Refinement of the crystal structures of biomimetic weddellites produced by microscopic fungus Aspergillus niger

NASA Astrophysics Data System (ADS)

Rusakov, A. V.; Frank-Kamenetskaya, O. V.; Gurzhiy, V. V.; Zelenskaya, M. S.; Izatulina, A. R.; Sazanova, K. V.

2014-05-01

The single-crystal structures of four biomimetic weddellites CaC2O4 · (2 + x)H2O with different contents of zeolitic water ( x = 0.10-0.24 formula units) produced by the microscopic fungus Aspergillus niger were refined from X-ray diffraction data ( R = 0.029-0.038). The effect of zeolitic water content on the structural stability of weddellite was analyzed. The parameter a was shown to increase with increasing x due to the increase in the distance between water molecules along this direction. The water content and structural parameters of the synthesized weddellites are similar to those of weddellites from biofilms and kidney stones.

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

Thimmaiah, Srinivasa; Tener, Zachary; Lamichhane, Tej N.

Here, the γ-region of the Mn–Al phase diagram between 45 and 70 at.% Al was re-investigated by a combination of powder and single crystal X-ray diffraction as well as EDS analysis to establish the distribution of Mn and Al atoms. Single crystals of γ-Mn 5–x Al 8+x were grown using Sn-flux at 650 °C. The crystal structure, atomic coordinates and site occupancy parameters of γ-Mn 5–x Al 8+x phases were refined from single crystal X-ray data. The γ-Mn 5-x Al 8+x phase adopts the rhombohedral Cr 5Al 8-type structure rather than a cubic γ-brass structure. The refined compositions from twomore » crystals extracted from the Al-rich and Mn-rich sides are, respectively, Mn 4.76Al 8.24(2) (I) and Mn 6.32Al 6.68(2) (II). The structure was refined in the acentric R3m space group (No.160, Z=6), in order to compare with other reported rhombohedral γ-brasses. In addition, according to X-ray powder diffraction analysis, at the Al-rich side the γ-phase coexists with LT–Mn 4Al 11 and, at the Mn-rich side, with a hitherto unknown phase. The refined lattice parameters from powder patterns fall in the range a=12.6814(7)–12.6012(5) Å and c=7.9444(2)–7.9311(2) Å from Al-rich to Mn-rich loadings, and the corresponding rhombohedral angles distorted from a pseudo-cubic cell were found to be 89.1(1)°–88.9(1)°. Magnetic susceptibility and magnetization studies of Mn 4.92Al 8.08(2) are consistent with moment bearing Mn and suggest a spin glass state below 27 K. Tight-binding electronic structure calculations (LMTO-ASA with LSDA) showed that the calculated Fermi level for γ-“Mn 5Al 8” falls within a pseudogap of the density of states, a result which is in accordance with a Hume-Rothery stabilization mechanism γ-brass type phases.« less

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.

A novel organic nonlinear optical crystal: Creatininium succinate

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

Thirumurugan, R.; Anitha, K., E-mail: singlecerystalxrd@gmail.ciom

2015-06-24

A novel organic material complex of creatininium succinate (CS) has been synthesized and single crystals were grown by the reaction of creatinine and succinic acid from aqueous solution by employing the technique of slow evaporation at room temperature. The structure of the grown crystal has been elucidated using single crystal X-ray diffraction analysis and the structure was refined by least-squares method to R = 0.027 for 1840 reflections. FT-IR spectral investigation has been carried out to identify the various functional groups in the title compound. UV–Vis transmission was carried out which shows the crystal has a good optical transmittance inmore » the visible region with lower cutoff wavelength around 220 nm. Nonlinear optical property of the crystal was confirmed by Kurtz-Perry powder technique.« less

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

Ramadhar, Timothy R.; Zheng, Shao-Liang; Chen, Yu-Sheng

This report describes complete practical guidelines and insights for the crystalline sponge method, which have been derived through the first use of synchrotron radiation on these systems, and includes a procedure for faster synthesis of the sponges. These guidelines will be applicable to crystal sponge data collected at synchrotrons or in-house facilities, and will allow researchers to obtain reliable high-quality data and construct chemically and physically sensible models for guest structural determination. A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported.more » The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.« less

Growth and structural characterization of single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) obtained by the partial melting technique

NASA Astrophysics Data System (ADS)

Yamaki, K.; Bamba, Y.; Mochiku, T.; Funahashi, S.; Matsushita, Y.; Irie, A.

2018-05-01

In this study, cubic single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) with typical dimensions of 100-150 μm in length were grown by the partial melting technique. Multiple 00l reflections were first observed by XRD measurements of the bulk RuGd-1212 single crystals. The resistivity of the obtained crystals was roughly estimated to be ∼24-80 mΩ cm and no superconducting transition was observed down to 4.2 K. From the XRD measurements and refinement of the crystal structure, it was apparent that the Ru and Sr sites of the single-crystal RuGd-1212 were partially substituted by Cu and Gd, respectively. Oxygen defects were found to be minor (δ ≈ 0.1). The lattice parameters a and c of the single crystals were found to be larger and smaller, respectively, than those of a polycrystalline sample.

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B] pyridine-3-carbonitrile

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

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K., E-mail: singlecrystalxrd@gmail.com

2016-05-23

The novel organic material C{sub 20}H{sub 21}ClN{sub 2}O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P2{sub 1}/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å{sup 3} and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. Themore » structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.« less

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

NASA Astrophysics Data System (ADS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D. M.; Conway, Barbara R.; Timmins, Peter

2007-03-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2NC(CH 3) 3-n(CH 2OH) n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family ( n=0, 1, 2), but significantly contrasting structural properties for the member with n=3.

Structure and magnetic properties of flux grown single crystals of Co3-xFexSn2S2 shandites

NASA Astrophysics Data System (ADS)

Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

2016-01-01

We report a successful single crystal growth of the shandite-type half-metallic ferromagnet Co3Sn2S2, and its Fe-substituted compounds, Co3-xFexSn2S2, by employing the flux method. Although Fe3Sn2S2 is unstable phase, we found that using the self Sn flux enables us to obtain single phase crystals up to x=0.53. The chemical composition of the grown plate-shaped single crystals was examined using wavelength-dispersive X-ray spectroscopy. The shandite structure with R 3 ̅m symmetry was confirmed by powder X-ray diffraction and the crystal structure parameters were refined using the Rietveld method. Magnetization measurements show suppression of the ferromagnetic order upon Fe-substitution , as well as in other substituted systems such as In- and Ni-substituted Co3Sn2S2. The almost identical magnetic phase diagrams of the Fe- and In-substituted compounds indicate that the electron number is dominantly significant to the magnetism in the Co-based shandite.

Key structure-activity relationships in the vanadium phosphorus oxide catalyst system

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

Thompson, M.R.; Ebner, J.R.

1990-04-01

The crystal structure of vanadyl pyrophosphate has been redetermined using single crystals obtained from a near solidified melt of a microcrystalline catalyst sample. Crystals that index as vanadyl pyrophosphate obtained from this melt are variable in color. Crystallographic refinement of the single crystal x-ray diffraction data indicates that structural differences among these materials can be described in terms of crystal defects associated with linear disorder of the vanadium atoms. The importance of the disorder is outlined in the context of its effect on the proposed surface topology parallel to (1,0,0). Models of the surface topology simply and intuitively account formore » the non-stoichometric surface atomic P/V ratio exhibited by selective catalysts of this phase. These models also point to the possible role of the excess phosphorus in providing site isolation of reactive centers at the surface. 33 refs., 7 figs.« less

Stochastic and Deterministic Crystal Structure Solution Methods in GSAS-II: Monte Carlo/Simulated Annealing Versus Charge Flipping

DOE PAGES

Von Dreele, Robert

2017-08-29

One of the goals in developing GSAS-II was to expand from the capabilities of the original General Structure Analysis System (GSAS) which largely encompassed just structure refinement and post refinement analysis. GSAS-II has been written almost entirely in Python loaded with graphics, GUI and mathematical packages (matplotlib, pyOpenGL, wxpython, numpy and scipy). Thus, GSAS-II has a fully developed modern GUI as well as extensive graphical display of data and results. However, the structure and operation of Python has required new approaches to many of the algorithms used in crystal structure analysis. The extensions beyond GSAS include image calibration/integration as wellmore » as peak fitting and unit cell indexing for powder data which are precursors for structure solution. Structure solution within GSAS-II begins with either Pawley or LeBail extracted structure factors from powder data or those measured in a single crystal experiment. Both charge flipping and Monte Carlo-Simulated Annealing techniques are available; the former can be applied to (3+1) incommensurate structures as well as conventional 3D structures.« less

Single crystal growth and characterization of kagomé-lattice shandites Co3Sn2-xInxS2

NASA Astrophysics Data System (ADS)

Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

2015-09-01

Single crystals of the shandite-type half metallic ferromagnet Co3Sn2S2, and its In-substituted compounds, Co3Sn2-xInxS2 (0

Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain

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

Bukrejewska, Malgorzata; Derewenda, Urszula; Radwanska, Malwina

2017-08-15

Two nonstructural proteins encoded byZika virusstrain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a boundS-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit.

Hydrogen positions in single nanocrystals revealed by electron diffraction

NASA Astrophysics Data System (ADS)

Palatinus, L.; Brázda, P.; Boullay, P.; Perez, O.; Klementová, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S.

2017-01-01

The localization of hydrogen atoms is an essential part of crystal structure analysis, but it is difficult because of their small scattering power. We report the direct localization of hydrogen atoms in nanocrystalline materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomography data. We used this method to locate hydrogen atoms in both an organic (paracetamol) and an inorganic (framework cobalt aluminophosphate) material. The results demonstrate that the technique can reliably reveal fine structural details, including the positions of hydrogen atoms in single crystals with micro- to nanosized dimensions.

Na 3Cr 2P 3S 12 and K 3Cr 2P 3S 12: Two New One-Dimensional Thiophosphate Compounds with a Novel Structure

NASA Astrophysics Data System (ADS)

Coste, S.; Kopnin, E.; Evain, M.; Jobic, S.; Payen, C.; Brec, R.

2001-12-01

Two new alkali metal chromium thiophosphates, Na3Cr2P3S12 and K3Cr2P3S12, have been synthesized and their structure determined from single-crystal or powder X-ray diffraction analyses. These isostructural compounds, which exhibit a novel structural arrangement, crystallize in the monoclinic system (space group P21/c) with the cell parameters a=17.4076(10) Å, b=11.1723(10) Å, c=19.2502(11) Å, β=149.731(3)° (V=1887.1(2) Å3, Z=4) and a=17.9690(14) Å, b=12.0607(5) Å, c=19.3109(16) Å, β=150.008(3)° (V=2091.98(16) Å3, Z=4) for Na3Cr2P3S12 (I) and K3Cr2P3S12 (II), respectively. For (I), the single-crystal refinement led to R/Rw(F2)=0.0417/0.0650 (for 4125 independent reflections and 182 refined parameters). For (II), the Rietveld refinement led to Rp/Rwp=0.0181/0.0233 (for 90 refined parameters). In both materials, the structures consist of 1∞[Cr2P3S12]3- chains built upon two edge-sharing [CrS6] octahedra capped by two [PS4] tetrahedra defining isolated [Cr2P2S12]-8 entities. These entities are linked to each other through an extra [PS4] tetrahedral group. Magnetic measurements evidence antiferromagnetic coupling between Cr3+ cations. The charge balance of the phase is MI3CrIII2PV3S-II12.

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

DOE PAGES

Zhang, Li; Popov, Dmitry; Meng, Yue; ...

2016-01-01

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

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

Zhang, Li; Popov, Dmitry; Meng, Yue

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

Improving virtual screening of G protein-coupled receptors via ligand-directed modeling

PubMed Central

Simms, John; Christopoulos, Arthur; Wootten, Denise

2017-01-01

G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology. In this study, we apply ligand-directed modeling (LDM) to available GPCR X-ray structures to improve VS performance and selectivity towards molecules of specific pharmacological profile. The described method refines a GPCR binding pocket conformation using a single known ligand for that GPCR. The LDM method is a computationally efficient, iterative workflow consisting of protein sampling and ligand docking. We developed an extensive benchmark comparing LDM-refined binding pockets to GPCR X-ray crystal structures across seven different GPCRs bound to a range of ligands of different chemotypes and pharmacological profiles. LDM-refined models showed improvement in VS performance over origin X-ray crystal structures in 21 out of 24 cases. In all cases, the LDM-refined models had superior performance in enriching for the chemotype of the refinement ligand. This likely contributes to the LDM success in all cases of inhibitor-bound to agonist-bound binding pocket refinement, a key task for GPCR SBDD programs. Indeed, agonist ligands are required for a plethora of GPCRs for therapeutic intervention, however GPCR X-ray structures are mostly restricted to their inactive inhibitor-bound state. PMID:29131821

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

Von Dreele, Robert

One of the goals in developing GSAS-II was to expand from the capabilities of the original General Structure Analysis System (GSAS) which largely encompassed just structure refinement and post refinement analysis. GSAS-II has been written almost entirely in Python loaded with graphics, GUI and mathematical packages (matplotlib, pyOpenGL, wxpython, numpy and scipy). Thus, GSAS-II has a fully developed modern GUI as well as extensive graphical display of data and results. However, the structure and operation of Python has required new approaches to many of the algorithms used in crystal structure analysis. The extensions beyond GSAS include image calibration/integration as wellmore » as peak fitting and unit cell indexing for powder data which are precursors for structure solution. Structure solution within GSAS-II begins with either Pawley or LeBail extracted structure factors from powder data or those measured in a single crystal experiment. Both charge flipping and Monte Carlo-Simulated Annealing techniques are available; the former can be applied to (3+1) incommensurate structures as well as conventional 3D structures.« less

A combined temperature-dependent electron and single-crystal X-ray diffraction study of the fresnoite compound Rb 2V 4+V 25+O 8

NASA Astrophysics Data System (ADS)

Withers, Ray L.; Höche, Thomas; Liu, Yun; Esmaeilzadeh, Saeid; Keding, Ralf; Sales, Brian

2004-10-01

High-purity Rb2V3O8 has been grown and temperature-dependent electron and single-crystal X-ray diffraction used to carefully investigate its fresnoite-type reciprocal lattice. In contrast to other recently investigated representatives of the fresnoite family of compounds, Rb2V3O8 is not incommensurately modulated with an incommensurate basal plane primary modulation wave vector given by q∼0.3 <110>*. A careful low-temperature electron diffraction study has, however, revealed the existence of weak incommensurate satellite reflections characterized by the primitive primary modulation wave vector q1∼0.16c*. The reciprocal space positioning of these incommensurate satellite reflections, the overall (3+1)-d superspace group symmetry, as well as the shapes of the refined displacement ellipsoids determined from single-crystal XRD refinement, are all consistent with their arising from a distinct type of condensed rigid unit modes (RUMs) of distortion of the Rb2V3O8 parent structure.

Synthesis, crystal structure investigation and magnetism of the complex metal-rich boride series Crx(Rh1-yRuy)7-xB3 (x=0.88-1; y=0-1) with Th7Fe3-type structure

NASA Astrophysics Data System (ADS)

Misse, Patrick R. N.; Mbarki, Mohammed; Fokwa, Boniface P. T.

2012-08-01

Powder samples and single crystals of the new complex boride series Crx(Rh1-yRuy)7-xB3 (x=0.88-1; y=0-1) have been synthesized by arc-melting the elements under purified argon atmosphere on a water-cooled copper crucible. The products, which have metallic luster, were structurally characterized by single-crystal and powder X-ray diffraction as well as EDX measurements. Within the whole solid solution range the hexagonal Th7Fe3 structure type (space group P63mc, no. 186, Z=2) was identified. Single-crystal structure refinement results indicate the presence of chromium at two sites (6c and 2b) of the available three metal Wyckoff sites, with a pronounced preference for the 6c site. An unexpected Rh/Ru site preference was found in the Ru-rich region only, leading to two different magnetic behaviors in the solid solution: The Rh-rich region shows a temperature-independent (Pauli) paramagnetism whereas an additional temperature-dependent paramagnetic component is found in the Ru-rich region.

Single crystals of the 96 K superconductor (Hg,Cu)Ba2CuO4+δ: Growth, structure and magnetism

NASA Astrophysics Data System (ADS)

Pelloquin, D.; Hardy, V.; Maignan, A.; Raveau, B.

1997-02-01

Single crystals of the 1201 (n = 1) (Hg,Cu)Ba2CuO4+δ mercury based cuprate have been grown by using a simple process without dry box. The as-synthesized crystals exhibit constant Tc(onset) of 96 K with sharp superconducting transitions. The electron microscopy coupled with EDX analyses evidence a ``1201''-type structure while a mercury deficiency is observed balanced by an excess of copper. The structural refinements based on single-crystal X-ray diffraction data confirm the electron deficiency on the Hg site (0,0,0) and show a splitting of the latter along the c axis correlated to the partial substitution of Cu for Hg. This structural study leads to the following formula Hg0.84Cu0.16Ba2CuO4.19. The magnetic study of a large crystal (1.1 × 0.38 × 0.065 mm3) shows that the (Hg,Cu)-1201 crystals exhibit an irreversibility line higher than that of the 1201 Hg0.8Bi0.2Ba2CuO4+δ crystal (Tc = 75 K). From the reversible magnetization, a λab(0) = 2470 Å value can be extrapolated. Using a 3D-2D decoupling formula, we obtain γ = 29 for the electronic anisotropy of this phase.

Low carrier semiconductor like behavior in Lu3Ir4Ge13 single crystal

NASA Astrophysics Data System (ADS)

Kumar, Anil; Matteppanavar, Shidaling; Thamizhavel, A.; Ramakrishnan, S.

2018-04-01

Single crystal of Lu3Ir4Ge13 crystallizing in the Yb3Rh4Sn13-type cubic crystal structure has been grown by Czochralski method in a tetra-arc furnace. In this paper we report on the crystal structure, magnetic and transport properties of Lu3Ir4Ge13. The analysis of the powder x-ray diffraction (XRD) studies revealed that Lu3Ir4Ge13 crystallizes in a cubic structure with the space group Pm-3n, no. 223. The lattice parameter was obtained from the Rietveld refinement of the room temperature XRD data which amounts to 8.904 (3) Å with low R factors. The temperature dependence of the resistivity exhibited semiconductor like behavior till 1.8 K, with a broad hump around 15 - 62 K. This hump was observed in both warming and cooling cycle with a very small hysteresis, it may be due to the existence of structural transition from high - low symmetry. The temperature dependent magnetization data shows the diamagnetic behavior with an anomaly around 70 K, which is well supported by the derivative of resistivity data.

Study of the specific features of single-crystal boron microstructure

NASA Astrophysics Data System (ADS)

Blagov, A. E.; Vasil'ev, A. L.; Dmitriev, V. P.; Ivanova, A. G.; Kulikov, A. G.; Marchenkov, N. V.; Popov, P. A.; Presnyakov, M. Yu.; Prosekov, P. A.; Pisarevskii, Yu. V.; Targonskii, A. V.; Chernaya, T. S.; Chernyshov, D. Yu.

2017-09-01

A complex study of the structure of β-boron single crystal grown by the floating-zone method, with sizes significantly exceeding the analogs known in the literature, has been performed. The study includes X-ray diffraction analysis and X-ray diffractometry (measurement of pole figures and rocking curves), performed on both laboratory and synchrotron sources; atomic-resolution scanning transmission electron microscopy with spherical aberration correction; and energy-dispersive microanalysis. X-ray diffraction analysis using synchrotron radiation has been used to refine the β-boron structure and find impurity Si atoms. The relative variations in the unit-cell parameters a and c for the crystal bulk are found to be δ a/ a ≈ 0.4 and δ c/ c ≈ 0.1%. X-ray diffractometry has revealed that the single-crystal growth axis coincides with the [2\\bar 2013] crystallographic axis and makes an angle of 21.12° with the [0001] threefold axis. Electron microscopy data have confirmed that the sample under study is a β-boron crystal, which may contain 0.3-0.4 at % Si as an impurity. Planar defects (stacking faults and dislocations) are found. The results of additional measurements of the temperature dependence of the thermal conductivity of the crystal in the range of 50-300 K are indicative of its high structural quality.

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

Absolute Configuration of Andrographolide and Its Proliferation of Osteoblast Cell Lines

NASA Astrophysics Data System (ADS)

Chantrapromma, S.; Boonnak, N.; Pitakpornpreecha, T.; Yordthong, T.; Chidan Kumar, C. S.; Fun, H. K.

2018-05-01

Andrographolide, C20H30O5, is a labdane diterpenoid which was isolated from the leave of Andrographis paniculata. Its crystal structure is determined by single crystal X-ray diffraction: monoclinic, sp. gr. P21, Z = 2. Absolute configuration is determined by the refinement of the Flack parameter to 0.21(19). In the crystal, molecules are linked by O-H···O hydrogen bonds and C-H···O interactions into two dimensional network parallel to the (001) plane. Its proliferation of osteoblast cell lines is reported.

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.

Structural and electronic evolution of Cr[subscript 2]O[subscript 3] on compression to 55 GPa

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

Dera, Przemyslaw; Lavina, Barbara; Meng, Yue

2016-08-15

Synchrotron single-crystal x-ray diffraction experiments have been performed on corundum-type Cr{sub 2}O{sub 3} up to a pressure of 55 GPa in Ne and He pressure transmitting media. Diffraction experiments were complemented by measurements of optical absorption spectra with single crystal samples up to 60 GPa. Results of the diffraction data analysis rule out the earlier reported monoclinic distortion at 15-30 GPa, but indicate evidence of two discontinuous transitions of electronic or magnetic nature, most likely associated with a change in magnetic ordering and charge transfer. The compression mechanism established from single crystal refinements indicates much smaller distortion of the Cr{supmore » 3+} coordination environment than was previously assumed.« less

Significance of structural changes in proteins: expected errors in refined protein structures.

PubMed Central

Stroud, R. M.; Fauman, E. B.

1995-01-01

A quantitative expression key to evaluating significant structural differences or induced shifts between any two protein structures is derived. Because crystallography leads to reports of a single (or sometimes dual) position for each atom, the significance of any structural change based on comparison of two structures depends critically on knowing the expected precision of each median atomic position reported, and on extracting it for each atom, from the information provided in the Protein Data Bank and in the publication. The differences between structures of protein molecules that should be identical, and that are normally distributed, indicating that they are not affected by crystal contacts, were analyzed with respect to many potential indicators of structure precision, so as to extract, essentially by "machine learning" principles, a generally applicable expression involving the highest correlates. Eighteen refined crystal structures from the Protein Data Bank, in which there are multiple molecules in the crystallographic asymmetric unit, were selected and compared. The thermal B factor, the connectivity of the atom, and the ratio of the number of reflections to the number of atoms used in refinement correlate best with the magnitude of the positional differences between regions of the structures that otherwise would be expected to be the same. These results are embodied in a six-parameter equation that can be applied to any crystallographically refined structure to estimate the expected uncertainty in position of each atom. Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters. PMID:8563637

Single-crystal diffraction at the Extreme Conditions beamline P02.2: procedure for collecting and analyzing high-pressure single-crystal data.

PubMed

Rothkirch, André; Gatta, G Diego; Meyer, Mathias; Merkel, Sébastien; Merlini, Marco; Liermann, Hanns Peter

2013-09-01

Fast detectors employed at third-generation synchrotrons have reduced collection times significantly and require the optimization of commercial as well as customized software packages for data reduction and analysis. In this paper a procedure to collect, process and analyze single-crystal data sets collected at high pressure at the Extreme Conditions beamline (P02.2) at PETRA III, DESY, is presented. A new data image format called `Esperanto' is introduced that is supported by the commercial software package CrysAlis(Pro) (Agilent Technologies UK Ltd). The new format acts as a vehicle to transform the most common area-detector data formats via a translator software. Such a conversion tool has been developed and converts tiff data collected on a Perkin Elmer detector, as well as data collected on a MAR345/555, to be imported into the CrysAlis(Pro) software. In order to demonstrate the validity of the new approach, a complete structure refinement of boron-mullite (Al5BO9) collected at a pressure of 19.4 (2) GPa is presented. Details pertaining to the data collections and refinements of B-mullite are presented.

Modelling dynamics in protein crystal structures by ensemble refinement

PubMed Central

Burnley, B Tom; Afonine, Pavel V; Adams, Paul D; Gros, Piet

2012-01-01

Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated Rfree values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a ‘molten core’ likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships. DOI: http://dx.doi.org/10.7554/eLife.00311.001 PMID:23251785

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.

Center for Macromolecular Crystallography, University of Alabama in Birmingham

NASA Technical Reports Server (NTRS)

Navia, Manuel A.

1991-01-01

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

Single crystal X-ray diffraction study of the HgBa2CuO4+δ superconducting compound

NASA Astrophysics Data System (ADS)

Bordet, P.; Duc, F.; Lefloch, S.; Capponi, J. J.; Alexandre, E.; Rosa-Nunes, M.; Antipov, E. V.; Putilin, S.

1996-02-01

A high precision X-ray diffraction analysis up to sin θ/λ = 1.15 of a HgBa2CuO4+δ single crystal having a Tc of ~ 90 K is presented. The cell parameters are a = 3.8815(4), c = 9.485 (7) Å. The refinements indicate the existence of a split barium site due to the presence of excess oxygen in the mercury layer. The position of this excess oxygen might be slightly displaced from the (1/2 1/2 0) position. A 6% mercury deficiency is observed. Models, including mercury defects, substitution by copper cations, or carbonate groups, are compared. However, we obtain no definite evidence for either of the three models. A possible disorder of the Hg position, due to the formation of chemical bonds with neighbouring extra oxygen anions, could correlate to the refinements of mixed species at the Hg site. A low temperature single crystal x-ray diffraction study, and comparison of refinements for the same single crystal with different extra oxygen contents, are in progress to help clarify this problem.

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

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

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2016-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:27248784

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2010-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy and neutron diffraction are well established and have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches and high-speed computing and visualization, now provide specialists and non-specialists alike with a steady flow of molecular images of unprecedented detail. The present chapter combines a general overview of diffraction methods with a step-by-step description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:20517991

Diffraction Techniques in Structural Biology.

PubMed

Egli, Martin

2016-06-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Accurate X-ray diffraction studies of KTiOPO{sub 4} single crystals doped with niobium

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

Novikova, N. E., E-mail: natnov@ns.crys.ras.ru; Sorokina, N. I.; Alekseeva, O. A.

2017-01-15

Single crystals of potassium titanyl phosphate doped with 4% of niobium (КТР:4%Nb) and 6% of niobium (KTP:6%Nb) are studied by accurate X-ray diffraction at room temperature. The niobium atoms are localized near the Ti1 and Ti2 atomic positions, and their positions are for the first time refined independent of the titanium atomic positions. Maps of difference electron density in the vicinity of K1 and K2 atomic positions are analyzed. It is found that in the structure of crystal КТР:4%Nb, additional positions of K atoms are located farther from the main positions and from each other than in КТР and KTP:6%Nbmore » crystals. The nonuniform distribution of electron density found in the channels of the КТР:4%Nb structure is responsible for ~20% increase in the signal of second harmonic generation.« less

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

PubMed

Rodrigues, João P G L M; Levitt, Michael; Chopra, Gaurav

2012-07-01

The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.

Purification, crystallization and initial crystallographic characterization of the Ginkgo biloba 11S seed globulin ginnacin

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

Jin, Tengchuan; Chen, Yu-Wei; Howard, Andrew

2008-07-01

The crystallization of ginnacin, the 11S seed storage protein from G. biloba, is reported. Ginkgo biloba, a well known ‘living fossil’ native to China, is grown worldwide as an ornamental shade plant. Medicinal and nutritional uses of G. biloba in Asia have a long history. However, ginkgo seed proteins have not been well studied at the biochemical and molecular level. In this study, the G. biloba 11S seed storage protein ginnacin was purified by sequential anion-exchange and gel-filtration chromatography. A crystallization screen was performed and well diffracting single crystals were obtained by the vapor-diffusion method. A molecular-replacement structural solution hasmore » been obtained. There are six protomers in an asymmetric unit. Structure refinement is currently in progress.« less

Hydrogen bonding in goldichite, KFe(SO4)2ṡ4H2O: structure refinement

NASA Astrophysics Data System (ADS)

Yang, Zhuming; Giester, Gerald

2018-02-01

The crystal structure of goldichite KFe(SO4)2ṡ4H2O was determined on a single crystal from the Baiyinchang copper deposit, Gansu, China. [ P121/ c1, a = 10.395(2), b = 10.475(2), c = 9.0875(18) Å, β = 101.65(3)°, V = 969.1(3) Å3, Z = 4]. All non-H atoms were refined with anisotropic displacement parameters and positions of H-atoms were determined by difference Fourier methods and refined from X-ray diffraction data. The crystal structure of goldichite consists of corrugated sheets parallel to the (100) plane by sharing corners between FeO6 octahedra and SO4 tetrahedra. The interstitial potassium atom exhibits a [KO7(H2O)2] nine-fold coordination, which shares edges to form a column parallel to the c-axis and to build a slab with the corrugated sheet. These slabs are linked in the [100] direction through a network of hydrogen bonds. Three types of hydrogen bonds involve links of slabs: Ow(3)-H(3B)···O(1), Ow(6)-H(6B)···O(11) and Ow(9)-H(9B)···O(11). The FTIR spectrum of goldichite shows a strong absorption between 3384 cm-1 and 3592 cm-1, which is in accordance with the O-H···O distances derived from structure data.

