi)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kussainova, Ardak M.; Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716; Akselrud, Lev G.

    2016-01-15

    The series of quaternary sulfides with general formula Ln{sub 2}CuMS{sub 5} (Ln=La, Ce; M=Sb, Bi) have been synthesized by solid-state reactions. Three representative members have been structurally characterized by single-crystal X-ray diffraction. La{sub 2}CuSbS{sub 5} crystallizes in a new structure type (space group Ima2 (no. 46), Z=4, a=13.401(2) Å, b=7.592(1) Å, c=7.598(1) Å, V=773.1(3) Å{sup 3}). The bismuth analogs of composition La{sub 2}CuBiS{sub 5} and Ce{sub 2}CuBiS{sub 5} crystallize with the La{sub 2}CuInSe{sub 5} structure type (space group Pnma (no. 62), Z=4). Lattice parameters for La{sub 2}CuBiS{sub 5}: a=11.9213(5) Å, b=3.9967(2) Å, c=17.0537(8) Å, V=812.56(7) Å{sup 3}; lattice parameters formore » Ce{sub 2}CuBiS{sub 5}: a=11.9179(15) Å, b=3.9596(5) Å, c=16.955(2) Å, V=800.13(17) Å{sup 3}). The similarities and the differences between the two structures are discussed. Electronic structure calculations for La{sub 2}CuSbS{sub 5} and La{sub 2}CuBiS{sub 5} are also presented; they suggest semiconducting behavior with energy gaps exceeding 1.7 eV. - Graphical abstract: La{sub 2}CuSbS{sub 5} crystallizes in a new structure type (space group Ima2 (no. 46). Its bismuth analog La{sub 2}CuBiS{sub 5} crystallizes in the La{sub 2}CuInSe{sub 5} structure type (space group Pnma (no. 62)). Z=4, a=11.9213(5) Å, b=3.9967(2) Å, c=17.0536(10) Å, V=813.53(10) Å{sup 3}). The structures are based on rare-earth metal atoms coordinated by S atoms in a trigonal-prismatic and/or square-antiprismatic fashion, Cu-centered tetrahedra, and pnictogen atoms in pyramidal or distorted octahedral coordination. - Highlights: • Ln{sub 2}CuSbS{sub 5} are complex quarternary phases crystallizing in their own structure type. • Ln{sub 2}CuSbS{sub 5} and Ce{sub 2}CuBiS{sub 5} are new compound in the respective ternary phase diagrams. • Ln{sub 2}CuSbS{sub 5} on one side, and Ln{sub 2}CuBiS{sub 5} on the other are not isotypic.« less

  10. Facile synthesis of gold nanomaterials with unusual crystal structures.

    PubMed

    Fan, Zhanxi; Huang, Xiao; Chen, Ye; Huang, Wei; Zhang, Hua

    2017-11-01

    Gold (Au) nanomaterials have attracted wide research attention, owing to their high chemical stability, promising catalytic properties, excellent biocompatibility, unique electronic structure and outstanding localized surface plasmon resonance (LSPR) absorption properties; all of which are closely related to their size and shape. Recently, crystal-phase-controlled synthesis of noble metal nanomaterials has emerged as a promising strategy to tune their physicochemical properties. This protocol describes the detailed experimental procedures for the crystal-phase-controlled syntheses of Au nanomaterials with unusual crystal structures under mild conditions. Briefly, pure hexagonal close-packed (hcp) Au square sheets (AuSSs) with a thickness of ∼2.4 nm are synthesized using a graphene-oxide-assisted method in which HAuCl 4 is reduced by oleylamine in a mixture of hexane and ethanol. By using pure hexane as the solvent, well-dispersed ultrathin hcp/face-centered cubic (fcc) Au nanowires with a diameter of ∼1.6 nm on graphene oxide can be obtained. Meanwhile, hcp/fcc Au square-like plates with a side length of 200-400 nm are prepared via the secondary growth of Au on the hcp AuSSs. Remarkably, hexagonal (4H) Au nanoribbons with a thickness of 2.0-6.0 nm can be synthesized with a one-pot colloidal method in which HAuCl 4 is reduced by oleylamine in a mixed solvent of hexane and 1,2-dichloropropane. It takes 17-37 h for the synthesis of these Au nanomaterials with unusual crystal structures. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) are used to characterize the resultant Au nanomaterials, which could have many promising applications, such as biosensing, near-IR photothermal therapy, catalysis and surface-enhanced Raman scattering (SERS).

  11. Crystal structure determination of new antimitotic agent bis(p-fluorobenzyl)trisulfide.

    PubMed

    An, Haoyun; Hu, Xiurong; Gu, Jianming; Chen, Linshen; Xu, Weiming; Mo, Xiaopeng; Xu, Wanhong; Wang, Xiaobo; Xu, Xiao

    2008-01-01

    The purpose of this research was to investigate the physical characteristics and crystalline structure of bis(p-fluorobenzyl)trisulfide, a new anti-tumor agent. Methods used included X-ray single crystal diffraction, X-ray powder diffraction (XRPD), Fourier-transform infrared (FT-IR) spectroscopy, differential scanning calorimetric (DSC) and thermogravimetric (TG) analyses. The findings obtained with X-ray single crystal diffraction showed that a monoclinic unit cell was a = 12.266(1) A, b = 4.7757(4) A, c = 25.510(1) A, beta = 104.25(1) degrees ; cell volume = 1,448.4(2) A(3), Z = 4, and space group C2/c. The XRPD studies of the four crystalline samples, obtained by recrystallization from four different solvents, indicated that they had the same diffraction patterns. The diffraction pattern stimulated from the crystal structure data is in excellent agreement with the experimental results. In addition, the identical FT-IR spectra of the four crystalline samples revealed absorption bands corresponding to S-S and C-S stretching as well as the characteristic aromatic substitution. Five percent weight loss at 163.3 degrees C was observed when TG was used to study the decomposition process in the temperature range of 20-200 degrees C. DSC also allowed for the determination of onset temperatures at 60.4(1)-60.7(3) degrees C and peak temperatures at 62.1(3)-62.4(3) degrees C for the four crystalline samples studied. The results verified that the single crystal structure shared the same crystal form with the four crystalline samples investigated.

  12. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Karayel, A., E-mail: matchlessjimmy@163.com, E-mail: yccaoh@hotmail.com; Özbey, S.; Ayhan-Kılcıgil, G.

    2015-12-15

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  13. The Crystal Structures of Potentially Tautomeric Compounds

    NASA Astrophysics Data System (ADS)

    Furmanova, Nina G.

    1981-08-01

    Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

  14. The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

    PubMed

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

    2012-11-23

    Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

  15. GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

    PubMed

    Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

    2018-04-10

    We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

  16. Crystal structure of product-bound complex of UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pampa, K.J., E-mail: sagarikakj@gmail.com; Lokanath, N.K.; Girish, T.U.

    Highlights: • Determined the structure of UDP-D-ManNAcADH to a resolution of 1.55 Å. • First complex structure of PhUDP-D-ManNAcADH with UDP-D-ManMAcA. • The monomeric structure consists of three distinct domains. • Cys258 acting as catalytic nucleophilic and Lys204 acts as acid/base catalyst. • Oligomeric state plays an important role for the catalytic function. - Abstract: UDP-N-acetyl-D-mannosamine dehydrogenase (UDP-D-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-D-mannosamine (UDP-D-ManNAc) to Uridine-diphospho-N-acetyl-D-mannosaminuronic acid (UDP-D-ManNAcA) through twofold oxidation of NAD{sup +}. In order to reveal the structural features of the Pyrococcus horikoshii UDP-D-ManNAcADH, we have determined the crystal structure of the product-bound enzyme bymore » X-ray diffraction to resolution of 1.55 Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-D-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.« less

  17. Computational Study of the Structure and Mechanical Properties of the Molecular Crystal RDX

    DTIC Science & Technology

    2011-01-01

    Doctor of Philosophy, 2011 Directed By: Assistant Professor Santiago D. Solares , Department of Mechanical Engineering Molecular crystals...Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour per response...NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed

  18. Demonstration of Crystal Structure.

    ERIC Educational Resources Information Center

    Neville, Joseph P.

    1985-01-01

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

  19. Crystal structure and functional characterization of SF216 from Shigella flexneri.

    PubMed

    Kim, Ha-Neul; Seok, Seung-Hyeon; Lee, Yoo-Sup; Won, Hyung-Sik; Seo, Min-Duk

    2017-11-01

    Shigella flexneri is a Gram-negative anaerobic bacterium that causes highly infectious bacterial dysentery in humans. Here, we solved the crystal structure of SF216, a hypothetical protein from the S. flexneri 5a strain M90T, at 1.7 Å resolution. The crystal structure of SF216 represents a homotrimer stabilized by intersubunit interactions and ion-mediated electrostatic interactions. Each subunit consists of three β-strands and five α-helices with the β-β-β-α-α-α-α-α topology. Based on the structural information, we also demonstrate that SF216 shows weak ribonuclease activity by a fluorescence quenching assay. Furthermore, we identify potential druggable pockets (putative hot spots) on the surface of the SF216 structure by computational mapping. © 2017 Federation of European Biochemical Societies.

  20. Transformations of the dislocation structure of nickel single crystals

    NASA Astrophysics Data System (ADS)

    Alfyorova, E. A.; Lychagin, D. V.; Lychagina, L. L.; Tsvetkov, N. A.

    2017-12-01

    A relationship between different-scale deformations of crystals has not been established yet. In order to solve this task, we investigate the development of a deformation relief and dislocation structure in nickel single crystals after deformation. The stress tensor, crystallography, and geometry of specimens affect the organization of some shear along corresponding systems of sliding. The organization of shear shows some features of self-organization. It is associated with the self-organization in the dislocation subsystem analyzed previously. The effectiveness of reducing external and internal stresses determines patterns of deformation processes at different scale levels.

  1. Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus.

    PubMed Central

    Prasad, G. S.; Stura, E. A.; McRee, D. E.; Laco, G. S.; Hasselkus-Light, C.; Elder, J. H.; Stout, C. D.

    1996-01-01

    We have determined the crystal structure of dUTP pyrophosphatase (dUTPase) from feline immunodeficiency virus (FIV) at 1.9 A resolution. The structure has been solved by the multiple isomorphous replacement (MIR) method using a P6(3) crystal form. The results show that the enzyme is a trimer of 14.3 kDa subunits with marked structural similarity to E. coli dUTPase. In both enzymes the C-terminal strand of an anti-parallel beta-barrel participates in the beta-sheet of an adjacent subunit to form an interdigitated, biologically functional trimer. In the P6(3) crystal form one trimer packs on the 6(3) screw-axis and another on the threefold axis so that there are two independent monomers per asymmetric unit. A Mg2+ ion is coordinated by three asparate residues on the threefold axis of each trimer. Alignment of 17 viral, prokaryotic, and eukaryotic dUTPase sequences reveals five conserved motifs. Four of these map onto the interface between pairs of subunits, defining a putative active site region; the fifth resides in the C-terminal 16 residues, which is disordered in the crystals. Conserved motifs from all three subunits are required to create a given active site. With respect to viral protein expression, it is particularly interesting that the gene for dUTPase (DU) resides in the middle of the Pol gene, the enzyme cassette of the retroviral genome. Other enzymes encoded in the Pol polyprotein, including protease (PR), reverse transcriptase (RT), and most likely integrase (IN), are dimeric enzymes, which implies that the stoichiometry of expression of active trimeric dUTPase is distinct from the other Pol-encoded enzymes. Additionally, due to structural constraints, it is unlikely that dUTPase can attain an active form prior to cleavage from the polyprotein. PMID:8976551

  2. Multiscale real-space quantum-mechanical tight-binding calculations of electronic structure in crystals with defects using perfectly matched layers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pourmatin, Hossein, E-mail: mpourmat@andrew.cmu.edu; Dayal, Kaushik, E-mail: kaushik@cmu.edu

    2016-10-15

    Graphical abstract: - Abstract: We consider the scattering of incident plane-wave electrons from a defect in a crystal modeled by the time-harmonic Schrödinger equation. While the defect potential is localized, the far-field potential is periodic, unlike standard free-space scattering problems. Previous work on the Schrödinger equation has been almost entirely in free-space conditions; a few works on crystals have been in one-dimension. We construct absorbing boundary conditions for this problem using perfectly matched layers in a tight-binding formulation. Using the example of a point defect in graphene, we examine the efficiency and convergence of the proposed absorbing boundary condition.

  3. High-throughput screening for thermoelectric sulphides by using crystal structure features as descriptors

    NASA Astrophysics Data System (ADS)

    Zhang, Ruizhi; Du, Baoli; Chen, Kan; Reece, Mike; Materials Research Insititute Team

    With the increasing computational power and reliable databases, high-throughput screening is playing a more and more important role in the search of new thermoelectric materials. Rather than the well established density functional theory (DFT) calculation based methods, we propose an alternative approach to screen for new TE materials: using crystal structural features as 'descriptors'. We show that a non-distorted transition metal sulphide polyhedral network can be a good descriptor for high power factor according to crystal filed theory. By using Cu/S containing compounds as an example, 1600+ Cu/S containing entries in the Inorganic Crystal Structure Database (ICSD) were screened, and of those 84 phases are identified as promising thermoelectric materials. The screening results are validated by both electronic structure calculations and experimental results from the literature. We also fabricated some new compounds to test our screening results. Another advantage of using crystal structure features as descriptors is that we can easily establish structural relationships between the identified phases. Based on this, two material design approaches are discussed: 1) High-pressure synthesis of metastable phase; 2) In-situ 2-phase composites with coherent interface. This work was supported by a Marie Curie International Incoming Fellowship of the European Community Human Potential Program.

  4. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    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; Roque, Paulo Sergio Silveira Belo Nascimento; 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.

    2016-01-01

    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 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. PMID:27633552

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

    PubMed Central

    Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D.

    2017-01-01

    In the crystal structure of the title compound, 5-fluoro­cytosinium picrate, C4H5FN3O+·C6H2N3O7 −, one N heteroatom of the 5-fluoro­cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA−) anion. In the crystal, the 5FC+ cation inter­acts with the PA− anion through three-centre N—H⋯O hydrogen bonds, forming two conjoined rings having R 2 1(6) and R 1 2(6) motifs, and is extended by N—H⋯O hydrogen bonds and C—H⋯O inter­actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C—F⋯π inter­actions. PMID:28316809

  6. Correlation between hierarchical structure of crystal networks and macroscopic performance of mesoscopic soft materials and engineering principles.

    PubMed

    Lin, Naibo; Liu, Xiang Yang

    2015-11-07

    This review examines how the concepts and ideas of crystallization can be extended further and applied to the field of mesoscopic soft materials. It concerns the structural characteristics vs. the macroscopic performance, and the formation mechanism of crystal networks. Although this subject can be discussed in a broad sense across the area of mesoscopic soft materials, our main focus is on supramolecular materials, spider and silkworm silks, and biominerals. First, the occurrence of a hierarchical structure, i.e. crystal network and domain network structures, will facilitate the formation kinetics of mesoscopic phases and boost up the macroscopic performance of materials in some cases (i.e. spider silk fibres). Second, the structure and performance of materials can be correlated in some way by the four factors: topology, correlation length, symmetry/ordering, and strength of association of crystal networks. Moreover, four different kinetic paths of crystal network formation are identified, namely, one-step process of assembly, two-step process of assembly, mixed mode of assembly and foreign molecule mediated assembly. Based on the basic mechanisms of crystal nucleation and growth, the formation of crystal networks, such as crystallographic mismatch (or noncrystallographic) branching (tip branching and fibre side branching) and fibre/polymeric side merging, are reviewed. This facilitates the rational design and construction of crystal networks in supramolecular materials. In this context, the (re-)construction of a hierarchical crystal network structure can be implemented by thermal, precipitate, chemical, and sonication stimuli. As another important class of soft materials, the unusual mechanical performance of spider and silkworm silk fibres are reviewed in comparison with the regenerated silk protein derivatives. It follows that the considerably larger breaking stress and unusual breaking strain of spider silk fibres vs. silkworm silk fibres can be interpreted

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

    NASA Technical Reports Server (NTRS)

    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

  8. Synthesis, structure and optical properties of two isotypic crystals, Na{sub 3}MO{sub 4}Cl (M=W, Mo)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han, Shujuan; Bai, Chunyan; Zhang, Bingbing

    Two isotypic compounds, Na{sub 3}MO{sub 4}Cl (M = W, Mo) have been obtained from the high temperature solution, and their structures were determined by single-crystal X-ray diffraction. Both of them crystallize in the space group P4/nmm of tetragonal system with the unit cells: a=7.5181(15), c=5.360(2) for Na{sub 3}WO{sub 4}Cl and a=7.4942(12), c=5.3409(18) for Na{sub 3}MoO{sub 4}Cl. The structure exhibits a 3D network built up by the ClNa{sub 6} groups, and the MO{sub 4} groups reside in the tunnels of the 3D network. The structural similarities and differences between Na{sub 3}MO{sub 4}Cl (M=W, Mo) and Sr{sub 3}MO{sub 4}F (M=Al, Ga) havemore » been discussed. Meanwhile, detailed structure comparison analyses between Na{sub 3}MO{sub 4}Cl (M=W, Mo) and Na{sub 3}MO{sub 4}F (M=W, Mo) indicate that the different connection modes of ClNa{sub 6} and FNa{sub 6} make Na{sub 3}MO{sub 4}Cl and Na{sub 3}MO{sub 4}F crystallize in different structures. The IR spectra were used to verify the validity of the structure. The diffuse reflectance spectra show that the UV absorption edges are about 249 nm (4.99 eV) and 265 nm (4.69 eV) for Na{sub 3}WO{sub 4}Cl and Na{sub 3}MoO{sub 4}Cl, respectively. In addition, the first-principles theoretical studies are also carried out to aid the understanding of electronic structures and linear optical properties. - Graphical abstract: Two isotypic compounds, Na{sub 3}MO{sub 4}Cl (M=W, Mo) have been obtained from the high temperature solution. Both of them crystallize in the space group P4/nmm of tetragonal system. The structure exhibits a 3D network built up by the ClNa{sub 6} groups, and the MO{sub 4} groups reside in the tunnels of the 3D network. - Highlights: • Structure and properties of Na{sub 3}MO{sub 4}Cl (M=W, Mo) are reported for the first time. • They show a 3D network built by ClNa{sub 6}, and WO{sub 4} lies in the tunnels of the network. • IR spectra were used to verify the validity of the structure. • Band structures

  9. Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maruyama, Yukie; Ochiai, Akihito; Mikami, Bunzo

    Research highlights: {yields} Bacterial alginate-binding Algp7 is similar to component EfeO of Fe{sup 2+} transporter. {yields} We determined the crystal structure of Algp7 with a metal-binding motif. {yields} Algp7 consists of two helical bundles formed through duplication of a single bundle. {yields} A deep cleft involved in alginate binding locates around the metal-binding site. {yields} Algp7 may function as a Fe{sup 2+}-chelated alginate-binding protein. -- Abstract: A gram-negative Sphingomonas sp. A1 directly incorporates alginate polysaccharide into the cytoplasm via the cell-surface pit and ABC transporter. A cell-surface alginate-binding protein, Algp7, functions as a concentrator of the polysaccharide in the pit.more » Based on the primary structure and genetic organization in the bacterial genome, Algp7 was found to be homologous to an M75 peptidase motif-containing EfeO, a component of a ferrous ion transporter. Despite the presence of an M75 peptidase motif with high similarity, the Algp7 protein purified from recombinant Escherichia coli cells was inert on insulin B chain and N-benzoyl-Phe-Val-Arg-p-nitroanilide, both of which are substrates for a typical M75 peptidase, imelysin, from Pseudomonas aeruginosa. The X-ray crystallographic structure of Algp7 was determined at 2.10 A resolution by single-wavelength anomalous diffraction. Although a metal-binding motif, HxxE, conserved in zinc ion-dependent M75 peptidases is also found in Algp7, the crystal structure of Algp7 contains no metal even at the motif. The protein consists of two structurally similar up-and-down helical bundles as the basic scaffold. A deep cleft between the bundles is sufficiently large to accommodate macromolecules such as alginate polysaccharide. This is the first structural report on a bacterial cell-surface alginate-binding protein with an M75 peptidase motif.« less

  10. Light-induced dynamic structural color by intracellular 3D photonic crystals in brown algae

    PubMed Central

    2018-01-01

    Natural photonic crystals are responsible for strong reflectance at selective wavelengths in different natural systems. We demonstrate that intracellular opal-like photonic crystals formed from lipids within photosynthetic cells produce vivid structural color in the alga Cystoseira tamariscifolia. The reflectance of the opaline vesicles is dynamically responsive to environmental illumination. The structural color is present in low light–adapted samples, whereas higher light levels produce a slow disappearance of the structural color such that it eventually vanishes completely. Once returned to low-light conditions, the color re-emerges. Our results suggest that these complex intracellular natural photonic crystals are responsive to environmental conditions, changing their packing structure reversibly, and have the potential to manipulate light for roles beyond visual signaling. PMID:29651457

  11. Light-induced dynamic structural color by intracellular 3D photonic crystals in brown algae.

    PubMed

    Lopez-Garcia, Martin; Masters, Nathan; O'Brien, Heath E; Lennon, Joseph; Atkinson, George; Cryan, Martin J; Oulton, Ruth; Whitney, Heather M

    2018-04-01

    Natural photonic crystals are responsible for strong reflectance at selective wavelengths in different natural systems. We demonstrate that intracellular opal-like photonic crystals formed from lipids within photosynthetic cells produce vivid structural color in the alga Cystoseira tamariscifolia . The reflectance of the opaline vesicles is dynamically responsive to environmental illumination. The structural color is present in low light-adapted samples, whereas higher light levels produce a slow disappearance of the structural color such that it eventually vanishes completely. Once returned to low-light conditions, the color re-emerges. Our results suggest that these complex intracellular natural photonic crystals are responsive to environmental conditions, changing their packing structure reversibly, and have the potential to manipulate light for roles beyond visual signaling.

  12. Investigation of selected structural parameters in Fe 95Si 5 amorphous alloy during crystallization process

    NASA Astrophysics Data System (ADS)

    Fronczyk, Adam

    2007-04-01

    In this study, we report on a crystallization behavior of the Fe 95Si 5 metallic glasses using a differential scanning cabrimetry (DSC), and X-ray diffraction. The paper presents the results of experimental investigation of Fe 95Si 5 amorphous alloy, subjected to the crystallizing process by the isothermal annealing. The objective of the experiment was to determine changes in the structural parameters during crystallization process of the examined alloy. Crystalline diameter and the lattice constant of the crystallizing phase were used as parameters to evaluate structural changes in material.

  13. Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

    PubMed Central

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

    2014-01-01

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

  14. Structuring β-Ga2O3 photonic crystal photocatalyst for efficient degradation of organic pollutants.

    PubMed

    Li, Xiaofang; Zhen, Xiuzheng; Meng, Sugang; Xian, Jiangjun; Shao, Yu; Fu, Xianzhi; Li, Danzhen

    2013-09-03

    Coupling photocatalysts with photonic crystals structure is based on the unique property of photonic crystals in confining, controlling, and manipulating the incident photons. This combination enhances the light absorption in photocatalysts and thus greatly improves their photocatalytic performance. In this study, Ga2O3 photonic crystals with well-arranged skeleton structures were prepared via a dip-coating infiltration method. The positions of the electronic band absorption for Ga2O3 photonic crystals could be made to locate on the red edge, on the blue edge, and away from the edge of their photonic band gaps by changing the pore sizes of the samples, respectively. Particularly, the electronic band absorption of the Ga2O3 photonic crystal with a pore size of 135 nm was enhanced more than other samples by making it locate on the red edge of its photonic band gap, which was confirmed by the higher instantaneous photocurrent and photocatalytic activity for the degradation of various organic pollutants under ultraviolet light irradiation. Furthermore, the degradation mechanism over Ga2O3 photonic crystals was discussed. The design of Ga2O3 photonic crystals presents a prospective application of photonic crystals in photocatalysis to address light harvesting and quantum efficiency problems through manipulating photons or constructing photonic crystal structure as groundwork.

  15. Crystal structure of the Japanese encephalitis virus envelope protein.

    PubMed

    Luca, Vincent C; AbiMansour, Jad; Nelson, Christopher A; Fremont, Daved H

    2012-02-01

    Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-Å resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

  16. Synthesis and crystal structure of chromium-bearing anhydrous wadsleyite

    NASA Astrophysics Data System (ADS)

    Sirotkina, E. A.; Bindi, L.; Bobrov, A. V.; Aksenov, S. M.; Irifune, T.

    2018-04-01

    A chromium-bearing wadsleyite (Cr- Wad) was synthesized in the model system Mg2SiO4-MgCr2O4 at 14 GPa and 1600 °C and studied from the chemical and structural point of views. Microprobe data gave the formula Mg1.930Cr0.120Si0.945O4, on the basis of 4 oxygen atoms. The crystal structure has been studied by single-crystal X-ray diffraction. The orthorhombic unit-cell parameters are: a = 5.6909(5) Å, b = 11.4640(10) Å, c = 8.2406(9) Å, V = 537.62(9) Å3, Z = 8. The structure, space group Imma, was refined to R 1 = 5.99% in anisotropic approximation using 1135 reflections with F o > 4σ( F o) and 43 parameters. Chromium was found to substitute for both Mg at the octahedral sites and Si at the tetrahedral site, according to the reaction VIMg2+ + IVSi4+ = VICr3+ + IVCr3+. On the whole, the structural topology is nearly identical to that of pure wadsleyite. The successful synthesis of Cr- Wad may be important for the thermobarometry of mantle phase associations.