Crystal structure of the non-stoichiometric argyrodite compound Ag 7- xGeSe 5I 1- x ( x=0.31). A highly disordered silver superionic conducting material

NASA Astrophysics Data System (ADS)

Belin, Renaud; Aldon, Laurent; Zerouale, Abdel; Belin, Claude; Ribes, Michel

2001-03-01

Single crystals of the Ag 6.69GeSe 5I 0.69 phase have been obtained by iodine transport of the iodine-partially substituted stoichiometric argyrodite compound Ag 7GeSe 5I. This phase crystallizes in the cubic space group F4¯3 m (argyrodite γ-phase, a=10.921(2) Å at -100°C, a=10.972(3) Å at 25°C, Z=4). It is highly disordered both at anion and cation sites. Crystal structure refinements were completed by an anharmonic Gram-Charlier development of the atomic displacement factors of iodine and silver atoms. The structure of Ag 6.69GeSe 5I 0.69 was determined at -100°C and +25°C and was refined to R( F) values of 5.80 and 6.51%, respectively. Both iodine and selenium (Se1) anions have been found disordered and iodine is slightly defective on its crystallographic site. This is correlated to the disorder observed for the two Ag1 and Ag2 cations that provides this material with superionic conducting properties. Analysis of the joint probability density function allowed the visualization of the Ag + diffusion paths within the anionic framework.

The single-crystal structure of the organic superconductor betaCO-(BEDT-TTF)2I3 from a powder grain.

PubMed

Madsen; Burghammer; Fiedler; Müller

1999-08-01

Synchrotron radiation diffraction data have been collected at 200 K on a microscopic single crystal (dimensions 12 x 10 x 2 µm) of the title compound, where BEDT-TTF is bis(ethylenedithio)tetrathiafulvalene, C(10)H(8)S(8). The quality of the diffraction data allowed a full structure refinement and enabled the determination of structural details such as the conformations of the ethylene groups as well as the occupancy of the triiodide sites. The compound was found to be slightly iodine-deficient and better described as beta(CO)-(BEDT-TTF)(2)I(3-x) [x = 0.014 (3)]. One of the ethylene groups of the BEDT-TTF cation is disordered at this temperature and exists in two distinct conformations with occupancies which are identical within the standard uncertainty.

Synthesis, crystal structure refinement, and nonlinear-optical properties of CaB{sub 3}O{sub 5}(OH): Comparative crystal chemistry of calcium triborates

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

Yamnova, N. A., E-mail: aks.crys@gmail.com; Aksenov, S. M.; Stefanovich, S. Yu.

Calcium triborate CaB{sub 3}O5(OH) obtained by hydrothermal synthesis in the Ca(OH){sub 2}–H{sub 3}BO{sub 3}–Na{sub 2}CO{sub 3}–KCl system is studied by single-crystal X-ray diffraction. The parameters of the orthorhombic unit cell are as follows: a = 13.490(1), b = 6.9576(3), and c = 4.3930(2) Å; V = 412.32(3) Å{sup 3} and space group Pna2{sub 1}. The structure is refined in the anisotropic approximation of the atomic displacement parameters to R = 4.28% using 972 vertical bar F vertical bar > 4σ(F). It is confirmed that the crystal structure of Ca triborate CaB{sub 3}O{sub 5}(OH) is identical to that described earlier. Themore » hydrogen atom is localized. An SHG signal stronger than that of the quartz standard is registered. The phase transition of calcium triborate into calciborite is found on heating. The comparative crystal-chemical analysis of a series of borates with the general chemical formula 2CaO · 3B{sub 2}O{sub 3} · nH{sub 2}O (n = 0–13) with the constant CaO: B{sub 2}O{sub 3}= 2: 3 ratio and variable content of water is performed.« less

Integration of neutron time-of-flight single-crystal Bragg peaks in reciprocal space

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

Schultz, Arthur J; Joergensen, Mads; Wang, Xiaoping

2014-01-01

The intensity of single crystal Bragg peaks obtained by mapping neutron time-of-flight event data into reciprocal space and integrating in various ways are compared. These include spherical integration with a fixed radius, ellipsoid fitting and integrating of the peak intensity and one-dimensional peak profile fitting. In comparison to intensities obtained by integrating in real detector histogram space, the data integrated in reciprocal space results in better agreement factors and more accurate atomic parameters. Furthermore, structure refinement using integrated intensities from one-dimensional profile fitting is demonstrated to be more accurate than simple peak-minus-background integration.

Ottensite, brizziite and mopungite from Pereta mine (Tuscany, Italy): new occurrences and crystal structure refinement of mopungite

NASA Astrophysics Data System (ADS)

Bittarello, Erica; Cámara, Fernando; Ciriotti, Marco E.; Marengo, Alessandra

2015-08-01

Ottensite, Na3 (Sb2O3)(SbS3)·3H2O, brizziite, NaSbO3, and mopungite, NaSb(OH)6, have been found on several specimens from the antimony mine of Pereta (Grosseto, Tuscany, Italy). Ottensite from Pereta mine occurs as brilliant reddish-brown spheroidal aggregates, with a diameter up to 0.2 mm, formed by radially oriented individuals. These aggregates are associated with well-shaped tabular and pseudocubic colourless crystals of mopungite and platy aggregates of brizziite. This is the second world occurrence of ottensite and brizziite. The mineral species were characterized by electron microprobe analysis, X-ray diffraction study and microRaman spectroscopy. Single-crystal X-ray diffraction data were collected on a twinned crystal of mopungite and the structure was for the first time refined on a natural sample in space group P42/ n [unit cell parameters a = 8.036(3) Å, c = 7.926(6) Å, V = 511.88(5) Å3, Z = 4] obtaining an R 1 -index of 5.17, wR 2 of 13.52 and GooF of 1.247.

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

Layered Structure and Swelling Behavior of a Multiple Hydrate-Forming Pharmaceutical Compound

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

Kiang, Y.; Xu, W; Stephens, P

2009-01-01

Investigation of one anhydrous and four hydrated forms of a pharmaceutical compound (1) using both single-crystal and high-resolution powder X-ray diffraction methods revealed a two-dimensional framework which, upon exposure to moisture, absorbed water between the layers, causing the lattice to expand by as much as 20% of the axial length along a. The single-crystal structure was solved and refined for the pentahydrate form in space group C2 with unit cell parameters a = 36.961(5) Angstroms, b = 7.458(2) Angstroms, c = 20.691(4) Angstroms, e = 99.461(1), and V = 5626(4) Angstroms3. In the single-crystal structure the water layers were parallelmore » to the bc plane and sandwiched by the crystalline compound 1 framework. Upon a change of relative humidity, water goes in and out of the interlayer space with the retention of the layer structure of the development compound. Starting from the anhydrous form, each additional water of hydration increased the interlayer spacing of the pharmaceutical solid by 1.3 Angstroms, half the size of a water molecule. In an exploratory formulation, this expansion of interlayer spacing caused tablets to crack upon storage at high relative humidity.« less

Crystal Structure and Ferroelectric Properties of ε-Ga2O3 Films Grown on (0001)-Sapphire.

PubMed

Mezzadri, Francesco; Calestani, Gianluca; Boschi, Francesco; Delmonte, Davide; Bosi, Matteo; Fornari, Roberto

2016-11-21

The crystal structure and ferroelectric properties of ε-Ga 2 O 3 deposited by low-temperature MOCVD on (0001)-sapphire were investigated by single-crystal X-ray diffraction and the dynamic hysteresis measurement technique. A thorough investigation of this relatively unknown polymorph of Ga 2 O 3 showed that it is composed of layers of both octahedrally and tetrahedrally coordinated Ga 3+ sites, which appear to be occupied with a 66% probability. The refinement of the crystal structure in the noncentrosymmetric space group P6 3 mc pointed out the presence of uncompensated electrical dipoles suggesting ferroelectric properties, which were finally demonstrated by independent measurements of the ferroelectric hysteresis. A clear epitaxial relation is observed with respect to the c-oriented sapphire substrate, with the Ga 2 O 3 [10-10] direction being parallel to the Al 2 O 3 direction [11-20], yielding a lattice mismatch of about 4.1%.

X-ray structure determination at low resolution

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

Brunger, Axel T., E-mail: brunger@stanford.edu; Department of Molecular and Cellular Physiology, Stanford University; Department of Neurology and Neurological Sciences, Stanford University

2009-02-01

Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alonemore » was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible.« less

High-pressure behavior of intermediate scapolite: compressibility, structure deformation and phase transition

NASA Astrophysics Data System (ADS)

Lotti, Paolo; Comboni, Davide; Merlini, Marco; Hanfland, Michael

2018-05-01

Scapolites are common volatile-bearing minerals in metamorphic rocks. In this study, the high-pressure behavior of an intermediate member of the scapolite solid solution series (Me47), chemical formula (Na1.86Ca1.86K0.23Fe0.01)(Al4.36Si7.64)O24[Cl0.48(CO3)0.48(SO4)0.01], has been investigated up to 17.79 GPa, by means of in situ single-crystal synchrotron X-ray diffraction. The isothermal elastic behavior of the studied scapolite has been described by a III-order Birch-Murnaghan equation of state, which provided the following refined parameters: V 0 = 1110.6(7) Å3, {K_{{V_0}}} = 70(2) GPa ({β _{{V_0}}} = 0.0143(4) GPa-1) and {K_{{V}}^' = 4.8(7). The refined bulk modulus is intermediate between those previously reported for Me17 and Me68 scapolite samples, confirming that the bulk compressibility among the solid solution increases with the Na content. A discussion on the P-induced structure deformation mechanisms of tetragonal scapolite at the atomic scale is provided, along with the implications of the reported results for the modeling of scapolite stability. In addition, a single-crystal to single-crystal phase transition, which is displacive in character, has been observed toward a triclinic polymorph at 9.87 GPa. The high-pressure triclinic polymorph was found to be stable up to the highest pressure investigated.

Advanced Structural Analyses by Third Generation Synchrotron Radiation Powder Diffraction

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

Sakata, M.; Aoyagi, S.; Ogura, T.

2007-01-19

Since the advent of the 3rd generation Synchrotron Radiation (SR) sources, such as SPring-8, the capabilities of SR powder diffraction increased greatly not only in an accurate structure refinement but also ab initio structure determination. In this study, advanced structural analyses by 3rd generation SR powder diffraction based on the Large Debye-Scherrer camera installed at BL02B2, SPring-8 is described. Because of high angular resolution and high counting statistics powder data collected at BL02B2, SPring-8, ab initio structure determination can cope with a molecular crystals with 65 atoms including H atoms. For the structure refinements, it is found that a kindmore » of Maximum Entropy Method in which several atoms are omitted in phase calculation become very important to refine structural details of fairy large molecule in a crystal. It should be emphasized that until the unknown structure is refined very precisely, the obtained structure by Genetic Algorithm (GA) or some other ab initio structure determination method using real space structural knowledge, it is not possible to tell whether the structure obtained by the method is correct or not. In order to determine and/or refine crystal structure of rather complicated molecules, we cannot overemphasize the importance of the 3rd generation SR sources.« less

Conformational Analysis of Free and Bound Retinoic Acid

PubMed Central

Fu, Zheng; Li, Xue; Merz, Kenneth M.

2012-01-01

The conformational profiles of unbound all-trans and 9-cis retinoic acid (RA) have been determined using classical and quantum mechanical calculations. Sixty-six all-trans-RA (ATRA) and forty-eight 9-cis-RA energy minimum conformers were identified via HF/6-31G* geometry optimizations in vacuo. Their relative conformational energies were estimated utilizing the M06, M06-2x and MP2 methods combined with the 6-311+G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets, as well as complete basis set MP2 extrapolations using the latter two basis sets. Single-point energy calculations performed with the M06-2x density functional were found to yield similar results to MP2/CBS for the low-energy retinoic acid conformations. Not unexpectedly, the conformational propensities of retinoic acid were governed by the orientation and arrangement of the torsion angles associated with the polyene tail. We also used previously reported QM/MM X-ray refinement results on four ATRA-protein crystal structures plus one newly refined 9-cis-RA complex (PDB ID 1XDK) in order to investigate the conformational preferences of bound retinoic acid. In the re-refined RA conformers the conjugated double bonds are nearly coplanar, which is consistent with the global minimum identified by the Omega/QM method rather than the corresponding crystallographically determined conformations given in the PDB. Consequently, a 91.3% average reduction of the local strain energy in the gas phase, as well as 92.1% in PCM solvent, was observed using the QM/MM refined structures versus the PDB deposited RA conformations. These results thus demonstrate that our QM/MM X-ray refinement approach can significantly enhance the quality of X-ray crystal structures refined by conventional refinement protocols, thereby providing reliable drug-target structural information for use in structure-based drug discovery applications. PMID:22844234

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 data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

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 molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

On the labyrinthine world of arsenites: a single-crystal neutron and X-ray diffraction study of cafarsite

NASA Astrophysics Data System (ADS)

Gatta, G. Diego; Rotiroti, Nicola; Cámara, Fernando; Meven, Martin

2018-03-01

The crystal chemistry of a cafarsite sample from the fengitic orthogneisses of the Mt. Leone-Arbola nappe (Lower Penninic), forming the central body of Mount Cervandone and cropping out both in Switzerland and Italy (Alpe Devero area, Verbano-Cusio-Ossola province), was investigated by electron microprobe analysis in wavelength-dispersive mode (EPMA-WDS), single-crystal Raman spectroscopy, and single-crystal X-ray and neutron diffraction at 293 K. The sample of cafarsite of this study was found experimentally to be anhydrous and the chemical formula obtained on the basis of the EPMA-WDS data and structural refinements is the following: Ca1,Ca2 (Ca15.56Na0.44)Σ16 Fe1 (Na0.53Fe2+ 0.17REE0.30)Σ1.00 Mn1,Ti,Fe2 (Ti7.46Fe3+ 4.47Fe2+ 3.20Mn2+ 0.85Al0.11) Σ16.11 As1,As2,As3 (AsO3)28 F F, with the general chemical formula Ca16(Na,Fe2+,REE)(Ti, Fe3+,Fe2+,Mn2+,Al)16(AsO3)28F [or Ca16(Na,Fe2+,REE)(Ti,Fe3+,Al)12(Fe2+,Mn)4(AsO3)28F]. Our experimental findings show that fluorine, which was unconsidered in the previous studies, is a key element. The anhydrous nature of this sample is also confirmed by its Raman spectrum, which does not show any evidence of active bands ascribable to the O-H stretching region. The X-ray and neutron structure refinements provide a structure model that is partially in agreement with the previous experimental findings. The space group (i.e. Pn3) and the unit-cell constant [i.e. 15.9507(4) Å] are conform to the literature data, but the structure of cafarsite, here refined, contains the following building units: three independent AsO3 groups (trigonal pyramids), one CaO6F polyhedron, one CaO8 polyhedron, two independent (Ti,Fe)O6 octahedra, one (Na,Fe,REE)O8 polyhedron, and one (Mn,Fe)O6 octahedron. Connections among polyhedra are mainly due to edge- or vertex-sharing; the AsO3 groups are not connected to each other.

Synthesis, crystal growth and characterization of bioactive material: 2- Amino-1H-benzimidazolium pyridine-3-carboxylate single crystal- a proton transfer molecular complex

NASA Astrophysics Data System (ADS)

Fathima, K. Saiadali; Kavitha, P.; Anitha, K.

2017-09-01

The 1:1 molecular adducts 2- Amino-1H-benzimidazolium pyridine-3-carboxylate (2ABPC) was synthesized and grown as single crystal where 2-aminobenzimidazole (ABI) acts as a donor and nicotinic acid (NA) acts as an acceptor. The presence of proton and carbon were predicted using 1H and 13C NMR spectral analysis. The molecular structure of the crystal was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R = 0.038 for 2469 reflections. The vibrational modes of functional group have been studied using FTIR and Raman spectroscopic analysis. The UV-Vis spectrum exhibited a visible band at 246 nm for 2ABPC due to the nicotinate anion of the molecule. Further, the antimicrobial activity of 2ABPC complex against B. subtilis, klebsiella pneumonia, Pseudomonas eruginos and E. coli pathogens was investigated. Minimum Inhibitory Concentration (MIC) for this crystal was obtained using UV spectrometer against MRSA pathogen. It was found that the benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of 2ABPC crystal.

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

PubMed

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

2007-05-01

A new polymorphic form of Alprazolam (Xanax), 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo-[4,3-alpha][1,4]benzodiazepine, C(17)H(13)ClN(4), has been investigated by means of X-ray powder diffraction (XRPD), single crystal X-ray diffraction, and differential scanning calorimetry (DSC). This polymorphic form (form III) was obtained during DSC experiments after the exothermic recrystallization of the melt of form I. The crystal unit cell dimensions for form III were determined from diffractometer methods. The monoclinic unit cell found for this polymorph using XRPD after indexing the powder diffractogram was confirmed by the cell parameters obtained from single crystal X-ray diffractometry on a crystal isolated from the DSC pans. The single crystal unit cell parameters are: a = 28.929(9), b = 13.844(8), c = 7.361(3) angstroms, beta = 92.82(3) degrees , V = 2944(2) angstroms(3), Z = 8, space group P2(1) (No.4), Dx = 1.393 Mg/m(3). The structure obtained from single crystal X-ray diffraction was used as initial model for Rietveld refinement on the powder diffraction data of form III. The temperature phase transformations of alprazolam were also studied using high temperature XRPD. A review of the different phases available in the Powder Diffraction File (PDF) database for this drug is described bringing some clarification and corrections. (c) 2007 Wiley-Liss, Inc. and the American Pharmacists Association.

Purification of Germanium Crystals by Zone Refining

NASA Astrophysics Data System (ADS)

Kooi, Kyler; Yang, Gang; Mei, Dongming

2016-09-01

Germanium zone refining is one of the most important techniques used to produce high purity germanium (HPGe) single crystals for the fabrication of nuclear radiation detectors. During zone refining the impurities are isolated to different parts of the ingot. In practice, the effective isolation of an impurity is dependent on many parameters, including molten zone travel speed, the ratio of ingot length to molten zone width, and number of passes. By studying the theory of these influential factors, perfecting our cleaning and preparation procedures, and analyzing the origin and distribution of our impurities (aluminum, boron, gallium, and phosphorous) identified using photothermal ionization spectroscopy (PTIS), we have optimized these parameters to produce HPGe. We have achieved a net impurity level of 1010 /cm3 for our zone-refined ingots, measured with van der Pauw and Hall-effect methods. Zone-refined ingots of this purity can be processed into a detector grade HPGe single crystal, which can be used to fabricate detectors for dark matter and neutrinoless double beta decay detection. This project was financially supported by DOE Grant (DE-FG02-10ER46709) and the State Governor's Research Center.

Structure and magnetic properties of Ce₃(Ni/Al/Ga)₁₁—A new phase with the La₃Al₁₁ structure type

DOE PAGES

Janka, Oliver; Shang, Tian; Baumbach, Ryan E.; ...

2015-03-01

Single crystals of Ce₃(Ni/Al/Ga)₁₁ were obtained from an Al flux reaction. Single crystals of the title compound crystallizing in the orthorhombic space group Immm (No. 71, Z = 2) with a = 436.38(14), b = 1004.5(3) and c = 1293.4(4) pm. This is a standardized unit cell of the previously published La₃Al₁₁ structure type. Wavelength dispersive microprobe provides the composition of Ce₃.₁₁₍₁₎Ni₀.₀₃₍₁₎Al₈.₉₅₍₁₎Ga₁.₉₀₍₁₎. Single crystal refinement provides the composition Ce₃Ni₀.₀₈Al₉.₁₃Ga₁.₇₈ with substitution of the Ni and Ga on the Al1 and Al4 sites with the Al2 and Al3 solely occupied by Al. Magnetic susceptibility measurements reveal antiferromagnetic ordering with T Nmore » = 4.8 K and there is no evidence for a ferromagnetic ordering that has been reported for Ce₃Al₁₁. The effective magnetic moment was found to be μ eff = 1.9μB/Ce, which is lower than the expected value for trivalent Ce (2.54μB/Ce).« less

Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity.

PubMed Central

Prasad, G. S.; Radhakrishnan, R.; Mitchell, D. T.; Earhart, C. A.; Dinges, M. M.; Cook, W. J.; Schlievert, P. M.; Ohlendorf, D. H.

1997-01-01

The structure of toxic shock syndrome toxin-1 (TSST-1), the causative agent in toxic shock syndrome, has been determined in three crystal forms. The three structural models have been refined to R-factors of 0.154, 0.150, and 0.198 at resolutions of 2.05 A, 2.90 A, and 2.75 A, respectively. One crystal form of TSST-1 contains a zinc ion bound between two symmetry-related molecules. Although not required for biological activity, zinc dramatically potentiates the mitogenicity of TSST-1 at very low concentrations. In addition, the structure of the tetramutant TSST-1H [T69I, Y80W, E132K, I140T], which is nonmitogenic and does not amplify endotoxin shock, has been determined and refined in a fourth crystal form (R-factor = 0.173 to 1.9 A resolution). PMID:9194182

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

Guo, Feng; Jin, Tengchuan; Howard, Andrew

The crystallization of the brazil nut allergen Ber e 2 is reported. Peanut and tree-nut allergies have attracted considerable attention because of their frequency and their lifelong persistence. Brazil-nut (Bertholletia excelsa) allergies have been well documented and the 11S legumin-like seed storage protein Ber e 2 (excelsin) is one of the two known brazil-nut allergens. In this study, Ber e 2 was extracted from brazil-nut kernels and purified to high purity by crystalline precipitation and gel-filtration chromatography. Well diffracting single crystals were obtained using the hanging-drop vapour-diffusion method. A molecular-replacement structural solution has been obtained. Refinement of the structure ismore » currently under way.« less

Magnetic and crystal structures of the honeycomb lattice Na2IrO3 and single layer Sr2IrO4

NASA Astrophysics Data System (ADS)

Ye, Feng

2013-03-01

5 d based iridates have recently attracted great attention due to the large spin-orbit coupling (SOC). It is now recognized that the SOC that competes with other relevant energies, particularly the on-site Coulomb interaction U, and have driven novel electronic and magnetic phases. Combining single crystal neutron and x-ray diffractions, we have investigated the magnetic and crystal structures of the honeycomb lattice Na2IrO3. The system orders magnetically below 18.1 K with Ir4+ ions forming zigzag spin chains within the layered honeycomb network with ordered moment of 0.22 μB /Ir site. Such a configuration sharply contrasts the Neel or stripe states proposed in the Kitaev-Heisenberg model. The structure refinement reveals that the Ir atoms form nearly ideal 2D honeycomb lattice while the IrO6 octahedra experience a trigonal distortion that is critical to the ground state. The results of this study provide much-needed experimental insights into the magnetic and crystal structure crucial to the understanding of the exotic magnetic order and possible topological characteristics in the 5 d-electron based honeycomb lattice. Neutron diffraction experiments are also performed to investigate the magnetic and crystal structure of the single layer iridate Sr2IrO4, where new structural information and spin order are obtained that is not available from previous neutron powder diffraction measurement. This work was sponsored in part by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy.

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Structure refinement of the δ1p phase in the Fe-Zn system by single-crystal X-ray diffraction combined with scanning transmission electron microscopy.

PubMed

Okamoto, Norihiko L; Tanaka, Katsushi; Yasuhara, Akira; Inui, Haruyuki

2014-04-01

The structure of the δ1p phase in the iron-zinc system has been refined by single-crystal synchrotron X-ray diffraction combined with scanning transmission electron microscopy. The large hexagonal unit cell of the δ1p phase with the space group of P63/mmc comprises more or less regular (normal) Zn12 icosahedra, disordered Zn12 icosahedra, Zn16 icosioctahedra and dangling Zn atoms that do not constitute any polyhedra. The unit cell contains 52 Fe and 504 Zn atoms so that the compound is expressed with the chemical formula of Fe13Zn126. All Fe atoms exclusively occupy the centre of normal and disordered icosahedra. Iron-centred normal icosahedra are linked to one another by face- and vertex-sharing forming two types of basal slabs, which are bridged with each other by face-sharing with icosioctahedra, whereas disordered icosahedra with positional disorder at their vertex sites are isolated from other polyhedra. The bonding features in the δ1p phase are discussed in comparison with those in the Γ and ζ phases in the iron-zinc system.

The importance of proper crystal-chemical and geometrical reasoning demonstrated using layered single and double hydroxides

PubMed Central

Richardson, Ian G.

2013-01-01

Atomistic modelling techniques and Rietveld refinement of X-ray powder diffraction data are widely used but often result in crystal structures that are not realistic, presumably because the authors neglect to check the crystal-chemical plausibility of their structure. The purpose of this paper is to reinforce the importance and utility of proper crystal-chemical and geometrical reasoning in structural studies. It is achieved by using such reasoning to generate new yet fundamental information about layered double hydroxides (LDH), a large, much-studied family of compounds. LDH phases are derived from layered single hydroxides by the substitution of a fraction (x) of the divalent cations by trivalent. Equations are derived that enable calculation of x from the a parameter of the unit cell and vice versa, which can be expected to be of widespread utility as a sanity test for extant and future structure determinations and computer simulation studies. The phase at x = 0 is shown to be an α form of divalent metal hydroxide rather than the β polymorph. Crystal-chemically sensible model structures are provided for β-Zn(OH)2 and Ni- and Mg-based carbonate LDH phases that have any trivalent cation and any value of x, including x = 0 [i.e. for α-M(OH)2·mH2O phases]. PMID:23719702

Pressure-induced changes of the structure and properties of monoclinic α -chalcocite Cu2S

NASA Astrophysics Data System (ADS)

Zimmer, D.; Ruiz-Fuertes, J.; Morgenroth, W.; Friedrich, A.; Bayarjargal, L.; Haussühl, E.; Santamaría-Pérez, D.; Frischkorn, S.; Milman, V.; Winkler, B.

2018-04-01

The high-pressure behavior of monoclinic (P 21/c ) α -chalcocite, Cu2S , was investigated at ambient temperature by single-crystal x-ray diffraction, electrical resistance measurements, and optical absorption spectroscopy up to 16 GPa. The experiments were complemented by density-functional-theory-based calculations. Single-crystal x-ray diffraction data show that monoclinic α -chalcocite undergoes two pressure-induced first-order phase transitions at ˜3.1 and ˜7.1 GPa. The crystal structure of the first high-pressure polymorph, HP1, was solved and refined in space group P 21/c with a =10.312 (4 )Å , b =6.737 (3 )Å , c =7.305 (1 )Å , and β =100.17 (2) ∘ at 6.2(3) GPa. The crystal structure of the second high-pressure polymorph, HP2, was solved and refined in space group P 21/c with a =6.731 (4 )Å , b =6.689 (2 )Å , c =6.967 (8 )Å , and β =93.18 (3) ∘ at 7.9(4) GPa. Electrical resistance measurements upon compression and optical absorption experiments upon decompression show that the structural changes in α -chalcocite are accompanied by changes of the electrical and optical properties. Upon pressure release, the band gap Eg of α -chalcocite (1.24 eV at ambient conditions) widens across the first structural phase transition, going from 1.24 eV at 2.2 GPa (α -chalcocite) to 1.35 eV at 2.6 GPa (HP1), and closes significantly across the second phase transition, going from 1.32 eV at 4.4 GPa (HP1) to 0.87 eV at 4.9 GPa (HP2). The electrical resistance shows similar behavior: its highest value is for the first high-pressure polymorph (HP1), and its lowest value is for the second high-pressure polymorph (HP2) of α -chalcocite. These results are interpreted on the basis of calculated electronic band structures.

The cluster compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} containing Mo{sub 14} clusters and the new mono- and bi-capped trioctahedral Mo{sub 15} and Mo{sub 16} clusters: Synthesis, crystal structure, and electrical and magnetic properties

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

Gall, Philippe; Guizouarn, Thierry; Gougeon, Patrick, E-mail: Patrick.Gougeon@univ-rennes1.fr

2015-07-15

Single crystals of the new quaternary compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} were obtained by solid state reaction. The crystal structure was determined by single-crystal X-ray diffraction. In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} crystallizes in the orthorhombic space group Pbca with unit-cell parameters a=9.4432(14) Å, b=11.4828(12) Å, c=20.299(4) Å and Z=4. Full-matrix least-squares refinement on F{sup 2} using 3807 independent reflections for 219 refinable parameters resulted in R{sub 1}=0.0259 and wR{sub 2}=0.0591. The crystal structure contains in addition to Mo{sub 14} clusters the first examples of mono- and bi-capped trioctahedral Mo{sub 14} i.e. Mo{sub 15} and Mo{sub 16} clusters.more » The oxygen framework derives from a stacking along the a direction of close-packed layers with sequence (…ABAC…). The Mo–Mo distances range between 2.6938(5) and 2.8420(6) Å and the Mo–O distances between 1.879(5) and 2.250(3) Å, as usually observed in molybdenum oxide clusters. The indium atoms form In{sub 4}{sup 6+} bent chains with In–In distances of 2.6682(5) and 2.6622(8) Å and the Ti atoms are in highly distorted octahedral sites of oxygen atoms with Ti–O distances ranging between 1.865(4) and 2.161(4) Å. Magnetic susceptibility measurements confirm the presence of Ti{sup 4+} cations and the absence of localized moments on the Mo network. Electrical resistivity measurements on a single crystal of In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} show a semimetallic behavior. - Graphical abstract: We present here the synthesis, the crystal structure, and the electrical and magnetic properties of the new compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} in which Mo{sub 14} clusters coexist statistically with mono- and bi-capped trioctahedral Mo{sub 14} that is Mo{sub 15} and Mo{sub 16} clusters. - Highlights: • Single crystals of In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} were obtained by solid state reaction. • The crystal structure contains Mo{sub 14}, Mo{sub 15} and Mo{sub 16} clusters. • The indium atoms form In{sub 4}{sup 6+} bent chains. • Poorly metallic behavior. • Absence of localized moments on the Mo network as well as on the Ti atoms.« less

Precursor Routes to Complex Ternary Intermetallics: Single-Crystal and Microcrystalline Preparation of Clathrate-I Na8Al8Si38 from NaSi + NaAlSi.

PubMed

Dong, Yongkwan; Chai, Ping; Beekman, Matt; Zeng, Xiaoyu; Tritt, Terry M; Nolas, George S

2015-06-01

Single crystals of the ternary clathrate-I Na8Al8Si38 were synthesized by kinetically controlled thermal decomposition (KCTD), and microcrystalline Na8Al8Si38 was synthesized by spark plasma sintering (SPS) using a NaSi + NaAlSi mixture as the precursor. Na8AlxSi46-x compositions with x ≤ 8 were also synthesized by SPS from precursor mixtures of different ratios. The crystal structure of Na8Al8Si38 was investigated using both Rietveld and single-crystal refinements. Temperature-dependent transport and UV/vis measurements were employed in the characterization of Na8Al8Si38, with diffuse-reflectance measurement indicating an indirect optical gap of 0.64 eV. Our results indicate that, when more than one precursor is used, both SPS and KCTD are effective methods for the synthesis of multinary inorganic phases that are not easily accessible by traditional solid-state synthesis or crystal growth techniques.

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

Davaasuren, Bambar; Dashjav, Enkhtsetseg; Kreiner, Guido

The carboferrates RE{sub 15}[Fe{sub 8}C{sub 25}] (RE=Dy, Ho) were prepared from mixtures of the elements by arc-melting followed with subsequent annealing at 1373 K. The crystal structures were determined from single crystal X-ray diffraction data and revealed an isotypic relationship to Er{sub 15}[Fe{sub 8}C{sub 25}] (hP48, P321). The main feature of the crystal structure is given by Fe{sub 6} cluster units characterized by covalent Fe–Fe bonding interactions. {sup 57}Fe Mössbauer spectra of Dy{sub 15}[Fe{sub 8}C{sub 25}] were fitted by three subspectra with relative spectral weights of about 3:3:2 which is in general agreement with the crystal structure. Below 50 K,more » an onset of magnetic hyperfine fields at the three iron sites is observed which is supposed to be caused by dipolar fields arising from neighboring, slowly relaxing Dy magnetic moments. - Graphical abstract: Fe{sub 6}-cluster in the crystal structure of RE{sub 15}[Fe{sub 8}C{sub 25}], RE=Dy, Ho. - Highlights: • New carboferrates RE{sub 15}[Fe{sub 8}C{sub 25}] with RE=Dy, Ho have been synthesized. • The crystal structures were refined using single crystal X-ray data. • An orientational relationship between Fe{sub 6}-clusters and Fe in γ-Fe is outlined. • {sup 57}Fe Mössbauer spectra are in agreement with structural data from X-rays. • Magnetic hyperfine fields below 50 K are explained by dipolar fields from Dy atoms.« less

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

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

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.

Redetermination of AgPO(3).

PubMed

Terebilenko, Katherina V; Zatovsky, Igor V; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2011-02-09

Single crystals of silver(I) polyphosphate(V), AgPO(3), were prepared via a phospho-ric acid melt method using a solution of Ag(3)PO(4) in H(3)PO(4). In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779-784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO(5)] polyhedra, giving rise to multidirectional ribbons, and from two types of PO(4) tetra-hedra linked into meandering chains (PO(3))(n) spreading parallel to the b axis with a repeat unit of four tetra-hedra. The calculated bond-valence sum value of one of the two Ag(I) ions indicates a significant strain of the structure.

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

Processing α-mercuric iodide by zone refining

NASA Astrophysics Data System (ADS)

Burger, A.; Morgan, S. H.; Henderson, D. O.; Biao, Y.; Zhang, K.; Silberman, E.; Nason, D.; van den Berg, L.; Ortale-Baccash, C.; Cross, E.

1993-03-01

An investigation is being conducted on zone refining α-mercuric iodide. Analytical studies using differential scanning calorimetry and anion chromatography indicate that impurities are accumulated mainly at the end where zone travel terminates. Early results indicate that single crystals can be readily grown from zone-refined material.

A combined experimental and in silico characterization to highlight additional structural features and properties of a potentially new drug

NASA Astrophysics Data System (ADS)

Bastos, Isadora T. S.; Costa, Fanny N.; Silva, Tiago F.; Barreiro, Eliezer J.; Lima, Lídia M.; Braz, Delson; Lombardo, Giuseppe M.; Punzo, Francesco; Ferreira, Fabio F.; Barroso, Regina C.

2017-10-01

LASSBio-1755 is a new cycloalkyl-N-acylhydrazone parent compound designed for the development of derivatives with antinociceptive and anti-inflammatory activities. Although single crystal X-ray diffraction has been considered as the golden standard in structure determination, we successfully used X-ray powder diffraction data in the structural determination of new synthesized compounds, in order to overcome the bottle-neck due to the difficulties experienced in harvesting good quality single crystals of the compounds. We therefore unequivocally assigned the relative configuration (E) to the imine double bond and a s-cis conformation of the amide function of the N-acylhydrazone compound. These features are confirmed by a computational analysis performed on the basis of molecular dynamics calculations, which are extended not only to the structural characteristics but also to the analysis of the anisotropic atomic displacement parameters, a further information - missed in a typical powder diffraction analysis. The so inferred data were used to perform additional cycles of refinement and eventually generate a new cif file with additional physical information. Furthermore, crystal morphology prediction was performed, which is in agreement with the experimental images acquired by scanning electron microscopy, thus providing useful information on possible alternative paths for better crystallization strategies.

X-Ray crystal structure of GarR—tartronate semialdehyde reductase from Salmonella typhimurium

PubMed Central

Osipiuk, J.; Zhou, M.; Moy, S.; Collart, F.

2009-01-01

Tartronate semialdehyde reductases (TSRs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using NAD as cofactor in the final stage of D-glycerate biosynthesis. These enzymes belong to family of structurally and mechanically related β-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. Here, we present the crystal structure of GarR a TSR from Salmonella typhimurium determined by the single-wavelength anomalous diffraction method and refined to 1.65 Å resolution. The active site of the enzyme contains L-tartrate which most likely mimics a position of a glycerate which is a product of the enzyme reaction. The analysis of the TSR structure shows also a putative NADPH binding site in the enzyme. PMID:19184529

X-ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium.

PubMed

Osipiuk, J; Zhou, M; Moy, S; Collart, F; Joachimiak, A

2009-09-01

Tartronate semialdehyde reductases (TSRs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using NAD as cofactor in the final stage of D-glycerate biosynthesis. These enzymes belong to family of structurally and mechanically related beta-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. Here, we present the crystal structure of GarR a TSR from Salmonella typhimurium determined by the single-wavelength anomalous diffraction method and refined to 1.65 A resolution. The active site of the enzyme contains L-tartrate which most likely mimics a position of a glycerate which is a product of the enzyme reaction. The analysis of the TSR structure shows also a putative NADPH binding site in the enzyme.

Structure of catalase determined by MicroED

PubMed Central

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

Collection of X-ray diffraction data from macromolecular crystals

PubMed Central

Dauter, Zbigniew

2017-01-01

Diffraction data acquisition is the final experimental stage of the crystal structure analysis. All subsequent steps involve mainly computer calculations. Optimally measured and accurate data make the structure solution and refinement easier and lead to more faithful interpretation of the final models. Here, the important factors in data collection from macromolecular crystals are discussed and strategies appropriate for various applications, such as molecular replacement, anomalous phasing, atomic-resolution refinement etc., are presented. Criteria useful for judging the diffraction data quality are also discussed. PMID:28573573

DiffPy-CMI-Python libraries for Complex Modeling Initiative

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

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

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-bearing magnesite, which spontaneously oxidises at HP/HT, forming Fe3+ carbonates, Fe3+ oxides and reduced carbon (diamonds). Single crystal diffraction approach allowed full structure determination of these phases, yielding to the discovery of few unpredicted structures, such as Mg2Fe2C4O13 and Fe13O19, which can be well reproduced in different experiments. Mg2Fe2C4O13 carbonate present truncated chain C4O13 groups, and Fe13O19 oxide, whose stoichiometry is intermediate between magnetite and hematite, is a one-layer structure, with features encountered in superconducting materials. The results fully support the ideas of unexpected complexities in the mineralogy of the lowermost mantle, and single crystal technique, once properly optimized in ad-hoc synchrotron beamlines, is fundamental for extracting accurate structural information, otherwise rarely accessible with other experimental techniques. References: [1] Merlini M., Hanfland M. (2013). Single crystal diffraction at Mbar conditions by synchrotron radiation. High Pressure Research, in press. [2] Dubrovinsky et al., (2010). High Pressure Research, 30, 620-633. [3] Arapan et al. (1997). Phys. Rev. Lett., 98, 268501. [4] Oganov et al. (2008) EPSL, 273, 38-47. [5] Boulard et al. (2011) PNAS, 108, 5184-5187.

Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis

PubMed Central

Cole, Jason C.

2017-01-01

The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal–organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein–ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement. PMID:28291758

[Pb2F2](SeO4): a heavier analogue of grandreefite, the first layered fluoride selenate

NASA Astrophysics Data System (ADS)

Charkin, Dmitri O.; Plokhikh, Igor V.; Zadoya, Anastasiya I.; Kazakov, Sergey M.; Zaloga, Alexander N.; Kozin, Michael S.; Depmeier, Wulf; Siidra, Oleg I.

2018-01-01

Co-precipitation of PbF2 and PbSeO4 in weakly acidic media results in the formation of [Pb2F2](SeO4), the selenate analogue of the naturally occurring mineral grandreefite, [Pb2F2](SO4). The new compound is monoclinic, C2/ c, a = 14.0784(2) Å, b = 4.6267(1) Å, c = 8.8628(1) Å, β = 108.98(1)°, V = 545.93(1) Å3. Its structure has been refined from powder data to R B = 1.55%. From thermal studies, it is established that the compound is stable in air up to about 300 °C, after which it gradually converts into a single phase with composition [Pb2O](SeO4), space group C2/ m, and lattice parameters a = 14.0332(1) Å, b = 5.7532(1) Å, c = 7.2113(1) Å, β = 115.07(1)°, V = 527.37(1) Å3. It is the selenate analogue of lanarkite, [Pb2O](SO4), and phoenicochroite, [Pb2O](CrO4), and its crystal structure was refined to R B = 1.21%. The formation of a single decomposition product upon heating in air suggests that this happens by a thermal hydrolysis mechanism, i.e., Pb2F2SeO4 + H2O (vapor) → Pb2OSeO4 + 2HF↑. This relatively low-temperature process involves complete rearrangement of the crystal structure—from a 2D architecture featuring slabs [Pb2F2]2+ formed by fluorine-centered tetrahedra into a structure characterized by 1D motifs based on [OPb2]2+ chains of oxocentered tetrahedra. The comparative crystal chemistry of the obtained anion-centered structural architectures is discussed.

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 nanpingite increases (001) separation between adjacent 2:1 layers, but has little effect on the dimensions in (001). The existence of rare 2M_2 polytype in nanpingite is attributed to this large layer separation, which minimizes the repulsion of the superimposed (along (001)) basal oxygens in neighboring tetrahedral layers.

REFMAC5 for the refinement of macromolecular crystal structures

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

Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk; Skubák, Pavol; Lebedev, Andrey A.

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

Flux free single crystal growth and characterization of FeTe1-xSx (x=0.00 and 0.10) crystals

NASA Astrophysics Data System (ADS)

Maheshwari, P. K.; Awana, V. P. S.

2018-05-01

We report synthesis of S doped FeTe1-xSx (x = 0.00 and 0.10) single crystals using flux free method via solid state reaction. Single crystal XRD patterns of FeTe1-xSx (x = 0.00 and 0.10) confirm the single crystalline property, as the crystals are grown in (00l) plane only. Powder XRD result of FeTe1-xSx (x = 0.00 and 0.10) crystals show that crystalline in tetragonal structure having P4/nmm space group. Rietveld refinement results show that both a and c lattice parameters decreases with S doping of 10% at Te site in FeTe1-xSx. Detailed scanning electron microscopy (SEM) image of FeTe0.90S0.10 shows that the growth of crystal is in slab-like morphology. Electrical resistivity measurement results onset confirm the superconductivity in S doped 10% sample at Te site and superconducting transition Tconset occurs at 9.5K and Tcoffset(ρ=0) occurs at 6.5K. ρ-T measurement has been performed under various magnetic field up to 12 Tesla down to 2K. Upper critical field Hc2(0), for x=0.10, which comes around 70Tesla, 60Tesla and 45Tesla of normal resistivity criterion ρn = 90%, 50% and 10% criterion respectively.

A Family of A-Site Cation-Deficient Double-Perovskite-Related Iridates: Ln9Sr2Ir4O24 (Ln = La, Pr, Nd, Sm).

PubMed

Ferreira, Timothy; Smith, Mark D; Zur Loye, Hans-Conrad

2018-06-21

The compositions of the general formula Ln 11- x Sr x Ir 4 O 24 (Ln = La, Pr, Nd, Sm; 1.37 ≥ x ≥ 2) belonging to a family of A-site cation-deficient double-perovskite-related oxide iridates were grown as highly faceted single crystals from a molten strontium chloride flux. Their structures were determined by single-crystal X-ray diffraction. On the basis of the single-crystal results, additional compositions, Ln 9 Sr 2 Ir 4 O 24 (Ln = La, Pr, Nd, Sm), were prepared as polycrystalline powders via solid-state reactions and structurally characterized by Rietveld refinement. The compositions Ln 9 Sr 2 Ir 4 O 24 (Ln = La, Pr, Nd, Sm) contain Ir(V) and Ir(IV) in a 1:3 ratio with an average iridium oxidation state of 4.25. The single-crystal compositions La 9.15 Sr 1.85 Ir 4 O 24 and Pr 9.63 Sr 1.37 Ir 4 O 24 contain relatively less Ir(V), with the average iridium oxidation states being 4.21 and 4.09, respectively. The magnetic properties of Ln 9 Sr 2 Ir 4 O 24 (Ln = La, Pr, Nd, Sm) were measured, and complex magnetic behavior was observed in all cases at temperatures below 30 K.

Redetermination of AgPO3

PubMed Central

Terebilenko, Katherina V.; Zatovsky, Igor V.; Ogorodnyk, Ivan V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2011-01-01

Single crystals of silver(I) polyphosphate(V), AgPO3, were prepared via a phospho­ric acid melt method using a solution of Ag3PO4 in H3PO4. In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779–784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO5] polyhedra, giving rise to multidirectional ribbons, and from two types of PO4 tetra­hedra linked into meandering chains (PO3)n spreading parallel to the b axis with a repeat unit of four tetra­hedra. The calculated bond-valence sum value of one of the two AgI ions indicates a significant strain of the structure. PMID:21522230

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

Electronic structure and optical properties of Cs2HgI4: Experimental study and band-structure DFT calculations

NASA Astrophysics Data System (ADS)

Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Shkumat, P. N.; Myronchuk, G. L.; Khvyshchun, M.; Fedorchuk, A. O.; Parasyuk, O. V.; Khyzhun, O. Y.

2015-04-01

High-quality single crystal of cesium mercury tetraiodide, Cs2HgI4, has been synthesized by the vertical Bridgman-Stockbarger method and its crystal structure has been refined. In addition, electronic structure and optical properties of Cs2HgI4 have been studied. For the crystal under study, X-ray photoelectron core-level and valence-band spectra for pristine and Ar+-ion irradiated surfaces have been measured. The present X-ray photoelectron spectroscopy (XPS) results indicate that the Cs2HgI4 single crystal surface is very sensitive with respect to Ar+ ion-irradiation. In particular, Ar+ bombardment of the single crystal surface alters the elemental stoichiometry of the Cs2HgI4 surface. To elucidate peculiarities of the energy distribution of the electronic states within the valence-band and conduction-band regions of the Cs2HgI4 compound, we have performed first-principles band-structure calculations based on density functional theory (DFT) as incorporated in the WIEN2k package. Total and partial densities of states for Cs2HgI4 have been calculated. The DFT calculations reveal that the I p states make the major contributions in the upper portion of the valence band, while the Hg d, Cs p and I s states are the dominant contributors in its lower portion. Temperature dependence of the light absorption coefficient and specific electrical conductivity has been explored for Cs2HgI4 in the temperature range of 77-300 K. Main optical characteristics of the Cs2HgI4 compound have been elucidated by the first-principles calculations.

The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

PubMed

Guizard, C; Chanzy, H; Sarko, A

1985-06-05

The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a resolution limit of 1.6 A. The X-ray intensities were measured from powder patterns recorded from collections of the single crystals. The structure crystallizes in a monoclinic unit cell with parameters a = 25.71 A, b = 10.21 A, c (chain axis) = 7.76 A and beta = 91.3 degrees. The space group is P2(1) with b axis unique. The unit cell contains six chains and eight water molecules, with three chains of the same polarity and four water molecules constituting the asymmetric unit. Along the chain direction the asymmetric unit is a dimer residue; however, the individual glucopyranose residues are very nearly related by a molecular 2-fold screw axis. The conformation of the chain is very similar to that in the anhydrous structure, but the chain packing differs in the two structures in that the rotational positions of the chains about the helix axes (the chain setting angles) are considerably different. The chains still pack in the form of sheets that are separated by water molecules. The difference in the chain setting angles between the anhydrous and hydrate structures corresponds to the angle between like unit cell axes observed in the diffraction diagrams recorded from hybrid crystals containing both polymorphs. Despite some beam damage effects, the structure was determined to a satisfactory degree of agreement, with the residuals R''(electron diffraction) = 0.258 and R(X-ray) = 0.127.

Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

PubMed

Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

2015-02-02

Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

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

Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more thanmore » the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.« less

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate.

PubMed

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-09-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=72.39, b=127.71, c=157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site.

Crystal structure of (Mo,W){sub 9}O{sub 25}, homologue of the Mo{sub 4}O{sub 11} (Orthorhombic)-type structure

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

D`Yachenko, O.G.; Tabachenko, V.V.; Sundberg, M.

The structure of Mo{sub 7.6}W{sub 1.4}O{sup 25} has been determined from single crystal X-ray data. The symmetry is monoclinic with lattice parameters a = 5.448(1), b = 27.639(8), c = 6.739 (1) {angstrom}, {beta} = 90.180(9){degrees}, and space group P2{sub 1}/n. The refinement led to R = 0.046 for 2060 observed unique reflections. The Mo:W ratio was confirmed by microanalysis. The (Mo, W){sub 9}O{sub 25} structure is built up of cornersharing distorted MO{sub 6} octahedra in slabs of ReO{sub 3}-type, cut parallel to (211) and seven octahedra wide along two subcell axes. The slabs appear alternatively in mirrored orientations. Themore » slabs are mutually linked by corner sharing of fairly regular MoO{sub 4} tetrahedra so that five-sided tunnels are formed. High-resolution electron microscopy images showed well-ordered crystal fragments.« less

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

Structures and phase transitions of the A7PSe6 (A = ag, Cu) argyrodite-type ionic conductors. III. alpha-Cu7PSe6

PubMed

Gaudin; Petricek; Boucher; Taulelle; Evain

2000-12-01

The crystal structure of the third polymorph of the Cu(7)PSe(6) argyrodite compound, alpha-Cu(7)PSe(6), heptacopper phosphorus hexaselenide, is determined by means of single-crystal diffraction from twinned crystals and X-ray powder diffraction, with the help of extensive NMR measurements. In the low-temperature form, i.e. below the last phase transition, alpha-Cu(7)PSe(6) crystallizes in orthorhombic symmetry, space group Pna2(1), with a = 14.3179 (4), b = 7.1112 (2), c = 10.1023 (3) A, V = 1028.590 (9) A(3) (deduced from powder data, T = 173 K) and Z = 4. Taking into account a twinning by reticular merohedry, the refinement of the alpha-Cu(7)PSe(6) structure leads to the residual factors R = 0.0466 and wR = 0.0486 for 127 parameters and 3714 observed, independent reflections (single-crystal data, T = 173 K). A full localization of the Cu(+)d(10) element is reached with one twofold-, one threefold- and five fourfold-coordinated Cu atoms. The observation of two phase transitions for Cu(7)PSe(6), to be compared with only one for Ag(7)PSe(6), is attributed to the d(10) element stability in a low coordination environment, copper being less prone to lower coordination sites than silver, especially at low temperature.

Investigation of Synthetic Mg(1.3)V(1.7)O4 Spinel with MgO Inclusions: Case Study of a Spinel with an Apparently occupied Interstitial Site

NASA Technical Reports Server (NTRS)

Uchida, Hinako; Righter, Kevin; Lavina, Barbara; Nowell, Matthew M.; Wright, Stuart I.; Downs, Robert T.; Yang, Hexiong

2007-01-01

A magnesium vanadate spinel crystal, ideally MgV2O4, synthesized at 1 bar, 1200 C and equilibrated under FMQ + 1.3 log f(sub o2) condition, was investigated using single-crystal X-ray diffraction, electron microprobe, and electron backscatter (EBSD). The initial X-ray structure refinements gave tetrahedral and octahedral site occupancies, along with the presence of 0.053 apfu Mg at an interstitial octahedral site . Back-scattered electron (BSE) images and electron microprobe analyses revealed the existence of an Mg-rich phase in the spinel matrix, which was too small (less than or equal to 3microns) for an accurate chemical determination. The EBSD analysis combined with X-ray energy dispersive spectroscop[y (XEDS) suggested that the Mg-rich inclusions are periclase oriented coherently with the spinel matrix. The final structure refinements were optimized by subtracting the X-ray intensity contributions (approx. 9%) of periclase reflections, which eliminated the interstitial Mg. This study provides insight into possible origins of refined interstitial cations reported in the the literature for spinel, and points to the difficulty of using only X-ray diffraction data to distinguish a spinel with interstitial cations from one with coherently oriented MgO inclusions.

Bridgman-Stockbarger growth of SrI2:Eu2+ single crystal

NASA Astrophysics Data System (ADS)

Raja, A.; Daniel, D. Joseph; Ramasamy, P.; Singh, S. G.; Sen, S.; Gadkari, S. C.

2018-05-01

Strontium Iodide (SrI2): Europium Iodide (EuI2) was purified by Zone-refinement process. Europium doped strontium iodide (SrI2:Eu2+) single crystal was grown by modified vertical Bridgman - Stockbarger technique. Photoluminescence (PL) excitation and emission (PLE) spectra were measured for Eu2+ doped SrI2 crystal. The sharp emission was recorded at 432 nm. Scintillation properties of the SrI2:Eu2+ crystal were checked by the gamma ray spectrometer using 137Cs gamma source.

Structure of new Hg0.75V0.25Ba2CuO4+δ superconducting single crystals.Effect of overdoping on the magnetization second peak

NASA Astrophysics Data System (ADS)

Villard, G.; Pelloquin, D.; Maignan, A.

1998-10-01

Superconducting crystals (Tc=88 K) of the `1201' mercury cuprate have been grown by using vanadium as stabilizer of the (HgOδ) mercury layer. Its shortened c-axis parameter, c=9.345 Å, is linked to the substitution of small VO4 tetrahedra for HgO2 stick deduced from the structural study. The regular layer stacking is confirmed by high resolution microscopy, and cationic analysis coupled to an electron microscope leads to the average formula Hg0.75V0.25Ba2CuO4+δ for these overdoped crystals in good agreement with the structural refinements. One of the major result of the structural part is the mobility of oxygens located at the [BaO]∞ layer level. The superconducting properties of crystals with typical 800×500×10 μm3 dimensions have been investigated by magnetic measurements. Well-marked fishtail features are exhibited on their M(H) curves. The corresponding second peak line differs from that of optimized 1201 crystals demonstrating the important consequences on the superconducting properties of the vanadium for mercury substitution.

Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum

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

Bhaumik, Prasenjit; Horimoto, Yasumi; Xiao, Huogen

2011-09-06

Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1 {angstrom}, respectively. The apoenzyme crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with twomore » molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4{sub 3} with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.« less

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

DOE PAGES

Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; ...

2014-06-17

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL)more » of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.« less

Crystal growth, characterization and theoretical studies of 4-aminopyridinium picrate

NASA Astrophysics Data System (ADS)

Aditya Prasad, A.; Muthu, K.; Rajasekar, M.; Meenatchi, V.; Meenakshisundaram, S. P.

2015-01-01

Single crystals of 4-aminopyridinium picrate (APP) were grown by slow evaporation of a mixed solvent system methanol-acetone (1:1, v/v) containing equimolar quantities of 4-aminopyridine and picric acid. Structure is elucidated by single crystal XRD analysis and the crystal belongs to monoclinic system with four molecules in the unit cell (space group P21/c) and the cell parameter values are, a = 8.513 Å (±0.015), b = 11.33 Å (±0.02), c = 14.33 Å (±0.03) and β = 104.15° (±0.019), V = 1340 A3 (±6) with refined R factors R1 = 0.0053 and wR2 = 0.0126. The electron density mapping is interpreted to find coordinates for each atom in the crystallized molecules. The various functional groups present in the molecule are confirmed by FT-IR analysis. UV-visible spectral analysis was used to determine the band gap energy of 4-aminopyridinium picrate. Powder X-ray diffraction pattern reveals the crystallinity of the as-grown crystal and it closely resembles the simulated XRD from the single crystal XRD analysis. Scanning electron microscopy reveals the surface morphology of the grown crystal. Optimized geometry is derived by Hartree-Fock theory calculations and the first-order molecular hyperpolarizability (β), theoretically calculated bond length, bond angles and excited state energy from theoretical UV-vis spectrum were estimated.

Crystal structure and chemistry of lithium-bearing trioctahedral micas-3T

USGS Publications Warehouse

Brigatti, M.F.; Kile, D.E.; Poppi, L.

2003-01-01

Chemical analyses and crystal structure refinements were performed on lithian siderophyllite-3T crystals from granitic pegmatites of the anorogenic Pikes Peak batholith (Colorado) to characterize the crystal chemistry and relations with trioctahedral lithium-bearing micas showing different stacking sequences. Chemical data show that the studied samples fall on the siderophyllite-polylithionite join, closer to the siderophyllite end-member. Single-crystal X-ray refinements were carried out on three samples (two of which were taken from core and rim of the same crystal) in space-group P31 12 (the agreement factor, Robs, varies between 0.034 and 0.036). Mean bond distances and mean electron counts of M1, M2 and M3 octahedral sites indicate an ordered cation distribution with M1 and M3 positions substantially larger than M2. In the sample with the largest iron content, the M2 mean electron count increases as well as the mean distance, whereas remains smaller than or . The tetrahedral cation-oxygen atom mean distances range from 1.614 to 1.638 A and from 1.663 to 1.678 A for T1 and T2 sites, respectively, being consistent with Al3+ enrichment in the T2 sites. The tetrahedral rotation angle, α, is generally small (3.1 ≤ α ≤ 4.6) and decreases with siderophyllite content. As Fe increases, the T1 tetrahedron becomes flatter (112.4 ≤ t1 ≤ 110.5??), whereas T2 tetrahedron distortion appears unchanged (110.7 ≤ T2 ≤ 110.9).

Structural and Crystal Chemical Properties of Alkali Rare-earth Double Phosphates

DOE PAGES

Farmer, James Matthew; Boatner, Lynn A.; Chakoumakos, Bryan C.; ...

2016-01-01

When appropriately activated, alkali rare-earth double phosphates of the form: M 3RE(PO 4) 2 (where M denotes an alkali metal and RE represents either a rare-earth element or Y or Sc) are of interest for use as inorganic scintillators for radiation detection at relatively long optical emission wavelengths. These compounds exhibit layered crystal structures whose symmetry properties depend on the relative sizes of the rare-earth and alkali-metal cations. Single-crystal X-ray and powder neutron diffraction methods were used here to refine the structures of the series of rare-earth double phosphate compounds: K 3RE(PO 4) 2 with RE = Lu, Er, Ho,more » Dy, Gd, Nd, Ce, plus Y and Sc - as well as the compounds: A 3Lu(PO 4) 2, with A = Rb, and Cs. The double phosphate K 3Lu(PO 4) 2 was reported and structurally refined previously. This material had a hexagonal unit cell at room temperature with the Lu ion six-fold coordinated with oxygen atoms of the surrounding phosphate groups. Additionally two lower-temperature phases were observed for K 3Lu(PO 4) 2. The first phase transition to a monoclinic P21/m phase occurred at ~230 K, and the Lu ion retained its six-fold coordination. The second K 3Lu(PO 4) 2 phase transition occurred at ~130 K. The P21/m space group symmetry was retained, however, one of the phosphate groups rotated to increase the oxygen coordination number of Lu from six to seven. This structure then became isostructural with the room-temperature form of the compound K 3Yb(PO 4) 2 reported here that also exhibits an additional high-temperature phase which occurs at T = 120 °C with a transformation to hexagonal P-3 space group symmetry and a Yb-ion coordination number reduction from seven to six. This latter result was confirmed using EXAFS. The single-crystal growth methods structural systematics, and thermal expansion properties of the present series of alkali rare-earth double phosphates, as determined by X-ray and neutron diffraction methods, are treated here.« less

Structural and Crystal Chemical Properties of Alkali Rare-earth Double Phosphates

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

Farmer, James Matthew; Boatner, Lynn A.; Chakoumakos, Bryan C.