  17. Crystal structure of the ternary silicide Gd2Re3Si5

    PubMed Central

    Fedyna, Vitaliia; Kozak, Roksolana; Gladyshevskii, Roman

    2014-01-01

    A single crystal of the title compound, the ternary silicide digadolinium trirhenium penta­silicide, Gd2Re3Si5, was isolated from an alloy of nominal composition Gd20Re30Si50 synthesized by arc melting and investigated by X-ray single-crystal diffraction. Its crystal structure belongs to the U2Mn3Si5 structure type. All atoms in the asymmetric lie on special positions. The Gd site has site symmetry m..; the two Mn atoms have site symmetries m.. and 2.22; the three Si atoms have site symmetries m.., ..2 and 4.. . The coordination polyhedra of the Gd atoms have 21 vertices, while those of the Re atoms are cubo­octa­hedra and 13-vertex polyhedra. The Si atoms are arranged as tricapped trigonal prisms, bicapped square anti­prisms, or 11-vertex polyhedra. The crystal structure of the title compound is also related to the structure types CaBe2Ge2 and W5Si3. It can be represented as a stacking of Gd-centred polyhedra of composition [GdSi9]. The Re atoms form infinite chains with an Re—Re distance of 2.78163 (5) Å and isolated squares with an Re—Re distance of 2.9683 (6) Å. PMID:25552967

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  19. An Efficient Scheme for Crystal Structure Prediction Based on Structural Motifs

    DOE PAGES

    Zhu, Zizhong; Wu, Ping; Wu, Shunqing; ...

    2017-05-15

    An efficient scheme based on structural motifs is proposed for the crystal structure prediction of materials. The key advantage of the present method comes in two fold: first, the degrees of freedom of the system are greatly reduced, since each structural motif, regardless of its size, can always be described by a set of parameters (R, θ, φ) with five degrees of freedom; second, the motifs could always appear in the predicted structures when the energies of the structures are relatively low. Both features make the present scheme a very efficient method for predicting desired materials. The method has beenmore » applied to the case of LiFePO 4, an important cathode material for lithium-ion batteries. Numerous new structures of LiFePO 4 have been found, compared to those currently available, available, demonstrating the reliability of the present methodology and illustrating the promise of the concept of structural motifs.« less

  20. An Efficient Scheme for Crystal Structure Prediction Based on Structural Motifs

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhu, Zizhong; Wu, Ping; Wu, Shunqing

    An efficient scheme based on structural motifs is proposed for the crystal structure prediction of materials. The key advantage of the present method comes in two fold: first, the degrees of freedom of the system are greatly reduced, since each structural motif, regardless of its size, can always be described by a set of parameters (R, θ, φ) with five degrees of freedom; second, the motifs could always appear in the predicted structures when the energies of the structures are relatively low. Both features make the present scheme a very efficient method for predicting desired materials. The method has beenmore » applied to the case of LiFePO 4, an important cathode material for lithium-ion batteries. Numerous new structures of LiFePO 4 have been found, compared to those currently available, available, demonstrating the reliability of the present methodology and illustrating the promise of the concept of structural motifs.« less

  1. Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

    DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP2 1lattice of hexagonal metric. The various twinning criteria give somewhatmore » conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.« less

  2. Crystallization, structure and dynamics of the proton-translocating P-type ATPase.

    PubMed

    Scarborough, G A

    2000-01-01

    Large single three-dimensional crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase (H(+) P-ATPase) can be grown in polyethylene-glycol-containing solutions optimized for moderate supersaturation of both the protein surfaces and detergent micellar region. Large two-dimensional H(+) P-ATPase crystals also grow on the surface of such mixtures and on carbon films located at such surfaces. Electron crystallographic analysis of the two-dimensional crystals grown on carbon films has recently elucidated the structure of the H(+) P-ATPase at a resolution of 0.8 nm in the membrane plane. The two-dimensional crystals comprise two offset layers of ring-shaped ATPase hexamers with their exocytoplasmic surfaces face to face. Side-to-side interactions between the cytoplasmic regions of the hexamers in each layer can be seen, and an interaction between identical exocytoplasmic loops in opposing hexamer layers holds the two layers together. Detergent rings around the membrane-embedded region of the hexamers are clearly visible, and detergent-detergent interactions between the rings are also apparent. The crystal packing forces thus comprise both protein-protein and detergent-detergent interactions, supporting the validity of the original crystallization strategy. Ten transmembrane helices in each ATPase monomer are well-defined in the structure map. They are all relatively straight, closely packed, moderately tilted at various angles with respect to a plane normal to the membrane surface and average approximately 3.5 nm in length. The transmembrane helix region is connected in at least three places to the larger cytoplasmic region, which comprises several discrete domains separated by relatively wide, deep clefts. Previous work has shown that the H(+) P-ATPase undergoes substantial conformational changes during its catalytic cycle that are not changes in secondary structure. Importantly, the results of hydrogen/deuterium exchange

  3. Determination of structure and properties of molecular crystals from first principles.

    PubMed

    Szalewicz, Krzysztof

    2014-11-18

    CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be

  4. Undergraduates improve upon published crystal structure in class assignment.

    PubMed

    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 protein sequence. With minimal direction from the instructor on how the students should complete the assignment, the students fared remarkably well in this task, with over half the class able to reconstruct the original sequence with over 77% sequence identity, and with structures whose median ranked in the 91(st) percentile of all structures of comparable resolution in terms of structure quality. Fourteen percent of the students' structures produced Molprobity steric clash validation scores even better than that of the original structure, suggesting that multiple students achieved an improvement in the overall structure quality compared to the published structure. Students were able to delineate limiting case chemical environments, such as charged interactions or complete solvent exposure, but were less able to distinguish finer details of hydrogen bonding or hydrophobicity. Our results prompt several questions: why were students able to perform so well in their structural validation scores? How were some students able to outperform the 88% sequence identity mark that would constitute a perfect score, given the level of degenerate density or surface residues with poor density? And how can the methodology used by the best students inform the practices of professional X-ray crystallographers? Copyright © 2014 Wiley Periodicals, Inc.

  5. Vivid structural colors with low angle dependence from long-range ordered photonic crystal films.

    PubMed

    Su, Xin; Xia, Hongbo; Zhang, Shufen; Tang, Bingtao; Wu, Suli

    2017-03-02

    Structural colored materials have attracted increasing attention due to their vivid color effects and non-photobleaching characteristics. However, the angle dependence of these structural colors severely restricts their practical applications, for example, in display and sensing devices. Here, a new strategy for obtaining low angle dependent structural colors is demonstrated by fabricating long-range ordered photonic crystal films. By using spheres with high refractive indices as building blocks, the angle dependence of the obtained colors has been strongly suppressed. Green, golden yellow and red structural colored films with low angle dependence were obtained by using 145 nm, 165 nm and 187 nm Cu 2 O spheres as building blocks, respectively. SEM images confirmed the long-range highly ordered arrays of the Cu 2 O photonic crystal films. Reflectance spectra and digital photographs clearly demonstrate the low angle dependence of these structural colors, which is in sharp comparison with the case of polystyrene (PS) and SiO 2 photonic crystal films. Furthermore, these structural colors are vivid with high color saturation, not only under black background, but also under white background and natural light without adding any light-absorbing agents. These low angle dependent structural colors endow Cu 2 O photonic crystal films with great potential in practical applications. Our findings may broaden the strategies for the design and fabrication of angle independent structural colored materials.

  6. Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4YbI 6

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wu, Yuntao; Chakoumakos, Bryan C.; Shi, Hongliang

    A self-activated Cs 4YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of more » $$\\bar{R}$$3 c. By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.« less

  7. Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4YbI 6

    DOE PAGES

    Wu, Yuntao; Chakoumakos, Bryan C.; Shi, Hongliang; ...

    2018-05-14

    A self-activated Cs 4YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of more » $$\\bar{R}$$3 c. By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.« less

  8. Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalasemore » (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.« less

  9. Structure-mechanical property correlations in mechanochromic luminescent crystals of boron difluoride dibenzoylmethane derivatives.

    PubMed

    Krishna, Gamidi Rama; Devarapalli, Ramesh; Prusty, Rajesh; Liu, Tiandong; Fraser, Cassandra L; Ramamurty, Upadrasta; Reddy, Chilla Malla

    2015-11-01

    The structure and mechanical properties of crystalline materials of three boron difluoride dibenzoylmethane (BF2dbm) derivatives were investigated to examine the correlation, if any, among mechanochromic luminescence (ML) behaviour, solid-state structure, and the mechanical behaviour of single crystals. Qualitative mechanical deformation tests show that the crystals of BF2dbm( (t) Bu)2 can be bent permanently, whereas those of BF2dbm(OMe)2 exhibit an inhomogeneous shearing mode of deformation, and finally BF2dbmOMe crystals are brittle. Quantitative mechanical analysis by nano-indentation on the major facets of the crystals shows that BF2dbm( (t) Bu)2 is soft and compliant with low values of elastic modulus, E, and hardness, H, confirming its superior suceptibility for plastic deformation, which is attributed to the presence of a multitude of slip systems in the crystal structure. In contrast, both BF2dbm(OMe)2 and BF2dbmOMe are considerably stiffer and harder with comparable E and H, which are rationalized through analysis of the structural attributes such as the intermolecular interactions, slip systems and their relative orientation with respect to the indentation direction. As expected from the qualitative mechanical behaviour, prominent ML was observed in BF2dbm( (t) Bu)2, whereas BF2dbm(OMe)2 exhibits only a moderate ML and BF2dbmOMe shows no detectable ML, all examined under identical conditions. These results confirm that the extent of ML in crystalline organic solid-state fluorophore materials can be correlated positively with the extent of plasticity (low recovery). In turn, they offer opportunities to design new and improved efficient ML materials using crystal engineering principles.

  10. a Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis.

    NASA Astrophysics Data System (ADS)

    Gomez de Anderez, Dora M.

    1990-01-01

    Available from UMI in association with The British Library. Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4-tetrahidro-1, 6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 Br.H_2O) has been determined, first using monochromatic Mo Kalpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed a R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop- 2-en-1-one, (C_{25 }H_{20}N _2O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analysis respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analysis of the benzil compound ((C_6H_5 O.CO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature -114 ^circC. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation

  11. A Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis

    NASA Astrophysics Data System (ADS)

    Gomez de Anderez, Dora M.

    1990-01-01

    Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4 -tetrahidro-1,6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 BrcdotH_2O) has been determined, first using monochromatic Mo K alpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed an R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop-2-en-1-one, (C_{25}H _{20}N_2 O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analyses respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analyses of the benzil compound ((C_6H_5 OcdotCO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new

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

    NASA Astrophysics Data System (ADS)

    Sheth, Agam R.

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Orlando, Benjamin J.; Malkowski, Michael G.

    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 conditionsmore » 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.« less

  14. Waveguide structures in anisotropic nonlinear crystals

    NASA Astrophysics Data System (ADS)

    Li, Da; Hong, Pengda; Meissner, Helmuth E.

    2017-02-01

    We report on the design and manufacturing parameters of waveguiding structures of anisotropic nonlinear crystals that are employed for harmonic conversions, using Adhesive-Free Bonding (AFB®). This technology enables a full range of predetermined refractive index differences that are essential for the design of single mode or low-mode propagation with high efficiency in anisotropic nonlinear crystals which in turn results in compact frequency conversion systems. Examples of nonlinear optical waveguides include periodically bonded walk-off corrected nonlinear optical waveguides and periodically poled waveguide components, such as lithium triborate (LBO), beta barium borate (β-BBO), lithium niobate (LN), potassium titanyl phosphate (KTP), zinc germanium phosphide (ZGP) and silver selenogallate (AGSE). Simulation of planar LN waveguide shows that when the electric field vector E lies in the k-c plane, the power flow is directed precisely along the propagation direction, demonstrating waveguiding effect in the planar waveguide. Employment of anisotropic nonlinear optical waveguides, for example in combination with AFB® crystalline fiber waveguides (CFW), provides access to the design of a number of novel high power and high efficiency light sources spanning the range of wavelengths from deep ultraviolet (as short as 200 nm) to mid-infrared (as long as about 18 μm). To our knowledge, the technique is the only generally applicable one because most often there are no compatible cladding crystals available to nonlinear optical cores, especially not with an engineer-able refractive index difference and large mode area.

  15. Crystal Structures of New Ammonium 5-Aminotetrazolates

    PubMed Central

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

    2015-01-01

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

  16. Brooker's merocyanine: Comparison of single crystal structures

    NASA Astrophysics Data System (ADS)

    Hayes, Kathleen L.; Lasher, Emily M.; Choczynski, Jack M.; Crisci, Ralph R.; Wong, Calvin Y.; Dragonette, Joseph; Deschner, Joshua; Cardenas, Allan Jay P.

    2018-06-01

    Brooker's merocyanine and its derivatives are well-studied molecules due to their very interesting optical properties. Merocyanine dyes exhibit different colors in solution depending on the solvent's polarity, pH, aggregation and intermolecular interactions. The synthesis of 1-methyl-4-[(oxocyclohexadienylidene)ethylidene]-1,4-dihydropyridine (MOED) dye yielded a particularly interesting solid state structure where in one crystal lattice, MOED and its protonated form are bound by hydrogen bonding interactions.

  17. X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.

    2014-10-01

    Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

  18. X-ray transparent microfluidic chip for mesophase-based crystallization of membrane proteins and on-chip structure determination

    DOE PAGES

    Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; ...

    2014-08-21

    Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. In addition, we validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

  19. [Crystal structure of SMU.2055 protein from Streptococcus mutans and its small molecule inhibitors design and selection].

    PubMed

    Xiaodan, Chen; Xiurong, Zhan; Xinyu, Wu; Chunyan, Zhao; Wanghong, Zhao

    2015-04-01

    The aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied. The three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures. The crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected. Protein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

  20. Structural coloration of chitosan-cationized cotton fabric using photonic crystals

    NASA Astrophysics Data System (ADS)

    Yavuz, G.; Zille, A.; Seventekin, N.; Souto, A. P.

    2017-10-01

    In this work, poly (styrene-methyl methacrylate-acrylic acid) P(St-MMA-AA) composite nanospheres were deposited onto chitosan-cationized woven cotton fabrics followed by a second layer of chitosan. The deposited photonic crystals (PCs) on the fabrics were evaluated for coating efficiency and resistance, chemical analysis and color variation by optical and SEM microscopy, ATR-FTIR, diffuse reflectance spectroscopy and washing fastness. Chitosan deposition on cotton fabric provided cationic groups on the fiber surface promoting electrostatic interaction with photonic crystals. SEM images of the washed samples indicate that the PCs are firmly coated on the cotton surface only in the chitosan treated sample. The photonic nanospheres show an average diameter of 280 nm and display a face-centered cubic closepacking structure with an average thickness of 10 μm. A further chitosan post-treatment enhances color yield of the samples due to the chitosan transparent covering layer that induce bright reflections where the angles of incidence and reflection are the same. After washing, no photonic crystal can be detected on control fabric surface. However, the sample that received a chitosan post-treatment showed a good washing fastness maintaining a reasonable degree of iridescence. Chitosan fills the spaces between the polymer spheres in the matrix stabilizing the photonic structure. Sizeable variations in lattice spacing will allow color variations using more flexible non-close-packed photonic crystal arrays in chitosan hydrogels matrices.

  1. Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gao, Jianzhao; Wu, Zhonghua; Hu, Gang

    Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community. We empirically evaluated and compared the predictive performance of seven representative methods. The analysis suggests that these methods produce quite accuratemore » propensities for the diffraction-quality crystallization. We also summarized results of the first study of the relation between these predictive propensities and the resolution of the crystallizable proteins. We found that the propensities predicted by several methods are significantly higher for proteins that have high resolution structures compared to those with the low resolution structures. Moreover, we tested a new meta-predictor, MetaXXC, which averages the propensities generated by the three most accurate predictors of the diffraction-quality crystallization. MetaXXC generates putative values of resolution that have modest levels of correlation with the experimental resolutions and it offers the lowest mean absolute error when compared to the seven considered methods. We conclude that protein sequences can be used to fairly accurately predict whether their corresponding protein structures can be solved using X-ray crystallography. Moreover, we also ascertain that sequences can be used to reasonably well predict the resolution of the resulting protein crystals.« less

  2. Abstraction in perceptual symbol systems.

    PubMed Central

    Barsalou, Lawrence W

    2003-01-01

    After reviewing six senses of abstraction, this article focuses on abstractions that take the form of summary representations. Three central properties of these abstractions are established: ( i ) type-token interpretation; (ii) structured representation; and (iii) dynamic realization. Traditional theories of representation handle interpretation and structure well but are not sufficiently dynamical. Conversely, connectionist theories are exquisitely dynamic but have problems with structure. Perceptual symbol systems offer an approach that implements all three properties naturally. Within this framework, a loose collection of property and relation simulators develops to represent abstractions. Type-token interpretation results from binding a property simulator to a region of a perceived or simulated category member. Structured representation results from binding a configuration of property and relation simulators to multiple regions in an integrated manner. Dynamic realization results from applying different subsets of property and relation simulators to category members on different occasions. From this standpoint, there are no permanent or complete abstractions of a category in memory. Instead, abstraction is the skill to construct temporary online interpretations of a category's members. Although an infinite number of abstractions are possible, attractors develop for habitual approaches to interpretation. This approach provides new ways of thinking about abstraction phenomena in categorization, inference, background knowledge and learning. PMID:12903648

  3. Syntheses, crystal structures, and properties of four complexes based on polycarboxylate and imidazole ligands

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Qiao, Rui; Chen, Shui-Sheng, E-mail: chenss@fync.edu.cn; Coordination Chemistry Institute, State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093

    2015-08-15

    Four metal–organic coordination polymers [Zn(HL)(H{sub 2}O)]·4H{sub 2}O (1), [Zn(HL)(L{sub 1})]·4H{sub 2}O (2), [Cu(HL)(H{sub 2}O)]·3H{sub 2}O (3) and [Cu(HL)(L{sub 1})]·5H{sub 2}O (4) were synthesized by reactions of the corresponding metal(II) salts with semirigid polycarboxylate ligand (5-((4-carboxypiperidin-1-yl)methyl)isophthalic acid hydrochloride, H{sub 3}L·HCl) or auxiliary ligand (1,4-di(1H-imidazol-4-yl)benzene, L{sub 1}). The structures of the compounds were characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The use of auxiliary ligand L{sub 1} has great influence on the structures of two pairs of complexes 1, 2 and 3, 4. Complex 1 is a uninodal 3-connected rare 2-fold interpenetrating ZnSc net with a Point (Schlafli) symbolmore » of (10{sup 3}) while 2 is a one-dimensional (1D) ladder structure. Compound 3 features a two-dimensional (2D) honeycomb network with typical 6{sup 3}-hcb topology, while 4 is 2D network with (4, 4) sql topology based on binuclear Cu{sup II} subunits. The non-covalent bonding interactions such as hydrogen bonds, π···π stacking and C–H···π exist in complexes 1–4, which contributes to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. And the photoluminescent property of 1 and 2 and gas sorption property of 4 have been investigated. - Graphical abstract: Four new coordination polymers have been obtained and their photoluminescent and gas sorption properties have also been investigated. - Highlights: • Two pairs of Zn{sup II}/ Cu{sup II} compounds have been synthesized. • Auxiliary ligand-controlled assembly of the complexes is reported. • The luminescent properties of complexes 1–2 were investigated. • The gas sorption property of 4 has been investigated.« less

  4. Novel Crystal Structure C60 Nanowire

    NASA Astrophysics Data System (ADS)

    Mickelson, William; Aloni, Shaul; Han, Weiqiang; Cumings, John; Zettl, Alex

    2003-03-01

    We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride (BN) nanotubes. For small-diameter BN tubes, the wire consists of a linear chain of C60's. With increasing BN tube inner diameter, novel C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) which are unknown for bulk or thin film forms of C60. C60 in BN nanotubes presents a model system for studying the properties of new dimensionally-constrained "silo" crystal structures.

  5. Chemical composition, crystal size and lattice structural changes after incorporation of strontium into biomimetic apatite.

    PubMed

    Li, Z Y; Lam, W M; Yang, C; Xu, B; Ni, G X; Abbah, S A; Cheung, K M C; Luk, K D K; Lu, W W

    2007-03-01

    Recently, strontium (Sr) as ranelate compound has become increasingly popular in the treatment of osteoporosis. However, the lattice structure of bone crystal after Sr incorporation is yet to be extensively reported. In this study, we synthesized strontium-substituted hydroxyapatite (Sr-HA) with different Sr content (0.3%, 1.5% and 15% Sr-HA in mole ratio) to simulate bone crystals incorporated with Sr. The changes in chemical composition and lattice structure of apetite after synthetic incorporation of Sr were evaluated to gain insight into bone crystal changes after incorporation of Sr. X-ray diffraction (XRD) patterns revealed that 0.3% and 1.5% Sr-HA exhibited single phase spectrum, which was similar to that of HA. However, 15% Sr-HA induced the incorporation of HPO4(2-) and more CO3(2-), the crystallinity reduced dramatically. Transmission electron microscopy (TEM) images showed that the crystal length and width of 0.3% and 1.5% Sr-HA increased slightly. Meanwhile, the length and width distribution were broadened and the aspect ratio decreased from 10.68+/-4.00 to 7.28+/-2.80. The crystal size and crystallinity of 15% Sr-HA dropped rapidly, which may suggest that the fundamental crystal structure is changed. The findings from this work indicate that current clinical dosage which usually results in Sr incorporation of below 1.5% may not change chemical composition and lattice structure of bone, while it will broaden the bone crystal size distribution and strengthen the bone.

  6. Radial wave crystals: radially periodic structures from anisotropic metamaterials for engineering acoustic or electromagnetic waves.

    PubMed

    Torrent, Daniel; Sánchez-Dehesa, José

    2009-08-07

    We demonstrate that metamaterials with anisotropic properties can be used to develop a new class of periodic structures that has been named radial wave crystals. They can be sonic or photonic, and wave propagation along the radial directions is obtained through Bloch states like in usual sonic or photonic crystals. The band structure of the proposed structures can be tailored in a large amount to get exciting novel wave phenomena. For example, it is shown that acoustical cavities based on radial sonic crystals can be employed as passive devices for beam forming or dynamically orientated antennas for sound localization.

  7. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

    PubMed Central

    Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

    2014-01-01

    The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

  8. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

    PubMed

    Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

    2014-07-01

    The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. © 2014 Sripathi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  9. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

  10. Protein nanocrystallography: growth mechanism and atomic structure of crystals induced by nanotemplates.

    PubMed

    Pechkova, E; Vasile, F; Spera, R; Fiordoro, S; Nicolini, C

    2005-11-01

    Protein nanocrystallography, a new technology for crystal growth based on protein nanotemplates, has recently been shown to produce diffracting, stable and radiation-resistant lysozyme crystals. This article, by computing these lysozyme crystals' atomic structures, obtained by the diffraction patterns of microfocused synchrotron radiation, provides a possible mechanism for this increased stability, namely a significant decrease in water content accompanied by a minor but significant alpha-helix increase. These data are shown to be compatible with the circular dichroism and two-dimensional Fourier transform spectra of high-resolution H NMR of proteins dissolved from the same nanotemplate-based crystal versus those from a classical crystal. Finally, evidence for protein direct transfer from the nanotemplate to the drop and the participation of the template proteins in crystal nucleation and growth is provided by high-resolution NMR spectrometry and mass spectrometry. Furthermore, the lysozyme nanotemplate appears stable up to 523 K, as confirmed by a thermal denaturation study using spectropolarimetry. The overall data suggest that heat-proof lysozyme presence in the crystal provides a possible explanation of the crystal's resistance to synchrotron radiation.

  11. Efficient green luminescence of terbium oxalate crystals: A case study with Judd-Ofelt theory and single crystal structure analysis and the effect of dehydration on luminescence

    NASA Astrophysics Data System (ADS)

    Alexander, Dinu; Joy, Monu; Thomas, Kukku; Sisira, S.; Biju, P. R.; Unnikrishnan, N. V.; Sudarsanakumar, C.; Ittyachen, M. A.; Joseph, Cyriac

    2018-06-01

    Design and synthesis of Lanthanide based metal organic framework is a frontier area of research owing to their structural diversity enabling specific applications. The luminescence properties of rare earths, tuned by the structural features of Ln-MOFs are investigated extensively. Rare earth oxalates which can be synthesized in a facile method, ensuring the structural features of MOFs with excellent photoluminescence characteristics deserves much attention. This work is the first time report on the single crystal structure and Judd-Ofelt (JO) theoretical analysis - their correlation with the intense and sharp green luminescence of Terbium oxalate crystals. The intense green luminescence observed for Terbium oxalate crystals for a wide range of excitation from DUV to visible region despite the luminescence limiting factors are discussed. The absence of concentration quenching and lifting up of forbidden nature of f-f transitions, allowing direct excitation of Terbium ions is analysed with the help of JO theory and single crystal structure analysis. The JO analysis predicted the asymmetry of Terbium sites, allowing the electric dipole transitions and from the JO intensity parameters, promising spectroscopic parameters - emission cross section, branching ratio, gain band width and gain coefficient of the material were calculated. The single crystal structure analysis revealed the asymmetry of Tb sites and structure of Terbium oxalate is formed by the hydrogen bonded stacking of overlapped six Terbium membered rings connected by the oxalate ligands. The molecularly thick layers thus formed on the crystal surface are imaged by the atomic force microscopy. The presence of water channels in the structure and the effect of lattice water molecules on the luminescence intensity are also investigated.