When appropriately activated, alkali rare-earth double phosphates of the form: M 3RE(PO 4) 2 (where M denotes an alkali metal and RE represents either a rare-earth element or Y or Sc) are of interest for use as inorganic scintillators for radiation detection at relatively long optical emission wavelengths. These compounds exhibit layered crystal structures whose symmetry properties depend on the relative sizes of the rare-earth and alkali-metal cations. Single-crystal X-ray and powder neutron diffraction methods were used here to refine the structures of the series of rare-earth double phosphate compounds: K 3RE(PO 4) 2 with RE = Lu, Er, Ho,more » Dy, Gd, Nd, Ce, plus Y and Sc - as well as the compounds: A 3Lu(PO 4) 2, with A = Rb, and Cs. The double phosphate K 3Lu(PO 4) 2 was reported and structurally refined previously. This material had a hexagonal unit cell at room temperature with the Lu ion six-fold coordinated with oxygen atoms of the surrounding phosphate groups. Additionally two lower-temperature phases were observed for K 3Lu(PO 4) 2. The first phase transition to a monoclinic P21/m phase occurred at ~230 K, and the Lu ion retained its six-fold coordination. The second K 3Lu(PO 4) 2 phase transition occurred at ~130 K. The P21/m space group symmetry was retained, however, one of the phosphate groups rotated to increase the oxygen coordination number of Lu from six to seven. This structure then became isostructural with the room-temperature form of the compound K 3Yb(PO 4) 2 reported here that also exhibits an additional high-temperature phase which occurs at T = 120 °C with a transformation to hexagonal P-3 space group symmetry and a Yb-ion coordination number reduction from seven to six. This latter result was confirmed using EXAFS. The single-crystal growth methods structural systematics, and thermal expansion properties of the present series of alkali rare-earth double phosphates, as determined by X-ray and neutron diffraction methods, are treated here.« less

Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.

PubMed

Orben, Claudia M; Dittrich, Birger

2014-06-01

For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.

The role of order-disorder transitions in the quest for molecular multiferroics: structural and magnetic neutron studies of a mixed valence iron(II)-iron(III) formate framework.

PubMed

Cañadillas-Delgado, Laura; Fabelo, Oscar; Rodríguez-Velamazán, J Alberto; Lemée-Cailleau, Marie-Hélène; Mason, Sax A; Pardo, Emilio; Lloret, Francesc; Zhao, Jiong-Peng; Bu, Xian-He; Simonet, Virginie; Colin, Claire V; Rodríguez-Carvajal, Juan

2012-12-05

Neutron diffraction studies have been carried out to shed light on the unprecedented order-disorder phase transition (ca. 155 K) observed in the mixed-valence iron(II)-iron(III) formate framework compound [NH(2)(CH(3))(2)](n)[Fe(III)Fe(II)(HCOO)(6)](n). The crystal structure at 220 K was first determined from Laue diffraction data, then a second refinement at 175 K and the crystal structure determination in the low temperature phase at 45 K were done with data from the monochromatic high resolution single crystal diffractometer D19. The 45 K nuclear structure reveals that the phase transition is associated with the order-disorder of the dimethylammonium counterion that is weakly anchored in the cavities of the [Fe(III)Fe(II)(HCOO)(6)](n) framework. In the low-temperature phase, a change in space group from P31c to R3c occurs, involving a tripling of the c-axis due to the ordering of the dimethylammonium counterion. The occurrence of this nuclear phase transition is associated with an electric transition, from paraelectric to antiferroelectric. A combination of powder and single crystal neutron diffraction measurements below the magnetic order transition (ca. 37 K) has been used to determine unequivocally the magnetic structure of this Néel N-Type ferrimagnet, proving that the ferrimagnetic behavior is due to a noncompensation of the different Fe(II) and Fe(III) magnetic moments.

Polymorphism in alkali metal uranyl nitrates: Synthesis and crystal structure of gamma-K(UO2)(NO3)3

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

Jouffret, Laurent J.; Krivovichev, Sergey V.; Burns, Peter C.

2011-07-20

Single crystals of γ-K(UO₂)(NO₃)₃ were prepared from aqueous solutions by evaporation. The crystal structure [orthorhombic, Pbca (61), a = 9.2559(3) Å, b = 12.1753(3) Å, c = 15.8076(5) Å, V = 1781.41(9) ų, Z = 8] was determined by direct methods and refined to R₁ = 0.0267 on the basis of 3657 unique observed reflections. The structure is composed of isolated anionic uranyl trinitrate units, [(UO₂)(NO₃)₃] –, that are linked through eleven-coordinated K + cations. Both known polymorphs of K(UO₂)(NO₃)₃ (α- and γ-phases) can be considered as based upon sheets of isolated complex [(UO₂)(NO₃)₃] – ions separated by K +more » cations. The existence of polymorphism in the two K[UO₂(NO₃)₃] polymorphs is due to the different packing modes of uranyl trinitrate clusters that adopt the same two-dimensional but different three-dimensional arrangements.« less

Synthesis and structural characterization of Li3K3Y7(BO3)9

NASA Astrophysics Data System (ADS)

Bräuchle, Sebastian; Huppertz, Hubert

2017-09-01

Li3K3Y7(BO3)9 was prepared by high-temperature solid state synthesis at 900 °C in a platinum crucible from lithium carbonate, potassium carbonate, boric acid, and yttrium(III) oxide. The compound crystallizes in the orthorhombic space group Pca21 (no. 29) (Z = 4). The structure was refined from single-crystal X-ray diffraction data: a = 20.743(8), b = 6.387(4), c = 17.474(4) Å, V = 2315.2(2) Å3, R1 = 0.0473, and wR2 = 0.0637 for all data. The crystal structure of Li3K3Y7(BO3)9 consists of isolated BO3 groups forming [Li3B4O21] units in combination with LiO6 octahedra in the ac plane, which are interconnected to each other by additional planar BO3 groups. The Y3+ and K+ cations are arranged in layers along the a-axis.

Neutron protein crystallography: A complementary tool for locating hydrogens in proteins.

PubMed

O'Dell, William B; Bodenheimer, Annette M; Meilleur, Flora

2016-07-15

Neutron protein crystallography is a powerful tool for investigating protein chemistry because it directly locates hydrogen atom positions in a protein structure. The visibility of hydrogen and deuterium atoms arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction at resolutions typical of protein crystals. Neutrons have the additional benefit to structural biology of not inducing radiation damage in protein crystals. The same crystal could be measured multiple times for parametric studies. Here, we review the basic principles of neutron protein crystallography. The information that can be gained from a neutron structure is presented in balance with practical considerations. Methods to produce isotopically-substituted proteins and to grow large crystals are provided in the context of neutron structures reported in the literature. Available instruments for data collection and software for data processing and structure refinement are described along with technique-specific strategies including joint X-ray/neutron structure refinement. Examples are given to illustrate, ultimately, the unique scientific value of neutron protein crystal structures. Copyright © 2015 Elsevier Inc. All rights reserved.

2Flux growth and characterization of Ce-substituted Nd 2 Fe 14 B single crystals

DOE PAGES

Susner, Michael A.; Conner, Benjamin S.; Saparov, Bayrammurad I.; ...

2016-10-27

Single crystals of (Nd 1-xCe x) 2Fe 14B are grown out of Fe-(Nd,Ce) flux. Chemical and structural analysis of the crystals indicate that (Nd 1-xCe x) 2Fe 14B forms a solid solution until at least x = 0.38 with a Vegard-like variation of the lattice constants with x. Refinements of single crystal neutron diffraction data indicate that Ce has a slight site preference (7:3) for the 4g rare earth site over the 4f site. Magnetization measurements at 300 K show only small decreases with increasing Ce content in saturation magnetization (M s) and anisotropy field (H A), and Curie temperaturemore » (T C). First principles calculations are carried out to understand the effect of Ce substitution on the electronic and magnetic properties. For a multitude of applications, it is expected that the advantage of incorporating lower-cost and more abundant Ce will outweigh the small adverse effects on magnetic properties. In conclusion, Ce-substituted Nd 2Fe 14B is therefore a potential high-performance permanent magnet material with substantially reduced Nd content.« less

Doping effects on the relaxation of frustration and magnetic properties of YMn0.9Cu0.1O3

NASA Astrophysics Data System (ADS)

Xiao, L. X.; Xia, Z. C.; Wang, X.; Ni, Y.; Yu, W.; Shi, L. R.; Jin, Z.; Xiao, G. L.

2017-12-01

The crystal structure and magnetic properties of hexagonal YMn0.9Cu0.1O3 single crystal are systematically investigated. The refinement results of XRD show the lattice constant decreases, which is unusually due to the doped Cu2+ ion has a larger ionic radius than the Mn3+ ions. The XPS results show that the coexistence of Mn2+, Mn3+ and Mn4+ ions in YMn0.9Cu0.1O3 single crystal. Magnetization measurements show that Cu doped YMn0.9Cu0.1O3 and parent YMnO3 have almost the same antiferromagnetic transition temperature TN, which indicates the AFM interaction is robust in the geometry frustrated system. Because doping directly destroy some of the Mn3+ ions nets, the relaxation of frustration of Mn in-plane 2D triangular geometry network leads to the significantly decrease of Mn3+ ions AFM interaction. In addition, the coexistence and competition between the ferromagnetic and antiferromagnetic interactions among the Mn2+, Mn3+ and Mn4+ ions lead to a complicated and irreversible magnetization behavior in YMn0.9Cu0.1O3 single crystal.

Growth, Faraday and inverse Faraday characteristics of Tb₂Ti₂O₇ crystal.

PubMed

Guo, Feiyun; Sun, Yilin; Yang, Xiongsheng; Chen, Xin; Zhao, Bin; Zhuang, Naifeng; Chen, Jianzhong

2016-03-21

Tb₂Ti₂O₇ (TTO) single crystal with dimensions of 20 × 20 × 16 mm³ was grown by the Czochralski method. Rietveld structure refinement of X-ray diffraction (XRD) data confirms that the compound crystallizes in the cubic system with pyrochlore structure. Transmission spectra, Magnetic circular dichroism (MCD) spectra, Faraday and inverse Faraday characteristics of TTO crystal have been measured and analyzed in detail. The results demonstrate that TTO crystal has high transmittance at 700-1400 nm waveband and a larger Verdat constant than that of TGG reported. Magnetic circular dichroism (MCD) spectra showed that the 4f→4f transitions of Tb³⁺ have significant contributions to the magneto-optical activity (MOA). In the time-resolved pump-probe spectroscopy, the rotation signals of the probe beam based on the inverse Faraday effect in magneto-optical crystal were observed at zero time delay, the full width at half maximum of the rotation and ellipticity signals can be as fast as ~500 fs, which indicates that TTO crystal can be a promising material for ultrafast all-optical magnetic switching.

Structure determination of two modulated gamma-brass structures in the Zn-Pd System through a (3 + 1)-dimensional space description.

PubMed

Gourdon, Olivier; Izaola, Zunbeltz; Elcoro, Luis; Petricek, Vaclav; Miller, Gordon J

2009-10-19

The structure determination of two composite compounds in the Zn-Pd system with close relationships to the cubic gamma-brass structure Zn(11-delta)Pd(2+delta) is reported. Their structures have been solved from single crystal X-ray diffraction data within a (3 + 1)-dimensional [(3 + 1)D] formalism. Zn(75.7(7))Pd(24.3) and Zn(78.8(7))Pd(21.2) crystallize with orthorhombic symmetry, superspace group Xmmm(00gamma)0s0 (X = [(1/2,1/2,0,0); (0,1/2,1/2,1/2); (1/2,0,1/2,1/2)]), with the following lattice parameters, respectively: a(s) = 12.929(3) A, b(s) = 9.112(4) A, c(s) = 2.5631(7) A, q = 8/13 c* and V(s) = 302.1(3) A(3) and a(s) = 12.909(3) A, b(s) = 9.115(3) A, c(s) = 2.6052(6) A, q = 11/18 c* and V(s) = 306.4(2) A(3). Their structures may be considered as commensurate because they can be refined in the conventional 3D space groups (Cmce and Cmcm, respectively) using supercells, but they also refined within the (3 + 1)D formalism to residual factors R = 3.14% for 139 parameters and 1184 independent reflections for Zn(75.7(7))Pd(24.3) and R = 3.16% for 175 parameters and 1804 independent reflections for Zn(78.8(7))Pd(21.2). The use of the (3 + 1)D formalism improves the results of the refinement and leads to a better understanding of the complexity of the atomic arrangement through the various modulations (occupation waves and displacive waves). Our refinements emphasize a unique Pd/Zn occupancy modulation at the center of distorted icosahedra, a modulation which correlates with the distortion of these polyhedra.

Structures and phase transitions of the A7PSe6 (A = Ag, Cu) argyrodite-type ionic conductors. II. Beta- and gamma-Cu7PSe6

PubMed

Gaudin; Boucher; Petricek; Taulelle; Evain

2000-06-01

The crystal structures of two of the three polymorphic forms of the Cu7PSe6 argyrodite compound are determined by means of single-crystal X-ray diffraction. In the high-temperature form, at 353 K, i.e. 33 K above the first phase transition, gamma-Cu7PSe6 crystallizes in cubic symmetry, space group F43m. The full-matrix least-squares refinement of the structure leads to the residual factors R = 0.0201 and wR = 0.0245 for 31 parameters and 300 observed independent reflections. In the intermediate form, at room temperature, beta-Cu7PSe6 crystallizes again in cubic symmetry, but with space group P2(1)3. Taking into account a merohedric twinning, the refinement of the beta-Cu7PSe6 structure leads to the residual factors R = 0.0297 and wR = 0.0317 for 70 parameters and 874 observed, independent reflections. The combination of a Gram-Charlier development of the Debye-Waller factor and a split model for copper cations reveals the possible diffusion paths of the d10 species in the gamma-Cu7PSe6 ionic conducting phase. The partial ordering of the Cu+ d10 element at the phase transition is found in concordance with the highest probability density sites of the high-temperature phase diffusion paths. A comparison between the two Cu7PSe6 and Ag7PSe6 analogues is carried out, stressing the different mobility of Cu+ and Ag+ and their relative stability in low-coordination chalcogenide environments.

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate

PubMed Central

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-01-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxy­acetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 72.39, b = 127.71, c = 157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. PMID:21904049

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

DOE PAGES

Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...

2016-08-31

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less

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

Plasticity of Cl-Te-Cl Fragments. Synthesis, Single-Crystal X-ray, and NBO Study of (1-Thia-2-tellura-1-phenyl-4-chloro)cyclopentane 2,2,2-Trichloride.

PubMed

Sundberg, Markku R.; Laitalainen, Tarja; Bergman, Jan; Uggla, Rolf; Matikainen, Jorma; Kaltia, Seppo

1998-06-01

Tellurium tetrachloride and allylphenyl sulfide react to form (1-thia-2-tellura-1-phenyl-4-chloro)cyclopentane 2,2,2-trichloride. The crystal and molecular structure were determined by single-crystal X-ray techniques. The crystals belong to the monoclinic system, space group P2(1)/c (No. 14) with a = 6.020(3) Å, b = 11.46(1) Å, c = 20.156(2) Å, beta = 97.53(2) degrees, V = 1379(1) Å(3), and Z = 4. The structure was refined to the final R value of 0.036. The coordination around Te(IV) is distorted psi octahedral with three Cl atoms in the equatorial positions. The axial Te(1)-C(1) bond opposite to the lone pair of electrons at the Te(IV) atom completes the coordination polyhedron. The intramolecular Te-S distance is 2.903(3) Å. Symmetric and asymmetric deformation modes were established to describe the plasticity of the Cl-Te-Cl fragments extracted from the Cambridge Structural Database. The hypervalency of Te(IV) manifests itself as plasticity in the equatorial plane of the coordination sphere. The NBO calculations show that all of the equatorial Te-Cl bonds are highly polarized and the electrons reside mainly on the Cl atoms.

Crystal Structure and Characterization of Ba 2V 3O 9: A Vanadyl(IV) Vanadate Containing Rutile-like Chains of VO 6Octahedra

NASA Astrophysics Data System (ADS)

Dhaussy, Anne-Claire; Abraham, Francis; Mentre, Olivier; Steinfink, Hugo

1996-11-01

The crystal structure of Ba2V3O9has been determined and refined to finalRandRwvalues of 0.025 and 0.028 from 1562 independent single crystal reflections. It crystallizes in the space groupP21/mwitha= 9.302(1) Å,b= 5.969(1) Å,c= 8.118(1) Å, and β = 113.96 (1)°. The structure consists of one-dimensional rutile-type chains of edge-sharing VO6octahedra parallel to thebaxis. The VO4tetrahedra share corners with VO6octahedra of a single rutile-type chain to form one-dimensional [V3O9]4-∞columns which are held together by Ba2+ions. In this mixed valence compound V4+and V5+ions are distributed in an ordered way in octahedra and tetrahedra, respectively. In the almost perfect O6octahedron the vanadium atom is off-center so that it forms a short vanadyl V_dbO bond of 1.686(3) Å, typical of a V4+ion. This compound is a barium vanadyl vanadate Ba2(VO)(VO4)2. It is the first example of isolated rutile-type chains found with V4+ions. Magnetic susceptibility measurements show that this phase is an antiferromagnet withTN≅ 58 K. At about 20 K magnetic anisotropy causes a canted spin arrangement.

Low-Ca pyroxenes from LL group chondritic meteorites: Crystal structural studies and implications for their thermal histories

NASA Astrophysics Data System (ADS)

Artioli, G.; Davoli, G.

1994-12-01

Crystal structural refinements of one orthorhombic (Pbca) and two monoclinic (P21/c) single crystals, from chondrules of low-Ca pyroxenes from unequilibrated chondritic meteorites of the LL group, were carried out. The intracrystalline Fe-Mg distribution between the M1 and M2 crystallographic sites of the Parnallee (LL-3) orthoenstatite is suggestive of very rapid cooling, whereas both the structural state and intracrystalline Fe-Mg distribution in the Soko Banja (LL-4) and Jolomba (LL-6) clinoenstaties indicate rapid cooling from the high temperature polymorphs, with no significant re-equilibration at lower temperatures. These results imply that thermal metamorphism in the parent body, if present, was insufficient to allow re-equilibration of the pyroxene minerals to low temperature, ordered crystal structures. The data also indicate that, assuming low or mild pressure and shock effects, there is no well defined correlation between equilibrium temperature of the mineral phases and the alleged petrologic type of the meteorites. This evidence is consistent with a rubble pile model for the parent body accretional history, or with an onion shell model with very low thermal peak metamorphism, as is assumed for a very small object.

Combining 27Al Solid-State NMR and First-Principles Simulations To Explore Crystal Structure in Disordered Aluminum Oxynitride.

PubMed

Tu, Bingtian; Liu, Xin; Wang, Hao; Wang, Weimin; Zhai, Pengcheng; Fu, Zhengyi

2016-12-19

The nuclear magnetic resonance (NMR) technique gives insight into the local information in a crystal structure, while Rietveld refinement of powder X-ray diffraction (PXRD) sketches out the framework of a crystal lattice. In this work, first-principles calculations were combined with the solid-state NMR technique and Rietveld refinement to explore the crystal structure of a disordered aluminum oxynitride (γ-alon). The theoretical NMR parameters (chemical shift, δ iso , quadrupolar coupling constants, C Q , and asymmetry parameter, η) of Al 22.5 O 28.5 N 3.5 , predicted by the gauge-including projector augmented wave (GIPAW) algorithm, were used to facilitate the analytical investigation of the 27 Al magic-angle spinning (MAS) NMR spectra of the as-prepared sample, whose formula was confirmed to be Al 2.811 O 3.565 N 0.435 by quantitative analysis. The experimental δ iso , C Q , and η of 27 Al showed a small discrepancy compared with theoretical models. The ratio of aluminum located at the 8a to 16d sites was calculated to be 0.531 from the relative integration of peaks in the 27 Al NMR spectra. The occupancies of aluminum at the 8a and 16d positions were determined through NMR investigations to be 0.9755 and 0.9178, respectively, and were used in the Rietveld refinement to obtain the lattice parameter and anion parameter of Al 2.811 O 3.565 N 0.435 . The results from 27 Al NMR investigations and PXRD structural refinement complemented each other. This work provides a powerful and accessible strategy to precisely understand the crystal structure of novel oxynitride materials with multiple disorder.

Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal

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

Zhu, Jin-Yi; Fu, Zheng-Qing; Argonne National Laboratory, Argonne, Illinois

2012-09-01

The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using data collected from a moderately diffracting crystal and 1.9 Å synchrotron X-rays. The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent amore » novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF{sub anom}/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R{sub free} = 26.8%) to 2.3 Å resolution. High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R{sub free} = 21.4%) to 1.85 Å resolution. AF1382 has a winged-helix–turn–helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1–82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.« less

Lunar troilite: Crystallography

USGS Publications Warehouse

Evans, H.T.

1970-01-01

Fine, euhedral crystals of troilite from lunar sample 10050 show a hexagonal habit consistent with the high-temperature NiAs-type structure. Complete three-dimensional counter intensity data have been measured and used to confirm and refine Bertaut's proposed low-temperature crystal structure.

Validation and extraction of molecular-geometry information from small-molecule databases.

PubMed

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Direct observation of the ferroelectric polarization in the layered perovskite Bi{sub 4}Ti{sub 3}O{sub 12}

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

Urushihara, Daisuke; Asaka, Toru, E-mail: asaka.toru@nitech.ac.jp; Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Nagoya 466-8555

We investigated the crystal structure and ferroelectric domains of Bi{sub 4}Ti{sub 3}O{sub 12} (BTO) by means of transmission electron microscopy (TEM) and single-crystal X-ray diffractometry. From the extinction rule, we determined that the space group in the ferroelectric phase of BTO is P1a1 rather than B2cb and B1a1 which have been proposed previously. We successfully refined the crystal structure based on the space group P1a1. The 180° and 90° ferroelectric domain structures were observed by the [001]-zone dark-field TEM imaging. In the 180° domain structure, we determined that one component of the polarization vector is parallel to the a-axis. Anmore » annular bright-field scanning transmission electron microscopy (ABF-STEM) was performed for the direct observation of the crystal structures. The ABF-STEM images displayed the contrasts with respect to every atomic position in spite of the highly distorted structure of BTO. We could evaluate the tilting and distortion of the [TiO{sub 6}] octahedra relatively. Therefore, we directly observed the ferroelectric displacements of Bi and Ti ions.« less

{sup 45}Sc Solid State NMR studies of the silicides ScTSi (T=Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt)

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

Harmening, Thomas; Eckert, Hellmut, E-mail: eckerth@uni-muenster.de; Fehse, Constanze M.

The silicides ScTSi (T=Fe, Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt) were synthesized by arc-melting and characterized by X-ray powder diffraction. The structures of ScCoSi, ScRuSi, ScPdSi, and ScIrSi were refined from single crystal diffractometer data. These silicides crystallize with the TiNiSi type, space group Pnma. No systematic influences of the {sup 45}Sc isotropic magnetic shift and nuclear electric quadrupolar coupling parameters on various structural distortion parameters calculated from the crystal structure data can be detected. {sup 45}Sc MAS-NMR data suggest systematic trends in the local electronic structure probed by the scandium atoms: both the electric field gradients andmore » the isotropic magnetic shifts relative to a 0.2 M aqueous Sc(NO{sub 3}){sub 3} solution decrease with increasing valence electron concentration and within each T group the isotropic magnetic shift decreases monotonically with increasing atomic number. The {sup 45}Sc nuclear electric quadrupolar coupling constants are generally well reproduced by quantum mechanical electric field gradient calculations using the WIEN2k code. Highlights: Black-Right-Pointing-Pointer Arc-melting synthesis of silicides ScTSi. Black-Right-Pointing-Pointer Single crystal X-ray data of ScCoSi, ScRuSi, ScPdSi, and ScIrSi. Black-Right-Pointing-Pointer {sup 45}Sc solid state NMR of silicides ScTSi.« less

The Leptospiral Antigen Lp49 is a Two-Domain Protein with Putative Protein Binding Function

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

Oliveira Giuseppe,P.; Oliveira Neves, F.; Nascimento, A.

2008-01-01

Pathogenic Leptospira is the etiological agent of leptospirosis, a life-threatening disease that affects populations worldwide. Currently available vaccines have limited effectiveness and therapeutic interventions are complicated by the difficulty in making an early diagnosis of leptospirosis. The genome of Leptospira interrogans was recently sequenced and comparative genomic analysis contributed to the identification of surface antigens, potential candidates for development of new vaccines and serodiagnosis. Lp49 is a membrane-associated protein recognized by antibodies present in sera from early and convalescent phases of leptospirosis patients. Its crystal structure was determined by single-wavelength anomalous diffraction using selenomethionine-labelled crystals and refined at 2.0 Angstromsmore » resolution. Lp49 is composed of two domains and belongs to the all-beta-proteins class. The N-terminal domain folds in an immunoglobulin-like beta-sandwich structure, whereas the C-terminal domain presents a seven-bladed beta-propeller fold. Structural analysis of Lp49 indicates putative protein-protein binding sites, suggesting a role in Leptospira-host interaction. This is the first crystal structure of a leptospiral antigen described to date.« less

Crystal structure of the true Nasicon: Na/sub 3/Zr/sub 2/Si/sub 2/PO/sub 12/

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

Boilot, J.P.; Collin, G.; Colomban, P.

For the first time, the results of single crystal determination of the true Nasicon are given. The structure refinement yielded the following composition: Na/sub 3.09(8)/Zr/sub 2.01(1)/P/sub 0.91/Si/sub 2.09/O/sub 12/. Evidence of the total occupancy of the Zr octahedron is found, displaying that only the Si/P non-stoichiometry mechanism is present in the Nasicon crystal. For the two temperatures which have been investigated (R.T. and 623K), the structures are very close to that of the Nasicon analog: Na/sub 3/Sc/sub 2/P/sub 3/O/sub 12/. However the Si/P substitution prevents the sodium long range ordering even in the monoclinic low temperature phase and therefore themore » cross over to the rhombohedral symmetry only involves very small atomic displacements. For both structures, a new sodium position (mid-Na) is displayed in the conduction channel, intermediate between the usual Na(1) and Na(2) sites.« less

Revealing the effect of edge contamination on vortex matter structure in a Nb single crystal with neutron diffraction techniques

NASA Astrophysics Data System (ADS)

Hanson, Helen; Wang, Xi; Luk, Michael; Shi, Jing; Ling, Xinsheng; Maranville, Brian; Majkrzak, Charles

2011-03-01

The vortex matter of type II superconductors provides a model system to study the effect of quenched random disorder on an elastic lattice, particularly in the framework of Bragg glass theory. Neutron scattering techniques are used to examine the structure of the vortex matter and to quantify the phase diagram. After measuring various thermal-magnetic histories, our data provided evidence for the edge contamination model in a Nb single crystal. Since surface oxidation is known to suppress the Bean-Livingston Surface barrier and the inhomogeneous distribution of surface impurities in Nb, we oxidize our sample surface and repeat our measurements. By comparing the data, we are able isolate the dynamic impact of the edge disorder from the static influence of bulk pinning. We discuss the various experimental obstacles in measuring the predicted Bragg glass state. We also report on Reverse Monte Carlo Refinement simulations modeling possible structures of our vortex matter. This research was supported by the U.S. DOE under grant DE- FG 02 - 07 ER46458.

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural, electronic and vibrational properties of LaF3 according to density functional theory and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Oreshonkov, A. S.; Roginskii, E. M.; Krylov, A. S.; Ershov, A. A.; Voronov, V. N.

2018-06-01

Crystal structure of LaF3 single crystal is refined in tysonite-type trigonal unit cell P c1 using density functional theory calculations and Raman spectroscopy. It is shown that trigonal structure with P c1 space group is more energy-efficient than hexagonal structure with space group P63 cm. Simulated Raman spectra obtained using LDA approximation is in much better agreement with experimental data than that obtained with PBE and PBEsol functionals of GGA. The calculated frequency value of silent mode B 2 in case of hexagonal structure P63 cm was found to be imaginary (unstable mode), thus the energy surface obtains negative curvature with respect to the corresponding normal coordinates of the mode which leads to instability of the hexagonal structure in harmonic approximation. The A 1g line at 214 cm‑1 in Raman spectra of LaF3 related to the translation of F2 ions along c axis can be connected with F2 ionic conductivity.

Evaluation of stability region for scandium-containing rare-earth garnet single crystals and their congruent-melting compositions

NASA Astrophysics Data System (ADS)

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

2017-06-01

Single crystals of scandium-containing rare-earth garnets in system R-Sc-C-O (R3+=Y, Gd; C3+=Al, Ga) have been grown by the Czochralski technique. X-ray diffraction analysis has been used to refine crystal compositions. The fundamental difference between the melt compositions and compositions of grown crystals has been found (except for compositions of congruent-melting compounds, CMC). The specific features of garnet solid solution formation have been established and the ternary diagrams with real or hypothetical phases have been built. The dinamics of coordination polyhedra changes with the formation of substitutional solid solutions have been proposed based on the mathematical modeling and experimental data. Possible existence of CMC with garnet structure in different systems as well as limit content of Sc ions in dodecahedral and octahedral sites prior to their partial substitution of ions, located in other sites, have been evaluated. It was established that the redistribution of cations over crystallographic sites (antistructural point defects) due to system self-organization to maintain its stability may be accompanied by cation ordering and the symmetry change of individual polyhedrons and/or the whole crystal.

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

DOE PAGES

Taddei, Keith M.; Sturza, M.; Chung, Duck -Yung; ...

2015-09-14

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate frommore » the majority phase. In order to better understand this minority phase, a series of high-quality Cs xFe 2–ySe 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.« less

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

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

Taddei, K. M.; Sturza, M.; Chung, D. Y.

2015-09-01

By simultaneously displaying magnetism and superconductivity in a single phase, the iron based superconductors provide a model system for the study of magnetism’s role in superconductivity. The class of intercalated iron selenide superconductors is unique amongst these in having the additional property of phase separation and coexistence of two distinct phases - one majority phase with iron vacancy ordering and strong antiferromagnetism and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfullymore » synthesized separate from the majority phase. In order to better understand this minority phase, a series of high quality CsxFe2-ySe2 single crystals with (0.8 ≤ x ≤ 1; 0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show the average structure of the minority phase to be I4/mmm, however, the temperature evolution of its lattice parameters shows it to be distinct from the high temperature I4/mmm parent structure. Neutron and x-ray diffraction experiments performed on single crystal samples reveal the presence of previously unobserved discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body-centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from a three-dimensional Cs vacancy ordering in the minority phase. This model predicts a 25% vacancy of the Cs site which is consistent with the site’s refined occupancy. Magnetization measurements performed in tandem with neutron single crystal diffraction provide evidence that the minority phase is the host of superconductivity. Our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the valence of iron.« less

Flow induced/ refined solution crystallization of a semiconducting polymer

NASA Astrophysics Data System (ADS)

Nguyen, Ngoc A.

Organic photovoltaics, a new generation of solar cells, has gained scientific and economic interests due to the ability of solution-processing and potentially low-cost power production. Though, the low power conversion efficiency of organic/ plastic solar cells is one of the most pertinent challenges that has appealed to research communities from many different fields including materials science and engineering, electrical engineering, chemical engineering, physics and chemistry. This thesis focuses on investigating and controlling the morphology of a semi-conducting, semi-crystalline polymer formed under shear-flow. Molecular structures and processing techniques are critical factors that significantly affect the morphology formation in the plastic solar cells, thus influencing device performance. In this study, flow-induced solution crystallization of poly (3-hexylthiophene) (P3HT) in a poor solvent, 2-ethylnapthalene (2-EN) was utilized to make a paint-like, structural liquid. The polymer crystals observed in this structured paint are micrometers long, nanometers in cross section and have a structure similar to that formed under quiescent conditions. There is pi-pi stacking order along the fibril axis, while polymer chain folding occurs along the fibril width and the order of the side-chain stacking is along fibril height. It was revealed that shear-flow not only induces P3HT crystallization from solution, but also refines and perfects the P3HT crystals. Thus, a general strategy to refine the semiconducting polymer crystals from solution under shear-flow has been developed and employed by simply tuning the processing (shearing) conditions with respect to the dissolution temperature of P3HT in 2-EN. The experimental results demonstrated that shear removes defects and allows more perfect crystals to be formed. There is no glass transition temperature observed in the crystals formed using the flow-induced crystallization indicating a significantly different morphology formation in comparison to that of the pristine (as-received) P3HT. As a result, single P3HT crystals with high surface energy chain folds were analyzed and determined. Previous reported results of infinite melting enthalpy of extended chain P3HT crystals are much higher than the result discovered in this study. The findings in this study revealed that the infinite melting enthalpy of chain-folded P3HT crystals is considerably decreased due to the presence of this P3HT chain-folded surface energy. In this study, the kinetics and mechanism of P3HT crystallization under shear-flow was thoroughly investigated as well. A homogeneous nucleation of P3HT was observed that allows one dimensional fibril crystal growth. The micrometer long P3HT crystals are formed and limited by the contact time between the P3HT molecules. Furthermore, it was found that phenyl-C61-butyric acid methyl ester (PCBM) nanoparticles inhibit the crystallization of P3HT under shear. However, the shear-flow leads to nanophase agglomeration of PCBM and creates percolation of P3HT fibril crystal networks and the PCBM phase separated domains that apparently present better pathways for transporting electrons and holes. Interestingly, the structured liquid was simply applied onto substrates with a paintbrush resulting in similar device performance to those made with current techniques in which the morphology is commonly formed during application or post-processing steps. These detailed findings are given and discussed in the thesis.

Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

NASA Astrophysics Data System (ADS)

Post, J. E.; Bish, D. L.; Heaney, P. J.

2006-05-01

Sepiolite is a hydrous Mg-silicate clay mineral with fibrous morphology that typically occurs as fine-grained, poorly crystalline masses. It occurs in a wide variety of geological environments and has been mined for centuries because of its many uses, e.g. in the pharmaceutical, fertilizer, and pesticide industries. Its versatile functionality derives from the large surface area and microporosity that are characteristic of the material. In recent years, sepiolite has received considerable attention with regard to the adsorption of organics, for use as a support for catalysts, as a molecular sieve, and as an inorganic membrane for ultrafiltration. Because of its fine-grained and poorly crystalline nature, it has not been possible to study sepiolite's crystal structure using single-crystal X-ray diffraction methods, and consequently many details of the structure are still not well known. In this study, Rietveld refinements using synchrotron powder X-ray diffraction data were used to investigate the crystal structure and dehydration behavior of sepiolite from Durango, Mexico. The room- temperature (RT) sepiolite structure in air compares well with previous models but reveals an additional zeolitic water site. The RT structure under vacuum retained only ~1/8 of the zeolitic water and the volume decreased 1.3%. Real-time, temperature-resolved synchrotron powder X-ray diffraction data and Rietveld refinements were used to investigate the behavior of the sepiolite structure from 300 to 925 K. Rietveld refinements revealed that most of the zeolitic water is lost by ~390 K, accompanied by a decrease in the a and c unit-cell parameters. Above ~600 K the sepiolite structure folds as one-half of the crystallographically bound water is lost. Rietveld refinements of the "anhydrous" sepiolite structure reveal that, in general, unit-cell parameters a, b, â and volume steadily decrease with increasing temperature; there is an obvious change in slope at ~820 K suggesting a phase transformation coinciding with the loss of the remaining bound water molecule. These temperature-resolved real-time powder X-ray diffraction studies provide the first comprehensive description of the sepiolite structure and the complex changes it undergoes as it dehydrates. Additional heating and cooling in situ powder X-ray diffraction experiments are underway in order to investigate the relative stabilities and rehydration behaviors of the partially-hydrated sepiolite phases. The results of these studies should provide a more robust model for predicting and modifying the properties and applications of this critical industrial material and environmentally important mineral.

Structure of the mixed-metal carbonate KAgCO₃ revisited: order-disorder (OD) polytypism and allotwinning.

PubMed

Hans, Philipp; Stöger, Berthold; Weil, Matthias; Zobetz, Erich

2015-04-01

Crystals of KAgCO3 belong to an order-disorder (OD) family of structures composed of layers of two kinds. There are two polytypes with a maximum degree of order [MDO1: Pccb; MDO2: Ibca, doubled a-axis compared with MDO1], which are both realised to a different extent in two crystals under investigation [volume fraction MDO1:MDO2 in crystal (I): 0.0216:0.9784 (3) and in crystal (II): 0.9657:0.0343 (3)]. Sharp diffraction spots and the absence of diffuse scattering indicate highly ordered macroscopic domains. The structure of KAgCO3 was refined concurrently against all reflections using an allotwin model (addition of the intensities of both domains). It is shown that a disorder model refined against reflections of only one domain can lead to a significant overestimation of the volume fraction of this domain.

Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from Arabidopsis thaliana in complex with AMP.

PubMed

Kim, Do Jin; Bitto, Eduard; Bingman, Craig A; Kim, Hyun-Jung; Han, Byung Woo; Phillips, George N

2015-07-01

Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain-containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N-terminal portion of a multi-domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP-like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann-like α/β overall fold. The bound AMP and conservation of residues in the ATP-binding loop suggest that the protein At3g01520 also belongs to the ATP-binding USP subfamily members. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

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.

Structural insight into arginine methylation by the mouse protein arginine methyltransferase 7: a zinc finger freezes the mimic of the dimeric state into a single active site.

PubMed

Cura, Vincent; Troffer-Charlier, Nathalie; Wurtz, Jean Marie; Bonnefond, Luc; Cavarelli, Jean

2014-09-01

Protein arginine methyltransferase 7 (PRMT7) is a type III arginine methyltransferase which has been implicated in several biological processes such as transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation and metastasis. PRMT7 is a unique but less characterized member of the family of PRMTs. The crystal structure of full-length PRMT7 from Mus musculus refined at 1.7 Å resolution is described. The PRMT7 structure is composed of two catalytic modules in tandem forming a pseudo-dimer and contains only one AdoHcy molecule bound to the N-terminal module. The high-resolution crystal structure presented here revealed several structural features showing that the second active site is frozen in an inactive state by a conserved zinc finger located at the junction between the two PRMT modules and by the collapse of two degenerated AdoMet-binding loops.

Crystal structure of human tooth enamel studied by neutron diffraction

NASA Astrophysics Data System (ADS)

Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

2015-02-01

Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

Structural Characterization Studies on Semiconducting ZnSnN 2 Films using Synchrotron X-ray Diffraction

NASA Astrophysics Data System (ADS)

Senabulya, Nancy

This work is motivated by the need for new visible frequency direct bandgap semiconductor materials that are earth abundant and low-cost to meet the increasing demand for optoelectronic device applications such as solid state lighting and photovoltaics. Zinc-Tin-Nitride (ZnSnN2), a member of the II-IV nitride semiconductor family has been proposed as an alternative to the more common III-nitride semiconductors for use in optoelectronic devices. This material has been synthesized under optimized conditions using plasma assisted molecular beam epitaxy. Though a lot of research has recently been done computationally to predict the electronic and structural properties of ZnSnN2, experimental verification of these theories in single crystal thin films is lacking and warrants investigation because the accurate determination of the crystal structure of ZnSnN2 is a fundamental prerequisite for controlling and optimizing optoelectronic properties. In this synchrotron x-ray diffraction study, we present experimental validation, through unit cell refinement and 3d reciprocal space maps, of the crystal structure of single domain ZnSnN2 films deposited on (111) Yttria stabilized zirconia (YSZ) and (001) Lithium gallate (LGO) substrates. We find that ZnSnN2 films grown on (111) YSZ can attain both the theoretically predicted disordered wurtzite and ordered orthorhombic Pna21 structures under carefully controlled MBE growth conditions, while films grown on (001) LGO have the ordered Pn21a orthorhombic crystal structure. Through a systematic annealing study, a temperature induced first order structural phase transition from the wurtzite to orthorhombic phase is realized, characterized by the appearance of superstructure reflections in.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Self-adjusted flux for the traveling solvent floating zone growth of YBaCuFeO5 crystal

NASA Astrophysics Data System (ADS)

Lai, Yen-Chung; Shu, Guo-Jiun; Chen, Wei-Tin; Du, Chao-Hung; Chou, Fang-Cheng

2015-03-01

A modified traveling solvent floating zone (TSFZ) technique was used to successfully grow a large size and high quality single crystal of multiferroic material YBaCuFeO5. This modified TSFZ growth uses a stoichiometric feed rod and pure copper oxide as the initial flux without prior knowledge of the complex phase diagram involving four elements, and the optimal flux for the growth of incongruently melt crystal is self-adjusted after a prolonged stable pulling. The wetting of the feed rod edge that often perturbs the molten zone stability was avoided by adding 2 wt% B2O3. The optimal flux concentration for the YBaCuFeO5 growth can be extracted to be near YBaCuFeO5:CuO=13:87 in molar ratio. The crystal quality was confirmed by the satisfactory refinement of crystal structure of space group P4mm and the two consecutive anisotropic antiferromagnetic phase transitions near 455 K and 170 K.

Undulated oxo-centered layers in PbLn3O4(VO4) (Ln= La and Nd) and relationship with Nd4O4(GeO4)

NASA Astrophysics Data System (ADS)

Colmont, Marie; Mentré, Olivier; Henry, Natacha; Pautrat, Alain; Leclercq, Bastien; Capet, Frédéric; Djelal, Nora; Roussel, Pascal

2018-04-01

Single crystals of PbLa3O4(VO4) have been synthesized using the flux growth technique and characterized by X-ray diffraction. The crystal structure of the tittle phase was solved by charge flipping and refined to R1 = 0.024 (wR2 = 0.031) for 2777 reflections [I>3σ(I)]. The compound is orthorhombic and crystallized in the space group Cmcm: a = 5.8686(6)Å, b = 17.898(2)Å, c = 7.9190(7)Å, V = 831.8(1)Å3, Z = 4. The structure is built on [PbLa3O4]3+ layers with zig-zag cross-sections, surrounded by isolated (VO4)3- tetrahedra. Its crystal structure shows direct relationship with the isoformular Nd4O4(GeO4) compound which crystallized in the primitive non centrosymmetric Pb21m sub-group. Its stability in temperature and under air was checked as well as optical properties. In a second part, lanthanum was substituted by neodymium giving rise to a paramagnet and f→ f electronic excitations superposed to the broad absorption front below 3.05 eV related to the presence of VO4 groups.

Single-crystal X-ray diffraction study of SrGeO3 high-pressure perovskite phase at 100 K

NASA Astrophysics Data System (ADS)

Nakatsuka, Akihiko; Arima, Hiroshi; Ohtaka, Osamu; Fujiwara, Keiko; Yoshiasa, Akira

2017-10-01

Single-crystal X-ray diffraction study of SrGeO3 perovskite (cubic; space group Pmɜ¯m) synthesized at 6 GPa and 1223 K was conducted at a low temperature of 100 K. The residual electron density revealed the presence of the bonding electron at the center of the Ge-O bond, in accordance with our previous conclusion that the Ge-O bond is strongly covalent. From comparison with our previous structure-refinement result at 296 K, the mean square displacement (MSD) of the O atom in the direction of the Ge-O bond is suggested to exhibit no significant temperature dependence, in contrast to that in the direction perpendicular to the bond. Thus, the strong covalency of the Ge-O bond can have a large influence on the temperature dependence of thermal vibration of the O atom.

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.

Structural studies on a high-pressure polymorph of NaYSi 2O 6

NASA Astrophysics Data System (ADS)

Kahlenberg, Volker; Konzett, Jürgen; Kaindl, Reinhard

2007-06-01

High-pressure synthesis experiments in the system Na 2O-Y 2O 3-SiO 2 revealed the existence of a previously unknown polymorph of NaYSi 2O 6 or Na 3Y 3[Si 3O 9] 2 which was quenched from 3.0 GPa and 1000 °C. Structural investigations on this modification have been performed using single-crystal X-ray diffraction data collected at ambient conditions. Furthermore, unpolarized micro-Raman spectra have been obtained from single-crystal material. The high-P modification of NaYSi 2O 6 crystallizes in the centrosymmetric space group C2/ c with 12 formula units per cell ( a=8.2131(9) Å, b=10.3983(14) Å, c=17.6542(21) Å, β=100.804(9)°, V=1481.0(3) Å 3, R(| F|)=0.033 for 1142 independent observed reflections) and belongs to the group of cyclo-silicates. Basic building units are isolated three-membered [Si 3O 9] rings located in layers parallel to (010). Within a single layer the rings are concentrated in strings parallel to [100]. The sequence of directedness of up ( U) or down ( D) pointing tetrahedra of a single ring is UUU or DDD, respectively. Stacking of the layers parallel to b results in the formation of a three-dimensional structure in which yttrium and sodium cations are incorporated for charge compensation. In more detail, four non-tetrahedral cation positions can be differentiated which are coordinated by 6 and 8 oxygen ligands. Refinements of the site occupancies did not reveal any indication for mixed Na-Y populations on these positions. Finally, several geometrical parameters of rings occurring in cyclo-trisilicate structures have been compiled and are discussed.

The Phase Transformation and Crystal Structure Studies of Strontium Substituted Barium Monoferrite

NASA Astrophysics Data System (ADS)

Mulyawan, A.; Adi, W. A.; Mustofa, S.; Fisli, A.

2017-03-01

Unlike other AFe2O4 ferrite materials, Barium Monoferrite (BaFe2O4) have an orthorhombic structure which is very interesting to further study the crystal structure and phase formation. In this study, Strontium substituted Barium Monoferrite in the form of Ba(1-x)Sr(x)Fe2O4 has successfully been synthesized through solid state reaction method which includes BaCO3, SrCO3, and Fe2O3 as starting materials. Ba(1-x)Sr(x)Fe2O4 was made by varying the dopant composition of Strontium (Sr2+) from x = 0, 0.1, 0.3, and 0.5. Each composition was assisted by ethanol and continued to the milling process for 5 hours then followed by sintering process at 900 °C for 5 hours. The phase transformation was studied by using X-ray diffractometer (XRD) and Rietveld refinement using General Structure Analysis System (GSAS) also 3D crystal visualization using VESTA. Referring to the refinement results, a single phase of BaFe2O4 was formed in x = 0 and 0.1. The composition has orthorhombic structure, space group B b21m, and lattice parameters of a = 19.0229, b = 5.3814 c = 8.4524 Å, α = β = γ = 90° and a = 18.9978, b = 5.3802 c = 8.4385 Å, α = β = γ = 90° respectively. In the composition of x = 0.3 it was found that the phase of BaSrFe4O8 begin to form due to the overload expansion of the Sr2+ occupancy which made the distortion of the initial lattice parameters and finally in the x = 0.5 composition the single phase of BaSrFe4O8 was clearly formed. Energy Dispersive Spectroscopy (EDS) was used to confirm the change of the material structure by measuring the elemental compound composition ratio. The result of EDS spectra clearly exhibited the dominant elements were Barium (Ba), Strontium (Sr), Iron (Fe), and Oxygen (O) with the compound ratio (Atomic percentage and mass percentage) correspond to the BaFe2O4 and BaSrFe4O8 phase.

Cloning, expression, purification, crystallization and preliminary X-ray characterization of the full-length single-stranded DNA-binding protein from the hyperthermophilic bacterium Aquifex aeolicus.

PubMed

Clarke, David J; Northey, Christopher G; Mack, Lynsey A; McNae, Iain W; Alexeev, Dmitriy; Sawyer, Lindsay; Campopiano, Dominic J

2004-11-01

Single-stranded DNA-binding (SSB) proteins stabilize single-stranded DNA, which is exposed by separation of the duplex during DNA replication, recombination and repair. The SSB protein from the hyperthermophile Aquifex aeolicus has been overexpressed in Escherichia coli, purified and characterized and crystals of the full-length protein (147 amino acids; M(r) 17 131.20) have been grown by vapour diffusion from ammonium sulfate pH 7.5 in both the absence and presence of ssDNA [dT(pT)(68)]. All crystals diffract to around 2.9 A resolution and those without bound DNA (native) belong to space group P2(1), with two tetramers in the asymmetric unit and unit-cell parameters a = 80.97, b = 73.40, c = 109.76 A, beta = 95.11 degrees . Crystals containing DNA have unit-cell parameters a = 108.65, b = 108.51, c = 113.24 A and could belong to three closely related space groups (I222, I2(1)2(1)2(1) or I4(1)) with one tetramer in the asymmetric unit. Electrospray mass spectrometry of the crystals confirmed that the protein was intact. Molecular replacement with a truncated E. coli SSB structure has revealed the position of the molecules in the unit cell and refinement of both native and DNA-bound forms is under way.

Crystal structure and magnetic properties of Sr 4Mn 2NiO 9

NASA Astrophysics Data System (ADS)

El Abed, Ahmed; Gaudin, Etienne; Lemaux, Sylvain; Darriet, Jacques

2001-12-01

The crystal structure of Sr 4Mn 2NiO 9 has been refined on single crystal. This phase belongs to the series A 1+ x(A 'xB 1- x)O 3 ( x=1/3) related to the 2H-hexagonal perovskite. The structure contains transition metals in chains of oxide polyhedra (trigonal prisms and octahedra); neighboring chains are separated from each other by the Sr atoms. The sequence of the face sharing polyhedra along the chains is two octahedra + one trigonal prism. Mn occupies the octahedra and Ni is disordered in the trigonal prism with ≈80% in the pseudo square faces of the prism and ≈20% at the centre. This result has been confirmed by XANES experiments at Mn K and Ni K edges, respectively. Sr 4Mn 2NiO 9 is antiferromagnetic with a Néel temperature at T=3 K. The Curie constant measured at high temperature is in good agreement with ≈80% of the Ni 2+ ions in the spin state configuration S=0.

Polymorphism in Alkali Metal Uranyl Nitrates: Synthesis and Crystal Structure of γ-K(UO2)(NO3)3

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

Jouffret, Laurent J.; Krivovichev, Sergey V.; Burns, Peter C.

2011-07-20

Single crystals of γ-K(UO2)(NO3)3 were prepared from aqueous solutions by evaporation. The crystal structure [orthorhombic, Pbca (61), a = 9.2559(3) Å, b = 12.1753(3) Å, c = 15.8076(5) Å, V = 1781.41(9) Å3, Z = 8] was determined by direct methods and refined to R1 = 0.0267 on the basis of 3657 unique observed reflections. The structure is composed of isolated anionic uranyl trinitrate units, [(UO2)(NO3)3]–, that are linked through eleven-coordinated K+ cations. Both known polymorphs of K(UO2)(NO3)3 (α- and γ-phases) can be considered as based upon sheets of isolated complex [(UO2)(NO3)3]– ions separated by K+ cations. The existence ofmore » polymorphism in the two K[UO2(NO3)3] polymorphs is due to the different packing modes of uranyl trinitrate clusters that adopt the same two-dimensional but different three-dimensional arrangements.« less

Ion channeling study of defects in compound crystals using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Turos, A.; Jozwik, P.; Nowicki, L.; Sathish, N.

2014-08-01

Ion channeling is a well-established technique for determination of structural properties of crystalline materials. Defect depth profiles have been usually determined basing on the two-beam model developed by Bøgh (1968) [1]. As long as the main research interest was focused on single element crystals it was considered as sufficiently accurate. New challenge emerged with growing technological importance of compound single crystals and epitaxial heterostructures. Overlap of partial spectra due to different sublattices and formation of complicated defect structures makes the two beam method hardly applicable. The solution is provided by Monte Carlo computer simulations. Our paper reviews principal aspects of this approach and the recent developments in the McChasy simulation code. The latter made it possible to distinguish between randomly displaced atoms (RDA) and extended defects (dislocations, loops, etc.). Hence, complex defect structures can be characterized by the relative content of these two components. The next refinement of the code consists of detailed parameterization of dislocations and dislocation loops. Defect profiles for variety of compound crystals (GaN, ZnO, SrTiO3) have been measured and evaluated using the McChasy code. Damage accumulation curves for RDA and extended defects revealed non monotonous defect buildup with some characteristic steps. Transition to each stage is governed by the different driving force. As shown by the complementary high resolution XRD measurements lattice strain plays here the crucial role and can be correlated with the concentration of extended defects.

Crystallization and preliminary crystallographic studies of human kallikrein 7, a serine protease of the multigene kallikrein family

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

Fernández, Israel S.; Ständker, Ludger; Hannover Medical School, Center of Pharmacology, 30625 Hannover

2007-08-01

The cloning, expression, purification and crystallization of recombinant human kallikrein 7, directly synthesized in the active form in E. coli, is described. Diffraction data were collected to 2.8 Å resolution from native crystals. Human kallikreins are a group of serine proteases of high sequence homology whose genes are grouped as a single cluster at chromosome 19. Although the physiological roles of kallikreins are generally still unknown, members of the kallikrein family have been clearly implicated in pathological situations such as cancer and psoriasis. Human kallikrein 7 (hK7) has been shown to be involved in pathological keratinization, psoriasis and ovarian cancer.more » In order to gain insight into the molecular structure of this protein, hK7 was crystallized after recombinant production in its folded and active form using a periplasmic secretion vector in Escherichia coli. The crystals belonged to the rhombohedral space group H32 and diffracted to 2.8 Å. The phase problem was solved by molecular replacement using the mouse kallikrein-related protein neuropsin. Completion of the model and structure refinement are under way.« less

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 where the data are sparse.« less

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 where the data are sparse.« less

TIMo/sub 2/ /SUP IV/ P/sub 3/O/sub 12/: a molybdenophosphate with a tunnel structure

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

Leclaire, A.; Monier, J.C.; Raveau, B.

1985-10-01

A molybdenophosphate, TIMo/sub 2/ /SUP IV/ P/sub 3/O/sub 12/, with an original tunnel structure, has been isolated. Its structure has been determined by X-ray diffraction on a single crystal. It crystallizes in the orthorhombic system with a = 8.836(1), b = 9.255(1), c = 12.288(1) A, possible space groups Pbcm and Pbc2/sub 1/ with /ZETA/ = 4. The structure was solved and refined in the centrosymmetric space group Pbcm. The host lattice ''Mo/sub 3/P/sub 3/O/sub 12/'' is built up from corner-sharing octahedra and tetrahedra and forms tunnels running along the b axis and cages where the TI+ ions are located.more » The relationships of this framework wit that of the phosphate tungsten bronze CsP/sub 8/W/sub 8/O/sub 40/ and that of the hexagonal tungsten bronze are discussed.« less

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

Polymorphism of the hydroxide perovskite Ga(OH)3 and possible proton-driven transformational behaviour

NASA Astrophysics Data System (ADS)

Welch, M. D.; Kleppe, A. K.

2016-07-01

The crystal structure of hydroxide perovskite Ga(OH)3, the mineral söhngeite, has been determined for a natural sample by single-crystal XRD in space group P42/ nmc to R 1 = 0.031, wR 2 = 0.071, GoF = 1.208, and for comparison also in space group P42/ n to R 1 = 0.031, wR 2 = 0.073, GoF = 1.076. Unit cell parameters are a = 7.4546(2) Å, c = 7.3915(2) Å, V = 410.75(2) Å3. The two structures are very similar and both have tilt system a + a + c -. The approximate positions of all H atoms in each structure have been refined. In the P42/ nmc structure all five H sites are half-occupied, whereas in the P42/ n structure four sites are half-occupied and one is fully occupied. The presence of five non-equivalent OH groups in söhngeite is confirmed by single-crystal Raman spectroscopy, but does not allow a choice between these two space groups to be made. There is only a single very weak violator of the c-glide of P42/ nmc and the two refined structures are essentially the same, but are significantly different from that of the original description in which orthorhombic space group Pmn21 was reported with corresponding tilt system a 0 a 0 c +. It is argued here that such a structure is very implausible for a hydroxide perovskite. On heating söhngeite to 423 K, transformation to a cubic structure with Imbar{3} symmetry ( a + a + a +) of the aristotype occurs. This cubic phase was recovered on cooling to 293 K without back-transformation to the tetragonal polymorph. As there is no continuous group/subgroup pathway from P42/ nmc (or P42/ n) to Imbar{3}, the transformation must be first-order, which is consistent with the large hysteresis observed. The change from the tetragonal to cubic structures involves a change in tilt system a + a + c - → a + a + a +, with a significant reconfiguration of hydrogen-bonding topology. The very different tilt systems and hydrogen-bonding configurations of the two polymorphs are responsible for hysteresis and metastable preservation of the cubic phase at 293 K. As the Ga(OH)6 octahedra of the low- and high- T polymorphs are very similar it is inferred that the transformation is driven by proton behaviour, presumably involving proton re-ordering.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).

PubMed

Park, HaJeung; González, Àlex L; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R; Fang, Pengfei; Guo, Min; Disney, Matthew D

2015-06-23

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10)

PubMed Central

Park, HaJeung; González, Àlex L.; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R.; Fang, Pengfei; Guo, Min; Disney, Matthew D.

2016-01-01

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA. PMID:26039897

A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

PubMed

Penttinen, Leena; Rutanen, Chiara; Saloheimo, Markku; Kruus, Kristiina; Rouvinen, Juha; Hakulinen, Nina

2018-01-01

Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

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

Schafer, Marion; Bobev, Svilen

This paper presents results from our exploratory work in the systems K-Cd-Ge, Rb-Cd-Ge, and Cs-Cd-Ge, which yielded the novel type-I clathrates with refined compositions K 8Cd 3.77(7)Ge 42.23, Rb 8Cd 3.65(7)Ge 42.35, and Cs 7.80(1)Cd 3.65(6)Ge 42.35. The three compounds represent rare examples of clathrates of germanium with the alkali metals, where a d 10 element substitutes a group 14 element. The three structures, established by single-crystal X-ray diffraction, indicate that the framework-building Ge atoms are randomly substituted by Cd atoms on only one of the three possible crystallographic sites. Furthermore, this and several other details of the crystal chemistrymore » are elaborated.« less

NMR spectroscopy of experimentally shocked single crystal quartz: A reexamination of the NMR shock barometer

NASA Technical Reports Server (NTRS)

Fiske, P. S.; Gratz, A. J.; Nellis, W. J.

1993-01-01

Cygan and others report a broadening of the Si-29 nuclear magnetic resonance (NMR) peak for synthetic quartz powders with increasing shock pressure which they propose as a shock wave barometer for natural systems. These results are expanded by studying single crystal quartz shocked to 12 and 33 GPa using the 6.5 m two-stage light-gas gun at Lawrence Livermore National Laboratories. Our NMR results differ substantially from those of Cygan and others and suggest that the proposed shock wave barometer may require refinement. The difference in results between this study and that of Cygan and others is most likely caused by different starting materials (single crystal vs. powder) and different shock loading histories. NMR results from single crystal studies may be more applicable to natural systems.