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Crystal Structures of Phosphite Dehydrogenase Provide Insights into Nicotinamide Cofactor Regeneration

    PubMed Central

    Zou, Yaozhong; Zhang, Houjin; Brunzelle, Joseph S.; Johannes, Tyler W.; Woodyer, Ryan; Hung, John E.; Nair, Nikhil; van der Donk, Wilfred A.; Zhao, Huimin; Nair, Satish K.

    2015-01-01

    The enzyme phosphite dehydrogenase (PTDH) catalyzes the NAD+-dependent conversion of phosphite to phosphate and represents the first biological catalyst that has been characterized to carry out the enzymatic oxidation of phosphorus. Despite over a decade’s worth of investigation into both the mechanism of its unusual reaction, as well as its utility in cofactor regeneration, there has been a lack of any structural data on PTDH. Here we present the co-crystal structure of an engineered thermostable variant of PTDH bound to NAD+ (1.7 Å resolution), as well as four other co-crystal structures of thermostable PTDH and its variants with different ligands (all between 1.85 – 2.3 Å resolution). These structures provide a molecular framework for understanding prior mutational analysis, and point to additional residues, located in the active site, that may contribute to the enzymatic activity of this highly unusual catalyst. PMID:22564171

  14. Crystal structure of yeast allantoicase reveals a repeated jelly roll motif.

    PubMed

    Leulliot, Nicolas; Quevillon-Cheruel, Sophie; Sorel, Isabelle; Graille, Marc; Meyer, Philippe; Liger, Dominique; Blondeau, Karine; Janin, Joël; van Tilbeurgh, Herman

    2004-05-28

    Allantoicase (EC 3.5.3.4) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 A by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.

  15. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  16. Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

    PubMed Central

    Zheng, Wenjun

    2010-01-01

    Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

  17. Use of Structure as a Basis for Abstraction in Air Traffic Control

    NASA Technical Reports Server (NTRS)

    Davison, Hayley J.; Hansman, R. John

    2004-01-01

    The safety and efficiency of the air traffic control domain is highly dependent on the capabilities and limitations of its human controllers. Past research has indicated that structure provided by the airspace and procedures could aid in simplifying the controllers cognitive tasks. In this paper, observations, interviews, voice command data analyses, and radar analyses were conducted at the Boston Terminal Route Control (TRACON) facility to determine if there was evidence of controllers using structure to simplify their cognitive processes. The data suggest that controllers do use structure-based abstractions to simplify their cognitive processes, particularly the projection task. How structure simplifies the projection task and the implications of understanding the benefits structure provides to the projection task was discussed.

  18. Structural properties and defects of GaN crystals grown at ultra-high pressures: A molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Gao, Tinghong; Li, Yidan; Xie, Quan; Tian, Zean; Chen, Qian; Liang, Yongchao; Ren, Lei; Hu, Xuechen

    2018-01-01

    The growth of GaN crystals at different pressures was studied by molecular dynamics simulation employing the Stillinger-Weber potential, and their structural properties and defects were characterized using the radial distribution function, the Voronoi polyhedron index method, and a suitable visualization technology. Crystal structures formed at 0, 1, 5, 10, and 20 GPa featured an overwhelming number of <4 0 0 0> Voronoi polyhedra, whereas amorphous structures comprising numerous disordered polyhedra were produced at 50 GPa. During quenching, coherent twin boundaries were easily formed between zinc-blende and wurtzite crystal structures in GaN. Notably, point defects usually appeared at low pressure, whereas dislocations were observed at high pressure, since the simultaneous growth of two crystal grains with different crystal orientations and their boundary expansion was hindered in the latter case, resulting in the formation of a dislocation between these grains.

  19. Crystal structure of a β-aminopeptidase from an Australian Burkholderia sp.

    PubMed

    John-White, Marietta; Dumsday, Geoff J; Johanesen, Priscilla; Lyras, Dena; Drinkwater, Nyssa; McGowan, Sheena

    2017-07-01

    β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.

  20. Crystal structure and density of helium to 232 kbar

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  1. Analysis of the crystal structure of an active MCM hexamer.

    PubMed

    Miller, Justin M; Arachea, Buenafe T; Epling, Leslie B; Enemark, Eric J

    2014-09-29

    In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis.

  2. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.

    2012-03-13

    Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimermore » in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.« less

  3. Crystal structure and texture changes during thermal cycling of TATB

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vogel, Sven C.; Yeager, John David

    2015-02-20

    Goals: Understand crystal structure and micro-structure changes during thermal cycling, understand reasons for ratcheting of TATB during thermal cycling, and Support of B61 LEP. Deliverables achieved: Completed in situ thermal cycling of loose powder and pressed pellet TATB on HIPPO, Quantified preferred orientation of pressed pellet, and quantified relative change of each of the six lattic parameters.

  4. Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.

    PubMed

    Zhang, Diana; Huang, Terry; Lukeman, Philip S; Paukstelis, Paul J

    2014-12-01

    We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Crystal structure and magnetic properties of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' containing residual {alpha}-Fe prepared by low-temperature ammonia nitridation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yamashita, S.; Masubuchi, Y.; Nakazawa, Y.

    2012-10-15

    Slight enhancement of saturation magnetization to 219 A m{sup 2} kg{sup -1} was observed from 199 A m{sup 2} kg{sup -1} for the original {alpha}-Fe on the intermediate nitrided mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' with residual {alpha}-Fe among the low temperature ammonia nitridation products under 5 T magnetic field at room temperature. The value changed not linearly against the yield as had been expected. Crystal structure refinement indicated that the phase similar to {alpha} Prime Prime -Fe{sub 16}N{sub 2} had deviations on its lattice constants and positional parameters, compared to previously reported values for {alpha} Prime Primemore » -Fe{sub 16}N{sub 2}. Spin-polarized total energy calculations were performed using the projector-augmented wave method as implemented in the Vienna ab-initio simulation package (VASP) to calculate magnetic moment on the refined crystal structure of the intermediate '{alpha} Prime Prime -Fe{sub 16}N{sub 2}'. The calculations supported the observed magnetization enhancement in the intermediate nitridation product. - Graphical abstract: Crystal structural parameters slightly change in the intermediate nitrided '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' from those in {alpha} Prime Prime -Fe{sub 16}N{sub 2} to show the magnetization maxima in the mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' and the residual {alpha}-F. Highlights: Black-Right-Pointing-Pointer Larger magnetization was observed than the value of Fe{sub 16}N{sub 2} on its intermediate nitrided mixture with residual {alpha}-Fe. Black-Right-Pointing-Pointer The enhancement was related to the crystal structural deviation from Fe{sub 16}N{sub 2} on the intermediate nitride. Black-Right-Pointing-Pointer It was supported by spin-polarized total energy calculation using the deviated structure.« less

  6. Continuous structural evolution of calcium carbonate particles: a unifying model of copolymer-mediated crystallization.

    PubMed

    Kulak, Alex N; Iddon, Peter; Li, Yuting; Armes, Steven P; Cölfen, Helmut; Paris, Oskar; Wilson, Rory M; Meldrum, Fiona C

    2007-03-28

    Two double-hydrophilic block copolymers, each comprising a nonionic block and an anionic block comprising pendent aromatic sulfonate groups, were used as additives to modify the crystallization of CaCO3. Marked morphological changes in the CaCO3 particles were observed depending on the reaction conditions used. A poly(ethylene oxide)-b-poly(sodium 4-styrenesulfonate) diblock copolymer was particularly versatile in effecting a morphological change in calcite particles, and a continuous structural transition in the product particles from polycrystalline to mesocrystal to single crystal was observed with variation in the calcium concentration. The existence of this structural sequence provides unique insight into the mechanism of polymer-mediated crystallization. We propose that it reflects continuity in the crystallization mechanism itself, spanning the limits from nonoriented aggregation of nanoparticles to classical ion-by-ion growth. The various pathways to polycrystalline, mesocrystal, and single-crystal particles, which had previously been considered to be distinct, therefore all form part of a unifying crystallization framework based on the aggregation of precursor subunits.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jiang, S. Q.; Li, M. Z., E-mail: maozhili@ruc.edu.cn; Wu, Z. W.

    2016-04-21

    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 crystalmore » 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 Zr{sub 85}Cu{sub 15} system, the stronger spatial correlation of Cu atoms could hinder the crystallization processes in deeply undercooled regions.« less

  8. An automated parallel crystallisation search for predicted crystal structures and packing motifs of carbamazepine.

    PubMed

    Florence, Alastair J; Johnston, Andrea; Price, Sarah L; Nowell, Harriott; Kennedy, Alan R; Shankland, Norman

    2006-09-01

    An automated parallel crystallisation search for physical forms of carbamazepine, covering 66 solvents and five crystallisation protocols, identified three anhydrous polymorphs (forms I-III), one hydrate and eight organic solvates, including the single-crystal structures of three previously unreported solvates (N,N-dimethylformamide (1:1); hemi-furfural; hemi-1,4-dioxane). Correlation of physical form outcome with the crystallisation conditions demonstrated that the solvent adopts a relatively nonspecific role in determining which polymorph is obtained, and that the previously reported effect of a polymer template facilitating the formation of form IV could not be reproduced by solvent crystallisation alone. In the accompanying computational search, approximately half of the energetically feasible predicted crystal structures exhibit the C=O...H--N R2(2)(8)dimer motif that is observed in the known polymorphs, with the most stable correctly corresponding to form III. Most of the other energetically feasible structures, including the global minimum, have a C=O...H--N C(4) chain hydrogen bond motif. No such chain structures were observed in this or any other previously published work, suggesting that kinetic, rather than thermodynamic, factors determine which of the energetically feasible crystal structures are observed experimentally, with the kinetics apparently favouring nucleation of crystal structures based on the CBZ-CBZ R2(2)(8) motif. (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association.

  9. Structural, spectral and birefringence studies of semiorganic nonlinear optical single crystal: Calcium5-sulfosalicylate

    NASA Astrophysics Data System (ADS)

    Shalini, D.; Kalainathan, S.; Ambika, V. Revathi; Hema, N.; Jayalakshmi, D.

    2017-11-01

    Semi-organic nonlinear optical crystal Calcium5-Sulfosalicylate (CA5SS) was grown by slow evaporation solution growth technique. The cell parameters and molecular structure of the grown crystal were studied by single crystal x-ray diffraction analysis. The presence of various functional groups of the grown crystal was confirmed using Fourier transform infrared (FT-IR), Fourier transform Raman (FT-Raman) analysis. UV-Visible spectrum shows that CA5SS crystals have high transmittance in the range of 330-900 nm. The refractive index, birefringence and transient photoluminescence properties of the grown crystal were analyzed. The frequency doubling of the grown crystal (CA5SS) were studied and compared with that of KDP.

  10. The Crystal and Molecular Structure of Acetatochlorobis(4-methylpyridine)oxovanadium (IV)

    NASA Technical Reports Server (NTRS)

    Schupp, John D.; Hepp, Aloysius F.; Duraj, Stan A.; Richman, Robert M.; Fanwick, Phillip E.; Hakimzadeh, Roshanak (Technical Monitor)

    2001-01-01

    The crystal and molecular structure of the title compound, VOCl(O2CCH3)(4-CH3C5H4N)2, has been determined by single-crystal x-ray diffraction. The material crystallizes in the space group P 1(bar) (#2) with a = 7.822(2), b = 8.023(l), c = 14.841(2) Angstroms, alpha = 99.73(l), beta = 91.41(l), and gamma = 117.13(l). The coordination geometry around the vanadium is a highly distorted octahedron. The molecule is remarkable for being a monomeric oxovanadium (IV) carboxylate. A generalized synthetic strategy is proposed for the preparation of oxovanadium (IV) monomers.

  11. In situ data collection and structure refinement from microcapillary protein crystallization

    PubMed Central

    Yadav, Maneesh K.; Gerdts, Cory J.; Sanishvili, Ruslan; Smith, Ward W.; Roach, L. Spencer; Ismagilov, Rustem F.; Kuhn, Peter; Stevens, Raymond C.

    2007-01-01

    In situ X-ray data collection has the potential to eliminate the challenging task of mounting and cryocooling often fragile protein crystals, reducing a major bottleneck in the structure determination process. An apparatus used to grow protein crystals in capillaries and to compare the background X-ray scattering of the components, including thin-walled glass capillaries against Teflon, and various fluorocarbon oils against each other, is described. Using thaumatin as a test case at 1.8 Å resolution, this study demonstrates that high-resolution electron density maps and refined models can be obtained from in situ diffraction of crystals grown in microcapillaries. PMID:17468785

  12. Growth and structure of a new photonic crystal: Chlorine substituted chalcone

    NASA Astrophysics Data System (ADS)

    Sarveshwara, H. P.; Raghavendra, S.; A, Jayarama; Menezes, Anthoni Praveen; Dharmaprakash, S. M.

    2015-06-01

    A new organic photonic material 3-(2, 4-dichlorophenyl)-1-(2,5-dimethylthiophen-3-yl)propan-1-one(DMTP) has been synthesized and crystallised in acetone solution. The functional groups present in the new material were identified by FTIR spectroscopy. The material is optically transparent in the wavelength range of 400-1100 nm. The crystal structure of DMTP was determined by single crystal X-ray diffraction. The title compound crystallizes in monoclinic system with a centrosymmetric space group P21/c. The Z-scan study revealed that the optical limiting property exhibited by the DMTP molecule is based on the reverse saturable absorption phenomena.

  13. Lead(ii) soaps: crystal structures, polymorphism, and solid and liquid mesophases.

    PubMed

    Martínez-Casado, F J; Ramos-Riesco, M; Rodríguez-Cheda, J A; Redondo-Yélamos, M I; Garrido, L; Fernández-Martínez, A; García-Barriocanal, J; da Silva, I; Durán-Olivencia, M; Poulain, A

    2017-07-05

    The long-chain members of the lead(ii) alkanoate series or soaps, from octanoate to octadecanoate, have been thoroughly characterized by means of XRD, PDF analysis, DSC, FTIR, ssNMR and other techniques, in all their phases and mesophases. The crystal structures at room temperature of all of the members of the series are now solved, showing the existence of two polymorphic forms in the room temperature crystal phase, different to short and long-chain members. Only nonanoate and decanoate present both forms, and this polymorphism is proven to be monotropic. At higher temperature, these compounds present a solid mesophase, defined as rotator, a liquid crystal phase and a liquid phase, all of which have a similar local arrangement. Since some lead(ii) soaps appear as degradation compounds in oil paintings, the solved crystal structures of lead(ii) soaps can now be used as fingerprints for their detection using X-ray diffraction. Pair distribution function analysis on these compounds is very similar in the same phases and mesophases for the different members, showing the same short range order. This observation suggests that this technique could also be used in the detection of these compounds in disordered phases or in the initial stages of formation in paintings.

  14. Discrete structures in continuum descriptions of defective crystals

    PubMed Central

    2016-01-01

    I discuss various mathematical constructions that combine together to provide a natural setting for discrete and continuum geometric models of defective crystals. In particular, I provide a quite general list of ‘plastic strain variables’, which quantifies inelastic behaviour, and exhibit rigorous connections between discrete and continuous mathematical structures associated with crystalline materials that have a correspondingly general constitutive specification. PMID:27002070

  15. One-dimensional dielectric bi-periodic photonic structures based on ternary photonic crystals

    NASA Astrophysics Data System (ADS)

    Dadoenkova, Nataliya N.; Dadoenkova, Yuliya S.; Panyaev, Ivan S.; Sannikov, Dmitry G.; Lyubchanskii, Igor L.

    2018-01-01

    We investigate the transmittivity spectra, fields, and energy distribution of the electromagnetic eigenwaves propagating in a one-dimensional (1D) dielectric photonic crystal [(TiO2/SiO2)NAl2O3]M with two periods formed by unit cells TiO2/SiO2 and (TiO2/SiO2)NAl2O3. Spectra of TE- and TM-modes depend on the geometric parameters of the structure and undergo modifications with the change in the period numbers, layer thicknesses, and incidence angle. Special attention is paid to the applicability of the hybrid effective medium approximation comprising the long-wave approximation and two-dimensional (2 × 2) transfer matrix method. We demonstrate spectral peculiarities of the bi-periodic structure and also show the differences between the band gap spectra of the bi-periodic and ternary 1D dielectric photonic crystals. The presented photonic crystal structure can find its applications in optoelectronics and nanophotonics areas as omnidirectional reflectors, optical ultra-narrow bandpass filters, and antireflection coatings.

  16. Crystal-to-Crystal Transition of Ultrasoft Colloids under Shear

    NASA Astrophysics Data System (ADS)

    Ruiz-Franco, J.; Marakis, J.; Gnan, N.; Kohlbrecher, J.; Gauthier, M.; Lettinga, M. P.; Vlassopoulos, D.; Zaccarelli, E.

    2018-02-01

    Ultrasoft colloids typically do not spontaneously crystallize, but rather vitrify, at high concentrations. Combining in situ rheo-small-angle-neutron-scattering experiments and numerical simulations we show that shear facilitates crystallization of colloidal star polymers in the vicinity of their glass transition. With increasing shear rate well beyond rheological yielding, a transition is found from an initial bcc-dominated structure to an fcc-dominated one. This crystal-to-crystal transition is not accompanied by intermediate melting but occurs via a sudden reorganization of the crystal structure. Our results provide a new avenue to tailor colloidal crystallization and the crystal-to-crystal transition at the molecular level by coupling softness and shear.

  17. Correlating Single Crystal Structure, Nanomechanical, and Bulk Compaction Behavior of Febuxostat Polymorphs.

    PubMed

    Yadav, Jayprakash A; Khomane, Kailas S; Modi, Sameer R; Ugale, Bharat; Yadav, Ram Naresh; Nagaraja, C M; Kumar, Navin; Bansal, Arvind K

    2017-03-06

    Febuxostat exhibits unprecedented solid forms with a total of 40 polymorphs and pseudopolymorphs reported. Polymorphs differ in molecular arrangement and conformation, intermolecular interactions, and various physicochemical properties, including mechanical properties. Febuxostat Form Q (FXT Q) and Form H1 (FXT H1) were investigated for crystal structure, nanomechanical parameters, and bulk deformation behavior. FXT Q showed greater compressibility, densification, and plastic deformation as compared to FXT H1 at a given compaction pressure. Lower mechanical hardness of FXT Q (0.214 GPa) as compared to FXT H1 (0.310 GPa) was found to be consistent with greater compressibility and lower mean yield pressure (38 MPa) of FXT Q. Superior compaction behavior of FXT Q was attributed to the presence of active slip systems in crystals which offered greater plastic deformation. By virtue of greater compressibility and densification, FXT Q showed higher tabletability over FXT H1. Significant correlation was found with anticipation that the preferred orientation of molecular planes into a crystal lattice translated nanomechanical parameters to a bulk compaction process. Moreover, prediction of compactibility of materials based on true density or molecular packing should be carefully evaluated, as slip-planes may cause deviation in the structure-property relationship. This study supported how molecular level crystal structure confers a bridge between particle level nanomechanical parameters and bulk level deformation behavior.

  18. Synthesis, growth, structural, spectroscopic and optical studies of a semiorganic NLO crystal: zinc guanidinium phosphate.

    PubMed

    Suvitha, A; Murugakoothan, P

    2012-02-01

    The semi-organic nonlinear optical (NLO) crystal, zinc guanidinium phosphate (ZGuP) has been grown through synthesis between zinc sulphate, guanidine carbonate and orthophosphoric acid from its aqueous solution by slow solvent evaporation technique. Solubility of the synthesized material has been determined for various temperatures using water as solvent. The grown crystal has been characterized by powder X-ray diffraction to confirm the crystal structure. Investigation has been carried out to assign the vibrational frequencies of the grown crystals by Fourier transform infrared spectroscopy technique. (1)H and (13)C FT-NMR have been recorded to elucidate the molecular structure. The optical absorption study confirms the suitability of the crystal for device applications. The second harmonic generation (SHG) efficiency of ZGuP is found to be 1.825 times that of potassium dihydrogen phosphate (KDP). Thermal behavior of the grown crystals has been studied by thermogravimetric and differential thermal analysis. The mechanical properties of the grown crystals have been studied using Vickers microhardness tester. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. The control of ice crystal growth and effect on porous structure of konjac glucomannan-based aerogels.

    PubMed

    Ni, Xuewen; Ke, Fan; Xiao, Man; Wu, Kao; Kuang, Ying; Corke, Harold; Jiang, Fatang

    2016-11-01

    Konjac glucomannan (KGM)-based aerogels were prepared using a combination of sol-gel and freeze-drying methods. Preparation conditions were chosen to control ice crystal growth and aerogel structure formation. The ice crystals formed during pre-freezing were observed by low temperature polarizing microscopy, and images of aerogel pores were obtained by scanning electron microscopy. The size of ice crystals were calculated and size distribution maps were drawn, and similarly for aerogel pores. Results showed that ice crystal growth and aerogel pore sizes may be controlled by varying pre-freezing temperatures, KGM concentration and glyceryl monostearate concentration. The impact of pre-freezing temperatures on ice crystal growth was explained as combining ice crystal growth rate with nucleation rate, while the impacts of KGM and glyceryl monostearate concentration on ice crystal growth were interpreted based on their influences on sol network structure. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Liquid crystal-based Mueller matrix spectral imaging polarimetry for parameterizing mineral structural organization.

    PubMed

    Gladish, James C; Duncan, Donald D

    2017-01-20

    Herein, we discuss the remote assessment of the subwavelength organizational structure of a medium. Specifically, we use spectral imaging polarimetry, as the vector nature of polarized light enables it to interact with optical anisotropies within a medium, while the spectral aspect of polarization is sensitive to small-scale structure. The ability to image these effects allows for inference of spatial structural organization parameters. This work describes a methodology for revealing structural organization by exploiting the Stokes/Mueller formalism and by utilizing measurements from a spectral imaging polarimeter constructed from liquid crystal variable retarders and a liquid crystal tunable filter. We provide results to validate the system and then show results from measurements on a mineral sample.

  1. Topological Classification of Crystalline Insulators through Band Structure Combinatorics

    NASA Astrophysics Data System (ADS)

    Kruthoff, Jorrit; de Boer, Jan; van Wezel, Jasper; Kane, Charles L.; Slager, Robert-Jan

    2017-10-01

    We present a method for efficiently enumerating all allowed, topologically distinct, electronic band structures within a given crystal structure in all physically relevant dimensions. The algorithm applies to crystals without time-reversal, particle-hole, chiral, or any other anticommuting or anti-unitary symmetries. The results presented match the mathematical structure underlying the topological classification of these crystals in terms of K -theory and therefore elucidate this abstract mathematical framework from a simple combinatorial perspective. Using a straightforward counting procedure, we classify all allowed topological phases of spinless particles in crystals in class A . Employing this classification, we study transitions between topological phases within class A that are driven by band inversions at high-symmetry points in the first Brillouin zone. This enables us to list all possible types of phase transitions within a given crystal structure and to identify whether or not they give rise to intermediate Weyl semimetallic phases.

  2. The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xu, Wenqian; Zhu, Qiang; Hu, Chunhua Tony

    2017-01-18

    Glycine, the simplest amino acid, is also the most polymorphous. Herein, we report the structure determination of an unknown phase of glycine which was firstly reported by Pyne and Suryanarayanan in 2001. To date, the new phase has only been prepared at 208 K as nanocrystals within ice. Through computational crystal structure prediction and powder X-ray diffraction methods, we identified this elusive phase as glycine dihydrate (GDH), representing a first report on a hydrated glycine structure. The structure of GDH has important implications for the state of glycine in aqueous solution, and the mechanisms of glycine crystallization. GDH may alsomore » be the form of glycine that comes to Earth from extraterrestrial sources.« less

  3. Passive Sensor Materials Based on Liquid Crystals

    DTIC Science & Technology

    2011-03-12

    REPORT Passive Sensor Materials based on Liquid Crystals 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Research supported by this grant entitled “Passive...Sensor Materials Based on Liquid Crystals” revolved around an investigation of liquid crystalline materials for use in passive sensors for chemical... based on Liquid Crystals Report Title ABSTRACT Research supported by this grant entitled “Passive Sensor Materials Based on Liquid Crystals” revolved

  4. Dual curved photonic crystal ring resonator based channel drop filter using two-dimensional photonic crystal structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chhipa, Mayur Kumar, E-mail: mayurchhipa1@gmail.com; Dusad, Lalit Kumar

    In this paper channel drop filter (CDF) is designed using dual curved photonic crystal ring resonator (PCRR). The photonic band gap (PBG) is calculated by plane wave expansion (PWE) method and the photonic crystal (PhC) based on two dimensional (2D) square lattice periodic arrays of silicon (Si) rods in air structure have been investigated using finite difference time domain (FDTD) method. The number of rods in Z and X directions is 21 and 20 respectively with lattice constant 0.540 nm and rod radius r = 0.1 µm. The channel drop filter has been optimized for telecommunication wavelengths λ = 1.591 µm with refractivemore » indices 3.533. In the designed structure further analysis is also done by changing whole rods refractive index and it has been observed that this filter may be used for filtering several other channels also. The designed structure is useful for CWDM systems. This device may serve as a key component in photonic integrated circuits. The device is ultra compact with the overall size around 123 µm{sup 2}.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bolotina, N. B., E-mail: bolotina@ns.crys.ras.ru; Brazhkin, V. V.; Dyuzheva, T. I.

    2013-01-15

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

  6. Electronic and crystal structure of NiTi martensite

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sanati, M.; Albers, R.C.; Pinski, F.J.