Single-crystal diffraction at megabar conditions by synchrotron radiation

NASA Astrophysics Data System (ADS)

Merlini, Marco; Hanfland, Michael

2013-08-01

Crystal structure determination at extreme pressures is currently possible at synchrotron beamlines optimized for such a purpose. We report the description of the experimental setup available at European Synchrotron Radiation Facility ID09 beamline (Grenoble, France) and, with two examples, we illustrate the state-of-the-art experiments currently performed at third-generation synchrotrons. The first example concerns the determination of the equation of state and the structural behavior of low-spin Fe-bearing siderite in the megabar pressure range. Siderite, in fact, undergoes a first-order isosymmetric transition at 45 GPa, and, above this pressure, it features Fe2+ in electronic low-spin configuration. The local configuration of Fe coordination polyhedra, determined by structural refinements, significantly deviates from a regular octahedron. Nevertheless, no further structural transition is detected up to the maximum pressure reached in our experiments, 135 GPa. The analysis of the Fe-O bond length extrapolated to ambient pressure, which indicates that the difference in ionic radii between the high- and the low-spin state of Fe2+ is 0.172 Å, in excellent agreement with the tabulated data by Shannon and Prewitt [Effective ionic radii in oxides and fluorides. Acta Crystallogr. 1969;B25:925-946]. The second example concerns the determination and refinement of the oP8 structure adopted by sodium in the pressure interval 118-125 GPa, using an experimental dataset collected at 118 GPa. The orthorhombic [a=4.7687(15) Å, b=3.0150(6) Å, c=5.2423(7) Å, V=75.4(3) Å3] oP8 structure is topologically related to the MnP structure, with two non-equivalent atoms in the unit cell. Despite the weak scattering factor of Na atoms, the quality of the data also allows meaningful displacement parameters refinements (R1=4.6%, 14 parameters, 190 diffractions, and 105 unique) demonstrating that the current accuracy of diffraction data at extreme pressures can be comparable with ambient condition measurements.

Crystal structure, quantum mechanical investigation, IR and NMR spectroscopy of two new organic salts: (C8H12NO)·[NO3] (I) and (C8H14N4)·[ClO4]2 (II)

NASA Astrophysics Data System (ADS)

Bayar, I.; Khedhiri, L.; Soudani, S.; Lefebvre, F.; Pereira da Silva, P. S.; Ben Nasr, C.

2018-06-01

Two new organic-inorganic hybrid materials, 4-methoxybenzylammonium nitrate, (C8H12NO)·[NO3] (I), and 2-(1-piperazinyl)pyrimidinium bis(perchlorate), (C8H14N4)·[ClO4]2(II), have been synthesized by an acid/base reaction at room temperature, their structures were determined by single crystal X-ray diffraction. Compound (I) crystallizes in the orthorhombic system and Pnma space group with a = 15.7908 (7), b = 6.8032 (3), c = 8.7091 (4) Å, V = 935.60 (7) Å3 with Z = 4. Full-matrix least-squares refinement converged at R = 0.038 and wR(F2) = 0.115. Compound (II) belongs to the monoclinic system, space group P21/c with the following parameters: a = 10.798(2), b = 7.330(1), c = 21.186(2) Å, β = 120.641 (4)°, V = 1442.7 (3) Å3and Z = 4. The structure was refined to R = 0.044, wR(F2) = 0.132. In the structures of (I) and (II), the anionic and cationic entities are interconnected by hydrogen bonding contacts forming three-dimensional networks. Intermolecular interactions were investigated by Hirshfeld surfaces and the contacts of the four different chloride atoms in (II) were compared. The Molecular Electrostatic Potential (MEP) maps and the HOMO and LUMO energy gaps of both compounds were computed. The vibrational absorption bands were identified by infrared spectroscopy. These compounds were also investigated by solid-state 13C, 35Cl and 15N NMR spectroscopy. DFT calculations allowed the attribution of the IR and NMR bands.

Synthesis, crystal structures and luminescence properties of the Eu 3+-doped yttrium oxotellurates(IV) Y 2Te 4O 11 and Y 2Te 5O 13

NASA Astrophysics Data System (ADS)

Höss, Patrick; Osvet, Andres; Meister, Frank; Batentschuk, Miroslaw; Winnacker, Albrecht; Schleid, Thomas

2008-10-01

Y 2Te 4O 11:Eu 3+ and Y 2Te 5O 13:Eu 3+ single crystals in sub-millimeter scale were synthesized from the binary oxides (Y 2O 3, Eu 2O 3 and TeO 2) using CsCl as fluxing agent. Crystallographic structures of the undoped yttrium oxotellurates(IV) Y 2Te 4O 11 and Y 2Te 5O 13 have been determined and refined from single-crystal X-ray diffraction data. In Y 2Te 4O 11, a layered structure is present where the reticulated sheets consisting of edge-sharing [YO 8] 13- polyhedra are interconnected by the oxotellurate(IV) units, whereas in Y 2Te 5O 13 only double chains of condensed yttrium-oxygen polyhedra with coordination numbers of 7 and 8 are left, now linked in two crystallographic directions by the oxotellurate(IV) entities. The Eu 3+ luminescence spectra and the decay time from different energy levels of the doped compounds were investigated and all detected emission levels were identified. Luminescence properties of the Eu 3+ cations have been interpreted in consideration of the now accessible detailed crystallographic data of the yttrium compounds, providing the possibility to examine the influence of the local symmetry of the oxygen coordination spheres.

Non-convergent ordering and displacive phase transition in pigeonite: in situ HT XRD study

NASA Astrophysics Data System (ADS)

Cámara, F.; Carpenter, M. A.; Domeneghetti, M. C.; Tazzoli, V.

A natural Ca-rich pigeonite (En47Fs43Wo10), free of augite exsolution products, was studied by in situ high-temperature single-crystal X-ray diffraction. The sample, monoclinic P21/c (a=9.719(7) Å, b=8.947(9) Å, c=5.251(3) Å, β=108.49(5), V=433.0(6) Å3), was annealed up to 1000 °C to induce a phase transition from P21/c to C2/c symmetry. Complete single-crystal X-ray diffraction data collections were carried out in situ at 650, 750, 850 and 950 °C after the crystal had reached equilibrium for the Fe-Mg intracrystalline exchange reaction at each temperature. The variation, with increasing temperature, of lattice parameters, of intensity of hkl reflections with h + k=2n + 1 (which vanish at high temperature) and of some geometrical parameters from structure refinement, showed that the displacive phase transition P21/cC2/c was continuous in character. This contrasts with the first-order character for the HT phase transition in pigeonite containing significantly less calcium.

Preparation of High Purity CdTe for Nuclear Detector: Electrical and Nuclear Characterization

NASA Astrophysics Data System (ADS)

Zaiour, A.; Ayoub, M.; Hamié, A.; Fawaz, A.; Hage-ali, M.

High purity crystal with controllable electrical properties, however, control of the electrical properties of CdTe has not yet been fully achieved. Using the refined Cd and Te as starting materials, extremely high-purity CdTe single crystals were prepared by the traditional vertical THM. The nature of the defects involved in the transitions was studied by analyzing the position of the energy levels by TSC method. The resolution of 4.2 keV (FWHM) confirms the high quality and stability of the detectors: TSC spectrum was in coherence with detectors spectrum with a horizontal plate between 0.2 and 0.6 eV. The enhancement in resolution of detectors with a full width at half- maximum (less than 0.31 meV), lead to confirm that the combination of vacuum distillation and zone refining was very effective to obtain more purified CdTe single crystals for photovoltaic or nuclear detectors with better physical properties.

Controlling the energy of defects and interfaces in the amplitude expansion of the phase-field crystal model

NASA Astrophysics Data System (ADS)

Salvalaglio, Marco; Backofen, Rainer; Voigt, Axel; Elder, Ken R.

2017-08-01

One of the major difficulties in employing phase-field crystal (PFC) modeling and the associated amplitude (APFC) formulation is the ability to tune model parameters to match experimental quantities. In this work, we address the problem of tuning the defect core and interface energies in the APFC formulation. We show that the addition of a single term to the free-energy functional can be used to increase the solid-liquid interface and defect energies in a well-controlled fashion, without any major change to other features. The influence of the newly added term is explored in two-dimensional triangular and honeycomb structures as well as bcc and fcc lattices in three dimensions. In addition, a finite-element method (FEM) is developed for the model that incorporates a mesh refinement scheme. The combination of the FEM and mesh refinement to simulate amplitude expansion with a new energy term provides a method of controlling microscopic features such as defect and interface energies while simultaneously delivering a coarse-grained examination of the system.

Ultra-low thermal conductivity of TlIn5Se8 and structure of the new complex chalcogenide Tl0.98In13.12Se16.7Te2.3

NASA Astrophysics Data System (ADS)

Lefèvre, Robin; Berthebaud, David; Pérez, Olivier; Pelloquin, Denis; Boudin, Sophie; Gascoin, Franck

2017-06-01

TlIn5Se8 has been synthesized by means of solid-state reaction and densified by Spark Plasma Sintering. The compound is a semiconductor with a band gap of 1.62 eV estimated from reflectance measurements. Its thermal conductivity is about 0.45 W m-1. K-1 in the temperature range 300-673 K, an extremely low value attributed to its complex pseudo-1D structure reminiscent of the pseudo-hollandite. While attempting to dope TlIn5Se8 with Te, a new complex chalcogenide was discovered and characterized by the combination of TEM and XRD diffraction. It belongs to the A2In12X19 family, crystallizing in the R 3 ̅:H space group. Single crystal X-ray diffraction study led to a refined composition of Tl0.98In13.12Se16.7Te2.3 with cell parameters: a=13.839(5) Å and c=35.18(3) Å. A static disorder is found on one indium site situated in an octahedral environment. The single crystal XRD study is in agreement with TEM analyses in STEM-HAADF image mode that do not show any extended defects or disorder at atomic scale.

Refinement of iron ore sinter phases: a silico-ferrite of calcium and aluminium (SFCA) and an Al-free SFC, and the effect on phase quantification by X-ray diffraction

NASA Astrophysics Data System (ADS)

Liles, David C.; de Villiers, Johan P. R.; Kahlenberg, Volker

2016-02-01

Crystals of a silico-ferrite of calcium and aluminium (SFCA) and an Al-free SFC were prepared from the melt by slow cooling of synthetically prepared mixtures and examined by single-crystal diffraction methods. Both crystals belong to the space group P-1. SFC has lattice parameters a = 9.1255(3) Å, b = 10.1189(3) Å, c = 10.6183(2) Å, α = 63.9554(9)°, β = 84.4964(11)°, γ = 65.6706(9)° with a final R(|F|) = 0.024. SFCA has a cell with a = 9.0738(9)Å, b = 10.0474(10)Å, c = 10.5611(10) Å, α = 64.061(3)°, β = 84.356(3)°, γ = 65.722(3)° with a final R(|F|) = 0.030. The SFC structure was transformed to the cell used by Hamilton et al. (1989) and refined to an R(|F|) = 0.024. All the atomic positions are equivalent to those reported by Hamilton et al. (1989) with the exception of one (Ca,Fe) position and two oxygen positions that are displaced from the published positions by 0.5 y (Ca,Fe1), 0.5 z (O4), or 0.5 x (O12). This is ascribed to transcription errors in the published crystal structure data. The calculated powder pattern of SFCA (this study) was compared with the experimental data and it shows that the low angle peak intensities agree significantly better than those calculated from the published atomic positions. Additional electron density is located in proximity to the octahedral and tetrahedral cation sites of the main structure. These positions, coupled with the partially occupied cation sites of the main structure, suggest a minor sharing of cations between the main cation sites and the additional sites.

Crystal Growth and Scintillation Properties of $${\\rm Cs}_{2}{\\rm NaGdBr}_{6}{:}{\\rm Ce}^{3+}$$

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

Yang, Pin; Zhou, Xiaowang; Deng, Haoran

2013-04-02

Single crystals of Cs 2NaGdBr 6 with different Ce +3 activator concentrations were grown by a two-zone Bridgman method. This new compound belongs to a large elpasolite halide (A 2BLnX 6) family. Many of these elpasolite compounds have shown high luminosity, good energy resolution and excellent proportionality in comparison to traditional scintillators such as CsI and NaI; therefore, they are particularly attractive for gamma-ray spectroscopy applications. This study investigated the scintillator properties of Cs 2NaGdBr 6:Ce +3 crystals as a new material for radiation detection. Special focus has been placed on the effects of activator concentration (0 to 50 mol.%)more » on the photoluminescence responses. Results of structural refinement, photoluminescence, radioluminescence, lifetime and proportionality measurements for this new compound are reported.« less

Incorporation of rare earth elements in titanite: Stabilization of the A2/a dimorph by creation of antiphase boundaries

USGS Publications Warehouse

Hughes, J.M.; Bloodaxe, E.S.; Hanchar, J.M.; Foord, E.E.

1997-01-01

The atomic arrangement of a natural rare-earth-rich titanite and two synthetic rare-earth-doped titanites have been refined in space group A2/a, and the atomic arrangement of an undoped P21/a synthetic titanite was also refined for comparison. Previous work has shown that titanite possesses a domain structure, with domains formed of like-displaced Ti atoms in the [100] octahedral chains. P21/a titanite results when the crystal is formed of a single domain, but as Ti-reversal sites occur in the octahedral chain the apparent A2/a structure results from the average of antiphase domains. Antiphase boundaries occur at O1, which is alternately overbonded or underbonded at the boundaries, depending on the displacement of the neighboring Ti atoms. Type 2 antiphase boundaries exist where two Ti atoms are displaced away from the intervening O1 atom and are energetically unfavorable because of underbonding of that O1 atom. However, substitution of a trivalent rare earth element in the adjacent Ca2+ site relieves that underbonding, favoring the creation of type 2 antiphase boundaries and stabilization of the A2/a dimorph. The results of high-precision crystal structure analyses demonstrate that rare earth substituents for Ca stabilize the A2/a dimorph at lower substitution levels than required for octahedral substitutions.

Direct Visualization of Orbital Flipping in Volborthite by Charge Density Analysis Using Detwinned Data

NASA Astrophysics Data System (ADS)

Sugawara, Kento; Sugimoto, Kunihisa; Fujii, Tatsuya; Higuchi, Takafumi; Katayama, Naoyuki; Okamoto, Yoshihiko; Sawa, Hiroshi

2018-02-01

The distribution of d-orbital valence electrons in volborthite [Cu3V2O7(OH)2 • 2H2O] was investigated by charge density analysis of the multipole model refinement. Diffraction data were obtained by synchrotron radiation single-crystal X-ray diffraction experiments. Data reduction by detwinning of the multiple structural domains was performed using our developed software. In this study, using high-quality data, we demonstrated that the water molecules in volborthite can be located by the hydrogen bonding in cavities that consist of Kagome lattice layers of CuO4(OH)2 and pillars of V2O7. Final multipole refinements before and after the structural phase transition directly visualized the deformation electron density of the valence electrons. We successfully directly visualized the orbital flipping of the d-orbital dx2-y2, which is the highest level of 3d orbitals occupied by d9 electrons in volborthite. The developed techniques and software can be employed for investigations of structural properties of systems with multiple structural domains.

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.

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

Rettie, Alexander J. E.; Sturza, Mihai; Malliakas, Christos D.

The two-dimensional material KCu 3–xSe 2 was synthesized using both a K 2Se 3 flux and directly from the elements. It crystallizes in the CsAg 3S 2 structure (monoclinic space group C2/m with a = 15.417(3) Å, b = 4.0742(8) Å, c = 8.3190(17) Å, and β = 112.94(3)°), and single-crystal refinement revealed infinite copper-deficient [Cu 3–xSe 2]– layers separated by K + ions. Thermal analysis indicated that KCu 3–xSe 2 melts congruently at ~755 °C. UV–vis spectroscopy showed an optical band gap of ~1.35 eV that is direct in nature, as confirmed by electronic structure calculations. Electronic transport measurementsmore » on single crystals yielded an in-plane resistivity of ~6 × 10 –1 Ω cm at 300 K that has a complex temperature dependence. The results of Seebeck coefficient measurements were consistent with a doped p-type semiconductor (S = +214 μV K –1 at 300 K), with doping being attributed to copper vacancies. Transport is dominated by low-mobility (on the order of 1 cm 2 V –1 s –1) holes caused by relatively flat valence bands with substantial Cu 3d character and a significant concentration of Cu ion vacancy defects (p ~ 10 19 cm –3) in this material. In conclusion, electronic band structure calculations showed that electrons should be significantly more mobile in this structure type.« less

Structural characterization and physicochemical features of new hybrid compound containing chlorate anions of cadmate (II)

NASA Astrophysics Data System (ADS)

Lassoued, Mohamed Saber; Abdelbaky, Mohammed S. M.; Lassoued, Abdelmajid; Gadri, Abdellatif; Ammar, Salah; Ben Salah, Abdelhamid; García-Granda, Santiago

2017-08-01

The present paper reports the synthesis of a single crystal of a new organic-inorganic hybrid compound, with the formula (C6H14N2) CdCl4·H2O, by slow evaporation method at room temperature. It was characterized by single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), Hirshfeld surface, spectroscopy measurement, thermal study and photoluminescence (PL) properties. A preliminary SCXRD structural analysis revealed that it crystallized in the monoclinic system (space group P21/c) with the following unit cell parameters: a = 12.95823(16) Å, b = 14.92449(16) Å, c = 7.13838(9) Å and β = 103.2108(12)° with Z = 4. The refinement converged to R = 0.0164 and ωR = 0.0393. Its atomic arrangement can be described as an alternation of organic and inorganic layers along the a-axis. The crystal packing was governed by the N-H⋯Cl and O-H⋯Cl hydrogen bonding interaction between the 1.2-diammoniumcyclohexane cations, the [CdCl42n-]n anions and water molecule. The Hirshfeld surface analysis was conducted to investigate intermolecular interactions and associated 2D fingerprint plots, revealing the relative contribution of these interactions in the crystal structure quantitatively. Furthermore, the room temperature infrared (IR) spectrum of the title compound was recorded and analyzed on the basis of data found in the literature. Besides, the thermal analysis studies were performed, but no phase transition was found in the temperature range between 30 and 450 °C. The optical and PL properties of the compound were investigated in the solid state at room temperature and exhibited three bands at 225, 268 and 315 nm and a strong fluorescence at 443 nm.

Crystal structure of N-[3-(di­methyl­aza­nium­yl)prop­yl]-N′,N′,N′′,N′′-tetra­methyl-N-(N,N,N′,N′-tetra­methyl­form­am­id­in­ium­yl)­guanidinium dibromide hydroxide monohydrate

PubMed Central

Tiritiris, Ioannis; Kantlehner, Willi

2015-01-01

The asymmetric unit of the title hydrated salt, C15H37N6 3+·2Br−·OH−·H2O, contains one cation, three partial-occupancy bromide ions, one hydroxide ion and one water mol­ecule. Refinement of the site-occupancy factors of the three disordered bromide ions converges with occupancies 0.701 (2), 0.831 (2) and 0.456 (2) summing to approximately two bromide ions per formula unit. The structure was refined as a two-component inversion twin with volume fractions 0.109 (8):0.891 (8) for the two domains. The central C3N unit of the bis­amidinium ion is linked to the aliphatic propyl chain by a C—N single bond. The other two bonds in this unit have double-bond character as have the four C—N bonds to the outer NMe2 groups. In contrast, the three C—N bonds to the central N atom of the (di­methyl­aza­nium­yl)propyl group have single-bond character. Delocalization of the two positive charges occurs in the N/C/N and C/N/C planes, while the third positive charge is localized on the di­methyl­ammonium group. The crystal structure is stabilized by O—H⋯O, N—H⋯Br, O—H⋯Br and C—H⋯Br hydrogen bonds, forming a three-dimensional network. PMID:26870507

Crystal structure of the mineral (Na,Ca,K)2(Ca,Na)4(Mg,Fe)5(Mg,Fe,Ti)5[Si12Al4O44](F,O)4: a triclinic representative of the amphibole family

NASA Astrophysics Data System (ADS)

Rastsvetaeva, R. K.; Aksenov, S. M.

2012-05-01

A mineral belonging to the amphibole family found at the Rothenberg paleovolcano (Eifel, Germany) was studied by single-crystal X-ray diffraction. The triclinic pseudomonoclinic unit-cell parameters are a = 5.3113(1) Å, b = 18.0457(3) Å; c = 9.8684(2) Å, α = 90.016(2)°, β = 105.543(4)°, γ = 89.985(2)°. The structure was solved by direct methods in sp. gr. P1 and refined to the R factor of 2.7% based on 6432 reflections with | F| > 3σ( F) taking into account twinning. The mineral with the idealized formula (Na,Ca,K)2(Ca,Na)4(Mg,Fe)5(Mg,Fe,Ti)5[Si12Al4O44](F,O)4 has some symmetry and structural features that distinguish it from other minerals of this family.

Refractive indices of CaF2 single crystals under elastic shock loading

NASA Astrophysics Data System (ADS)

Li, Y.; Zhou, X. M.; Liu, C. L.; Luo, S. N.

2017-07-01

Refractive indices and Hugoniots of CaF2 single crystals are investigated by laser displacement interferometry under shock loading below 5 GPa. Birefringence is observed for the [110] loading. We obtain the Hugoniot equation of states for [100], [110] and [111], and refractive indices for these orientations with consideration of their polarization. The measured refractive indices are in reasonable agreement with predictions based on the piezo-optic theory, and are used to refine the elasto-optic coefficients.

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

Growth, Crystal Structure and Magnetic Characterization of Zn-Stabilized CePtIn4

NASA Astrophysics Data System (ADS)

Carnicom, Elizabeth M.; Klimczuk, Tomasz; von Rohr, Fabian; Winiarski, Michal J.; Kong, Tai; Stolze, Karoline; Xie, Weiwei; Kushwaha, Satya K.; Cava, Robert J.

2017-08-01

The growth and characterization of CePtIn4, stabilized by 10% Zn substitution for In, is reported. The new material is orthorhombic, space group Cmcm (No. 63), with lattice parameters a = 4.51751(4) Å, b = 16.7570(2) Å, and c = 7.36682(8) Å, and the refined crystal composition has 10% of Zn substituted for In, i.e., the crystals are CePt(In0.9Zn0.1)4. Crystals were grown using a self-flux method: only growths containing Zn yielded CePtIn4 crystals, while Ce3Pt4In13 crystals formed when Zn was not present. Anisotropic temperature-dependent magnetic susceptibilities for single crystals show that Zn-stabilized CePtIn4 orders magnetically at ˜1.9 K. High-temperature Curie-Weiss fits indicate an effective moment of ˜2.49 μB/Ce and a directionally averaged Weiss-temperature of approximately -31 K. Specific heat data shows a peak consistent with the ordering temperature seen in the magnetic susceptibility data. Zn-stabilized CePtIn4 is metallic and displays no superconducting transition down to 0.14 K.

Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation.

PubMed

Fadel, Valmir; Canduri, Fernanda; Olivieri, Johnny R; Smarra, André L S; Colombo, Marcio F; Bonilla-Rodriguez, Gustavo O; de Azevedo, Walter F

2003-12-01

Crystal structure of hemoglobin isolated from the Brazilian maned wolf (Chrysocyon brachyurus) was determined using standard molecular replacement technique and refined using maximum-likelihood and simulated annealing protocols to 1.87A resolution. Structural and functional comparisons between hemoglobins from the Chrysocyon brachyurus and Homo sapiens are discussed, in order to provide further insights in the comparative biochemistry of vertebrate hemoglobins.

Cloning, overexpression, purification and preliminary crystallographic studies of a mitochondrial type II peroxiredoxin from Pisum sativum.

PubMed

Barranco-Medina, Sergio; López-Jaramillo, Francisco Javier; Bernier-Villamor, Laura; Sevilla, Francisca; Lázaro, Juan José

2006-07-01

A cDNA encoding an open reading frame of 199 amino acids corresponding to a type II peroxiredoxin from Pisum sativum with its transit peptide was isolated by RT-PCR. The 171-amino-acid mature protein (estimated molecular weight 18.6 kDa) was cloned into the pET3d vector and overexpressed in Escherichia coli. The recombinant protein was purified and crystallized by the hanging-drop vapour-diffusion technique. A full data set (98.2% completeness) was collected using a rotating-anode generator to a resolution of 2.8 angstroms from a single crystal flash-cooled at 100 K. X-ray data revealed that the protein crystallizes in space group P1, with unit-cell parameters a = 61.88, b = 66.40, c = 77.23 angstroms, alpha = 102.90, beta = 104.40, gamma = 99.07 degrees, and molecular replacement using a theoretical model predicted from the primary structure as a search model confirmed the presence of six molecules in the unit cell as expected from the Matthews coefficient. Refinement of the structure is in progress.

Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli

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

Alexopoulos, Eftichia; Department of Medical Biophysics, University of Toronto, Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto Medical Discovery Tower, 101 College Street, Toronto, Ontario M5G 1L7; Kanjee, Usheer

2008-08-01

The structure of the decameric inducible lysine decarboxylase from E. coli was determined by SIRAS using a hexatantalum dodecabromide (Ta{sub 6}Br{sub 12}{sup 2+}) derivative. Model building and refinement are under way. The decameric inducible lysine decarboxylase (LdcI) from Escherichia coli has been crystallized in space groups C2 and C222{sub 1}; the Ta{sub 6}Br{sub 12}{sup 2+} cluster was used to derivatize the C2 crystals. The method of single isomorphous replacement with anomalous scattering (SIRAS) as implemented in SHELXD was used to solve the Ta{sub 6}Br{sub 12}{sup 2+}-derivatized structure to 5 Å resolution. Many of the Ta{sub 6}Br{sub 12}{sup 2+}-binding sites hadmore » twofold and fivefold noncrystallographic symmetry. Taking advantage of this feature, phase modification was performed in DM. The electron-density map of LdcI displays many features in agreement with the low-resolution negative-stain electron-density map [Snider et al. (2006 ▶), J. Biol. Chem.281, 1532–1546].« less

Structure refinement of Zn and Pr-doped Y-Ba-Cu-oxides

NASA Astrophysics Data System (ADS)

Naik, M. S.; Sarode, P. R.; Priolkar, K. R.; Prabhu, R. B.

2018-05-01

Superconducting compounds of composition Y0.9 Pr0.1Ba2 [Cu1-yZny]3O7-δ (0 ≤ y ≤ 0.10) have been synthesized. The structure of these materials has been studied using powder X-ray diffraction technique and refinement has been carried out by using Rietveld refinement procedure. It has been shown that all these compounds crystallize in orthorhombic structure with slight change in c parameter. Increase of parameter O(2) and decrease of parameter O(3)suggest the changes in the Cu-O2 plane of these orthorhombic materials on Zn substitution.

Re-refinement of the spliceosomal U4 snRNP core-domain structure

PubMed Central

Li, Jade; Leung, Adelaine K.; Kondo, Yasushi; Oubridge, Chris; Nagai, Kiyoshi

2016-01-01

The core domain of small nuclear ribonucleoprotein (snRNP), comprised of a ring of seven paralogous proteins bound around a single-stranded RNA sequence, functions as the assembly nucleus in the maturation of U1, U2, U4 and U5 spliceosomal snRNPs. The structure of the human U4 snRNP core domain was initially solved at 3.6 Å resolution by experimental phasing using data with tetartohedral twinning. Molecular replacement from this model followed by density modification using untwinned data recently led to a structure of the minimal U1 snRNP at 3.3 Å resolution. With the latter structure providing a search model for molecular replacement, the U4 core-domain structure has now been re-refined. The U4 Sm site-sequence AAUUUUU has been shown to bind to the seven Sm proteins SmF–SmE–SmG–SmD3–SmB–SmD1–SmD2 in an identical manner as the U1 Sm-site sequence AAUUUGU, except in SmD1 where the bound U replaces G. The progression from the initial to the re-refined structure exemplifies a tortuous route to accuracy: where well diffracting crystals of complex assemblies are initially unavailable, the early model errors are rectified by exploiting preliminary interpretations in further experiments involving homologous structures. New insights are obtained from the more accurate model. PMID:26894541

A detailed experimental and theoretical study of two novel substituted trifluoromethylchromones. The influence of the bulky bromine atom on the crystal packing.

PubMed

Alcívar León, C D; Echeverría, G A; Piro, O E; Ulic, S E; Jios, J L

2015-02-05

The new 3-methyl-2-trifluoromethylchromone (1) and 3-bromomethyl-2-trifluoromethylchromone (2) compounds were synthesized and characterized by vibrational (IR, Raman), UV-Vis and NMR ((1)H, (13)C and (19)F) spectroscopy and MS spectrometry. The crystal structures of 1 and 2 were determined by X-ray diffraction methods. Both compounds crystallize in the monoclinic P21/c space group with Z=4 molecules per unit cell. The structures were solved from 1423 (1) and 1856 (2) reflections with I>2σ (I) and refined by full-matrix least-squares to agreement R1-values of 0.0403 (1) and 0.0554 (2). Because of π-bonding delocalization, the organic molecular skeletons are planar and the molecular bonding structures can be described by formally single, double and resonant bonds. In 2, the CF3 group revealed a strong rotational disorder around the CCF3 bond, which could be explained in terms of four split positions with about uniform angular distribution. The vibrational, electronic and NMR, spectra were discussed and assigned with the assistance of DFT calculations. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural change in lead fluorapatite at high pressure

NASA Astrophysics Data System (ADS)

Fleet, Michael E.; Liu, Xi; Shieh, Sean R.

2010-01-01

The structure of lead fluorapatite [PbFAP; Pb10(PO4)6F2], crystallized from the melt in a platinum capsule at 1,000°C and 1 atm, has been investigated by single-crystal X-ray diffraction. Crystal data are a = 9.7638 (6), c = 7.2866 (4) Å, space group P63/ m, R = 0.043, R w = 0.034. We have also studied the compressional behaviour of the c-axis channel of PbFAP up to 9 GPa at 25°C, using a diamond-anvil cell, synchrotron X-radiation, and Rietveld powder structure refinement. Pressure-volume data for the channel polyhedron of PbFAP fitted to the third-order Birch-Murnaghan equation resulted in K T = 33.2 ± 1.2 GPa when K T ' is fixed at 4. The c-axis channel of PbFAP is about twice as compressible as the unit-cell volume of PbFAP and the channel of calcium apatites. This is attributed to the anomalous narrowing of the channel of PbFAP with increase in confining pressure. Flexibility of the apatite channel is a key factor in the scavenging of toxic heavy metals by calcium apatites.

A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution.

PubMed

Gessmann, Renate; Axford, Danny; Brückner, Hans; Berg, Albrecht; Petratos, Kyriacos

2017-02-01

Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained from methanol solutions of purified bergofungin mixed with water. Although there are differences in the intramolecular hydrogen-bonding scheme of samarosporin I, the overall folding is very similar for both peptaibols, namely 3 10 -helical at the termini and α-helical in the middle of the molecules. Bergofungin A and samarosporin I molecules are arranged in a similar way in both lattices. However, the packing of bergofungin A exhibits a second solvent channel along the twofold axis. This latter channel occurs in the vicinity of the N-terminus, where the natural substitution resides.

Facile synthesis and structure characterization of hexagonal tungsten bronzes crystals

NASA Astrophysics Data System (ADS)

Lee, Jiann-Shing; Liu, Hao-Chuan; Peng, Gao-De; Tseng, Yawteng

2017-05-01

A facile molten-salt route was used to synthesize hexagonal Cs0.33WO3, Rb0.33WO3 and K0.30WO3 crystals. The three isostructural compounds were successfully prepared from the reaction of MxWO3 powders (M = Cs, Rb, K) in the CsCl/NaCl, RbCl/NaCl and KCl/NaCl fluxes, respectively. The structure determination and refinement, based on single-crystal X-ray diffraction data, are in agreement with previous works, possessing space group P63/mcm. The a and c parameters vary non-linearly with increasing radii of the M+ cations (rM) that is coordinated to twelve oxygen atoms. Both the volumes of unit-cell and WO6 octahedra vary linearly with rM, which become smaller from Cs0.33WO3 to K0.30WO3. The distortion of WO6 octahedra as well as isotropic displacement parameters increases from Cs0.33WO3 to K0.30WO3. The geometry of the WO6 octahedron becomes more regular with increasing rM. These structural trends arise from the effective size of the M+ cation.

Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65 Å resolution

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

Maraite, Andy; Schmidt, Thomas; Ansörge-Schumacher, Marion B.

2007-07-01

The X-ray crystal structure of the ThDP-dependent enzyme benzaldehyde lyase has been refined to 1.65 Å. Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 Å using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005 ▶), FEBS J.272, 6067–6076]. In this communication of parallel studies, BAL was crystallized in an alternative spacemore » group (P2{sub 1}2{sub 1}2{sub 1}) and its structure refined to a resolution of 1.65 Å, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.« less

Enzymatic Synthesis of Refined Olive Oil-Based Structured Lipid Containing Omega -3 and -6 Fatty Acids for Potential Application in Infant Formula.

PubMed

Li, Ruoyu; Sabir, Jamal S M; Baeshen, Nabih A; Akoh, Casimir C

2015-11-01

Structured lipids (SLs) containing palmitic, docosahexaenoic (DHA), and gamma-linolenic (GLA) acids were produced using refined olive oil, tripalmitin, and ethyl esters of DHA single cell oil and GLA ethyl esters. Immobilized Lipozyme TL IM lipase was used as the biocatalyst. The SLs were characterized for fatty acid profile, triacylglycerol (TAG) molecular species, solid fat content, oxidative stability index, and melting and crystallization profiles and compared to physical blend of substrates, extracted fat from commercial infant formula (IFF), and milk fat. 49.28 mol% of palmitic acid was found at the sn-2 position of SL TAG and total DHA and GLA composition were 0.73 and 5.00 mol%, respectively. The total oleic acid content was 36.13 mol% which was very close to the 30.49% present in commercial IFF. Comparable solid fat content profiles were also found between SLs and IFF. The SLs produced have potential for use in infant formulas. © 2015 Institute of Food Technologists®

Mott localization in a pure stripe antiferromagnet Rb 1 - δ Fe 1.5 - σ S 2

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

Wang, Meng; Yi, Ming; Cao, Huibo

A combination of neutron diffraction and angle-resolved photoemission spectroscopy measurements on a pure antiferromagnetic stripe Rb 1-δFe 1.5-σS 2 is reported. A neutron diffraction experiment on a powder sample shows that a 98% volume fraction of the sample is in the antiferromagnetic stripe phase with rhombic iron vacancy order and a refined composition of Rb 0.66Fe 1.36S 2, and that only 2% of the sample is in the block antiferromagnetic phase with √5×√5 iron vacancy order. Furthermore, a neutron diffraction experiment on a single crystal shows that there is only a single phase with the stripe antiferromagnetic order with themore » refined composition of Rb 0.78Fe 1.35S 2, while the phase with block antiferromagnetic order is absent. Angle-resolved photoemission spectroscopy measurements on the same crystal with the pure stripe phase reveal that the electronic structure is gapped at the Fermi level with a gap larger than 0.325 eV. The data collectively demonstrate that the extra 10% iron vacancies in addition to the rhombic iron vacancy order effectively impede the formation of the block antiferromagnetic phase; the data also suggest that the stripe antiferromagnetic phase with rhombic iron vacancy order is a Mott insulator.« less

Synthesis, structural and optical properties of (ALa)(FeMn)O6 (A = Ba and Sr) double perovskites

NASA Astrophysics Data System (ADS)

Kumar, Dinesh; Sudarshan, V.; Singh, Akhilesh Kumar

2018-05-01

Here, we report structural and optical properties of ALaFeMnO6 (A = Ba and Sr) double perovskite synthesized via auto-combustion followed by calcinations process. Rietveld refinement of structure using x-ray diffraction data reveals that BaLaFeMnO6 crystallizes into cubic crystal structure with space group Pm-3m while SrLaFeMnO6 crystallizes into rhombohedral crystal structure having space group R-3c. The absorption spectrum measurement using UV-Vis spectroscopy reveals that these samples are prefect insulator having energy band gap between conduction and valence band of the order of 6 eV.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

PubMed

Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

2016-02-26

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

Structural analysis according to reduced data: VIII. Refinement of the extended model of aspherical atoms

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

Dudka, A. P.

A program for the refinement of the model of aspherical atoms within the Stewart-Hansen-Coppens formalism has been developed. Deformation scattering up to the 8th expansion order in multipoles has been taken into account for the first time. The program was tested for 11 crystals. The effect of the result of interpolation of radial scattering curves on the model parameters is considered. The importance of introduction of multipoles of high (5th-8th) orders into the model for a number of crystals is shown. The use of the extended multipole model for a silicon crystal revealed some new specific features of the electronicmore » structure: consideration of multipoles up to the 7th order makes it possible to explain the intensity of the forbidden 222 reflection.« less

A grid-enabled web service for low-resolution crystal structure refinement.

PubMed

O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

2012-03-01

Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

PubMed

Gueddida, Saber; Yan, Zeyin; Kibalin, Iurii; Voufack, Ariste Bolivard; Claiser, Nicolas; Souhassou, Mohamed; Lecomte, Claude; Gillon, Béatrice; Gillet, Jean-Michel

2018-04-28

In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO 3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO 3 crystal along the Ti-O 1 -Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

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

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl; Waleń, Tomasz; University of Warsaw, Banacha 2, 02-097 Warsaw

2015-03-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure ismore » RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.« less

The structural and Raman spectral studies on Ni0.5Cu0.5Fe2O4 ferrite

NASA Astrophysics Data System (ADS)

Somani, M.; Saleem, M.

2018-05-01

Spinel ferrite Ni0.5Cu0.5Fe2O4 has been successfully prepared via solid state reaction. The crystal structure studies using XRD technique revealed cubic structure of the sample. The XRD spectra was further refined via Retvield Refinement and all the parameters regarding structure were obtained which confirmed cubic structure. The assigned space group was found to be Fd-3m. Particle size was calculated to be 56 nm. The Raman Spectra revealed five active Raman modes which confirmed spinel structure.

Ammonium–cobalt–nickel phosphates, NH{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·H{sub 2}O

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

Torre-Fernández, Laura; Trobajo, Camino; Pedro, Imanol de

The ammonium–cobalt–nickel phosphates, NH{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·H{sub 2}O (x=0.00, 0.34, 0.59, 0.70, 1.00), and the deuterated forms, ND{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·D{sub 2}O (x=0.00, 0.38, 0.48, 0.69, 0.85), have been synthesized under mild hydrothermal conditions and characterised using X-ray and neutron diffraction, chemical and thermal analysis, and magnetic measurements. Their crystal structures, including hydrogen positions, were determined by Rietveld refinement using single-crystal X-ray and neutron powder diffraction data. The space group of these orthorhombic crystals modifies as a function of their composition. The magnetic susceptibility and magnetization measurements of these ammonium–cobalt–nickel phosphates show antiferromagnetic behaviour, and the Neel temperaturemore » evolves from 5.5 K (x=0.00) up to 13.2 K (x=1.00). - Graphical abstract: We obtained single crystals for all the members of the family. In this series, although all crystals are orthorhombic, the space group changes as a function of the composition, showing how the single-crystal diffraction data is capable to manifest structural subtleties that had not been described before for this group of materials. All the investigated materials behave antiferromagnetically with ordering temperatures from 5.5 K up to 13.2 K. Display Omitted - Highlights: • The ammonium–cobalt–nickel phosphates, NH{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·H{sub 2}O (x=0.00, 0.34, 0.59, 0.70, 1.00) and the deuterated forms ND4[Co1-xNixPO4]·D{sub 2}O (x=0.00, 0.38, 0.49, 0.68, 0.85) have synthesized by hydrothermal synthesis. • The structural studies of these compounds are introduced as a function of the composition. • The magnetic studies show an antiferromagnetically behavior with ordering temperatures from 5.5 K to 13.2 K.« less

Optimization of the crystal growth of the superconductor CaKFe4As4 from solution in the FeAs -CaFe2As2-KFe2As2 system

NASA Astrophysics Data System (ADS)

Meier, W. R.; Kong, T.; Bud'ko, S. L.; Canfield, P. C.

2017-06-01

Measurements of the anisotropic properties of single crystals play a crucial role in probing the physics of new materials. Determining a growth protocol that yields suitable high-quality single crystals can be particularly challenging for multicomponent compounds. Here we present a case study of how we refined a procedure to grow single crystals of CaKFe4As4 from a high temperature, quaternary liquid solution rich in iron and arsenic ("FeAs self-flux"). Temperature dependent resistance and magnetization measurements are emphasized, in addition to the x-ray diffraction, to detect intergrown CaKFe4As4 , CaFe2As2 , and KFe2As2 within what appear to be single crystals. Guided by the rules of phase equilibria and these data, we adjusted growth parameters to suppress formation of the impurity phases. The resulting optimized procedure yielded phase-pure single crystals of CaKFe4As4 . This optimization process offers insight into the growth of quaternary compounds and a glimpse of the four-component phase diagram in the pseudoternary FeAs -CaFe2As2-KFe2As2 system.

KH2PO4 single crystals activated with the Ti4+ ions in the form of TiO2-x × nH2O nanoparticles: Structural peculiarities, point defects, and dielectric properties

NASA Astrophysics Data System (ADS)

Kuz'micheva, Galina M.; Timaeva, Olesya I.; Kaurova, Irina A.; Svetogorov, Roman D.; Mühlbauer, Martin J.

2018-03-01

Potassium dihydrogen phosphate KH2PO4 (KDP) single crystals activated with Ti4+ ions in the form of TiO2-x × nH2O nanoparticles in the η-phase, synthesized by the sulfate method using TiOSO4 × xH2SO4 × yH2O, have been first grown by the temperature lowering method and cut from pyramidal (P) and prismatic (Pr) growth sectors. The first-performed neutron powder diffraction investigation of P and Pr samples cut from the KDP:Ti4+ crystal allowed us to reveal vacancies in the K and H sites for both samples, their number being larger in the Pr structure compared to the P one. Taking into account the deficiency of the K and H sites, full occupation of the O site, presence of Ti4+ ions in the structure, and the electroneutrality condition, a partial substitution of (PO4)3- anion by the (SO4)2- one, larger for the Pr sample, was observed. The real compositions of P and Pr samples, correlated with the cation-anion internuclear distances, were refined. The dielectric permittivity of the Pr sample was significantly lower than that of the P one; it decreases with decreasing K-O, P-O, and O...H distances and increasing deficiency of the K and H sites.

High-pressure phases of cordierite from single-crystal X-ray diffraction to 15 GPa

DOE PAGES

Finkelstein, Gregory J.; Dera, Przemyslaw K.; Duffy, Thomas S.

2015-08-14

High-pressure single-crystal X-ray diffraction experiments were conducted on natural cordierite crystals with composition Mg1.907(18)Fe0.127(6)Al4.01(2)Si4.96(3)Na0.026(3)O18.12(9) using a synchrotron X-ray source. The samples were compressed at 300 K in a diamond anvil cell to a maximum pressure of 15.22(15) GPa with a neon pressure-transmitting medium and a gold pressure calibrant. We observed a recently described orthorhombic to triclinic transition, as well as a further transition to a second triclinic phase. We solved and refined both new triclinic hases in space group P1, and designate them cordierite II and III. The structures of cordierite II and III were refined at 7.52(3) GPa atmore » 15.22(15) GPa, respectively. The lattice parameters at these pressures are a = 15.567(3) Å, b = 9.6235(4) Å, c = 9.0658(6) Å, α = 89.963(5)°, β = 86.252(10)°, and γ = 90.974(8)° for cordierite II, and a = 8.5191(19) Å, b = 8.2448(3) Å, c = 9.1627(4) Å, α = 85.672(4)°, β = 85.986(7)°, and γ = 70.839(10)° for cordierite III. Across the phase transitions there is a significant reduction in the length of the a-axis (~2 Å per phase transition), whereas both the b- and c-axis remain largely unchanged. Cordierite II has four- and five-coordinated Si and Al, while cordierite III has four-, five-, and six-coordinated Si, four- and five-coordinated Al, and five- and six-coordinated Mg. The sequence of high-pressure phases shows increasing polymerization of coordination polyhedra. These results, together with other recent studies, suggest that mixed 4-, 5-, and 6-fold coordination states may occur more commonly in silicate structures compressed at 300 K than previously recognized.« less

Structure cristalline, caractérisation spectroscopique, calcul DFT et analyse de surface Hirshfeld du perchlorate de p-toluidinium.

PubMed

Ben Jomaa, Meriam; Chebbi, Hammouda; Fakhar Bourguiba, Noura; Zid, Mohamed Faouzi

2018-02-01

The synthesis of p -toluidinium perchlorate (systematic name: 4-methyl-anilinium perchlorate), C 7 H 10 N + ·ClO 4 - , was carried out from an aqueous reaction of perchloric acid with p -toluidine. This compound was characterized by powder XRD, IR and UV-Vis spectroscopy. The structure was further confirmed by a single-crystal X-ray diffraction study. The crystal structure is formed by a succession of two-dimensional mol-ecular layers consisting of perchlorate anions and organic cations parallel to the (100) plane and located at x = 2 n  + ½ ( n ∈ Z ). Each mixed layer is formed by infinite chains {C 7 H 10 N + ·ClO 4 - } n parallel to the [010] direction and developing along the c axis, generating R 2 4 (8), R 2 2 (4) and R 4 4 (12) graph-set motifs. The results of a theoretical study using the DFT method at the B3LYP/6-311++G(d,p) level are in good agreement with the experimental data. Hirshfeld surface and fingerprint plots reveal that the structure is dominated by O⋯H/H⋯O (54.2%), H⋯H (26.9%) and C-H ⋯π (14.3%) contacts. The studied crystal was refined as a two-component twin.

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

Structural, magnetic, magneto-caloric and Mössbauer spectral study of Tb{sub 2}Fe{sub 17} compound synthesized by arc melting

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

Charfeddine, S.; LVMU, Centre National de Recherches en Sciences des Matériaux, Technopole de Borj-Cédria, BP 73 Soliman 8027; Zehani, K.

We have synthesized the intermetallic Tb{sub 2}Fe{sub 17} compound in hexagonal crystal structure by arc-melting without annealing. X-ray diffraction pattern has been refined by Rietveld method. The crystal structure is hexagonal with P6{sub 3}/mmc space group (Th{sub 2}Ni{sub 17}-type). The Mössbauer spectrum of Tb{sub 2}Fe{sub 17} compound has been analyzed with seven magnetic sextets assigned to the inequivalent crystallographic sites. The temperature dependence of magnetization data revealed that Tb{sub 2}Fe{sub 17} exhibits a second-order ferromagnetic to paramagnetic phase transition in the vicinity of Curie temperature (T{sub C}=412 K). The relative cooling power around the magnetic transition and the Arrott plotsmore » are also reported. - Graphical abstract: A 3D surface showing the temperature and applied magnetic field dependencies of the magnetization for Tb{sub 2}Fe{sub 17} compound (left). Rietveld analysis of the XRD pattern (right). Crystal structure for the hexagonal P6{sub 3}/mmc Tb{sub 2}Fe{sub 17} (bottom). Display Omitted - Highlights: • Tb{sub 2}Fe{sub 17} single-phase synthesized by simple arc-melting without any heat treatment. • The crystal structure is hexagonal with P6{sub 3}/mmc space group. • The magnetic entropy change of the sample was determined by Maxwell relation. • Hyperfine parameters, magnetic and magnetocaloric properties were studied.« less

SINGLE CRYSTAL DIFFRACTION OF SIDERITE UP TO 54 GPA AND HIGH PRESSURE-HIGH TEMPERATURE PHASES IN THE Fe-C-O SYSTEM (Invited)

NASA Astrophysics Data System (ADS)

Lavina, B.; Dera, P. K.; Downs, R. T.

2009-12-01

Phases in the Fe-C-O system are of interest for the deep carbon cycle, they might play an important role in buffering the mantle fO2. Carbon is also common in the fluid phases that greatly influence the Earth’s processes. The study of the high pressure behavior of siderite and of the phases synthesized after laser heating offers a good opportunity to illustrate the advantages and importance of single crystal diffraction in the high pressure science. The structure of siderite, FeCO3, has been refined up to 54 GPa across the spin pairing transition. Splitting of the diffraction peaks at the transition pressure provides unequivocal evidence of the sharpness of the spin crossover and of the absence of any intermediate volume and therefore of an intermediate spin state at ambient temperature. Diffraction intensities were collected in about 30 minutes at a bending magnet station (HPCAT, APS) and in about one minute at an insertion device station (GSECARS, APS). The quality of the refinement is unvaried in the investigated range, and the results obtained from the two different radiation and detectors are consistent. The refinements provide an accurate and robust determination of the dependence of bond distances and angles with pressure. Subtle structural rearrangements associated with the collapse of the octahedral cation size will be discussed. In situ laser heating is a very powerful method to study minerals at the actual P-T of the Earth’s deep interior. Overcoming the kinetic barriers required for bond breaking and atom diffusion, high pressure-high temperature phases may be synthesized. The analysis of high-pressure phases is very challenging. Diffraction patterns are usually of moderate quality and resolution, furthermore in addition to the sample, the pattern contains the contribution of other phases such as those used to insulate the anvils, to provide a pressure medium and a pressure marker. In several cases after laser heating, we observed phase transitions and growth of large crystallites, here the contribution of different phases could be better distinguished by analyzing the 3-dimensional distribution in the reciprocal space of the diffraction peaks. Laser heating experiments in the Fe-C-O system were conducted in the pressure range 20-140 GPa. The siderite stability field seems narrower than the previous investigations suggested. At least one of the extracted single crystal phases provides evidence of oxidation-reduction reactions.

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

Kahlenberg, Volker; Konzett, Juergen; Kaindl, Reinhard

High-pressure synthesis experiments in the system Na{sub 2}O-Y{sub 2}O{sub 3}-SiO{sub 2} revealed the existence of a previously unknown polymorph of NaYSi{sub 2}O{sub 6} or Na{sub 3}Y{sub 3}[Si{sub 3}O{sub 9}]{sub 2} which was quenched from 3.0 GPa and 1000 deg. C. Structural investigations on this modification have been performed using single-crystal X-ray diffraction data collected at ambient conditions. Furthermore, unpolarized micro-Raman spectra have been obtained from single-crystal material. The high-P modification of NaYSi{sub 2}O{sub 6} crystallizes in the centrosymmetric space group C2/c with 12 formula units per cell (a=8.2131(9) A, b=10.3983(14) A, c=17.6542(21) A, {beta}=100.804(9){sup o}, V=1481.0(3) A{sup 3}, R(|F|)=0.033 formore » 1142 independent observed reflections) and belongs to the group of cyclo-silicates. Basic building units are isolated three-membered [Si{sub 3}O{sub 9}] rings located in layers parallel to (010). Within a single layer the rings are concentrated in strings parallel to [100]. The sequence of directedness of up (U) or down (D) pointing tetrahedra of a single ring is UUU or DDD, respectively. Stacking of the layers parallel to b results in the formation of a three-dimensional structure in which yttrium and sodium cations are incorporated for charge compensation. In more detail, four non-tetrahedral cation positions can be differentiated which are coordinated by 6 and 8 oxygen ligands. Refinements of the site occupancies did not reveal any indication for mixed Na-Y populations on these positions. Finally, several geometrical parameters of rings occurring in cyclo-trisilicate structures have been compiled and are discussed. - Graphical abstract: Projection of the whole structure of high-P NaYSi{sub 2}O{sub 6} parallel to [100].« less

Rietveld refinement of the crystal structures of Rb2 XSi5O12 (X = Ni, Mn).

PubMed

Bell, Anthony M T; Henderson, C Michael B

2016-02-01

The synthetic leucite silicate framework mineral analogues Rb2 XSi5O12 {X = Ni [dirubidium nickel(II) penta-silicate] and Mn [dirubidium manganese(II) penta-silicate]} have been prepared by high-temperature solid-state synthesis. The results of Rietveld refinements, using X-ray powder diffraction data collected using Cu Kα X-rays, show that the title compounds crystallize in the space group Pbca and adopt the cation-ordered structure of Cs2CdSi5O12 and other leucites. The structures consist of tetra-hedral SiO4 and XO4 units sharing corners to form a partially substituted silicate framework. Extraframework Rb(+) cations sit in channels in the framework. All atoms occupy the 8c general position for this space group. In these refined structures, silicon and X atoms are ordered onto separate tetra-hedrally coordinated sites (T-sites). However, the Ni displacement parameter and the Ni-O bond lengths suggest that for the X = Ni sample, there may actually be some T-site cation disorder.

Rietveld refinement of the crystal structures of Rb2 XSi5O12 (X = Ni, Mn)

PubMed Central

Bell, Anthony M. T.; Henderson, C. Michael B.

2016-01-01

The synthetic leucite silicate framework mineral analogues Rb2 XSi5O12 {X = Ni [dirubidium nickel(II) penta­silicate] and Mn [dirubidium manganese(II) penta­silicate]} have been prepared by high-temperature solid-state synthesis. The results of Rietveld refinements, using X-ray powder diffraction data collected using Cu Kα X-rays, show that the title compounds crystallize in the space group Pbca and adopt the cation-ordered structure of Cs2CdSi5O12 and other leucites. The structures consist of tetra­hedral SiO4 and XO4 units sharing corners to form a partially substituted silicate framework. Extraframework Rb+ cations sit in channels in the framework. All atoms occupy the 8c general position for this space group. In these refined structures, silicon and X atoms are ordered onto separate tetra­hedrally coordinated sites (T-sites). However, the Ni displacement parameter and the Ni—O bond lengths suggest that for the X = Ni sample, there may actually be some T-site cation disorder. PMID:26958399

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

PubMed

Pawlak, Tomasz; Potrzebowski, Marek J

2014-03-27

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

Crystal structure of the heptamolybdate(VI) (paramolybdate) ion, [Mo7O24]6-, in the ammonium and potassium tetrahydrate salts

USGS Publications Warehouse

Evans, H.T.; Gatehouse, B.M.; Leverett, P.

1975-01-01

The crystal structures of the isomorphous salts MI6 [Mo7O24],4H2O (M = NH4 or K) have been refined by three-dimensional X-ray diffraction methods. Unit cell dimensions of these monoclinic compounds, space group P21/C with Z = 4, are, ammonium salt: a = 8.3934 ?? 0.0008, b = 36.1703 ?? 0.0045, c = 10.4715 ?? 0.0011 A??, ?? = 115.958?? ?? 0.008??; and potassium salt: a = 8.15 ?? 0.02, b = 35.68 ?? 0.1, c = 10.30 ?? 0.02 A??, ?? = 115.2?? ?? 02??. By use of multiple Weissenberg patterns, 8197 intensity data (Mo-K?? radiation) for the ammonium compound and 2178 (Cu-K?? radiation) for the potassium compound were estimated visually and used to test and refine Lindqvist's proposed structure in the space group P21/c. Lindqvist's structure was confirmed and the full matrix least-squares isotropic refinement led to R 0.076 (ammonium) 0.120 (potassium), with direct unambiguous location of the cations and water molecules in the potassium compound.

Copper Vacancies and Heavy Holes in the Two-Dimensional Semiconductor KCu 3–xSe 2

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

Rettie, Alexander J. E.; Sturza, Mihai; Malliakas, Christos D.

The two-dimensional material KCu 3–xSe 2 was synthesized using both a K 2Se 3 flux and directly from the elements. It crystallizes in the CsAg 3S 2 structure (monoclinic space group C2/m with a = 15.417(3) Å, b = 4.0742(8) Å, c = 8.3190(17) Å, and β = 112.94(3)°), and single-crystal refinement revealed infinite copper-deficient [Cu 3–xSe 2]– layers separated by K + ions. Thermal analysis indicated that KCu 3–xSe 2 melts congruently at ~755 °C. UV–vis spectroscopy showed an optical band gap of ~1.35 eV that is direct in nature, as confirmed by electronic structure calculations. Electronic transport measurementsmore » on single crystals yielded an in-plane resistivity of ~6 × 10 –1 Ω cm at 300 K that has a complex temperature dependence. The results of Seebeck coefficient measurements were consistent with a doped p-type semiconductor (S = +214 μV K –1 at 300 K), with doping being attributed to copper vacancies. Transport is dominated by low-mobility (on the order of 1 cm 2 V –1 s –1) holes caused by relatively flat valence bands with substantial Cu 3d character and a significant concentration of Cu ion vacancy defects (p ~ 10 19 cm –3) in this material. In conclusion, electronic band structure calculations showed that electrons should be significantly more mobile in this structure type.« less

Copper Vacancies and Heavy Holes in the Two-Dimensional Semiconductor KCu 3–xSe 2

DOE PAGES

Rettie, Alexander J. E.; Sturza, Mihai; Malliakas, Christos D.; ...

2017-06-21

The two-dimensional material KCu 3–xSe 2 was synthesized using both a K 2Se 3 flux and directly from the elements. It crystallizes in the CsAg 3S 2 structure (monoclinic space group C2/m with a = 15.417(3) Å, b = 4.0742(8) Å, c = 8.3190(17) Å, and β = 112.94(3)°), and single-crystal refinement revealed infinite copper-deficient [Cu 3–xSe 2]– layers separated by K + ions. Thermal analysis indicated that KCu 3–xSe 2 melts congruently at ~755 °C. UV–vis spectroscopy showed an optical band gap of ~1.35 eV that is direct in nature, as confirmed by electronic structure calculations. Electronic transport measurementsmore » on single crystals yielded an in-plane resistivity of ~6 × 10 –1 Ω cm at 300 K that has a complex temperature dependence. The results of Seebeck coefficient measurements were consistent with a doped p-type semiconductor (S = +214 μV K –1 at 300 K), with doping being attributed to copper vacancies. Transport is dominated by low-mobility (on the order of 1 cm 2 V –1 s –1) holes caused by relatively flat valence bands with substantial Cu 3d character and a significant concentration of Cu ion vacancy defects (p ~ 10 19 cm –3) in this material. In conclusion, electronic band structure calculations showed that electrons should be significantly more mobile in this structure type.« less

Influence of Melt Superheating Treatment on Solidification Characteristics and Rupture Life of a Third-Generation Ni-Based Single-Crystal Superalloy

NASA Astrophysics Data System (ADS)

Su, Haijun; Wang, Haifeng; Zhang, Jun; Guo, Min; Liu, Lin; Fu, Hengzhi

2018-05-01

The influence of melt superheating treatment on the melt properties, solidification characteristics, and rupture life of a third-generation Ni-based single-crystal superalloy was investigated to reveal the critical temperature range of melt structure evolution and its effect on rupture life. The results showed that the viscosity of superalloy decreased but the surface tension increased with increasing superheating temperature. Two characteristic temperature points where the melt viscosity and undercooling degree suddenly change were determined to be 1600 °C and 1700 °C, respectively. Similarly, the stability of the solidification interface firstly improved and then weakened with increasing superheating temperature. The dendrite arms were well refined and the segregation was reduced at 1700 °C. In addition, the rupture life obtained at 1100 °C and 137 MPa increased by approximately 30 pct, approaching the rupture life of the corresponding superalloy containing 2 pct Ru, with increasing superheating temperature from 1500 °C to 1700 °C. When the melt was further heated to 1800 °C, the rupture life decreased. The evolutions of solidification characteristics and rupture life with increasing melt superheating temperature were attributed to changes in the melt structure.