    1998-11-01

    All of the first-principles electronic-structure calculations for the martensitic structure of NiTi have used the experimental atomic parameters reported by Michal and Sinclair [Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. {bold B37}, 1803 (1981)]. We have used first-principles, full-potential, linear muffin-tin orbital calculations to examine the total energy of all the experimental martensitic structures reported in the literature. We find that another crystal structure, that of Kudoh {ital et al.} [Acta Metall. Mater. {bold 33}, 2049 (1985)], has the lowest total energy at zero temperature. Ground-state and formation energies were calculated for all of the experimental structures. Total andmore » local densities of states were calculated and compared with each other for the structures of both Kudoh {ital et al.} and Michal and Sinclair thinsp {copyright} {ital 1998} {ital The American Physical Society}« less

  7. Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.

    2001-11-01

    In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

  8. Crystal Structural Effect of AuCu Alloy Nanoparticles on Catalytic CO Oxidation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhan, Wangcheng; Wang, Jinglin; Wang, Haifeng

    2017-06-07

    Controlling the physical and chemical properties of alloy nanoparticles (NPs) is an important approach to optimize NP catalysis. Unlike other tuning knobs, such as size, shape, and composition, crystal structure has received limited attention and not been well understood for its role in catalysis. This deficiency is mainly due to the difficulty in synthesis and fine-tuning of the NPs’ crystal structure. Here, Exemplifying by AuCu alloy NPs with face centered cubic (fcc) and face centered tetragonal (fct) structure, we demonstrate a remarkable difference in phase segregation and catalytic performance depending on the crystal structure. During the thermal treatment in air,more » the Cu component in fcc-AuCu alloy NPs segregates more easily onto the alloy surface as compared to that in fct-AuCu alloy NPs. As a result, after annealing at 250 °C in air for 1 h, the fcc- and fct-AuCu alloy NPs are phase transferred into Au/CuO and AuCu/CuO core/shell structures, respectively. More importantly, this variation in heterostructures introduces a significant difference in CO adsorption on two catalysts, leading to a largely enhanced catalytic activity of AuCu/CuO NP catalyst for CO oxidation. Furthermore, the same concept can be extended to other alloy NPs, making it possible to fine-tune NP catalysis for many different chemical reactions.« less

  9. Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca.

    PubMed

    Singh, D D; Saikrishnan, K; Kumar, Prashant; Dauter, Z; Sekar, K; Surolia, A; Vijayan, M

    2004-11-01

    The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit. The structure has been solved using molecular replacement to a resolution of 3 A. The structure of the subunit is similar to that of jacalin-like lectins.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

    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. Themore » 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.« less

  11. Comparing data accuracy between structured abstracts and full-text journal articles: implications in their use for informing clinical decisions.

    PubMed

    Fontelo, Paul; Gavino, Alex; Sarmiento, Raymond Francis

    2013-12-01

    The abstract is the most frequently read section of a research article. The use of 'Consensus Abstracts', a clinician-oriented web application formatted for mobile devices to search MEDLINE/PubMed, for informing clinical decisions was proposed recently; however, inaccuracies between abstracts and the full-text article have been shown. Efforts have been made to improve quality. We compared data in 60 recent-structured abstracts and full-text articles from six highly read medical journals. Data inaccuracies were identified and then classified as either clinically significant or not significant. Data inaccuracies were observed in 53.33% of articles ranging from 3.33% to 45% based on the IMRAD format sections. The Results section showed the highest discrepancies (45%) although these were deemed to be mostly not significant clinically except in one. The two most common discrepancies were mismatched numbers or percentages (11.67%) and numerical data or calculations found in structured abstracts but not mentioned in the full text (40%). There was no significant relationship between journals and the presence of discrepancies (Fisher's exact p value =0.3405). Although we found a high percentage of inaccuracy between structured abstracts and full-text articles, these were not significant clinically. The inaccuracies do not seem to affect the conclusion and interpretation overall. Structured abstracts appear to be informative and may be useful to practitioners as a resource for guiding clinical decisions.

  12. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    PubMed

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

  13. Crystal Structure Characterization of Thin Layer Zinc Oxide

    NASA Astrophysics Data System (ADS)

    Doyan, Aris; Susilawati; Azizatul Fitri, Siti; Ahzan, Sukainil

    2017-05-01

    In this research the characterization of the crystal structure of a thin layer of ZnO (zinc oxide) were synthesized by sol - gel method and spin coating deposited on a glass substrate. The samples were divided into three sol concentrations of 0.1, 0.3, 0.5 Molar and two deposition temperature is 350 °C, and 550 °C. UV-Vis. spectrophotometer results showed that in the spectrum of visible light (wavelength range 300-800 nm) has a transmittance value of which increases with increasing concentration and temperature deposition of zinc oxide, otherwise the value of the absorption and the band gap energy decreases with the addition of concentration and deposition temperature. The transmittances value of the highest and lowest absorption was 93.5% and 0.03 is at a concentration of 0.1 M and zinc oxide deposition temperature of 550 °C, with a value of band gap energy of 2.98 eV. The XRD results showed that the zinc oxide crystal orientation in the field of 013 with a crystal grain size 14.4472 nm. SEM results showed the surface morphology of zinc oxide such as rod-like.

  14. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yennawar, Hemant; Møller, Magda; University of Copenhagen, DK-2100 Copenhagen

    The X-ray crystal structure and a small-angle X-ray scattering solution structure of sheep liver sorbitol dehydrogenase have been determined. The details of the interactions that enable the tetramer scaffold to be the functional biological unit have been analyzed. The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystalmore » symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.« less

  15. Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM

    PubMed Central

    Gupta, Gagan Deep; Madamwar, Datta

    2015-01-01

    Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein. PMID:25923120

  16. Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions.

    PubMed

    Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

    2018-04-06

    Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

  17. Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions

    NASA Astrophysics Data System (ADS)

    Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

    2018-04-01

    Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

  18. From protein structure to function via single crystal optical spectroscopy

    PubMed Central

    Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

    2015-01-01

    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 maps, 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 infereing 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. PMID:25988179

  19. Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.

    PubMed

    Luo, Fangjia; Shinzawa-Itoh, Kyoko; Hagimoto, Kaede; Shimada, Atsuhiro; Shimada, Satoru; Yamashita, Eiki; Yoshikawa, Shinya; Tsukihara, Tomitake

    2017-07-01

    Cytochrome c oxidase (CcO) couples proton pumping to O 2 reduction. Its enzymatic activity depends sensitively on pH over a wide range. However, owing to difficulty in crystallizing this protein, X-ray structure analyses of bovine CcO aimed at understanding its reaction mechanism have been conducted using crystals prepared at pH 5.7, which is significantly lower than that in the cell. Here, oxidized CcO at pH 7.3 was crystallized using a fluorinated octyl-maltoside derivative, and the structure was determined at 1.77 Å resolution. No structural differences between crystals obtained at the neutral pH and the acidic pH were detected within the molecules. On the other hand, some differences in intermolecular interactions were detected between the two types of crystal. The influence of pH on the molecular surface is likely to contribute to the pH dependency of the aerobic oxidation of ferrocytochrome c.

  20. Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures.

    PubMed

    Tasolamprou, Anna C; Zhang, Lei; Kafesaki, Maria; Koschny, Thomas; Soukoulis, Costas M

    2015-06-01

    We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. The angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

  1. Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tasolamprou, Anna C.; Zhang, Lei; Kafesaki, Maria

    2015-05-19

    We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. Furthermore, the angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

  2. Probing the Crystal Structure and Formation Mechanism of Lanthanide-Doped Upconverting Nanocrystals

    DOE PAGES

    Hudry, Damien; Abeykoon, A. M. M.; Dooryhee, E.; ...

    2016-11-23

    Lanthanide (Ln)-doped upconverting nanocrystals (UCNCs), such as NaLnF 4 (with Ln = lanthanide), constitute an important class of nanoscale materials due to their capacity to convert near-infrared photons into near-ultraviolet or visible light. Although under intense investigation for more than a decade, UCNCs have been relatively underexplored especially regarding their crystal structure and mechanisms of formation in organic media. The former is needed to explain the relationship between atomic scale structure and upconversion (UC) properties of UCNCs (i.e., local symmetry for 4f–4f transition probability, Ln 3+ distances for energy migration), while the latter is essential to finely tune the size, morphology, chemical composition, and architecture of well-defined upconverting nanostructures, which constitute the experimental levers to modify the optical properties. In this contribution, we use synchrotron-based diffraction experiments coupled to Rietveld and pair distribution function (PDF) analyses to understand the formation of NaGdF 4:Yb:Er UCNCs in organic media and to investigate their crystal structure. Our results reveal a complex mechanism of the formation of NaGdF 4:Yb:Er UCNCs based on chemical reactions involving molecular clusters and in situ-generated, crystalline sodium fluoride at high temperature. Additionally, a detailed crystallographic investigation of NaGdF 4:Yb:Er UCNCs is presented. Our Rietveld and PDF analyses show that the space group Pmore » $$\\bar{6}$$ is the one that best describes the crystal structure of NaGdF 4:Yb:Er UCNCs contrary to what has been recently proposed. Further, our Rietveld and PDF data reveal the formation of bulk-like crystal structure down to 10 nm with limited distortions. Finally, the results presented in this paper constitute an important step toward the comprehensive understanding of the underlying picture that governs UC properties of lanthanide-doped nanostructures.« less

  3. Transmission electron microscopy: direct observation of crystal structure in refractory ceramics.

    PubMed

    Shaw, T M; Thomas, G

    1978-11-10

    Using high-resolution multibeam interference techniques in the transmission electron microscope, images have been obtained that make possible a real-space structure analysis of a beryllium-silicon-nitrogen compound. The results illustrate the usefulness of lattice imaging in the analysis of local crystal structure in these technologically promising ceramic materials.

  4. Discrete structures in continuum descriptions of defective crystals.

    PubMed

    Parry, G P

    2016-04-28

    I discuss various mathematical constructions that combine together to provide a natural setting for discrete and continuum geometric models of defective crystals. In particular, I provide a quite general list of 'plastic strain variables', which quantifies inelastic behaviour, and exhibit rigorous connections between discrete and continuous mathematical structures associated with crystalline materials that have a correspondingly general constitutive specification. © 2016 The Author(s).

  5. Structure of Bacillus halmapalus α-amylase crystallized with and without the substrate analogue acarbose and maltose

    PubMed Central

    Lyhne-Iversen, Louise; Hobley, Timothy J.; Kaasgaard, Svend G.; Harris, Pernille

    2006-01-01

    Recombinant Bacillus halmapalus α-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 Å. It was found that the crystal belonged to space group P212121, with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 Å. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES–HEPES–boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 Å. The crystal belonged to space group P212121, with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 Å. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates. PMID:16946462

  6. Crystal Structure of the Catalytic Domain of Drosophila [beta]1,4-Galactosyltransferase-7

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ramakrishnan, Boopathy; Qasba, Pradman K.

    2010-11-03

    The {beta}1,4-galactosyltransferase-7 ({beta}4Gal-T7) enzyme, one of seven members of the {beta}4Gal-T family, transfers in the presence of manganese Gal from UDP-Gal to an acceptor sugar (xylose) that is attached to a side chain hydroxyl group of Ser/Thr residues of proteoglycan proteins. It exhibits the least protein sequence similarity with the other family members, including the well studied family member {beta}4Gal-T1, which, in the presence of manganese, transfers Gal from UDP-Gal to GlcNAc. We report here the crystal structure of the catalytic domain of {beta}4Gal-T7 from Drosophila in the presence of manganese and UDP at 1.81 {angstrom} resolution. In the crystalmore » structure, a new manganese ion-binding motif (HXH) has been observed. Superposition of the crystal structures of {beta}4Gal-T7 and {beta}4Gal-T1 shows that the catalytic pocket and the substrate-binding sites in these proteins are similar. Compared with GlcNAc, xylose has a hydroxyl group (instead of an N-acetyl group) at C2 and lacks the CH{sub 2}OH group at C5; thus, these protein structures show significant differences in their acceptor-binding site. Modeling of xylose in the acceptor-binding site of the {beta}4Gal-T7 crystal structure shows that the aromatic side chain of Tyr{sup 177} interacts strongly with the C5 atom of xylose, causing steric hindrance to any additional group at C5. Because Drosophila Cd7 has a 73% protein sequence similarity to human Cd7, the present crystal structure offers a structure-based explanation for the mutations in human Cd7 that have been linked to Ehlers-Danlos syndrome.« less

  7. Crystal Structure of a Ube2S-Ubiquitin Conjugate

    PubMed Central

    Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

    2016-01-01

    Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

  8. Surface photonic crystal structures for LED emission modification

    NASA Astrophysics Data System (ADS)

    Uherek, Frantisek; Škriniarová, Jaroslava; Kuzma, Anton; Šušlik, Łuboš; Lettrichova, Ivana; Wang, Dong; Schaaf, Peter

    2017-12-01

    Application of photonic crystal structures (PhC) can be attractive for overall and local enhancement of light from patterned areas of the light emitting diode (LED) surface. We used interference and near-field scanning optical microscope lithography for patterning of the surface of GaAs/AlGaAs based LEDs emitted at 840 nm. Also new approach with patterned polydimethylsiloxane (PDMS) membrane applied directly on the surface of red emitting LED was investigated. The overall emission properties of prepared LED with patterned structure show enhanced light extraction efficiency, what was documented from near- and far-field measurements.

  9. Structural variability in Cu(I) and Ag(I) coordination polymers with a flexible dithione ligand: Synthesis, crystal structure, microbiological and theoretical studies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beheshti, Azizolla, E-mail: a.beheshti@scu.ac.ir; Nozarian, Kimia; Babadi, Susan Soleymani

    Two new compounds namely [Cu(SCN)(µ-L)]{sub n} (1) and ([Ag (µ{sub 2}-L)](ClO{sub 4})){sub n} (2) have been synthesized at room temperature by one-pot reactions between the 1,1-(1,4-butanediyl)bis(1,3-dihydro-3-methyl-1H-imidazole- 2-thione) (L) and appropriate copper(I) and silver(I) salts. These polymers have been characterized by single crystal X-ray diffraction, XRPD, TGA, elemental analysis, infrared spectroscopy, antibacterial activity and scanning probe microscopy studies. In the crystal structure of 1, copper atoms have a distorted trigonal planar geometry with a CuS{sub 2}N coordination environment. Each of the ligands in the structure of 1 acting as a bidentate S-bridging ligand to form a 1D chain structure. Additionally, themore » adjacent 1D chains are interconnected by the intermolecular C-H…S interactions to create a 2D network structure. In contrast to 1, in the cationic 3D structure of 2 each of the silver atoms exhibits an AgS{sub 4} tetrahedral geometry with 4-membered Ag{sub 2}S{sub 2} rings. In the structure of 2, the flexible ligand adopts two different conformations; gauche-anti-gauche and anti-anti-anti. The antibacterial studies of these polymers showed that polymer 2 is more potent antibacterial agent than 1. Scanning probe microscopy (SPM) study of the treated bacteria was carried out to investigate the structural changes cause by the interactions between the polymers and target bacteria. Theoretical study of polymer 1 investigated by the DFT calculations indicates that observed transitions at 266 nm and 302 nm in the UV–vis spectrum could be attributed to the π→π* and MLCT transitions, respectively. - Graphical abstract: Two new Cu(I) and Ag(I) coordination polymers have been have been synthesized by one-pot reactions. Copper complex has a 2D non-covalent structure, but silver compound is a 3D coordination compound. These compounds have effective antibacterial activity. - Highlights: • Cu(I) and Ag(I) based coordination

  10. The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space.

    PubMed

    Xu, Wenqian; Zhu, Qiang; Hu, Chunhua Tony

    2017-02-13

    Glycine, the simplest amino acid, is also the most polymorphous. Herein, we report the structure determination of a long unknown phase of glycine, which was first reported by Pyne and Suryanarayanan in 2001. To date, this phase has only been prepared at 208 K as nanocrystals within ice. Through computational crystal-structure prediction and powder X-ray diffraction methods, we identified this elusive phase as glycine dihydrate (GDH), representing the first report on the structure of a hydrated glycine structure. The structure of GDH has important implications for the state of glycine in aqueous solution and the mechanisms of glycine crystallization. GDH may also be the form of glycine that comes to Earth from extraterrestrial sources. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Crystal Structure of Bacillus subtilis α-Amylase in Complex with Acarbose

    PubMed Central

    Kagawa, Masayuki; Fujimoto, Zui; Momma, Mitsuru; Takase, Kenji; Mizuno, Hiroshi

    2003-01-01

    The crystal structure of Bacillus subtilis α-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process. PMID:14617662

  12. Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

    PubMed

    Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

    2012-05-01

    We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

  13. Synthesis, crystal structure, Hirshfeld surfaces analysis and anti-ischemic activity of cinnamide derivatives

    NASA Astrophysics Data System (ADS)

    Zhong, Jian-gang; Han, Jia-pei; Li, Xiao-feng; Xu, Yi; Zhong, Yan; Wu, Bin

    2018-02-01

    Two cinnamide derivatives, namely, (E)-1-(4-(bis(4-methylphenyl)- methyl)piperazin-1-yl)-3-(3,4-diethoxyphenyl)prop-2-en-1-one (5) and (E)-1-(4-(bis- (4-fluorophenyl)methyl)piperazin-1-yl)-3-(4-methoxyphenyl)prop-2-en-1-one (6), have been synthesized and characterized by IR spectra, High resolution mass spectra, 1H NMR spectra, 13C NMR spectra. The compound 5 is a novel compound and has never been reported in the literature. Their crystal structures were studied by single-crystal X-ray diffraction. They all crystallize in the monoclinic system. The single-crystal X-ray revealed that compound 5 has infinite X-shaped 1-D polymeric chains structure and compound 6 has a layered 3-D structure by intermolecular interactions. Hirshfeld surface analysis demonstrated the presence of H⋯H, O⋯H, C⋯H, F⋯H, Csbnd H⋯π and π⋯π intermolecular interactions. In addition, the MTT assay results indicated that the compounds 5 and 6 display effective activities against neurotoxicity which is induced by glutamine in PC12 cells. The in vivo experiment indicated that the compound 6 has a good protective effect on cerebral infarction.

  14. Four-port coupled channel-guide device based on 2D photonic crystal structure

    NASA Astrophysics Data System (ADS)

    Camargo, Edilson A.; Chong, Harold M. H.; De La Rue, Richard M.

    2004-12-01

    We have fabricated and measured a four-port coupled channel-waveguide device using W1 channel waveguides oriented along ΓK directions in a two-dimensional (2D) hole-based planar photonic crystal (PhC) based on silicon-on-insulator (SOI) waveguide material, at operation wavelengths around 1550 nm. 2D FDTD simulations and experimental results are shown and compared. The structure has been designed using a mode conversion approach, combined with coupled-mode concepts. The overall length of the photonic crystal structure is typically about 39 μm and the structure has been fabricated using a combination of direct-write electron-beam lithography (EBL) and dry-etch processing. Devices were measured using a tunable laser with end-fire coupling into the planar structure.

  15. A comparative study on the crystal structure of bicycle analogues to the natural phytotoxin helminthosporins

    NASA Astrophysics Data System (ADS)

    Barbosa, Luiz Cláudio de Almeida; Teixeira, Robson Ricardo; Nogueira, Leonardo Brandão; Maltha, Celia Regina Alvares; Doriguetto, Antônio Carlos; Martins, Felipe Terra

    2016-02-01

    Herein we described structural insights of a series of analogues to helminthosporin phytotoxins. The key reaction used to prepare the compounds corresponded to the [3 + 4] cycloaddition between the oxyallyl cation generated from 2,4-dibromopentan-3-one and different furans. Their structures were confirmed upon IR, NMR and X-ray diffraction analyses. While bicycles 7, 8 and 9 crystallize in the centrosymmetric monoclinic space group P21/c, compound 10 was solved in the noncentrosymmetric orthorhombic space group P212121. The solid materials obtained were shown to be racemic crystals (7, 8, 9) or racemic conglomerate (10). In all compounds, there is formation of a bicycle featured by fused tetrahydropyranone and 2,5-dihydrofuran rings. They adopt chair and envelope conformations, respectively. Crystal packing of all compounds is stabilized through C-H•••O contacts. Conformational aspects as well as similarities and differences among the crystal structures of the synthesized analogues are discussed.

  16. Antiferromagnetic defect structure in LaNi O3 -δ single crystals

    NASA Astrophysics Data System (ADS)

    Wang, Bi-Xia; Rosenkranz, S.; Rui, X.; Zhang, Junjie; Ye, F.; Zheng, H.; Klie, R. F.; Mitchell, J. F.; Phelan, D.

    2018-06-01

    The origins of the metal-insulator and magnetic transitions exhibited by perovskite rare-earth nickelates, RNiO3 (where R is a rare-earth element), remain open issues, with charge disproportionation, magnetic interactions, and lattice response across multiple length scales being among the many possible origins. Recently, growth of single crystals of LaNiO3, which is the only member of these compounds that remains metallic in its ground state, has been reported, opening a new chapter in the investigation of the perovskite nickelates. Here, using a combination of magnetometry, heat capacity, and neutron scattering on as-grown and purposely reduced LaNi O3 -δ crystals, we show that both antiferromagnetic and ferromagnetic phases with a Néel temperature of ˜152 K and a Curie temperature of ˜225 K can be induced by reduction of the oxygen content. Transmission electron microscopy shows that these phases are characterized by ordered oxygen vacancy defect structures that exist as dilute secondary phases in as-grown crystals despite growth in partial oxygen pressures up to at least 130 bar. The demonstration of antiferromagnetism resulting from oxygen vacancy ordered structures implies that stoichiometry must be explicitly considered when interpreting the bulk properties of LaNi O3 -δ single crystals; accordingly, the implications of our results for putative oxygen-stoichiometric LaNiO3 are discussed.

  17. Influence law of structural characteristics on the surface roughness of a magnetorheological-finished KDP crystal.

    PubMed

    Chen, Shaoshan; Li, Shengyi; Hu, Hao; Li, Qi; Tie, Guipeng

    2014-11-01

    A new nonaqueous and abrasive-free magnetorheological finishing (MRF) method is adopted for processing potassium dihydrogen phosphate (KDP) crystal due to its low hardness, high brittleness, temperature sensitivity, and water solubility. This paper researches the influence of structural characteristics on the surface roughness of MRF-finished KDP crystal. The material removal by dissolution is uniform layer by layer when the polishing parameters are stable. The angle between the direction of the polishing wheel's linear velocity and the initial turning lines will affect the surface roughness. If the direction is perpendicular to the initial turning lines, the polishing can remove the lines. If the direction is parallel to the initial turning lines, the polishing can achieve better surface roughness. The structural characteristic of KDP crystal is related to its internal chemical bonds due to its anisotropy. During the MRF finishing process, surface roughness will be improved if the structural characteristics of the KDP crystal are the same on both sides of the wheel. The processing results of (001) plane crystal show we can get the best surface roughness (RMS of 0.809 nm) if the directions of cutting and MRF polishing are along the (110) direction.

  18. Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

    2010-05-01

    Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

  19. Single-crystal growth, structure refinement and the properties of Bis(glycine) Strontium Chloride

    NASA Astrophysics Data System (ADS)

    Balaji, S. R.; Balu, T.; Rajasekaran, T. R.

    2018-02-01

    Single crystals of Bis (glycine) Strontium Chloride (BGSC) were grown by means of slow evaporation process by using analar grade Glycine and Strontium Chloride Hexahydrate as a parent compound from its aqueous solution at room temperature. The final chemical composition, [{{Sr}}{({{{C}}}2{{{H}}}5{{{NO}}}2)}2{{{Cl}}}2].{{{H}}}4{{{O}}}3+{{{H}}}8{{{O}}}3, formed were metallic light colorless block, about the size of 28 mm × 9 mm × 8 mm. A single-crystal x-ray diffraction study revealed an ordered superstructure with orthorhombic symmetry that could be assigned to the space group Pbcn. The structure in BGSC, revealed in the electron density distribution was analyzed by the direct methods (SHELXS-2014) and refined by least squares full matrix method (SHELXL-2014). The crystal structure, including anisotropic atomic displacement parameters for each atom and isotropic atomic displacement parameters for hydrogen atom, was refined to R1 = 0.0395, wR2 = 0.0776 using 1097 independent reflections. The FTIR spectrum of BGSC confirms the protonation of amino groups and the different molecular groups present in BGSC vibrate in different modes. Reverse Indentation Size Effect (RISE) was revealed in BGSC in the micro-hardness analysis using Vicker’s micro-hardness analysis. DTA and DSC results ruled out the possibility of structural change independent of mass change. The AFM studies shows fine nano size fiber like structure of the grown crystals.

  20. Crystal structure of a cocaine-binding antibody.

    PubMed

    Larsen, N A; Zhou, B; Heine, A; Wirsching, P; Janda, K D; Wilson, I A

    2001-08-03

    Murine monoclonal antibody GNC92H2 was elicited by active immunization with a cocaine immunoconjugate and binds free cocaine with excellent specificity and moderate affinity. Improvement of affinity, as well as humanization of GNC92H2, would be advantageous in immunopharmacotherapy for cocaine addiction, and for emergency cases of drug overdose. Toward this end, the crystal structure of an engineered murine-human chimeric Fab of GNC92H2 complexed with cocaine was determined at 2.3 A resolution. Structural analysis reveals a binding pocket with high shape and charge complementarity to the cocaine framework, which explains the specificity for cocaine, as opposed to the pharmacologically inactive cocaine metabolites. Importantly, the structure provides a foundation for mutagenesis to enhance the binding affinity for cocaine and potent cocaine derivatives, such as cocaethylene, and for additional humanization of the antibody. Copyright 2001 Academic Press.

  1. Structural differences between single crystal and polycrystalline UBe 13

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Volz, Heather Michelle; Vogel, Sven C.; Smith, Alice Iulia

    Here, we report on observations of structural and chemical differences between samples of UBe 13 that were synthesised using two different methods. Unexplained discrepancies in properties between samples with differing synthesis had previously been found in this heavy fermion superconductor. A polycrystalline UBe13 sample was made by arc-melting the constituents. Single crystals were grown using an aluminium flux and had a consistently slightly larger lattice parameter than the polycrystals, which merited further study. Neutron diffraction data were collected at the Lujan Center at LANSCE on the HIPPO diffractometer. Aluminium was detected by inductively coupled plasma mass spectrometry (ICP-MS) in themore » flux-grown single crystal (0.803 wt%), and small amounts (~0.2 wt%) of thorium were detected in the UBe 13 polycrystalline sample. In order to probe the implications of the presence of Al, calculations by spin-polarised DFT-GGA+U show that the incorporation of Al onto the 96i site (the lowest symmetry site in the structure) is energetically more favourable than on other sites. In general, the trends calculated by DFT for bond lengths and lattice parameter increases are consistent with bond lengths experimentally observed by neutron diffraction, but specific percentage changes with aluminium incorporation may be obscured by the unexpected thorium in the polycrystalline sample. The aggregate of our initial observations suggests that incorporation of aluminium from the flux into single crystal UBe 13 is significant.« less

  2. Structural differences between single crystal and polycrystalline UBe 13

    DOE PAGES

    Volz, Heather Michelle; Vogel, Sven C.; Smith, Alice Iulia; ...

    2018-05-16

    Here, we report on observations of structural and chemical differences between samples of UBe 13 that were synthesised using two different methods. Unexplained discrepancies in properties between samples with differing synthesis had previously been found in this heavy fermion superconductor. A polycrystalline UBe13 sample was made by arc-melting the constituents. Single crystals were grown using an aluminium flux and had a consistently slightly larger lattice parameter than the polycrystals, which merited further study. Neutron diffraction data were collected at the Lujan Center at LANSCE on the HIPPO diffractometer. Aluminium was detected by inductively coupled plasma mass spectrometry (ICP-MS) in themore » flux-grown single crystal (0.803 wt%), and small amounts (~0.2 wt%) of thorium were detected in the UBe 13 polycrystalline sample. In order to probe the implications of the presence of Al, calculations by spin-polarised DFT-GGA+U show that the incorporation of Al onto the 96i site (the lowest symmetry site in the structure) is energetically more favourable than on other sites. In general, the trends calculated by DFT for bond lengths and lattice parameter increases are consistent with bond lengths experimentally observed by neutron diffraction, but specific percentage changes with aluminium incorporation may be obscured by the unexpected thorium in the polycrystalline sample. The aggregate of our initial observations suggests that incorporation of aluminium from the flux into single crystal UBe 13 is significant.« less

  3. Crystal structure analysis of Great Cormorant (Phalacrocorax carbo) Hemoglobin.

    PubMed

    Ganapathy, Jagadeesan; Palayam, Malathy; Pennathur, Gautam; Sanmargam, Aravindhan; Krishnasamy, Gunasekaran

    2018-06-20

    Hemoglobin (Hb) molecule consists of α2β2 dimers arranged in fashion having pseudo-222 symmetry. The subunits are composed of the specific functional prosthetic group "heme'' and a protein moiety "globin". Bird Hbs are functionally similar to mammalian Hbs and regulated by inositol pentaphosphate (IPP) but they are structurally dissimilar with mammalian Hbs in adaptation to vital environment such as high altitudes, high speed flights and oxygen affinity. The insufficient structural studies on avian Hbs limit us to understand their degree of adaptation to such critical environments. So far, detailed structural studies of bar-headed goose (BHG) and graylag goose (GLG) Hb structures were reported to expose their remarkable difference in molecular level adaptation. The striking contrasts to its close relative the bar headed goose, which lives at high altitude and capable of tolerating severe hypoxic environment is mainly due its structural features. The Great Cormorant (GCT) can fly and swim, the dual characteristic of GCT leads to study the details of adaptation of high oxygen affinity in avian species and to know about the role of amino acid substitutions at α1β1 interface, the crystal structure of Great cormorant is studied. The structure of GCT Hb has been solved at 3.5Å resolution and it is compared with the other high oxygen affinity Hb (graylag goose (GLG), bar headed goose (BHG) and human (HMN) hemoglobin) structures. To determine the crystal structure of Great Cormorant (GCT) Hemoglobin and to compare its three dimensional structure with other high and low oxygen affinity hemoglobin species to understand its characteristic features of high oxygen affinity. The GCT hemoglobin has been purified, crystallized and data sets were processed using iMosflm. The integrated data has been solved using Molecular replacement method using Graylag hemoglobin (1FAW) as the template. The structure refinement has been carried out using Refmac which reduced the Rwork and

  4. TaRh2B2 and NbRh2B2: Superconductors with a chiral noncentrosymmetric crystal structure.

    PubMed

    Carnicom, Elizabeth M; Xie, Weiwei; Klimczuk, Tomasz; Lin, Jingjing; Górnicka, Karolina; Sobczak, Zuzanna; Ong, Nai Phuan; Cava, Robert J

    2018-05-01

    It is a fundamental truth in solid compounds that the physical properties follow the symmetry of the crystal structure. Nowhere is the effect of symmetry more pronounced than in the electronic and magnetic properties of materials-even the projection of the bulk crystal symmetry onto different crystal faces is known to have a substantial impact on the surface electronic states. The effect of bulk crystal symmetry on the properties of superconductors is widely appreciated, although its study presents substantial challenges. The effect of a lack of a center of symmetry in a crystal structure, for example, has long been understood to necessitate that the wave function of the collective electron state that gives rise to superconductivity has to be more complex than usual. However, few nonhypothetical materials, if any, have actually been proven to display exotic superconducting properties as a result. We introduce two new superconductors that in addition to having noncentrosymmetric crystal structures also have chiral crystal structures. Because the wave function of electrons in solids is particularly sensitive to the host material's symmetry, crystal structure chirality is expected to have a substantial effect on their superconducting wave functions. Our two experimentally obtained chiral noncentrosymmetric superconducting materials have transition temperatures to superconductivity that are easily experimentally accessible, and our basic property characterization suggests that their superconducting properties may be unusual. We propose that their study may allow for a more in-depth understanding of how chirality influences the properties of superconductors and devices that incorporate them.

  5. On the symmetry and crystal structures of Ba{sub 2}LaIrO{sub 6}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fu, W.T., E-mail: w.fu@chem.leidenuniv.n; Goetz, R.J.; IJdo, D.J.W.

    2010-02-15

    Accurate profile analysis of X-ray diffraction data was carried out to settle recent dispute on the symmetry and crystal structures of the double perovskite Ba{sub 2}LaIrO{sub 6}. Even through careful comparison of the full-width at half-maximum values, we found no evidence for Ba{sub 2}LaIrO{sub 6} adopting either monoclinic (I2/m) or mixed rhombohedral (R3-bar) and monoclinic (I2/m) structures at room temperature, becoming triclinic (I1-bar) at below about 200 K. The correct space group is just R3-bar at temperatures between 82 and 653 K. Furthermore, the R3-bar->Fm3-barm phase transition does occur in Ba{sub 2}LaIrO{sub 6}, but the transition temperature is found tomore » be much higher than the reported value. - Graphical abstract: Observed (crosses) and calculated (continuous line) profiles of Ba{sub 2}LaIrO{sub 6} at some selected temperature showing the region containing the basic (222), (321) and (400) reflections. Tick marks below indicate the positions of the allowed Bragg's reflections.« less

  6. Non-linear thermal evolution of the crystal structure and phase transitions of LaFeO{sub 3} investigated by high temperature X-ray diffraction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Selbach, Sverre M.; Tolchard, Julian R.; Fossdal, Anita

    2012-12-15

    The crystal structure, anisotropic thermal expansion and structural phase transition of the perovskite LaFeO{sub 3} has been studied by high-temperature X-ray diffraction from room temperature to 1533 K. The structural evolution of the orthorhombic phase with space group Pbnm and the rhombohedral phase with R3{sup Macron }c structure of LaFeO{sub 3} is reported in terms of lattice parameters, thermal expansion coefficients, atomic positions, octahedral rotations and polyhedral volumes. Non-linear lattice expansion across the antiferromagnetic to paramagnetic transition of LaFeO{sub 3} at T{sub N}=735 K was compared to the corresponding behavior of the ferroelectric antiferromagnet BiFeO{sub 3} to gain insight tomore » the magnetoelectric coupling in BiFeO{sub 3}, which is also multiferroic. The first order phase transition of LaFeO{sub 3} from Pbnm to R3{sup Macron }c was observed at 1228{+-}9 K, and a subsequent transition to Pm3{sup Macron }m was extrapolated to occur at 2140{+-}30 K. The stability of the Pbnm and R3{sup Macron }c polymorphs of LaFeO{sub 3} is discussed in terms of the competing enthalpy and entropy of the two crystal polymorphs and the thermal evolution of the polyhedral volume ratio V{sub A}/V{sub B}. - Graphical abstract: Aniostropic thermal evolution of the lattice parameters and phase transition of LaFeO{sub 3}. Highlights: Black-Right-Pointing-Pointer The crystal structure of LaFeO{sub 3} is studied by HTXRD from RT to 1533 K. Black-Right-Pointing-Pointer A non-linear expansion across the Neel temperature is observed for LaFeO{sub 3}. Black-Right-Pointing-Pointer The ratio V{sub A}/V{sub B} is used to rationalize the thermal evolution of the structure.« less

  7. Investigation of 2D photonic crystal structure based channel drop filter using quad shaped photonic crystal ring resonator for CWDM system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chhipa, Mayur Kumar, E-mail: mayurchhipa1@gmail.com; Dusad, Lalit Kumar; Rajasthan Technical University, Kota, Rajasthan

    In this paper, the design & performance of two dimensional (2-D) photonic crystal structure based channel drop filter is investigated using quad shaped photonic crystal ring resonator. In this paper, Photonic Crystal (PhC) based on square lattice periodic arrays of Gallium Indium Phosphide (GaInP) rods in air structure have been investigated using Finite Difference Time Domain (FDTD) method and photonic band gap is being calculated using Plane Wave Expansion (PWE) method. The PhC designs have been optimized for telecommunication wavelength λ= 1571 nm by varying the rods lattice constant. The number of rods in Z and X directions is 21 andmore » 20, with lattice constant 0.540 nm it illustrates that the arrangement of Gallium Indium Phosphide (GaInP) rods in the structure which gives the overall size of the device around 11.4 µm × 10.8 µm. The designed filter gives good dropping efficiency using 3.298, refractive index. The designed structure is useful for CWDM systems. This device may serve as a key component in photonic integrated circuits. The device is ultra compact with the overall size around 123 µm{sup 2}.« less

  8. Monoclinic crystal structure of α - RuCl 3 and the zigzag antiferromagnetic ground state

    DOE PAGES

    Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; ...

    2015-12-10

    We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, inmore » contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition

  9. Progress in thin-film silicon solar cells based on photonic-crystal structures

    NASA Astrophysics Data System (ADS)

    Ishizaki, Kenji; De Zoysa, Menaka; Tanaka, Yoshinori; Jeon, Seung-Woo; Noda, Susumu

    2018-06-01

    We review the recent progress in thin-film silicon solar cells with photonic crystals, where absorption enhancement is achieved by using large-area resonant effects in photonic crystals. First, a definitive guideline for enhancing light absorption in a wide wavelength range (600–1100 nm) is introduced, showing that the formation of multiple band edges utilizing higher-order modes confined in the thickness direction and the introduction of photonic superlattice structures enable significant absorption enhancement, exceeding that observed for conventional random scatterers. Subsequently, experimental evidence of this enhancement is demonstrated for a variety of thin-film Si solar cells: ∼500-nm-thick ultrathin microcrystalline silicon cells, few-µm-thick microcrystalline silicon cells, and ∼20-µm-thick thin single-crystalline silicon cells. The high short-circuit current densities and/or efficiencies observed for each cell structure confirm the effectiveness of using multiple band-edge resonant modes of photonic crystals for enhancing broadband absorption in actual solar cells.

  10. Highly Efficient and Simple Route to Synthesize N-(4-Acetylphenyl)-4-chlorobenzenesulfonamide and Its Crystal Structure

    NASA Astrophysics Data System (ADS)

    Kobkeatthawin, T.; Chantrapromma, S.; Chidan Kumar, C. S.; Fun, H.-K.

    2017-12-01

    The one-pot synthesis of N-(4-acetylphenyl)-4-chlorobenzenesulfonamide under base conditions is carried out. The present method offers several advantages such as excellent yields, short reaction times and high purity. The chemical structure was elucidated using 1H-NMR, FT-IR and UV-Vis spectroscopy. The crystal structure of the substance was determined by single crystal X-ray structure analysis. The molecule is in a V-shape. The two substituted benzene rings make the dihedral angle of 84.31(9)°. In the crystal packing, the molecules are linked by N-H···O and C-H···O hydrogen bonds into double chains along the b-axis. The crystal is further stabilized by weak C-H···O, C-Cl···π and π···π interactions.

  11. Protein crystal structure from non-oriented, single-axis sparse X-ray data

    DOE PAGES

    Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.; ...

    2016-01-01

    X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases

  12. Protein crystal structure from non-oriented, single-axis sparse X-ray data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.

    X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases

  13. Ultra-thin ZnSe: Anisotropic and flexible crystal structure

    NASA Astrophysics Data System (ADS)

    Bacaksiz, C.; Senger, R. T.; Sahin, H.

    2017-07-01

    By performing density functional theory-based calculations, we investigate the structural, electronic, and mechanical properties of the thinnest ever ZnSe crystal [11]. The vibrational spectrum analysis reveals that the monolayer ZnSe is dynamically stable and has flexible nature with its soft phonon modes. In addition, a direct electronic band gap is found at the gamma point for the monolayer structure of ZnSe. We also elucidate that the monolayer ZnSe has angle dependent in-plane elastic parameters. In particular, the in-plane stiffness values are found to be 2.07 and 6.89 N/m for the arm-chair and zig-zag directions, respectively. The angle dependency is also valid for the Poisson ratio of the monolayer ZnSe. More significantly, the in-plane stiffness of the monolayer ZnSe is the one-tenth of Young modulus of bulk zb-ZnSe which indicates that the monolayer ZnSe is a quite flexible single layer crystal. With its flexible nature and in-plane anisotropic mechanical properties, the monolayer ZnSe is a good candidate for nanoscale mechanical applications.

  14. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

  15. X-ray structure investigation of some substituted indoles, and the x-ray crystal of 1,1'-bishomocubane

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Quarles, William G.

    1970-05-01

    The crystal structures of 5-methoxytryptamine, melatonin, and the p-bromobenzoate of 1,1'-bishomocubane have been solved by x-ray diffraction methods. A computer program for the trial and error solution of crystal structures is also described here.

  16. Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels.

    PubMed

    Yamamoto, Masataka; Hayakawa, Naoki; Murakami, Midori; Kouyama, Tsutomu

    2009-10-30

    The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.

  17. Synthesis and crystal structure determination of yttrium ultraphosphate YP 5O 14

    NASA Astrophysics Data System (ADS)

    Mbarek, A.; Graia, M.; Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

    2009-03-01

    The crystal structure of monoclinic YP 5O 14 (space group C2/ c, a=12.919(2) Å, b=12.796(4) Å, c=12.457(2) Å, β=91.30(1)°, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F2 using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ( ωR=0.069). The structure is isotypic with HoP 5O 14. This structure is built up from infinite layers of PO 4 tetrahedra linked through isolated YO 8 polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu 3+ ion incorporated in the monoclinic C2/ c polymorph of YP 5O 14 as local structural probe show that in YP 5O 14: 5% Eu 3+ sample, the Eu 3+ ions are distributed over the two Y 3+ crystallographic sites of C 2 symmetry of this structure.

  18. Crystal structure and thermal expansion of a CsCe 2Cl 7 scintillator

    DOE PAGES

    Zhuravleva, M.; Lindsey, A.; Chakoumakos, B. C.; ...

    2015-04-06

    Here we used single-crystal X-ray diffraction data to determine crystal structure of CsCe 2Cl 7. It crystallizes in a P112 1/b space group with a = 19.352(1) Å, b = 19.352(1) Å, c = 14.838(1) Å, γ = 119.87(2) ° , and V = 4818.6(5) Å 3. Differential scanning calorimetry measurements combined with the structural evolution of CsCe 2Cl 7 via X-ray diffractometry over a temperature range from room temperature to the melting point indicates no obvious intermediate solid-solid phase transitions. The anisotropy in the average linear coefficient of thermal expansion of the a axis (21.3 10 -6/ °C) withmore » respect to the b and c axes (27.0 10 -6/ °C) was determined through lattice parameter refinement of the temperature dependent diffraction patterns. Lastly, these findings suggest that the reported cracking behavior during melt growth of CsCe 2Cl 7 bulk crystals using conventional Bridgman and Czochralski techniques may be largely attributed to the anisotropy in thermal expansion.« less

  19. Ge K-Edge Extended X-Ray Absorption Fine Structure Study of the Local Structure of Amorphous GeTe and the Crystallization

    NASA Astrophysics Data System (ADS)

    Maeda, Yoshihito; Wakagi, Masatoshi

    1991-01-01

    The local structure and crystallization of amorphous GeTe (a-GeTe) were examined by means of Ge K-edge EXAFS. In a-GeTe, both Ge-Ge and Ge-Te bonds were observed to exist in nearest neighbors of Ge. The average coordination number around Ge is 3.7, which is close to the tetrahedral structure. A random covalent network (RCN) model seems to be suitable for the local Structure. After a-GeTe crystallizes at 129°C, the Ge-Ge bond disappears and the Ge-Te bond length increases considerably. As temperature rises, in a-GeTe the Debye-Waller factor of the Ge-Te bond increases greatly, while that of the Ge-Ge bond increases only slightly. At the crystallization, it is found that the fluctuation of the Ge-Te bond length plays a major role in the change of the local structure and bonding state around Ge.

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

    PubMed Central

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  1. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

  2. Studies on the growth, structural, optical, mechanical properties of 8-hydroxyquinoline single crystal by vertical Bridgman technique

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Prabhakaran, SP.; Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in; Velusamy, P.

    2011-11-15

    Highlights: {yields} Growth of bulk single crystal of 8-hydroxyquinoline (8-HQ) by vertical Bridgman technique for the first time. {yields} The crystalline perfection is reasonably good. {yields} The photoluminescence spectrum shows that the material is suitable for blue light emission. -- Abstract: Single crystal of organic nonlinear optical material, 8-hydroxyquinoline (8-HQ) of dimension 52 mm (length) x 12 mm (dia.) was grown from melt using vertical Bridgman technique. The crystal system of the material was confirmed by powder X-ray diffraction analysis. The crystalline perfection of the grown crystal was examined by high-resolution X-ray diffraction study. Low angular spread around 400'' ofmore » the diffraction curve and the low full width half maximum values show that the crystalline perfection is reasonably good. The recorded photoluminescence spectrum shows that the material is suitable for blue light emission. Optical transmittance for the UV and visible region was measured and mechanical strength was estimated from Vicker's microhardness test along the growth face of the grown crystal.« less

  3. Magnetic and Crystal Structure of α-RuCl3

    NASA Astrophysics Data System (ADS)

    Sears, Jennifer

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

  4. Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank

    PubMed Central

    Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

    2010-01-01

    Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution. PMID:21293729

  5. Niobium hyperfine structure in crystal calcium tungstate

    NASA Technical Reports Server (NTRS)

    Tseng, D. L.; Kikuchi, C.

    1972-01-01

    A study of the niobium hyperfine structure in single crystal calcium tungstate was made by the combination of the technique of electron paramagnetic resonance and electron nuclear double resonance (EPR/ENDOR). The microwave frequency was about 9.4 GHz and the radio frequency from 20MHz to 70 MHz. The rare earth ions Nd(3+), U(3+), or Tm(3+) were added as the charge compensator for Nb(5+). To create niobium paramagnetic centers, the sample was irradiated at 77 deg K with a 10 thousand curie Co-60 gamma source for 1 to 2 hours at a dose rate of 200 K rads per hour and then transferred quickly into the cavity. In a general direction of magnetic field, the spectra showed 4 sets of 10 main lines corresponding to 4 nonequivalent sites of niobium with I = 9/2. These 4 sets of lines coalesced into 2 sets of 10 in the ab-plane and into a single set of 10 along the c-axis. This symmetry suggested that the tungsten ions are substituted by the niobium ions in the crystal.

  6. Crystal and Magnetic Structures in Layered, Transition Metal Dihalides and Trihalides

    DOE PAGES

    McGuire, Michael A.

    2017-04-27

    Materials composed of two dimensional layers bonded to one another through weak van der Waals interactions often exhibit strongly anisotropic behaviors and can be cleaved into very thin specimens and sometimes into monolayer crystals. Interest in such materials is driven by the study of low dimensional physics and the design of functional heterostructures. Binary compounds with the compositions MX 2 and MX 3 where M is a metal cation and X is a halogen anion often form such structures. Magnetism can be incorporated by choosing a transition metal with a partially filled d-shell for M, enabling ferroic responses for enhancedmore » functionality. Here we give a brief overview of binary transition metal dihalides and trihalides, summarizing their crystallographic properties and long-range-ordered magnetic structures, focusing on those materials with layered crystal structures and partially filled d-shells required for combining low dimensionality and cleavability with magnetism.« less

  7. Rapid crystallization and morphological adjustment of zeolite ZSM-5 in nonionic emulsions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang Ying, E-mail: yingzh1977@163.co; Jin Chao; Research Institute of Petroleum Processing, Beijing 100083

    2011-01-15

    Zeolite ZSM-5 was synthesized for the first time in a nonionic emulsion composed of polyoxyethylated alkylphenol, butanol, cyclohexane and tetraethylammonium hydroxide (TEAOH)-containing zeolite synthesis mixture. The crystallization kinetics in the emulsion was investigated and the ZSM-5 product was characterized in detail by XRD, SEM, FT-IR, TG, N{sub 2} adsorption and CHN analysis techniques. Compared with the conventionally hydrothermal synthesis with the same structure directing agent TEAOH, the emulsion system allows rapid crystallization of ZSM-5. The ZSM-5 product exhibits unusual agglomerated structure and possesses larger specific surface area. The FT-IR, TG results plus CHN analysis show the encapsulation of a tracemore » of emulsion components in the emulsion ZSM-5. Control experiments show the emulsion system exerts the crystallization induction and morphological adjustment effects mainly during the aging period. The effects are tentatively attributed to the confined space domains, surfactant-water interaction as well as surfactant-growing crystals interaction existing in the emulsion. -- Graphical abstract: The nonionic emulsion synthesis allows rapid crystallization and morphological adjustment of zeolite ZSM-5 compared with the conventional hydrothermal synthesis. Display Omitted« less

  8. Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

    PubMed Central

    Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.; Polikarpov, Igor

    2016-01-01

    Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues. PMID:27050262

  9. Amplified Emission and Field-Effect Transistor Characteristics of One-Dimensionally Structured 2,5-Bis(4-biphenylyl)thiophene Crystals.

    PubMed

    Hashimoto, Kazumasa; Sasaki, Fumio; Hotta, Shu; Yanagi, Hisao

    2016-04-01

    One-dimensional (1D) structures of 2,5-bis(4-biphenylyl)thiophene (BP1T) crystals are fabricated for light amplification and field-effect transistor (FET) measurements. A strip-shaped 1D structure (10 µm width) made by photolitography of a vapor-deposited polycrystalline film shows amplified spontaneous emission and lasing oscillations under optical pumping. An FET fabricated with this 1D structure exhibits hole-conduction with a mobility of µh = 8.0 x 10(-3) cm2/Vs. Another 1 D-structured FET is fabricated with epitaxially grown needle-like crystals of BP1T. This needle-crystal FET exhibits higher mobility of µh = 0.34 cm2/Vs. This improved hole mobility is attributed to the single-crystal channel of epitaxial needles while the grain boudaries in the polycrystalline 1 D-structure decrease the carrier transport.

  10. Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

    PubMed

    Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

    2014-12-11

    The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

  11. OsN2: Crystal structure and electronic properties

    NASA Astrophysics Data System (ADS)

    Montoya, Javier A.; Hernandez, Alexander D.; Sanloup, Chrystèle; Gregoryanz, Eugene; Scandolo, Sandro

    2007-01-01

    Osmium nitride belongs to a family of nitrides synthesized recently at high pressures from their parent elements. Here we show, based on first-principles calculations, that the crystal structure of osmium nitride is isostructural to marcasite. Excellent agreement is obtained between the authors' results and x-ray, Raman, and compressibility measurements. In the OsN2 marcasite structure single-bonded N2 units occupy the interstitial sites of the Os close-packed lattice, giving rise to a metallic compound. A comparison between the formation energies of OsN2 and PtN2 explains the similar thermodynamic conditions of formation reported experimentally for the two compounds.

  12. Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Radka, Christopher D.; DeLucas, Lawrence J.; Wilson, Landon S.

    2017-06-30

    Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. InYersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA ismore » polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.« less

  13. Crystal Structure of an L-Carnitine Complex with Pyrogallol[4]arene

    NASA Astrophysics Data System (ADS)

    Fujisawa, I.; Takeuchi, D.; Kitamura, Y.; Okamoto, R.; Aoki, K.

    2012-03-01

    L-Carnitine is essential for the transport of long-chain fatty acids from cytosol into mitochondria for generating metabolic energy. The survey of crystal structures of carnitine-containing proteins in the Protein Data Bank reveals that carnitine can take several conformations with the quarternary trimethylammonium terminal being always bound to aromatic residues through cation-π interactions in acyltransferases or carnitine-binding proteins. In order to demonstrate the importance of cation-π interaction as a carnitine recognition mechanism in the artificial receptor-ligand system that mimics the carnitine-binding sites, we have determined the crystal structure of a complex formed between L-carnitine and pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT) as a carnitine receptor, 2PCT·2(L-carnitine)·4EtOH. There form two crystallographically independent monomeric [PCT·L-carnitine] substructures, which further form an obliquely arranged capsule-like dimeric [PCT·L-carnitine]2 structure through a pair of O-H (PCT)···O (L-carnitine) hydrogen bonds. This is the first report of PCT complex with chiral molecules. In each of the two monomeric [PCT·L-carnitine] substructures, the L-carnitine molecule takes the elongated form with an intramolecular hydrogen bond between the hydroxyl group and the carboxylate oxygen, and the cationic trimethylammonium moiety is incorporated into the cavity of the bowl-shaped PCT molecule through cation-π interactions. These features are similar to those at the D-carnitine-binding site in the crystal structure of the glycine betaine/carnitine/choline-binding protein complex.

  14. Surface Structure Spread Single Crystals (S4C): Preparation and characterization

    NASA Astrophysics Data System (ADS)

    de Alwis, A.; Holsclaw, B.; Pushkarev, V. V.; Reinicker, A.; Lawton, T. J.; Blecher, M. E.; Sykes, E. C. H.; Gellman, A. J.

    2013-02-01

    A set of six spherically curved Cu single crystals referred to as Surface Structure Spread Single Crystals (S4Cs) has been prepared in such a way that their exposed surfaces collectively span all possible crystallographic surface orientations that can be cleaved from the face centered cubic Cu lattice. The method for preparing these S4Cs and for finding the high symmetry pole point is described. Optical profilometry has been used to determine the true shapes of the S4Cs and show that over the majority of the surface, the shape is extremely close to that of a perfect sphere. The local orientations of the surfaces lie within ± 1° of the orientation expected on the basis of the spherical shape; their orientation is as good as that of many commercially prepared single crystals. STM imaging has been used to characterize the atomic level structure of the Cu(111) ± 11°-S4C. This has shown that the average step densities and the average step orientations match those expected based on the spherical shape. In other words, although there is some distribution of step-step spacing and step orientations, there is no evidence of large scale reconstruction or faceting. The Cu S4Cs have local structures based on the ideal termination of the face centered cubic Cu lattice in the direction of termination. The set of Cu S4Cs will serve as the basis for high throughput investigations of structure sensitive surface chemistry on Cu.

  15. The structural and content aspects of abstracts versus bodies of full text journal articles are different

    PubMed Central

    2010-01-01

    Background An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research. Results We examined the structural and linguistic aspects of abstracts and bodies of full text articles, the performance of text mining tools on both, and the distribution of a variety of semantic classes of named entities between them. We found marked structural differences, with longer sentences in the article bodies and much heavier use of parenthesized material in the bodies than in the abstracts. We found content differences with respect to linguistic features. Three out of four of the linguistic features that we examined were statistically significantly differently distributed between the two genres. We also found content differences with respect to the distribution of semantic features. There were significantly different densities per thousand words for three out of four semantic classes, and clear differences in the extent to which they appeared in the two genres. With respect to the performance of text mining tools, we found that a mutation finder performed equally well in both genres, but that a wide variety of gene mention systems performed much worse on article bodies than they did on abstracts. POS tagging was also more accurate in abstracts than in article bodies. Conclusions Aspects of structure and content differ markedly between article abstracts and article bodies. A number of these differences may pose problems as the text mining field moves more into the area of processing full-text articles. However, these differences also present a number of opportunities for the extraction of data types, particularly that found in parenthesized text

  16. Characterization of molecular associations involving L-ornithine and α-ketoglutaric acid: crystal structure of L-ornithinium α-ketoglutarate.

    PubMed

    Allouchi, H; Céolin, R; Berthon, L; Tombret, F; Rietveld, I B

    2014-07-01

    The crystal structure of L-ornithinium α-ketoglutarate (C5H13N2O2, C5H5O5) has been solved by direct methods using single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group P21, unit cell parameters a=15.4326(3), b=5.2015(1), c=16.2067(3) Å and β=91.986(1)°, containing two independent pairs of molecular ions in the asymmetric unit. An extensive hydrogen-bond network and electrostatic charges due to proton transfer provide an important part of the cohesive energy of the crystal. The conformational versatility of L-ornithine and α-ketoglutaric acid is illustrated by the present results and crystal structures available from the Cambridge Structural Database. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  17. Na3Tb(PO4)2: Synthesis, crystal structure and greenish emitting properties

    NASA Astrophysics Data System (ADS)

    Zhao, Dan; Ma, Zhao; Liu, Bao-Zhong; Zhang, Rui-Juan; Wu, Zhi-Qiang; Wang, Jian; Duan, Pei-Gao

    2018-03-01

    A anhydrous orthoborate Na3Tb(PO4)2 has been prepared and its crystal structure was determined by X-Ray diffraction of a non-merohedral twinned single crystal. The results show that the compound crystallizes in monoclinic space group C2/c and the structure features a 3D framework containing PO4, NaO6, NaO7, NaO8 and TbO8 polyhedra. Under near-UV excitation (370 nm), Na3Tb(PO4)2 shows intense characteristic emission bands of Tb3+ (490 nm, 543 nm, 585 nm and 620 nm) with the CIE coordinate of (0.3062, 0.5901), corresponding to greenish color. The excitation spectrum covers a wide range from 340 nm to 390 nm, which indicates that phosphor Na3Tb(PO4)2 can be efficiently activated by near-UV LED ship.

  18. Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

    NASA Astrophysics Data System (ADS)

    Hu, Changjun; Bai, He; He, Xinfu; Zhang, Boyao; Nie, Ningming; Wang, Xianmeng; Ren, Yingwen

    2017-02-01

    Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

  19. Structure of the toxic core of α-synuclein from invisible crystals

    DOE PAGES

    Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.; ...

    2015-09-09

    We report that the protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates thatmore » this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. Finally, the NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.« less

  20. Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

    NASA Astrophysics Data System (ADS)

    Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

    2017-05-01

    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

  1. The synthesis and crystal structure of α-Ca 3UO 6

    NASA Astrophysics Data System (ADS)

    Holc, J.; Golic̆, L.

    1983-07-01

    Single crystals of α-Ca 3UO 6 were grown from a UO 3CaCl 2CaO melt by the slow cooling method from 950°C. The crystal structure was determined by means of X-ray diffraction with R = 0.032 and Rw = 0.019. The structure of α-Ca 3UO 6 is of Mg 3TeO 6 type. α-Ca 3UO 6 is rhombohedral with a = 6.729 (1)Å, α = 90.30 (1)°, Z = 2, Dc = 4.955 g/cm 3, Dm = 4.79 g/cm 3, space group R overline3. Uranium and calcium atoms are six-coordinated. At 1200°C rhombohedral α-Ca 3UO 6 irreversibly transforms to monoclinic β-Ca 3UO 6.

  2. Crystal structures, in-silico study and anti-microbial potential of synthetic monocarbonyl curcuminoids

    NASA Astrophysics Data System (ADS)

    Ud Din, Zia; Serrano, N. F. G.; Ademi, Kastriot; Sousa, C. P.; Deflon, Victor Marcelo; Maia, Pedro Ivo da Silva; Rodrigues-Filho, Edson

    2017-09-01

    In this work the screening of 20 unsymmetrical chalcone and curcuminoids analogues in regard of their antimicrobial properties was conducted. Electron donating groups in the aromatic rings in the chalcone and curcuminoid derivatives produced higher antimicrobial effect. Compounds 1, 9 and 15 exhibited good activity against Escherichia coli and Staphylococcus aureus. These compounds were further evaluated against nine micro-organisms of pathological interest. Pharmmaper was used for target fishing of compounds against important bacterial targets. Molecular Docking helped to verify the results of these compounds against the selected bacterial target D-alanyl-D-alanine carboxypeptidase (PDB ID: 1PW1). The crystal structure of ligand and docked conformers in the active site of 1PW1 were analyzed. As a result structure-activity relationships are proposed. Structures of compounds 14 and 16 were obtained through single crystals X-ray diffraction studies. Compound 14 crystallizes in monoclinic space group P21/c with unit cell dimensions a = 13.1293(3) Å, b = 17.5364(4) Å, c = 15.1433(3) Å, β = 95.6440(10), V = 3469.70(13) Å3 and Z = 8. Compound 16 crystallizes in triclinic space group Pī with unit cell dimensions a = 6.8226(4) Å, b = 7.2256(4) Å, c = 18.1235(12) Å, β = 87.322(4), V = 850.57(9) Å3 and Z = 2.

  3. Structure, dynamics and bifurcations of discrete solitons in trapped ion crystals

    NASA Astrophysics Data System (ADS)

    Landa, H.; Reznik, B.; Brox, J.; Mielenz, M.; Schaetz, T.

    2013-09-01

    We study discrete solitons (kinks) accessible in the state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-three-dimensional configurations, both theoretically and experimentally. We first extend the theoretical understanding of different phenomena predicted and recently experimentally observed in the structure and dynamics of these topological excitations. Employing tools from topological degree theory, we analyze bifurcations of crystal configurations in dependence on the trapping parameters, and investigate the formation of kink configurations and the transformations of kinks between different structures. This allows us to accurately define and calculate the effective potential experienced by solitons within the Wigner crystal, and study how this (so-called Peierls-Nabarro) potential gets modified to a non-periodic globally trapping potential in certain parameter regimes. The kinks' rest mass (energy) and spectrum of modes are computed and the dynamics of linear and nonlinear kink oscillations are analyzed. We also present novel, experimentally observed, configurations of kinks incorporating a large-mass defect realized by an embedded molecular ion, and of pairs of interacting kinks stable for long times, offering the perspective for exploring and exploiting complex collective nonlinear excitations, controllable on the quantum level.

  4. Crystal structure of a two-subunit TrkA octameric gating ring assembly

    DOE PAGES

    Deller, Marc C.; Johnson, Hope A.; Miller, Mitchell D.; ...

    2015-03-31

    The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K⁺ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K⁺ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K⁺ ions acrossmore » the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K⁺ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K⁺ gating ring assemblies.« less

  5. Crystal structure of the mutant D52S hen egg white lysozyme with an oligosaccharide product.

    PubMed

    Hadfield, A T; Harvey, D J; Archer, D B; MacKenzie, D A; Jeenes, D J; Radford, S E; Lowe, G; Dobson, C M; Johnson, L N

    1994-11-11

    The crystal structure of a mutant hen egg white lysozyme, in which the key catalytic residue aspartic acid 52 has been changed to a serine residue (D52S HEWL), has been determined and refined to a crystallographic R value of 0.173 for all data F > 0 between 8 and 1.9 A resolution. The D52S HEWL structure is very similar to the native HEWL structure (r.m.s. deviation of main-chain atoms 0.20 A). Small shifts that result from the change in hydrogen bonding pattern on substitution of Asp by Ser were observed in the loop between beta-strands in the region of residues 46 to 49. D52S HEWL exhibits less than 1% activity against the bacterial cell wall substrate. Cocrystallisation experiments with the hexasaccharide substrate beta(1-4) polymer of N-acetyl-D-glucosamine (GlcNAc6) resulted in crystals between 5 days and 14 days after the initial mixing of enzyme and substrate. Analysis by laser absorption mass spectrometry of the oligosaccharides present after incubation with native and D52S HEWL under conditions similar to those used for crystal growth showed that after 14 days with native HEWL complete catalysis to GlcNAc3. GlcNAc2 and GlcNac had occurred but with D52S HEWL only partial catalysis to the major products GlcNAc4 and GlcNAc2 had occurred and at least 50% of the GlcNAc6 remained intact. X-ray analysis of the D52S-oligosaccharide complex crystals showed that they contained the product GlcNAc4. The structure of the D52S HEWL-GlcNAc4 complex has been determined and refined to an R value of 0.160 for data between 8 and 2 A resolution. GlcNAc4 occupies sites A to D in the active site cleft. Careful refinement and examination of 2Fo-Fc electron density maps showed that the sugar in site D has the sofa conformation, a conformation previously observed with the HEWL complex with tetra-N-acetylglucosamine lactone transition state analogue, the HEWL complex with the cell wall trisaccharide and the phage T4 lysozyme complex with a cell wall product. The semi-axial C(5)-C(6

  6. Abstracts, Third Space Processing Symposium, Skylab results

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Skylab experiments results are reported in abstracts of papers presented at the Third Space Processing Symposium. Specific areas of interest include: exothermic brazing, metals melting, crystals, reinforced composites, glasses, eutectics; physics of the low-g processes; electrophoresis, heat flow, and convection demonstrations flown on Apollo missions; and apparatus for containerless processing, heating, cooling, and containing materials.

  7. Clay Mineral Crystal Structure Tied to Composition

    NASA Image and Video Library

    2016-12-13

    This diagram illustrates how the dimensions of clay minerals' crystal structure are affected by which ions are present in the composition of the mineral. Different clay minerals were identified this way at two sites in Mars' Gale Crater: "Murray Buttes" and "Yellowknife Bay." In otherwise identical clay minerals, a composition that includes aluminum and ferric iron ions (red dots) results in slightly smaller crystalline unit cells than one that instead includes magnesium and ferrous iron ions (green dots). Ferric iron is more highly oxidized than ferrous iron. Crystalline cell units are the basic repeating building blocks that define minerals. X-ray diffraction analysis, a capability of the Chemistry and Mineralogy (CheMin) instrument on NASA's Curiosity Mars rover, identifies minerals from their crystalline structure. http://photojournal.jpl.nasa.gov/catalog/PIA21148

  8. Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

    NASA Astrophysics Data System (ADS)

    Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

    2018-04-01

    The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

  9. ‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

    PubMed Central

    Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

    2015-01-01

    The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

  10. Relationship between mechanical properties and crystal structure in cocrystals and salt of paracetamol.

    PubMed

    Ahmed, Hamzah; Shimpi, Manishkumar R; Velaga, Sitaram P

    2017-01-01

    Objectives were to study mechanical properties of various solid forms of paracetamol and relate to their crystal structures. Paracetamol form I (PRA), its cocrystals with oxalic acid (PRA-OXA) and 4,4-bipyridine (PRA-BPY) and hydrochloride salt (PRA-HCL) were selected. Cocrystals and salt were scaled-up using rational crystallization methods. The resulting materials were subjected to different solid-state characterizations. The powders were sieved and 90-360 µm sieve fraction was considered. These powders were examined by scanning electron microscopy (SEM) and densities were determined. Tablets were made at applied pressures of 35-180 MPa under controlled conditions and the tablet height, diameter and hardness were measured. Tensile strength and porosity of the tablets were estimated using well known models. Crystal structures of these systems were visualized and slip planes were identified. Cocrystal and salt of PRA were physically pure. Sieved powders had comparable morphologies and particle size. The apparent and theoretical densities of powders were similar, but no clear trends were observed. The tensile strengths of these compacts were increased with increasing pressure whereas tabletability decreased in the order oxalic acid > PRA-HCL ≈ PRA-OXA > BPY > PRA-BPY. Tablet tensile strength decreases exponentially with increasing porosity with the exception of PRY-BPY and BPY. Slip plane prediction based on attachment energies may not be independently considered. However, it was possible to explain the improved mechanical properties of powders based on the crystal structure. Cocrystallization and salt formation have introduced structural features that are responsible for improved tableting properties of PRA.

  11. Purification and Bicelle Crystallization for Structure Determination of the E. coli Outer Membrane Protein TamA.

    PubMed

    Gruss, Fabian; Hiller, Sebastian; Maier, Timm

    2015-01-01

    TamA is an Omp85 protein involved in autotransporter assembly in the outer membrane of Escherichia coli. It comprises a C-terminal 16-stranded transmembrane β-barrel as well as three periplasmic POTRA domains, and is a challenging target for structure determination. Here, we present a method for crystal structure determination of TamA, including recombinant expression in E. coli, detergent extraction, chromatographic purification, and bicelle crystallization in combination with seeding. As a result, crystals in space group P21212 are obtained, which diffract to 2.3 Å resolution. This protocol also serves as a template for structure determination of other outer membrane proteins, in particular of the Omp85 family.

  12. A first principles prediction of the crystal structure of C6Br2ClFH2

    NASA Astrophysics Data System (ADS)

    Misquitta, Alston J.; Welch, Gareth W. A.; Stone, Anthony J.; Price, Sarah L.

    2008-04-01

    We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-fluorobenzene molecule from first principles using SAPT(DFT) interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of CBrClFH and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.

  13. Specific Features of the Domain Structure of BaTiO3 Crystals during Thermal Heating and Cooling

    NASA Astrophysics Data System (ADS)

    Kiselev, D. A.; Ilina, T. S.; Malinkovich, M. D.; Sergeeva, O. N.; Bolshakova, N. N.; Semenova, E. M.; Kuznetsova, Yu. V.

    2018-04-01

    This paper presents the results of the study of the domain structure of barium titanate crystals in a wide temperature range including the Curie point ( T C) using the polarization-optical method in the reflected light and the force microscopy of the piezoelectric response. It is shown that a new a-c domain structure forms during cyclic heating of the crystal above T C and subsequent cooling to the ferroelectric phase. The role of uncompensated charges appeared on the crystal surface during the phase transition and their influence on the formation of the domain structure during cooling are discussed.

  14. The magnetic and crystal structures of Sr2IrO4: A neutron diffraction study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ye, Feng; Chi, Songxue; Chakoumakos, Bryan C

    2013-01-01

    We report a single-crystal neutron diffraction study of the layered Sr2IrO4. This work unambigu- ously determines the magnetic and crystal structures, and reveals that the spin orientation rigidly tracks the staggered rotation of the IrO6 octahedra in Sr2IrO4. The long-range antiferromagnetic order has a canted spin configuration with an ordered moment of 0.208(3) B/Ir site within the basal plane; a detailed examination of the spin canting yields 0.202(3) and 0.049(2) B/site for the a-axis and the b-axis, respectively. It is intriguing that forbidden nuclear reflections of space group I41/acd are also observed in a wide temperature range from 4 Kmore » to 600 K, which suggests a reduced crystal structure symmetry. This neutron scattering work provides a direct, well-refined experimen- tal characterization of the magnetic and crystal structures that are crucial to the understanding of the unconventional magnetism existent in this unusual magnetic insulator.« less

  15. Crystal structure and biochemical characterization of beta-keto thiolase B from polyhydroxyalkanoate-producing bacterium Ralstonia eutropha H16

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Eun-Jung; Son, Hyeoncheol Francis; Kim, Sangwoo

    Highlights: • We determined a crystal structure of β-keto thiolase from Ralstonia eutropha H16 (ReBktB). • Distinct substrate binding mode ReBktB was elucidated. • Enzymatic kinetic parameters of ReBktB were revealed. - Abstract: ReBktB is a β-keto thiolase from Ralstonia eutropha H16 that catalyzes condensation reactions between acetyl-CoA with acyl-CoA molecules that contains different numbers of carbon atoms, such as acetyl-CoA, propionyl-CoA, and butyryl-CoA, to produce valuable bioproducts, such as polyhydroxybutyrate, polyhydroxybutyrate-hydroxyvalerate, and hexanoate. We solved a crystal structure of ReBktB at 2.3 Å, and the overall structure has a similar fold to that of type II biosynthetic thiolases, suchmore » as PhbA from Zoogloea ramigera (ZrPhbA). The superposition of this structure with that of ZrPhbA complexed with CoA revealed the residues that comprise the catalytic and substrate binding sites of ReBktB. The catalytic site of ReBktB contains three conserved residues, Cys90, His350, and Cys380, which may function as a covalent nucleophile, a general base, and second nucleophile, respectively. For substrate binding, ReBktB stabilized the ADP moiety of CoA in a distinct way compared to ZrPhbA with His219, Arg221, and Asp228 residues, whereas the stabilization of β-mercaptoethyamine and pantothenic acid moieties of CoA was quite similar between these two enzymes. Kinetic study of ReBktB revealed that K{sub m}, V{sub max}, and K{sub cat} values of 11.58 μM, 1.5 μmol/min, and 102.18 s{sup −1}, respectively, and the catalytic and substrate binding sites of ReBktB were further confirmed by site-directed mutagenesis experiments.« less

  16. High-throughput crystallization screening.

    PubMed

    Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

    2014-01-01

    Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

  17. Crystal structure and chemical bonding in the mixed anion compound BaSF.

    PubMed

    Driss, D; Cadars, S; Deniard, P; Mevellec, J-Y; Corraze, B; Janod, E; Cario, L

    2017-11-28

    BaSF was synthesised by a solid state reaction at high temperature and its crystal structure was determined thanks to X-ray diffraction on a single crystal. This transparent yellow fluorochalcogenide has an intergrowth structure built from the stacking of fluorite type layers and sulfur layers. In BaSF sulfur atoms form dimers with interatomic distances as short as 2.1074(10) Å. DFT calculations confirm that this compound is a band insulator with the Fermi level lying in between the antibonding π* and σ* molecular orbitals of the sulfur dimers. Reflectance measurements show that the optical band gap of BaSF is about 2.7 eV in good agreement with the value found from DFT calculations.

  18. Structural, optical, mechanical and dielectric studies of pure and doped L-Prolinium trichloroacetate single crystals.

    PubMed

    Renuka, N; Ramesh Babu, R; Vijayan, N; Vasanthakumar, Geetha; Krishna, Anuj; Ramamurthi, K

    2015-02-25

    In the present work, pure and metal substituted L-Prolinium trichloroacetate (LPTCA) single crystals were grown by slow evaporation method. The grown crystals were subjected to single crystal X-ray diffraction (XRD), powder X-ray diffraction, FTIR, UV-Visible-NIR, hardness, photoluminescence and dielectric studies. The dopant concentration in the crystals was measured by inductively coupled plasma (ICP) analysis. Single crystal X-ray diffraction studies of the pure and metal substituted LPTCA revealed that the grown crystals belong to the trigonal system. Ni(2+) and Co(2+) doping slightly altered the lattice parameters of LPTCA without affecting the basic structure of the crystal. FTIR spectral analysis confirms the presence of various functional groups in the grown crystals. The mechanical behavior of pure and doped crystals was analyzed by Vickers's microhardness test. The optical transmittance, dielectric and photoluminescence properties of the pure and doped crystals were analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Crystal structure, conformational analysis, and molecular dynamics of tetra-0-methyl-(+)-catechin

    Treesearch

    Frank R. Fronczek; Richard W. Hemingway; G. Wayne McGraw; Jan P. Steynberg; Carin A. Helfer; Wayne L. Mattice

    1993-01-01

    The structure of tetra-O-methyl-(+)-catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1, a=4.8125(2) Ǻ, b=12.9148(8) Ǻ, c=13.8862(11) Ǻ, α=86.962(6)°, β=89.120(5)°, γ=...

  20. The perfection and defect structure of organic hourglass inclusion K 2SO 4 crystals

    NASA Astrophysics Data System (ADS)

    Vetter, William M.; Totsuka, Hirono; Dudley, Michael; Kahr, Bart

    2002-06-01

    Hourglass inclusion crystals of K 2SO 4 were grown from aqueous solutions containing the dye acid fuchsin, and studied by synchrotron white-beam X-ray topography and reciprocal space mapping. Both self-nucleated and larger, seeded dye-included crystals were prepared, as well as comparable undoped crystals. While the dye modified the crystals' habit strongly, X-ray topographs showed it had no influence on their dislocation configurations, which were typical for solution-grown crystals. No kinematical contrast arising from the presence of the dye was observed that indicated dye-induced strain in the crystal lattice. Growth sector boundaries were visible in the dyed crystals but not in undoped crystals, implying there was a slightly higher lattice mismatch across growth sector boundaries in the dye-included crystals. Reciprocal space maps of small areas on an hourglass inclusion crystal within either a dye-included growth sector or an undoped growth sector showed single peaks with the same perfect crystal rocking curve width and no dilatation or tilt of the host lattice resulting from the dye's presence. These results showed hourglass inclusion crystals can be grown in which the presence of the dye disturbs the crystalline structure of the host salt minimally, and that hourglass inclusions have the nature of a solid solution.

  1. Editors' Introduction: Abstract Concepts: Structure, Processing, and Modeling.

    PubMed

    Bolognesi, Marianna; Steen, Gerard

    2018-06-22

    Our ability to deal with abstract concepts is one of the most intriguing faculties of human cognition. Still, we know little about how such concepts are formed, processed, and represented in mind. For example, because abstract concepts do not designate referents that can be experienced through our body, the role of perceptual experiences in shaping their content remains controversial. Current theories suggest a variety of alternative explanations to the question of "how abstract concepts are represented in the human mind." These views pinpoint specific streams of semantic information that would play a prominent role in shaping the content of abstract concepts, such as situation-based information (e.g., Barsalou & Wiemer-Hastings, ), affective information (Kousta, Vigliocco, Vinson, Andrews, & Del Campo, ), and linguistic information (Louwerse, ). Rarely, these theoretical views are directly compared. In this special issue, current views are presented in their most recent and advanced form, and directly compared and discussed in a debate, which is reported at the end of each article. As a result, new exciting questions and challenges arise. These questions and challenges, reported in this introductory article, can arguably pave the way to new empirical studies and theoretical developments on the nature of abstract concepts. © 2018 Cognitive Science Society, Inc.

  2. Synthesis, growth, structural and optical studies of a novel organic Piperazine (bis) p-toluenesulfonate single crystal.

    PubMed

    Rekha, P; Peramaiyan, G; NizamMohideen, M; Kumar, R Mohan; Kanagadurai, R

    2015-03-15

    A novel organic single crystal of Piperazinium (bis) p-toluenesulfonate (PPTS) was grown by a slow evaporation solution growth technique. The structure of the grown crystal was determined using single crystal X-ray diffraction analysis. The PPTS crystal belongs to the triclinic crystal system with space group of P1¯. The presence of functional groups was confirmed by FTIR spectral analysis. The optical transmittance range and cut-off wavelength were identified by UV-vis-NIR spectral studies. The luminescent properties of PPTS crystal were investigated. The thermal behavior of PPTS crystal was studied by TG-DT analyses. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Bismuth doping effect on crystal structure and photodegradation activity of Bi-TiO2 nanoparticles

    NASA Astrophysics Data System (ADS)

    Wu, Ming-Chung; Chang, Yin-Hsuan; Lin, Ting-Han

    2017-04-01

    The bismuth precursor is adopted as dopant to synthesize bismuth doped titanium dioxide nanoparticles (Bi-TiO2 NPs) with sol-gel method following by the thermal annealing treatment. We systematically developed a series of Bi-TiO2 NPs at several calcination temperatures and discovered the corresponding crystal structure by varying the bismuth doping concentration. At a certain 650 °C calcination temperature, the crystal structure of bismuth titanate (Bi2Ti2O7) is formed when the bismuth doping concentration is as high as 10.0 mol %. The photocatalytic activity of Bi-TiO2 NPs is increased by varying the doping concentration at the particular calcination temperature. By the definition X-ray diffraction (XRD) structural identification, a phase diagram of Bi-TiO2 NPs in doping concentration versus calcination temperature is provided. It can be useful for further study in the crystal structure engineering and the development of photocatalyst.

  4. Structural morphology of crystals with the barite (BaSO 4) structure: A revision and extension

    NASA Astrophysics Data System (ADS)

    Hartman, P.; Strom, C. S.

    1989-09-01

    The structural morphology of crystals with the barite (BaSO 4) structure (sulphates, chromates, perchlorates, permanganates and tetrafluoroborates) has been determined with the use of computer programs. Uniquely defined F forms are {002}, {210}, {211}, {020} and {201}. Two different F slices were found for {101} and {200}, 33 for {011}. Attachment energies and specific surface energies have been calculated for an electrostatic point charge model as a function of the charge distribution in the anion. On this basis it is concluded that {101} behaves as an F form, {200} as an S form and {011} as a K form. The theoretical growth form shows {210}, {101} and {002} as main forms. A comparison is made with habits of natural and synthetic crystals. Experiments on KCIO 4 show that {011} appears at high supersaturations (>38; ;20%). It is shown that a broken bond model provides relative attachment energies that are higher by a factor of about three.

  5. Microgravity protein crystallization

    PubMed Central

    McPherson, Alexander; DeLucas, Lawrence James

    2015-01-01

    Over the past 20 years a variety of technological advances in X-ray crystallography have shortened the time required to determine the structures of large macromolecules (i.e., proteins and nucleic acids) from several years to several weeks or days. However, one of the remaining challenges is the ability to produce diffraction-quality crystals suitable for a detailed structural analysis. Although the development of automated crystallization systems combined with protein engineering (site-directed mutagenesis to enhance protein solubility and crystallization) have improved crystallization success rates, there remain hundreds of proteins that either cannot be crystallized or yield crystals of insufficient quality to support X-ray structure determination. In an attempt to address this bottleneck, an international group of scientists has explored use of a microgravity environment to crystallize macromolecules. This paper summarizes the history of this international initiative along with a description of some of the flight hardware systems and crystallization results. PMID:28725714

  6. The crystal and magnetic structures of Sr 2LaFe 3O 8

    NASA Astrophysics Data System (ADS)

    Battle, P. D.; Gibb, T. C.; Lightfoot, P.

    1990-02-01

    The crystal and magnetic structures of the anion-deficient perovskite Sr 2LaFe 3O 8 (space group Pmma, a = 5.5095(1), b = 11.8845(5), c = 5.6028(1)AÅ) have been refined from X-ray and neutron powder diffraction data collected at room temperature. The crystal structure consists of layers of octahedral (O) and tetrahedral (T) iron-oxygen polyhedra arranged in the stacking sequence … OOTOOT … perpendicular to theyˆaxis of the unit cell. The magnetic structure is that of a G-type antiferromagnet with ordered magnetic moments of 3.77(5) and 3.15(11) μ B at the octahedral and tetrahedral sites, respectively. The low moment at the tetrahedral site is consistent with the observed disorder and magnetic anisotropy.

  7. Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27}: Solid-state synthesis, crystal structure and site-preference

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jeon, Beom-Yong; Nam, Gnu; Lee, Dong Woo

    A novel intermetallic compound of Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27} has been synthesized through the high-temperature solid-state reaction using Nb-ampoules. A batch of well grown block-/short bar-shaped single-crystals has been obtained, and the crystal structure of the title compound has been characterized by single-crystal X-ray diffraction analyses. Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27} adopts the Ho{sub 11}Ge{sub 10}-type structure belonging to the tetragonal space group I4/mmm (Z=4, Pearson symbol tI84) with nine crystallographically unique atomic positions in the asymmetric unit. The lattice parameters are a=12.0163(1) Å and c=16.5396(2) Å. The overall crystal structure can simply be depicted as an assembly of three differentmore » types of co-facial cationic polyhedra centered by anions, which is further enclosed by the three-dimensional (3-D) cage-like anionic framework. The extra amount of In is observed in one of three isolated anionic sites resulting in introducing the Ge/In-mixed site at the Wyckoff 4e site. This unique site-preference of In substitution for Ge at the 4e site has been enlightened via the atomic size-aspect which was fully supported and rationalized by the site- and bond-energies analyses using tight-binding linear muffin-tin orbital (TB-LMTO) calculations. Energy-dispersive X-ray spectroscopy (EDS), density of states (DOS), crystal orbital Hamilton population (COHP), and electron localization function (ELF) analyses for the title compound are also presented. Magnetic susceptibility measurement proves that an antiferromagnetic ordering of Ce atoms at a low temperature with a paramagnetic Curie temperature of −23.2 K. - Graphical abstract: Reported is experimental and theoretical investigations for Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27}, which is the first reported example having the extra amounts of In substitution for Ge at one of three “isolated” anionic sites in the Ho{sub 11}Ge{sub 10}-type phase. The observed In site

  8. Crystal Structures of T Cell Receptor (Beta) Chains Related to Rheumatoid Arthritis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li,H.; van Vranken, S.; Zhao, Y.

    The crystal structures of the V{beta}17+ {beta} chains of two human T cell receptors (TCRs), originally derived from the synovial fluid (SF4) and tissue (C5-1) of a patient with rheumatoid arthritis (RA), have been determined in native (SF4) and mutant (C5-1{sub F104{yields}Y/C187{yields}S}) forms, respectively. These TCR {beta} chains form homo-dimers in solution and in crystals. Structural comparison reveals that the main-chain conformations in the CDR regions of the C5-1 and SF4 V{beta}17 closely resemble those of a V{beta}17 JM22 in a bound form; however, the CDR3 region shows different conformations among these three V{beta}17 structures. At the side-chain level, conformationalmore » differences were observed at the CDR2 regions between our two ligand-free forms and the bound JM22 form. Other significant differences were observed at the V{beta} regions 8-12, 40-44, and 82-88 between C5-1/SF4 and JM22 V{beta}17, implying that there is considerable variability in the structures of very similar {beta} chains. Structural alignments also reveal a considerable variation in the V{beta}-C{beta} associations, and this may affect ligand recognition. The crystal structures also provide insights into the structure basis of T cell recognition of Mycoplasma arthritidis mitogen (MAM), a superantigen that may be implicated in the development of human RA. Structural comparisons of the V{beta} domains of known TCR structures indicate that there are significant similarities among V{beta} regions that are MAM-reactive, whereas there appear to be significant structural differences among those V{beta} regions that lack MAM-reactivity. It further reveals that CDR2 and framework region (FR) 3 are likely to account for the binding of TCR to MAM.« less

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2016-04-14

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

  11. Preparation and crystal structure of U3Fe2C5: An original uranium-iron carbide

    NASA Astrophysics Data System (ADS)

    Henriques, M. S.; Paixão, J. A.; Henriques, M. S. C.; Gonçalves, A. P.

    2015-09-01

    The U3Fe2C5 compound was prepared from the elements by arc-melting, followed by an heat-treatment in an induction furnace, at 1250 °C for 1 h and 1300 °C for 2 h. The crystal structure of this phase was determined by direct methods from single crystal X-ray diffraction data. U3Fe2C5 crystallizes in an original tetragonal crystal structure, with space group I4/mmm, a = 3.4980(3) Å and c = 19.8380(15) Å as lattice constants and two formula units per cell. This new type structure is characterized by the simultaneous presence of isolated and pairs of carbon atoms, the interatomic distances in the pairs being similar to a typical carbon-carbon double bond length found in a molecule. U3Fe2C5 is closely related to UC and UFeC2, and can be seen as build from two (distorted) UFeC2 unit cells and a UC layer.

  12. Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

    NASA Astrophysics Data System (ADS)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2016-11-01

    The synthesis, crystal structure and spectroscopic characterization of a new chlorocadmate template by the 1-(2-hydroxyethyl)piperazine ligand are reported. In the atomic arrangement, the CdCl5O entities are deployed in corrugated rows along the a-axis at y = 1/4 and y = 3/4 to form layers parallel to the (a,b) plane. In these crystals, piperazinediium cations are in a chair conformation and are inserted between these layers through Nsbnd H⋯Cl, Csbnd H⋯Cl, Osbnd H⋯Cl and Nsbnd H⋯O hydrogen bonds to form infinite three-dimensional network. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that H⋯Cl and Csbnd H⋯Hsbnd C intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The crystal contacts enrichments reveals that, the Cd++ … Cl- salt bridges, the Cd⋯O complexation and Osbnd H⋯Cl- and Nsbnd H⋯Cl-strong H-bonds are the driving forces in the packing formation. The presence of twelve independent chloride anions and four organic cation in the asymmetric unit allowed comparing their contact propensities. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. Additional characterization of this compound has also been performed by IR spectroscopy.

  13. Crystal Structure of Manganese Lipoxygenase of the Rice Blast Fungus Magnaporthe oryzae*

    PubMed Central

    Wennman, Anneli; Oliw, Ernst H.; Karkehabadi, Saeid; Chen, Yang

    2016-01-01

    Lipoxygenases (LOX) are non-heme metal enzymes, which oxidize polyunsaturated fatty acids to hydroperoxides. All LOX belong to the same gene family, and they are widely distributed. LOX of animals, plants, and prokaryotes contain iron as the catalytic metal, whereas fungi express LOX with iron or with manganese. Little is known about metal selection by LOX and the adjustment of the redox potentials of their protein-bound catalytic metals. Thirteen three-dimensional structures of animal, plant, and prokaryotic FeLOX are available, but none of MnLOX. The MnLOX of the most important plant pathogen, the rice blast fungus Magnaporthe oryzae (Mo), was expressed in Pichia pastoris. Mo-MnLOX was deglycosylated, purified to homogeneity, and subjected to crystal screening and x-ray diffraction. The structure was solved by sulfur and manganese single wavelength anomalous dispersion to a resolution of 2.0 Å. The manganese coordinating sphere is similar to iron ligands of coral 8R-LOX and soybean LOX-1 but is not overlapping. The Asn-473 is positioned on a short loop (Asn-Gln-Gly-Glu-Pro) instead of an α-helix and forms hydrogen bonds with Gln-281. Comparison with FeLOX suggests that Phe-332 and Phe-525 might contribute to the unique suprafacial hydrogen abstraction and oxygenation mechanism of Mo-MnLOX by controlling oxygen access to the pentadiene radical. Modeling suggests that Arg-525 is positioned close to Arg-182 of 8R-LOX, and both residues likely tether the carboxylate group of the substrate. An oxygen channel could not be identified. We conclude that Mo-MnLOX illustrates a partly unique variation of the structural theme of FeLOX. PMID:26783260

  14. [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    PubMed

    Abaturov, L V; Nosova, N G

    2013-01-01

    The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

  15. Preparation, characterization and crystal structures of three salts of the quaterpyridine ligand

    NASA Astrophysics Data System (ADS)

    Ciesielski, Artur; Stefankiewicz, Artur R.; Patroniak, Violetta; Kubicki, Maciej

    2009-07-01

    As a result of a reaction between 6,6'''-dimethyl-2,2':6',2'':6'',2'''-quaterpyridine C 22H 18N 4 and lanthanide(III) salts, compounds, [C 22H 20N 4] 2+·2(CF 3SO 3) - ( 1) and [C 22H 20N 4] 2+·2(ClO 4) - ( 2), have been obtained. They were characterized by spectroscopic techniques (ESI-MS, NMR, IR), elemental analysis, and their formulae were confirmed on the basis of X-ray crystallography. It turned out that the perchlorate crystallizes as two solvates: with acetonitrile and disordered water molecules. These are the first structural characterization of a 6,6'″-dimethyl-2,2':6',2″:6″,2'″-quaterpyridinium dication. Due to the intramolecular hydrogen bond it adopts the previously unobserved cis/trans/cis conformation. In all three crystals the dications have C i symmetry, they occupy the special positions in their respective space groups. In the crystal structures the π-π stacking and weak hydrogen bonds add directionality to the dominating electrostatic interactions between cations and anions.

  16. Band structures in two-dimensional phononic crystals with periodic Jerusalem cross slot

    NASA Astrophysics Data System (ADS)

    Li, Yinggang; Chen, Tianning; Wang, Xiaopeng; Yu, Kunpeng; Song, Ruifang

    2015-01-01

    In this paper, a novel two-dimensional phononic crystal composed of periodic Jerusalem cross slot in air matrix with a square lattice is presented. The dispersion relations and the transmission coefficient spectra are calculated by using the finite element method based on the Bloch theorem. The formation mechanisms of the band gaps are analyzed based on the acoustic mode analysis. Numerical results show that the proposed phononic crystal structure can yield large band gaps in the low-frequency range. The formation mechanism of opening the acoustic band gaps is mainly attributed to the resonance modes of the cavities inside the Jerusalem cross slot structure. Furthermore, the effects of the geometrical parameters on the band gaps are further explored numerically. Results show that the band gaps can be modulated in an extremely large frequency range by the geometry parameters such as the slot length and width. These properties of acoustic waves in the proposed phononic crystals can potentially be applied to optimize band gaps and generate low-frequency filters and waveguides.

  17. The Crystal Structure of Coxsackievirus A21 and Its Interaction with ICAM-1

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xiao, Chuan; Bator-Kelly, Carol M.; Rieder, Elizabeth

    2010-11-30

    CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 {angstrom} resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 {angstrom} resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1{sup Kilifi}. The cryo-EM map was fitted with the crystal structuresmore » of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.« less

  18. Stabilizing subnanometer Ag(0) nanoclusters by thiolate and diphosphine ligands and their crystal structures

    NASA Astrophysics Data System (ADS)

    Yang, Huayan; Wang, Yu; Zheng, Nanfeng

    2013-03-01

    The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions.The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions. Electronic supplementary information (ESI) available: Experimental details, more pictures of the structure and XPS spectra of the clusters. CCDC 916463 and 916464. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr34328f

  19. Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

    NASA Astrophysics Data System (ADS)

    Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

    2015-04-01

    The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.

  20. Structure of a new crystal form of human Hsp70 ATPase domain.

    PubMed

    Osipiuk, J; Walsh, M A; Freeman, B C; Morimoto, R I; Joachimiak, A

    1999-05-01

    Hsp70 proteins are highly conserved proteins induced by heat shock and other stress conditions. An ATP-binding domain of human Hsp70 protein has been crystallized in two major morphological forms at pH 7.0 in the presence of PEG 8000 and CaCl2. Both crystal forms belong to the orthorhombic space group P212121, but show no resemblance in unit-cell parameters. Analysis of the crystal structures for both forms shows a 1-2 A shift of one of the subdomains of the protein. This conformational change could reflect a 'natural' flexibility of the protein which might be relevant to ATP binding and may facilitate the interaction of other proteins with Hsp70 protein.

  1. Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.

    2016-03-16

    Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase fromBifidobacterium bifidumS17 (BbGal43A) are described.BbGal43A was successfully produced and showed activitymore » towards synthetic galactosides.BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences betweenBbGal43A and its characterized homologues.« less

  2. Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1.

    PubMed

    Hosaka, Toshiaki; Okazaki, Masateru; Kimura-Someya, Tomomi; Ishizuka-Katsura, Yoshiko; Ito, Kaori; Yokoyama, Shigeyuki; Dodo, Kosuke; Sodeoka, Mikiko; Shirouzu, Mikako

    2017-09-01

    Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P22 1 2 1 , which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P22 1 2 1 were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family. © 2017 The Protein Society.

  3. AACSD: An atomistic analyzer for crystal structure and defects

    NASA Astrophysics Data System (ADS)

    Liu, Z. R.; Zhang, R. F.

    2018-01-01

    We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

  4. Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Thompson, Michael C.; Cascio, Duilio; Yeates, Todd O.

    Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the datamore » sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less

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

    NASA Technical Reports Server (NTRS)

    1975-01-01

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

  6. Natural Cr3+-rich ettringite: occurrence, properties, and crystal structure

    NASA Astrophysics Data System (ADS)

    Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.; Murashko, Mikhail N.

    2017-08-01

    Cr3+-rich ettringite with Cr3+→Al substitution and Cr/(Cr + Al) ratios up to 0.40-0.50 was found in mineral assemblages of the Ma'aleh Adumim area of Mottled Zone (Judean Desert). The Cr3+-rich compositions were the latest in the thaumasite → ettringite-thaumasite solid solution → ettringite → ettringite-bentorite solid solution series. The mineral-forming solution was enriched in Cr3+ and had a pH buffered by afwillite at 11-12. Chromium was inherited from larnite rocks produced by high-temperature combustion metamorphic alteration of bioproductive calcareous sediments. The Cr/(Cr + Al) ratios are within 0.10-0.15 in most of the analysed crystals. This degree of substitution imparts pink colouration to the crystals, but does not affect their habit (a combination of monohedra and a prism). The habit changes to pyramid faces in coarse and later Cr3+-bearing crystals as Cr/(Cr + Al) ratios increase abruptly to 0.40-0.50. Single-crystal XRD analysis of one Cr-free and two Cr3+-rich samples and their structure determination and refinement indicate that the Cr-rich crystals (with Cr/(Cr + Al) to 0.3) preserve the symmetry and metrics of ettringite. The Ca-O bonding network undergoes differentiation with increase of Cr3+ concentration at octahedral M sites. The compression of Ca2 and expansion of Ca1 polyhedra sub-networks correlates with the degree of Cr3+→Al substitution.

  7. Crystal Structure of Oligomeric β1-Adrenergic G Protein- Coupled Receptors in Ligand-Free Basal State

    PubMed Central

    Huang, Jianyun; Chen, Shuai; Zhang, J. Jillian; Huang, Xin-Yun

    2013-01-01

    G protein-coupled receptors (GPCRs) mediate transmembrane signaling. Before ligand binding, GPCRs exist in a basal state. Crystal structures of several GPCRs bound with antagonists or agonists have been solved. However, the crystal structure of the ligand-free basal state of a GPCR, the starting point of GPCR activation and function, has not been determined. Here we report the X-ray crystal structure of the first ligand-free basal state of a GPCR in a lipid membrane-like environment. Oligomeric turkey β1-adrenergic receptors display two alternating dimer interfaces. One interface involves the transmembrane domain (TM) 1, TM2, the C-terminal H8, and the extracellular loop 1. The other interface engages residues from TM4, TM5, the intracellular loop 2 and the extracellular loop 2. Structural comparisons show that this ligand-free state is in an inactive conformation. This provides the structural information regarding GPCR dimerization and oligomerization. PMID:23435379

  8. Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein.

    PubMed

    Tanaka, Yoshiki; Iwaki, Shigehiro; Tsukazaki, Tomoya

    2017-09-05

    The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins. Here, we describe the crystal structure of a MATE protein from the plant Camelina sativa at 2.9 Å resolution. Two sets of six transmembrane α helices, assembled pseudo-symmetrically, possess a negatively charged internal pocket with an outward-facing shape. The crystal structure provides insight into the diversity of plant MATE proteins and their substrate recognition and transport through the membrane. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Structural, optical and electronic properties of K2Ba(NO3)4 crystal

    NASA Astrophysics Data System (ADS)

    Isaenko, L. I.; Korzhneva, K. E.; Goryainov, S. V.; Goloshumova, A. A.; Sheludyakova, L. A.; Bekenev, V. L.; Khyzhun, O. Y.

    2018-02-01

    Nitrate crystals reveal nonlinear optical properties and could be considered as converters of laser radiation in the short-wave region. The conditions for obtaining and basic properties of K2Ba(NO3)4 double nitrate crystals were investigated. Crystal growth was implemented by slow cooling in the temperature range of 72-49 °C and low rate evaporation. The structural analysis of K2Ba(NO3)4 formation on the basis of two mixed simple nitrate structures is discussed. The main groups of oscillations in K2Ba(NO3)4 crystal were revealed using Raman and IR spectroscopy, and the table of vibrations for this compound was compiled. The electronic structure of K2Ba(NO3)4 was elucidated in the present work from both experimental and theoretical viewpoints. In particular, X-ray photoelectron spectroscopy (XPS) was employed in the present work to measure binding energies of the atoms constituting the titled compound and its XPS valence-band spectrum for both pristine and Ar+ ion-bombarded surfaces. Further, total and partial densities of states of constituent atoms of K2Ba(NO3)4 have been calculated. The calculations reveal that the O 2p states dominate in the total valence-band region of K2Ba(NO3)4 except of its bottom, where K 3p and Ba 5p states are the principal contributors, while the bottom of the conduction band is composed mainly of the unoccupied O 2p states, with somewhat smaller contributions of the N 2p∗ states as well. With respect to the occupation of the valence band by the O 2p states, the present band-structure calculations are confirmed by comparison on a common energy scale of the XPS valence-band spectrum and the X-ray emission O Kα band for the K2Ba(NO3)4 crystal under study. Furthermore, the present calculations indicate that the K2Ba(NO3)4 compound is a direct-gap material.

  10. Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing

    2005-09-01

    Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in themore » mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion.« less

  11. Synthesis, crystal structure, vibrational spectroscopy and photoluminescence of new hybrid compound containing chlorate anions of stanate (II)

    NASA Astrophysics Data System (ADS)

    Lassoued, Mohamed Saber; Abdelbaky, Mohammed S. M.; Lassoued, Abdelmajid; Meroño, Rafael Mendoza; Gadri, Abdellatif; Ammar, Salah; Ben Salah, Abdelhamid; García-Granda, Santiago

    2017-08-01

    The present work aimed at studying a new organic-inorganic bis (4-amino quinolinium) hexachloro stanate (II) dihydrate compound. It was prepared and characterized by single crystal X-ray diffraction, X-ray powder, Hirshfeld surface, Spectroscopy measurement, thermal study and photoluminescence properties. It was found to crystallize in the monoclinic system (P21/c space group) with the following lattice parameters: a = 7.2558(6) Å, b = 13.4876(5) Å, c = 17.2107(13) Å, β = 102.028 (12)°. Its crystal structure was determined and refined down to an R value of 0.06 and a wR value of 0.087. The structure consisted of two different alternating organic-inorganic layers. The crystal packing was stabilized by Nsbnd H⋯Cl and Osbnd H⋯Cl hydrogen bonds and π-π interactions. Hirshfeld surface analysis was used to investigate intermolecular interactions, as well 2D finger plots were conducted to reveal the contribution of these interactions in the crystal structure quantitatively. The X-ray powder is in agreement with the X-ray structure. Scanning electronic microscopy (SEM) was carried out. Furthermore, the room temperature Infra Red (IR) spectrum of the title compound was analyzed on the basis of data found in the literature. Solid state 13C NMR spectrum shows ten signals, confirming the solid state structure determined by X-ray diffraction. Thermal analysis shows two anomalies at 380 and 610 °C. The optical properties of the crystal were studied using optical absorption UV-visible and photoluminescence (PL) spectroscopy, which were investigated at room temperature.

  12. Antiferromagnetic defect structure in LaNi O 3 – δ single crystals

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Bi -Xia; Rosenkranz, Stephan; Rui, X.

    Here, the origins of the metal-insulator and magnetic transitions exhibited by perovskite rare-earth nickelates, RNiO 3 (where R is a rare-earth element), remain open issues, with charge disproportionation, magnetic interactions, and lattice response across multiple length scales being among the many possible origins. Recently, growth of single crystals of LaNiO 3, which is the only member of these compounds that remains metallic in its ground state, has been reported, opening a new chapter in the investigation of the perovskite nickelates. Here, using a combination of magnetometry, heat capacity, and neutron scattering on as-grown and purposely reduced LaNiO 3–δ crystals, wemore » show that both antiferromagnetic and ferromagnetic phases with a Néel temperature of ~152 K and a Curie temperature of ~225 K can be induced by reduction of the oxygen content. Transmission electron microscopy shows that these phases are characterized by ordered oxygen vacancy defect structures that exist as dilute secondary phases in as-grown crystals despite growth in partial oxygen pressures up to at least 130 bar. The demonstration of antiferromagnetism resulting from oxygen vacancy ordered structures implies that stoichiometry must be explicitly considered when interpreting the bulk properties of LaNiO 3–δ single crystals; accordingly, the implications of our results for putative oxygen-stoichiometric LaNiO 3 are discussed.« less

  13. Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lenz, Dominic A.; Likos, Christos N.; Blaak, Ronald

    We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, amore » transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed.« less

  14. Antiferromagnetic defect structure in LaNi O 3 – δ single crystals

    DOE PAGES

    Wang, Bi -Xia; Rosenkranz, Stephan; Rui, X.; ...

    2018-06-12

    Here, the origins of the metal-insulator and magnetic transitions exhibited by perovskite rare-earth nickelates, RNiO 3 (where R is a rare-earth element), remain open issues, with charge disproportionation, magnetic interactions, and lattice response across multiple length scales being among the many possible origins. Recently, growth of single crystals of LaNiO 3, which is the only member of these compounds that remains metallic in its ground state, has been reported, opening a new chapter in the investigation of the perovskite nickelates. Here, using a combination of magnetometry, heat capacity, and neutron scattering on as-grown and purposely reduced LaNiO 3–δ crystals, wemore » show that both antiferromagnetic and ferromagnetic phases with a Néel temperature of ~152 K and a Curie temperature of ~225 K can be induced by reduction of the oxygen content. Transmission electron microscopy shows that these phases are characterized by ordered oxygen vacancy defect structures that exist as dilute secondary phases in as-grown crystals despite growth in partial oxygen pressures up to at least 130 bar. The demonstration of antiferromagnetism resulting from oxygen vacancy ordered structures implies that stoichiometry must be explicitly considered when interpreting the bulk properties of LaNiO 3–δ single crystals; accordingly, the implications of our results for putative oxygen-stoichiometric LaNiO 3 are discussed.« less

  15. Abstract shapes of RNA.

    PubMed

    Giegerich, Robert; Voss, Björn; Rehmsmeier, Marc

    2004-01-01

    The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.

  16. Abstract numeric relations and the visual structure of algebra.

    PubMed

    Landy, David; Brookes, David; Smout, Ryan

    2014-09-01

    Formal algebras are among the most powerful and general mechanisms for expressing quantitative relational statements; yet, even university engineering students, who are relatively proficient with algebraic manipulation, struggle with and often fail to correctly deploy basic aspects of algebraic notation (Clement, 1982). In the cognitive tradition, it has often been assumed that skilled users of these formalisms treat situations in terms of semantic properties encoded in an abstract syntax that governs the use of notation without particular regard to the details of the physical structure of the equation itself (Anderson, 2005; Hegarty, Mayer, & Monk, 1995). We explore how the notational structure of verbal descriptions or algebraic equations (e.g., the spatial proximity of certain words or the visual alignment of numbers and symbols in an equation) plays a role in the process of interpreting or constructing symbolic equations. We propose in particular that construction processes involve an alignment of notational structures across representation systems, biasing reasoners toward the selection of formal notations that maintain the visuospatial structure of source representations. For example, in the statement "There are 5 elephants for every 3 rhinoceroses," the spatial proximity of 5 and elephants and 3 and rhinoceroses will bias reasoners to write the incorrect expression 5E = 3R, because that expression maintains the spatial relationships encoded in the source representation. In 3 experiments, participants constructed equations with given structure, based on story problems with a variety of phrasings. We demonstrate how the notational alignment approach accounts naturally for a variety of previously reported phenomena in equation construction and successfully predicts error patterns that are not accounted for by prior explanations, such as the left to right transcription heuristic.

  17. Synthesis, crystal structure, and electrical and magnetic properties of BaMo{sub 6}Te{sub 6}: A novel reduced molybdenum telluride containing infinite chains of trans-face shared Mo{sub 6} octahedra

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gall, Philippe; Guizouarn, Thierry; Potel, Michel

    Powder samples and single crystals of the new ternary compound BaMo{sub 6}Te{sub 6} were obtained by solid state reaction. The structure was determined by single-crystal X-ray diffraction. BaMo{sub 6}Te{sub 6} crystallizes in the hexagonal space group P6{sub 3}/m (No. 176) with unit-cell parameters a=9.3941(2) Å, c=4.5848(1) Å and Z=1. Full-matrix least-squares refinement on F{sup 2} using 452 independent reflections for 17 refinable parameters resulted in R1=0.0208 and wR2=0.0539. The structure consists of one-dimensional infinite chains of trans-face shared Mo{sub 6} octahedra capped by Se atoms. These chains that are running along the c axis are separated from each other bymore » nine-coordinate Ba atoms. Resistivity measurements on a single crystal indicated that the BaMo{sub 6}Te{sub 6} compound is metallic down to 160 K and semiconductor below. Magnetic susceptibility measurements showed that BaMo{sub 6}Te{sub 6} is weakly diamagnetic with no anomaly at the metal–semiconductor transition. - Graphical abstract: We present here the synthesis, the crystal structure, and the electrical and magnetic properties of the new compound BaMo{sub 6}Te{sub 6} containing infinite chains of trans-face shared Mo{sub 6} octahedra. - Highlights: • BaMo{sub 6}Te{sub 6} contains infinite chains of trans-face-sharing Mo{sub 6} octahedra |Mo{sub 6/2}|{sub ∞}{sup 1}. • Synthesis by solid state reaction. • Single-crystal X-ray study. • Continuous metal–nonmetal transition. • Anderson localization.« less

  18. Crystal Initiation Structures in Developing Enamel: Possible Implications for Caries Dissolution of Enamel Crystals

    PubMed Central

    Robinson, Colin; Connell, Simon D.

    2017-01-01

    Investigations of developing enamel crystals using Atomic and Chemical Force Microscopy (AFM, CFM) have revealed a subunit structure. Subunits were seen in height images as collinear swellings about 30 nM in diameter on crystal surfaces. In friction mode they were visible as positive regions. These were similar in size (30–50 nM) to collinear spherical structures, presumably mineral matrix complexes, seen in developing enamel using a freeze fracturing/freeze etching procedure. More detailed AFM studies on mature enamel suggested that the 30–50 nM structures were composed of smaller units, ~10–15 nM in diameter. These were clustered in hexagonal or perhaps a spiral arrangement. It was suggested that these could be the imprints of initiation sites for mineral precipitation. The investigation aimed at examining original freeze etched images at high resolution to see if the smaller subunits observed using AFM in mature enamel were also present in developing enamel i.e., before loss of the organic matrix. The method used was freeze etching. Briefly samples of developing rat enamel were rapidly frozen, fractured under vacuum, and ice sublimed from the fractured surface. The fractured surface was shadowed with platinum or gold and the metal replica subjected to high resolution TEM. For AFM studies high-resolution tapping mode imaging of human mature enamel sections was performed in air under ambient conditions at a point midway between the cusp and the cervical margin. Both AFM and freeze etch studies showed structures 30–50 nM in diameter. AFM indicated that these may be clusters of somewhat smaller structures ~10–15 nM maybe hexagonally or spirally arranged. High resolution freeze etching images of very early enamel showed ~30–50 nM spherical structures in a disordered arrangement. No smaller units at 10–15 nM were clearly seen. However, when linear arrangements of 30–50 nM units were visible the picture was more complex but also smaller units including

  19. Binary ionic porphyrin nanosheets: electronic and light-harvesting properties regulated by crystal structure

    NASA Astrophysics Data System (ADS)

    Tian, Yongming; M. Beavers, Christine; Busani, Tito; Martin, Kathleen E.; Jacobsen, John L.; Mercado, Brandon Q.; Swartzentruber, Brian S.; van Swol, Frank; Medforth, Craig J.; Shelnutt, John A.

    2012-02-01

    Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room temperature preparation of the nanosheets has provided the first X-ray crystal structure of a cooperative binary ionic (CBI) solid. The unit cell contains one and one-half molecules of aquo-ZnTPPS4- (an electron donor) and three half molecules of dihydroxy-SnTNMePyP4+ (an electron acceptor). Charge balance in the solid is reached without any non-porphyrinic ions, as previously determined for other CBI nanomaterials by non-crystallographic means. The crystal structure reveals a complicated molecular arrangement with slipped π-π stacking only occurring in isolated dimers of one of the symmetrically unique zinc porphyrins. Consistent with the crystal structure, UV-visible J-aggregate bands indicative of exciton delocalization and extended π-π stacking are not observed. XRD measurements show that the structure of the Zn/Sn nanosheets is distinct from that of Zn/Sn four-leaf clover-like CBI solids reported previously. In contrast with the Zn/Sn clovers that do exhibit J-aggregate bands and are photoconductive, the nanosheets are not photoconductive. Even so, the nanosheets act as light-harvesting structures in an artificial photosynthesis system capable of reducing water to hydrogen but not as efficiently as the Zn/Sn clovers.Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room

  20. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de; Brosi, Richard W. W.; Steinmetz, Andrea

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein,more » but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.« less

  1. Band structure analysis of leaky Bloch waves in 2D phononic crystal plates.

    PubMed

    Mazzotti, Matteo; Miniaci, Marco; Bartoli, Ivan

    2017-02-01

    A hybrid Finite Element-Plane Wave Expansion method is presented for the band structure analysis of phononic crystal plates with two dimensional lattice that are in contact with acoustic half-spaces. The method enables the computation of both real (propagative) and imaginary (attenuation) components of the Bloch wavenumber at any given frequency. Three numerical applications are presented: a benchmark dispersion analysis for an oil-loaded Titanium isotropic plate, the band structure analysis of a water-loaded Tungsten slab with square cylindrical cavities and a phononic crystal plate composed of Aurum cylinders embedded in an epoxy matrix. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri

    2010-09-28

    Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailedmore » study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.« less

  3. Crystal Structures of Inhibitir Complexes of Human T-Cell Leukemia Virus (HTLV-1) Protease

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri

    2010-09-17

    Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailedmore » study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.« less

  4. Concept Formation and Abstraction.

    ERIC Educational Resources Information Center

    Lunzer, Eric A.

    1979-01-01

    This paper examines the nature of concepts and conceptual processes and the manner of their formation. It argues that a process of successive abstraction and systematization is central to the evolution of conceptual structures. Classificatory processes are discussed and three levels of abstraction outlined. (Author/SJL)

  5. Crystal structure and superconductivity in atomic hydrogen: Deformation between I41/amd and Fddd

    NASA Astrophysics Data System (ADS)

    Ishikawa, T.; Nagara, H.; Oda, T.; Suzuki, N.; Shimizu, K.

    2017-10-01

    We investigated crystal structures of solid metallic hydrogen using the potential energy surface trekking for structure search. We applied this technique to a tetragonal I41/amd structure at pressures of 500 and 600 GPa and obtained the transformation into multiple orthorhombic Fddd structures, which are formed by distortions in the ab plane of I41/amd. The potential barriers are easily surmounted by few trekking steps, which indicates that in solid metallic hydrogen crystal structure is softened with respect to the distortion and is easily fluctuated among the I41/amd and Fddd structures. Calculated superconducting critical temperatures show 269 K for I41/amd and 263 K for Fddd at 500 GPa. The structures are softened and the electron-phonon coupling are enhanced with pressurization to 600 GPa. As the results, the superconducting critical temperature is increased to 281 K for I41/amd, whereas it is decreased to 252 K for Fddd owing to its larger phonon softening than that of I41/amd.

  6. Growth and structural analysis of ammonium nickel cobalt sulfate hexahydrate crystals

    NASA Astrophysics Data System (ADS)

    de Oliveira, Michelle; Ghosh, Santunu; Pacheco, Tiago S.; Perpétuo, Genivaldo J.; Franco, Carlos J.

    2017-10-01

    We have obtained a set of crystals of the empirical formula (NH4)2Ni x Co(1-x)(SO4)2 · 6H2O with the different concentrations of Ni and Co, by employing the growth from the solution technique. We have chosen the monocrystal (NH4)2Ni0.3Co0.7(SO4)2 · 6H2O for the structural analysis. The structure was resolved by x-ray diffraction method and refined by the full-matrix least-squares method with the help of SHELXS software. This crystal belongs to a monoclinic space group P21/c with crystal parameters, a  =  6.2455 (2) Å, b  =  12.5065 (3) Å, c  =  9.2303 (2) Å, α  =  γ  =  90°, β  =  106.995 (3)°, V  =  689.49 (3) Å3, Z  =  2. We have shown the configuration of the unit cell of the above monocrystal, along with that we have also reported the length, angles between the bonds and the geometry of the hydrogen bonds of the monocrystal.

  7. The crystal structure of the new ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2)

    NASA Astrophysics Data System (ADS)

    Fedyna, L. O.; Bodak, O. I.; Fedorchuk, A. O.; Tokaychuk, Ya. O.

    2005-06-01

    New ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2) was synthesized and its crystal structure was determined by direct methods from X-ray powder diffraction data (diffractometer DRON-3M, Cu Kα-radiation, R=6.99%,R=12.27%,R=11.55%). The compound crystallizes with the own cubic structure type: space group F 4¯ 3m, Pearson code cF272, a=16.6150(2) Å,Z=8. The structure of the Dy 3Cu 20Sb 11-x ( x≈2) can be obtained from the structure type BaHg 11 by doubling of the lattice parameter and subtraction of 16 atoms. The studied structure was compared with the structures of known compounds, which crystallize in the same space group with similar cell parameters.

  8. Structural, quantum chemical, vibrational and thermal studies of a hydrogen bonded zwitterionic co-crystal (nicotinic acid: pyrogallol)

    NASA Astrophysics Data System (ADS)

    Prabha, E. Arockia Jeya Yasmi; Kumar, S. Suresh; Athimoolam, S.; Sridhar, B.

    2017-02-01

    In the present work, a new co-crystal of nicotinic acid with pyrogallol (NICPY) has been grown in the zwitterionic form and the corresponding structural, vibrational, thermal, solubility and anti-cancer characteristics have been reported. The single crystal X-ray diffraction analysis confirms that the structural molecular packing of the crystal stabilized through N-H⋯O and O-H⋯O hydrogen bond. The stabilization energy of the hydrogen bond motifs were calculated in the solid state. Vibrational spectral studies such as Fourier transform-infrared (FT-IR) and FT-Raman were adopted to understand the zwitterionic co-crystalline nature of the compound, which has been compared with theoretically calculated vibrational frequencies. The thermal stability of the grown co-crystal was analyzed by TG/DTA study. The solubility of the NICPY co-crystal was investigated in water at different temperature and compared with that of the nicotinic acid, which is the parent compound of NICPY co-crystal. The grown crystals were treated with human cervical cancer cell line (HeLa) to analyze the cytotoxicity of NICPY crystals and compared with the parent compound, which shows that NICPY has moderate activity against human cervical cancer cell line.

  9. On the Relationship Between Scintillation Anisotropy and Crystal Structure in Pure Crystalline Organic Scintillator Materials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schuster, Patricia; Feng, Patrick; Brubaker, Erik

    We report the scintillation anisotropy effect for proton recoil events has been investigated in five pure organic crystalline materials: anthracene, trans-stilbene, p-terphenyl, bibenzyl, and diphenylacetylene. These measurements include characterization of the scintillation response for one hemisphere of proton recoil directions in each crystal. In addition to standard measurements of the total light output and pulse shape at each angle, the prompt and delayed light anisotropies are analyzed, allowing for investigation of the singlet and triplet molecular excitation behaviors independently. This work provides new quantitative and qualitative observations that make progress toward understanding the physical mechanisms behind the scintillation anisotropy. Thesemore » measurements show that the relationship between the prompt and delayed light anisotropies is correlated with crystal structure, as it changes between the pi-stacked crystal structure materials (anthracene and p-terphenyl) and the herringbone crystal structure materials (stilbene, bibenzyl, and diphenylacetylene). The observations are consistent with a model in which there are preferred directions of kinetic processes for the molecular excitations. Finally, these processes and the impact of their directional dependencies on the scintillation anisotropy are discussed.« less

  10. On the Relationship Between Scintillation Anisotropy and Crystal Structure in Pure Crystalline Organic Scintillator Materials

    DOE PAGES

    Schuster, Patricia; Feng, Patrick; Brubaker, Erik

    2018-05-03

    We report the scintillation anisotropy effect for proton recoil events has been investigated in five pure organic crystalline materials: anthracene, trans-stilbene, p-terphenyl, bibenzyl, and diphenylacetylene. These measurements include characterization of the scintillation response for one hemisphere of proton recoil directions in each crystal. In addition to standard measurements of the total light output and pulse shape at each angle, the prompt and delayed light anisotropies are analyzed, allowing for investigation of the singlet and triplet molecular excitation behaviors independently. This work provides new quantitative and qualitative observations that make progress toward understanding the physical mechanisms behind the scintillation anisotropy. Thesemore » measurements show that the relationship between the prompt and delayed light anisotropies is correlated with crystal structure, as it changes between the pi-stacked crystal structure materials (anthracene and p-terphenyl) and the herringbone crystal structure materials (stilbene, bibenzyl, and diphenylacetylene). The observations are consistent with a model in which there are preferred directions of kinetic processes for the molecular excitations. Finally, these processes and the impact of their directional dependencies on the scintillation anisotropy are discussed.« less

  11. Crystal structure of hydrocortisone acetate, C23H32O6

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kaduk, James A.; Gindhart, Amy M.; Blanton, Thomas N.

    The crystal structure of hydrocortisone acetate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Hydrocortisone acetate crystallizes in space groupP2 1(#4) witha= 8.85173(3) Å,b= 13.53859(3) Å,c= 8.86980(4) Å,β= 101.5438(3)°,V= 1041.455(6) Å 3, andZ= 2. Both hydroxyl groups form hydrogen bonds to the ketone oxygen atom on the steroid ring system, resulting in a three-dimensional hydrogen bond network. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

  12. Synthesis, crystal structure, and ionic conductivity of a new layered metal phosphate, Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Sung-Chul; Kwak, Hyun-Jung; Yoo, Chung-Yul

    2016-11-15

    A new layered metal phosphate, Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3}, was synthesized in the form of either a single-crystal or polycrystalline powder using the molten hydroxide flux method or a solid-state reaction, respectively. Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3} crystallizes to the P2{sub 1}/n (Z=4) monoclinic space group with lattice parameters a≈4.95 Å, b≈22.06 Å, c≈8.63 Å, and β≈91.5°. The structure is composed of stacked [LiSrAl(PO{sub 4}){sub 2}] layers alternating regularly with [LiSrPO{sub 4}] layers. In the [LiSrAl(PO{sub 4}){sub 2}] sublattice, the AlO{sub 6} octahedra and PO{sub 4} tetrahedra are tilted cooperatively to form an anionic, corrugated, two-dimensional [Al(PO{sub 4}){sub 2}]{supmore » 3−} framework that can be regarded as a “distorted-glaserite” structure. The [LiSrPO{sub 4}] sublattice is that of a layered block containing a six-membered ring formed from alternating linkages of LiO{sub 4} and PO{sub 4} tetrahedra. The six-membered rings show a boat-type arrangement with the up(U) or down(D) pointing sequence, UUDUUD. The interspace between the two sublattices generates a two-dimensional pathway for Li{sup +} ion conduction. The impedance measurement indicated that Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3} had a moderate ion conductivity (σ≈1.30×10{sup −4} S cm{sup −1} at 667 K), with an activation energy E{sub a}≈1.02 eV. - Graphical abstract: Polyhedral view of Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3}. Li{sup +} ions are represented by green spheres, Sr atoms by white spheres, AlO{sub 6} groups by octahedra, and PO{sub 4} groups by tetrahedra. - Highlights: • New compound Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3} is reported. • The crystal structure is investigated by single-crystal XRD analysis. • The structure is formed by the alternate stacking of two different sublattices. • Correlation between the crystal structure and ionic conductivity is discussed.« less

  13. Synthesis, crystal structure and optical properties of two new layered cadmium iodates: Cd(IO{sub 3})X (X=Cl, OH)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Bing-Ping, E-mail: ybp@fjirsm.ac.cn; Mao, Jiang-Gao

    Systematic explorations of new compounds in the cadmium iodate system by hydrothermal reactions led to two layered iodates, namely, Cd(IO{sub 3})X (X=Cl, OH). Cd(IO{sub 3})Cl crystallizes in the orthorhombic space group Cmca (No. 64) whereas Cd(IO{sub 3})(OH) crystallizes in the orthorhombic space group Pnma (No. 62). Cd(IO{sub 3})Cl displays a unique double layered structure composed of {sup 1}{sub ∞}[Cd−O{sub 3}Cl]{sub n} chains. Cadmium octahedrons form a 1D chain along the a-axis through edge sharing, and such chains are further interconnected via IO{sub 3} groups to form a special double layer on (020) plane. Cd(IO{sub 3})(OH) also exhibits a layered structuremore » that is composed of cadmium cations, IO{sub 3} groups and hydroxyl ions. Within a layer, chains of CdO{sub 6} edge-shared octahedra are observed along the b-axis. And these chains are connected by IO{sub 3} groups into a layer parallel to the bc plane. Spectroscopic characterizations, elemental analysis, and thermogravimetric analysis for the reported two compounds are also presented. - Graphical abstract: Two new layered cadmium iodates Cd(IO{sub 3})X (X=Cl, OH) are reported. Cd(IO{sub 3})Cl features a unique double layered structure whereas Cd(IO{sub 3})(OH) displays an ordinary layered structure. - Highlights: • Two new layered cadmium iodates Cd(IO{sub 3})X (X=Cl, OH) are reported. • Cd(IO{sub 3})Cl features a unique double layered structure. • Cd(IO{sub 3})(OH) displays an ordinary layered structure. • The spectroscopic and thermal properties have been studied in detail.« less

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

    DOE PAGES

    Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; ...

    2016-04-12

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. Furthermore, this observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn 3N 4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Caskey, Christopher M.; Colorado School of Mines, Golden, Colorado 80401; Larix Chemical Science, Golden, Colorado 80401

    2016-04-14

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

  16. Crystal structure and explosive performance of a new CL-20/caprolactam cocrystal

    NASA Astrophysics Data System (ADS)

    Guo, Changyan; Zhang, Haobin; Wang, Xiaochuan; Xu, Jinjiang; Liu, Yu; Liu, Xiaofeng; Huang, Hui; Sun, Jie

    2013-09-01

    Co-crystallization is an effective way to improve performance of the high explosive 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20). A new CL-20/caprolactam (CPL) cocrystal has been prepared by a rapid solvent evaporation method, and the crystal structure investigations show that the cocrystal is formed by strong intermolecular hydrogen bond interaction. The cocrystal can only be prepared with low moisture content of the air, because water in the air has a profound effect on the cocrystal formation, and it can lead to crystal form conversion of CL-20, but not the formation of cocrystal. The CL20/CPL explosive possess very low sensitivity, and may be used as additive in explosives formulation to desensitize other high explosives.

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

    PubMed

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

    2010-06-21

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

  18. Crystal structure, spectrum character and explosive property of a new cocrystal CL-20/DNT

    NASA Astrophysics Data System (ADS)

    Liu, Ke; Zhang, Gao; Luan, Jieyu; Chen, Zhiqun; Su, Pengfei; Shu, Yuanjie

    2016-04-01

    A new cocrystal explosive of 2,4,6,8,10,12-hexanitrohexaazaiso-wurtzitane(CL-20) and 2,5-dinitrotoluene(DNT) in a molar ratio of 1:2 has been prepared by slow solvent evaporation method. Crystal structure of the cocrystal characterized by single crystal X-ray diffraction (SXRD) reveals that the cocrystal is formed by intermolecular hydrogen bond interactions and belongs to the triclinic system with P-1 group. Moreover, the obivious differences of powder X-ray diffraction (PXRD) patterns, infrared spectroscopy and Raman spectroscopy confirm that the intermolecular interactions have great influence for the crystal structure and formation of cocrystal. The cocrystal exhibits a lower impact height of 44 cm, suggesting a substantial reduction of sensitivity in comparison with CL-20. And thermal test results showed cocrystal obtains a lower melting point than DNT, which means huge advantages in blasting engineering.

  19. Tailoring the structures and photonic properties of low-dimensional organic materials by crystal engineering.

    PubMed

    Li, Qing; Jin, Wang; Chu, Manman; Zhang, Wei; Gu, Jianmin; Shahid, Bilal; Chen, Aibing; Yu, Yifeng; Qiao, Shanlin; Zhao, Yong Sheng

    2018-03-08

    Low-dimensional organic materials have given rise to tremendous interest in optoelectronic applications, owing to their controllable photonic properties. However, the controlled-synthesis approaches for organic nano-/micro-architectures are very difficult to attain, because the weak interaction (van der Waals force) between the organic molecules cannot dominate the kinetic process of crystal growth. We report a simple method, which involves selective adhesion to the organic crystal plane by hydrogen-bonding interaction for modulating the crystal growth process, which leads either to the self-assembly of one organic molecule into two-dimensional (2D) microsheets with an obvious asymmetric light propagation or one-dimensional (1D) microrods with low propagation loss. The method of tailoring the structures and photonic properties for fabricating different micro-structures would provide enlightenment for the development of tailor-made mini-sized devices for photonic integrated circuits.

  20. Analysis of zinc binding sites in protein crystal structures.

    PubMed

    Alberts, I L; Nadassy, K; Wodak, S J

    1998-08-01

    The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.