Synthesis, Crystal Structure, and Topology-Symmetry Analysis of a New Modification of NaIn[IO3]4

NASA Astrophysics Data System (ADS)

Belokoneva, E. L.; Karamysheva, A. S.; Dimitrova, O. V.; Volkov, A. S.

2018-01-01

Crystals of new iodate NaIn[IO3]4 were prepared by the hydrothermal synthesis. The unit cell parameters are a = 7.2672(2) Å, b = 15.2572(6) Å, c = 15.0208(6) Å, β = 101.517(3)°, sp. gr. P21/ c. The formula was determined during the structure determination and refinement of a twinned crystal based on a set of reflections from the atomic planes of the major individual. The refinement with anisotropic displacement parameters was performed for both twin components to the final R factor of 0.050. The In and Na atoms are in octahedral coordination formed by oxygen atoms. The oxygen octahedra are arranged into columns by sharing edges, and the columns are connected by isolated umbrella-like [IO3]- groups to form layers. The new structure is most similar to the isoformular iodate NaIn[IO3]4, which crystallizes in the same sp. gr. P21/ c and is structurally similar, but has a twice smaller unit cell and is characterized by another direction of the monoclinic axis. The structural similarity and difference between the two phases were studied by topologysymmetry analysis. The formation of these phases is related to different combinations of identical one-dimensional infinite chains of octahedra.

Embarras de richesses - It is not good to be too anomalous: Accurate structure of selenourea, a chiral crystal of planar molecules.

PubMed

Luo, Zhipu; Dauter, Zbigniew

2017-01-01

Selenourea, SeC(NH2)2, recently found an application as a derivatization reagent providing a significant anomalous diffraction signal used for phasing macromolecular crystal structures. The crystal structure of selenourea itself was solved about 50 years ago, from data recorded on films and evaluated by eye and refined to R = 0.15 with errors of bond lengths and angles about 0.1 Å and 6°. In the current work this structure is re-evaluated on the basis of synchrotron data and refined to R1 = 0.021 with bond and angle errors about 0.007 Å and 0.5°. The nine planar molecules of selenourea pack either in the P31 or in the P32 unit cell. All unique molecules are connected by a complex network of Se•••H-N hydrogen bonds and Se•••Se contacts. The packing of selenourea molecules is highly pseudosymmetric, approximating either of the P31(2)12, R3, and R32 space groups. Because the overwhelming majority of diffracted X-ray intensity originates form the anomalously scattering selenium atoms, the measurable anomalous Bijvoet differences are diminished and it was not possible to solve this crystal structure based on the anomalous signal alone.

Two-Step Vapor/Liquid/Solid Purification

NASA Technical Reports Server (NTRS)

Holland, L. R.

1986-01-01

Vertical distillation system combines in single operation advantages of multiple zone refining with those of distillation. Developed specifically to load Bridgman-Stockbarger (vertical-solidification) growth ampoules with ultrapure tellurium and cadmium, system, with suitable modifications, serves as material refiner. In first phase of purification process, ampoule heated to drive off absorbed volatiles. Second phase, evaporator heated to drive off volatiles in charge. Third phase, slowly descending heater causes distillation from evaporator to growing crystal in ampoule.

Effect of strain and stress on the relative dimensions of the 'hard' and 'soft' regions in crept NaCl single crystals

NASA Technical Reports Server (NTRS)

Raj, S. V.; Freed, Alan D.

1992-01-01

It is shown that the L exp h and L exp s ratio, where these are respectively the average dimensions of the hard and soft regions as a function of stress and strain in crept NaCl single crystals, significantly influences the steady-state creep and power-law breakdown in these crystals. This is suggested to be due to a change in the internal stresses of the material. The present observations also indicate that steady-state creep is more likely to be influenced by the degree of refinement in the cell boundaries within the subgrains than by the formation of equiaxed subgrains under power-law conditions.

Crystal structure and thermal expansion of CsCaI3:Eu and CsSrBr3:Eu scintillators

NASA Astrophysics Data System (ADS)

Loyd, Matthew; Lindsey, Adam; Patel, Maulik; Koschan, Merry; Melcher, Charles L.; Zhuravleva, Mariya

2018-01-01

The distorted-perovskite scintillator materials CsCaI3:Eu and CsSrBr3:Eu prepared as single crystals have shown promising potential for use in radiation detection applications requiring a high light yield and excellent energy resolution. We present a study using high temperature powder X-ray diffraction experiments to examine a deleterious high temperature phase transition. High temperature phases were identified through sequential diffraction pattern Rietveld refinement in GSAS II. We report the linear coefficients of thermal expansion for both high and low temperature phases of each compound. Thermal expansion for both compositions is greatest in the [0 0 1] direction. As a result, Bridgman growth utilizing a seed oriented with the [0 0 1] along the growth direction should be used to mitigate thermal stress.

Structure and transport properties of dense polycrystalline clathrate-II (K,Ba) 16(Ga,Sn) 136 synthesized by a new approach employing SPS

DOE PAGES

Wei, Kaya; Zeng, Xiaoyu; Tritt, Terry M.; ...

2016-08-26

Tin clathrate-II framework-substituted compositions are of current interest as potential thermoelectric materials for medium-temperature applications. A review of the literature reveals different compositions reported with varying physical properties, which depend strongly on the exact composition as well as the processing conditions. We therefore initiated an approach whereby single crystals of two different (K,Ba) 16(Ga,Sn) 136 compositions were first obtained, followed by grinding of the crystals into fine powder for low temperature spark plasma sintering consolidation into dense polycrystalline solids and subsequent high temperature transport measurements. Powder X-ray refinement results indicate that the hexakaidecahedra are empty, K and Ba occupying onlymore » the decahedra. Their electrical properties depend on composition and have very low thermal conductivities. As a result, the structural and transport properties of these materials are compared to that of other Sn clathrate-II compositions.« less

The new silver borate Ag{sub 3}B{sub 5}O{sub 9}

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

Sohr, Gerhard; Falkowski, Viktoria; Huppertz, Hubert, E-mail: hubert.huppertz@uibk.ac.at

2015-05-15

Single crystals of Ag{sub 3}B{sub 5}O{sub 9} were obtained via high-pressure synthesis at 3 GPa and 600 °C, using a Walker-type multianvil high-pressure device. Ag{sub 3}B{sub 5}O{sub 9} crystalizes with a=674.7(2), b=943.5(2), c=1103.5(2) pm, V=0.7025(2) nm{sup 3}, and Z=4 in the noncentrosymmetric space group P2{sub 1}2{sub 1}2{sub 1} (no. 19). The orthorhombic structure was refined from 3740 independent reflections with R1=0.0496 and wR2=0.587 (all data). It is built up from infinite corner-sharing chains of BO{sub 4} tetrahedra along the a axis, which are interconnected by BO{sub 3} groups to form a network. In the structure, three crystallographically independent sites aremore » occupied with Ag{sup +} cations exhibiting argentophillic interactions. The synthetic conditions as well as the results of the single crystal structure analysis are presented. - Graphical abstract: Noncentrosymmetric silver borate: During investigations in the system Ag–B–O, a new noncentrosymmetric silver borate Ag{sub 3}B{sub 5}O{sub 9} was discovered. The new structure type is built up from corner-sharing BO{sub 3} and BO{sub 4} groups, forming a network. Argentophillic interactions are clearly indicated by the Ag{sup +}⋯Ag{sup +} distances present in the structure. - Highlights: • A noncentrosymmetric borate Ag{sub 3}B{sub 5}O{sub 9} is accessible via high-pressure synthesis. • Ag{sub 3}B{sub 5}O{sub 9} is the second high-pressure silver borate. • Ag{sup +}⋯Ag{sup +} distances in Ag3B5O9 clearly indicate the presence of argentophillic interactions.« less

Crystallography of waxes - an electron diffraction study of refined and natural products

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1997-02-01

The crystal structure of four waxes has been investigated by electron crystallography. Two of these waxes, including a refined petroleum product (Gulfwax) and a material from lignite (montan wax), form well ordered crystals and their structure could be solved quantitatively from the observed 0022-3727/30/3/018/img1 diffraction patterns. As also found previously for simpler binary n-paraffin solid solutions, the average structure resembles that of a pure paraffin (e.g. n-0022-3727/30/3/018/img2) but with a Gaussian distribution of atomic occupancies near the chain ends to account for the statistical distribution of chain lengths within a lamella. Two other waxes from living organisms, South African bee honeycomb and the leaves of the Brazilian carnauba palm, are much less ordered, even though they share the same methylene subcell packing of the most crystalline parts of the previous materials. It appears that these waxes cannot fully separate into distinct lamellae, perhaps due to the presence of very long `tie' molecules, and are therefore `frustrated' crystal structures.

Structural and electron charge density studies of a nonlinear optical compound 4,4 di-methyl amino cyano biphenyl

NASA Astrophysics Data System (ADS)

Naima, Boubegra; Abdelkader, Chouaih; Mokhtaria, Drissi; Fodil, Hamzaoui

2014-01-01

The 4,4 dimethyl amino cyano biphenyl crystal (DMACB) is characterized by its nonlinear activity. The intra molecular charge transfer of this molecule results mainly from the electronic transmission of the electro-acceptor (cyano) and electro-donor (di-methyl-amino) groups. An accurate electron density distribution around the molecule has been calculated based on a high-resolution X-ray diffraction study. The data were collected at 123 K using graphite-monochromated Mo K α radiation to sin(β)/λ = 1.24 Å-1. The integrated intensities of 13796 reflections were measured and reduced to 6501 independent reflections with I >= 3σ(I). The crystal structure was refined using the experimental model of Hansen and Coppens (1978). The crystal structure has been validated and deposited at the Cambridge Crystallographic Data Centre with the deposition number CCDC 876507. In this article, we present the thermal motion and the structural analysis obtained from the least-square refinement based on F2 and the electron density distribution obtained from the multipolar model.

Structure of Mesorhizobium loti arylamine N-acetyltransferase 1

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

Holton, Simon J.; Dairou, Julien; Sandy, James

2005-01-01

The crystal structure of a M. loti arylamine N-acetyltransferase 1 has been determined at 2.0 Å resolution. The arylamine N-acetyltransferase (NAT) enzymes have been found in a broad range of both eukaryotic and prokaryotic organisms. The NAT enzymes catalyse the transfer of an acetyl group from acetyl Co-enzyme A onto the terminal nitrogen of a range of arylamine, hydrazine and arylhydrazine compounds. Recently, several NAT structures have been reported from different prokaryotic sources including Salmonella typhimurium, Mycobacterium smegmatis and Pseudomonas aeruginosa. Bioinformatics analysis of the Mesorhizobium loti genome revealed two NAT paralogues, the first example of multiple NAT isoenzymes inmore » a eubacterial organism. The M. loti NAT 1 enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme was crystallized in 0.5 M Ca(OAc){sub 2}, 16% PEG 3350, 0.1 M Tris–HCl pH 8.5 using the sitting-drop vapour-diffusion method. A data set diffracting to 2.0 Å was collected from a single crystal at 100 K. The crystal belongs to the orthorhombic spacegroup P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 53.2, b = 97.3, c = 114.3 Å. The structure was refined to a final free-R factor of 24.8%. The structure reveals that despite low sequence homology, M. loti NAT1 shares the common fold as reported in previous NAT structures and exhibits the same catalytic triad of residues (Cys-His-Asp) in the active site.« less

Neutron diffraction and μ SR studies of two polymorphs of nickel niobate NiNb 2 O 6

DOE PAGES

Munsie, T. J. S.; Wilson, M. N.; Millington, A.; ...

2017-10-13

Neutron diffraction and muon spin relaxation (μSR) studies are presented in this paper for the newly characterized polymorph of NiNb 2O 6 (β-NiNb 2O 6) with space group P4 2/n and μSR data only for the previously known columbite structure polymorph with space group Pbcn. The magnetic structure of the P4 2/n form was determined from neutron diffraction using both powder and single-crystal data. Powder neutron diffraction determined an ordering wave vector →k=( 1/ 2, 1/ 2, 1/ 2). Single-crystal data confirmed the same →k vector and showed that the correct magnetic structure consists of antiferromagnetically coupled chains running alongmore » the a or b axis in adjacent Ni 2+ layers perpendicular to the c axis, which is consistent with the expected exchange interaction hierarchy in this system. The refined magnetic structure is compared with the known magnetic structures of the closely related trirutile phases, NiSb 2O 6 and NiTa 2O 6. μSR data finds a transition temperature of T N~15K for this system, while the columbite polymorph exhibits a lower T N=5.7(3) K. Our μSR measurements also allowed us to estimate the critical exponent of the order parameter β for each polymorph. We found β =0.25(3) and 0.16(2) for the β and columbite polymorphs, respectively. The single-crystal neutron scattering data give a value for the critical exponent β =0.28(3) for β-NiNb 2O 6, in agreement with the μSR value. While both systems have β values less than 0.3, which is indicative of reduced dimensionality, this effect appears to be much stronger for the columbite system. Finally, in other words, although both systems appear to be well described by S=1 spin chains, the interchain interactions in the β polymorph are likely much larger.« less

Neutron diffraction and μ SR studies of two polymorphs of nickel niobate NiNb2O6

NASA Astrophysics Data System (ADS)

Munsie, T. J. S.; Wilson, M. N.; Millington, A.; Thompson, C. M.; Flacau, R.; Ding, C.; Guo, S.; Gong, Z.; Aczel, A. A.; Cao, H. B.; Williams, T. J.; Dabkowska, H. A.; Ning, F.; Greedan, J. E.; Luke, G. M.

2017-10-01

Neutron diffraction and muon spin relaxation (μ SR ) studies are presented for the newly characterized polymorph of NiNb2O6 (β -NiNb2O6) with space group P4 2/n and μ SR data only for the previously known columbite structure polymorph with space group P b c n . The magnetic structure of the P4 2/n form was determined from neutron diffraction using both powder and single-crystal data. Powder neutron diffraction determined an ordering wave vector k ⃗=(1/2 ,1/2 ,1/2 ) . Single-crystal data confirmed the same k ⃗ vector and showed that the correct magnetic structure consists of antiferromagnetically coupled chains running along the a or b axis in adjacent Ni2 + layers perpendicular to the c axis, which is consistent with the expected exchange interaction hierarchy in this system. The refined magnetic structure is compared with the known magnetic structures of the closely related trirutile phases, NiSb2O6 and NiTa2O6 . μ SR data finds a transition temperature of TN˜15 K for this system, while the columbite polymorph exhibits a lower TN=5.7 (3 ) K. Our μ SR measurements also allowed us to estimate the critical exponent of the order parameter β for each polymorph. We found β =0.25 (3 ) and 0.16(2) for the β and columbite polymorphs, respectively. The single-crystal neutron scattering data give a value for the critical exponent β =0.28 (3 ) for β -NiNb2O6 , in agreement with the μ SR value. While both systems have β values less than 0.3, which is indicative of reduced dimensionality, this effect appears to be much stronger for the columbite system. In other words, although both systems appear to be well described by S =1 spin chains, the interchain interactions in the β polymorph are likely much larger.

Neutron diffraction and μ SR studies of two polymorphs of nickel niobate NiNb 2 O 6

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

Munsie, T. J. S.; Wilson, M. N.; Millington, A.

Neutron diffraction and muon spin relaxation (μSR) studies are presented in this paper for the newly characterized polymorph of NiNb 2O 6 (β-NiNb 2O 6) with space group P4 2/n and μSR data only for the previously known columbite structure polymorph with space group Pbcn. The magnetic structure of the P4 2/n form was determined from neutron diffraction using both powder and single-crystal data. Powder neutron diffraction determined an ordering wave vector →k=( 1/ 2, 1/ 2, 1/ 2). Single-crystal data confirmed the same →k vector and showed that the correct magnetic structure consists of antiferromagnetically coupled chains running alongmore » the a or b axis in adjacent Ni 2+ layers perpendicular to the c axis, which is consistent with the expected exchange interaction hierarchy in this system. The refined magnetic structure is compared with the known magnetic structures of the closely related trirutile phases, NiSb 2O 6 and NiTa 2O 6. μSR data finds a transition temperature of T N~15K for this system, while the columbite polymorph exhibits a lower T N=5.7(3) K. Our μSR measurements also allowed us to estimate the critical exponent of the order parameter β for each polymorph. We found β =0.25(3) and 0.16(2) for the β and columbite polymorphs, respectively. The single-crystal neutron scattering data give a value for the critical exponent β =0.28(3) for β-NiNb 2O 6, in agreement with the μSR value. While both systems have β values less than 0.3, which is indicative of reduced dimensionality, this effect appears to be much stronger for the columbite system. Finally, in other words, although both systems appear to be well described by S=1 spin chains, the interchain interactions in the β polymorph are likely much larger.« less

Cloning, overexpression, purification and preliminary crystallographic studies of a mitochondrial type II peroxiredoxin from Pisum sativum

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

Barranco-Medina, Sergio; López-Jaramillo, Francisco Javier, E-mail: fjljara@ugr.es; Bernier-Villamor, Laura

2006-07-01

The isolation, purification, crystallization and molecular-replacement solution of mitochondrial type II peroxiredoxin from P. sativum is reported. A cDNA encoding an open reading frame of 199 amino acids corresponding to a type II peroxiredoxin from Pisum sativum with its transit peptide was isolated by RT-PCR. The 171-amino-acid mature protein (estimated molecular weight 18.6 kDa) was cloned into the pET3d vector and overexpressed in Escherichia coli. The recombinant protein was purified and crystallized by the hanging-drop vapour-diffusion technique. A full data set (98.2% completeness) was collected using a rotating-anode generator to a resolution of 2.8 Å from a single crystal flash-cooledmore » at 100 K. X-ray data revealed that the protein crystallizes in space group P1, with unit-cell parameters a = 61.88, b = 66.40, c = 77.23 Å, α = 102.90, β = 104.40, γ = 99.07°, and molecular replacement using a theoretical model predicted from the primary structure as a search model confirmed the presence of six molecules in the unit cell as expected from the Matthews coefficient. Refinement of the structure is in progress.« less

Optimization of crystallization conditions for biological macromolecules.

PubMed

McPherson, Alexander; Cudney, Bob

2014-11-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Optimization of crystallization conditions for biological macromolecules

PubMed Central

McPherson, Alexander; Cudney, Bob

2014-01-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success. PMID:25372810

Crystal Structure Studies of Low-Ca Pyroxenes from LL-Group Chondritic Meteorites

NASA Astrophysics Data System (ADS)

Artioli, G.; Davoli, G.; Sighinolfi, G. P.

1993-07-01

One orthorhombic (Pbca) and two monoclinic (P2(sub)1/c) single crystals of low-Ca pyroxenes were extracted from unequilibrated chondritic meteorites of the LL-group. The results of the crystal structure refinements performed using x-ray diffraction data indicate that: (1) the intracrystalline Fe-Mg distribution over the M1 and M2 crystallographic sites of the Parnallee (LL-3) orthoenstatite is consistent with a temperature of 960 degrees C for the closure of the exchange equilibrium process; and (2) the structural state and intracristalline Fe-Mg order in the Soko Banja (LL-4) and Jolomba (LL-6) clinoenstatites indicate a closing temperature of at least 1000-1100 degrees C, with no significant reequilibration at lower temperatures. The present data represent the first detailed crystallographic investigation of pyroxenes from LL-chondrites and support the hypothesis that the chondrule pyroxenes bear a distinct memory of rapid cooling in the solar nebular and that thermal metamorphism in the parent body, if present, was totally unsufficient to allow reequilibration of the pyroxene minerals to the low-temperature ordered crystal structures. The data also indicate that, assuming low or mild pressure and shock effects, there is no well-defined correlation between equilibrium temperature of the mineral phases and the alleged petrologic type of the meteorites. This evidence is consistent with a rubble-pile model for the parent body accretional history, or with an onion-shell model with very low thermal-peak metamorphism, as it is assumed for a very small object.

Growth of single crystals of organic salts with large second-order optical nonlinearities by solution processes for devices

NASA Technical Reports Server (NTRS)

Leslie, Thomas M.

1995-01-01

Data obtained from the electric field induced second harmonic generation (EFISH) and Kurtz Powder Methods will be provided to MSFC for further refinement of their method. A theoretical model for predicting the second-order nonlinearities of organic salts is being worked on. Another task is the synthesis of a number of salts with various counterions. Several salts with promising SHG activities and new salts will be tested for the presence of two crystalline forms. The materials will be recrystallized from dry and wet solvents and compared for SHG efficiency. Salts that have a high SHG efficiency and no tendency to form hydrates will be documented. The synthesis of these materials are included in this report. A third task involves method to aid in the growth of large, high quality single crystals by solution processes. These crystals will be characterized for their applicability in the fabrication of devices that will be incorporated into optical computers in future programs. Single crystals of optimum quality may be obtained by crystal growth in low-gravity. The final task is the design of a temperature lowering single crystal growth apparatus for ground based work. At least one prototype will be built.

Crystal structure of the mineral (Na,Ca,K){sub 2}(Ca,Na){sub 4}(Mg,Fe){sub 5}(Mg,Fe,Ti){sub 5}[Si{sub 12}Al{sub 4}O{sub 44}](F,O){sub 4}: a triclinic representative of the amphibole family

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

Rastsvetaeva, R. K., E-mail: rast@ns.crys.ras.ru; Aksenov, S. M.

2012-05-15

A mineral belonging to the amphibole family found at the Rothenberg paleovolcano (Eifel, Germany) was studied by single-crystal X-ray diffraction. The triclinic pseudomonoclinic unit-cell parameters are a = 5.3113(1) Angstrom-Sign , b = 18.0457(3) Angstrom-Sign ; c = 9.8684(2) Angstrom-Sign , {alpha} = 90.016(2) Degree-Sign , {beta} = 105.543(4) Degree-Sign , {gamma} = 89.985(2) Degree-Sign . The structure was solved by direct methods in sp. gr. P1 and refined to the R factor of 2.7% based on 6432 reflections with |F| > 3{sigma}(F) taking into account twinning. The mineral with the idealized formula (Na,Ca,K){sub 2}(Ca,Na){sub 4}(Mg,Fe){sub 5}(Mg,Fe,Ti){sub 5}[Si{sub 12}Al{sub 4}O{submore » 44}](F,O){sub 4} has some symmetry and structural features that distinguish it from other minerals of this family.« less

Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7}: Structural, spectroscopic and computational studies on a sorosilicate

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

Kahlenberg, Volker, E-mail: volker.kahlenberg@uibk.ac.at; Brunello, Emanuele; Hejny, Clivia

2015-05-15

Synthesis experiments in the system Li{sub 2}O–CaO–SiO{sub 2} resulted in the formation of single-crystals of Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7}. Structural investigations were based on single-crystal diffraction. At ambient conditions the compound has the following basic crystallographic data: hexagonal symmetry, space group P6{sub 1}22, a=5.0961(2) Å, c=41.264(2) Å, V=928.07(6) Å{sup 3}, Z=6. Structure solution was performed using direct methods. The final least-squares refinement calculations converged at a residual of R(|F|)=0.0260. From a structural point the lithium calcium silicate belongs to the group of pyrosilicates containing [Si{sub 2}O{sub 7}]-groups. Additional lithium and calcium cations are incorporated between the silicate dimers andmore » are coordinated by four and six nearest oxygen neighbours, respectively. Each [LiO{sub 4}]-tetrahedron shares two common corners with directly neighboring tetrahedra forming zweier single-chains which are running parallel to 〈1 0 0〉 in z-levels defined by the presence of the 6{sub 1}{sup [0} {sup 0} {sup 1]}-screw axes. From the corner-sharing [LiO{sub 4}]- and [SiO{sub 4}]-moieties a three dimensional framework can be constructed. An interesting feature of this framework is the presence of an O{sup [3]}-type bridging oxygen linking three tetrahedra (one [LiO{sub 4}]- and two [SiO{sub 4}]-units). Structural similarities with other silicates are discussed in detail. The high-temperature behavior of the Si–O, Ca–O and Li–O bond distances in Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7} was investigated by in{sub -}situ single-crystal X-ray diffraction in the range between 65 and 700 °C. From the evolution of the lattice parameters, the thermal expansion tensor α{sub ij} has been determined. The structural characterization has been supplemented by micro-Raman spectroscopy. Interpretation of the spectroscopic data including the allocation of the bands to certain vibrational species has been aided by DFT-calculations. - Graphical abstract: Framework of [SiO{sub 4}]- and [LiO{sub 4}]-tetrahedra in the crystal structure of Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7}. - Highlights: • We report the crystal structure of the sorosilicate Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7} at ambient conditions. • The thermal expansion tensor as well as the evolution of the structure between 25 and 700 °C was studied. • A topological analysis of the tetrahedral framework based on [SiO{sub 4}]- and [LiO{sub 4}]-units is presented. • The crystal structure of Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7} is discussed with respect to related compounds. • Interpretation of the Raman spectra of the crystals has been aided by DFT-calculations.« less

Average structure and M2 site configurations in C2/c clinopyroxenes along the Di-En join

NASA Astrophysics Data System (ADS)

Tribaudino, M.; Benna, P.; Bruno, E.

1989-12-01

In order to clarify the structural configurations observed in Diss in the Ca-rich region of the Di-En join (in which TEM observations show neither exsolution microstructures nor evidence of spinodal decomposition) single crystals large enough for X-ray diffraction analyses, with composition (Ca0.66Mg0.34)MgSi2O6, have been equilibrated close to the solvus at T=1350° C for 317 h, and quenched at room temperature. The refinement in C2/c space group shows that in the M2 site Ca and Mg are fully ‘ordered’ in two split positions (M2occ: 0.66 Ca; M2'occ: 0.34 Mg). Since the average structure shows a relevant elongation of anisotropic thermal ellipsoids of the O2 and O3 oxygen atoms, the refinement has been carried out according to a split model for O2 and O3 atoms: Ca appears 8-coordinated (as in diopside) and Mg shows a sixfold coordination similar to that of high-pigeonite. This coordination for Mg is significantly different from the fourfold coordination (Zn-like in Zn-cpx) proposed previously and it is a more probable coordination for Mg from a crystalchemical point of view. The same results were obtained refining a Di80En20 cpx, equilibrated at T=1230° C, according to the same O-split model. The data support the coexistence of a Di-like configuration for Ca and of a highPig-like configuration for Mg away from the solvus also. At T very near to T solidus the different configurations, observed at room temperature in the quenched samples, should converge and Ca and Mg should retain a single disordered configuration in the M2 site.

Transport properties of Nd0.67Sr0.33Mn0.85Co0.15O3 manganite

NASA Astrophysics Data System (ADS)

Bhargav, Abhinav; Tank, Tejas M.; Sanyal, Sankar P.

2018-05-01

We have studied the structural and electrical transport properties of Nd0.67Sr0.33Mn0.85Co0.15O3 manganite prepared through conventional solid state reaction technique. The investigation of X-ray diffraction data and rietvield refinement show that the synthesized sample is single phase in nature and crystallizes in orthorhombic perovskite structure with Pbnm space group. The resistivity versus temperature measurement for sample Nd0.67Sr0.33Mn0.85Co0.15O3 was performed in the range 0-300K and at 0T field. The electrical transport mechanism of the sample is analyzed by different theoretical models, for temperatures below and above TP.

On the Use of Dynamical Diffraction Theory To Refine Crystal Structure from Electron Diffraction Data: Application to KLa5O5(VO4)2, a Material with Promising Luminescent Properties.

PubMed

Colmont, Marie; Palatinus, Lukas; Huvé, Marielle; Kabbour, Houria; Saitzek, Sébastien; Djelal, Nora; Roussel, Pascal

2016-03-07

A new lanthanum oxide, KLa5O5(VO4)2, was synthesized using a flux growth technique that involved solid-state reaction under an air atmosphere at 900 °C. The crystal structure was solved and refined using an innovative approach recently established and based on three-dimensional (3D) electron diffraction data, using precession of the electron beam and then validated against Rietveld refinement and denisty functional theory (DFT) calculations. It crystallizes in a monoclinic unit cell with space group C2/m and has unit cell parameters of a = 20.2282(14) Å, b = 5.8639(4) Å, c = 12.6060(9) Å, and β = 117.64(1)°. Its structure is built on Cresnel-like two-dimensional (2D) units (La5O5) of 4*3 (OLa4) tetrahedra, which run parallel to (001) plane, being surrounded by isolated VO4 tetrahedra. Four isolated vanadate groups create channels that host K(+) ions. Substitution of K(+) cations by another alkali metal is possible, going from lithium to rubidium. Li substitution led to a similar phase with a primitive monoclinic unit cell. A complementary selected area electron diffraction (SAED) study highlighted diffuse streaks associated with stacking faults observed on high-resolution electron microscopy (HREM) images of the lithium compound. Finally, preliminary catalytic tests for ethanol oxidation are reported, as well as luminescence evidence. This paper also describes how solid-state chemists can take advantages of recent progresses in electron crystallography, assisted by DFT calculations and powder X-ray diffraction (PXRD) refinements, to propose new structural types with potential applications to the physicist community.

Growth, properties, and applications of potassium niobate single crystals

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

Mizell, G.; Fay, W.R.; Alekel, T. III

1994-12-31

Production refinements and pragmatic optical properties of the frequency converter crystal KNbO{sub 3} (KN) are highlighted regarding its commercialization. The growth, morphological orientation, and processing of KN crystals into devices are outlined. Passive absorption data are presented that define the effective window range for KN devices. An absorption band at 2.85 {mu}m is attributed to the presence of OH groups in the crystal, and its vibrational strength varies with crystal growth conditions and incident polarized light orientation. Although blue light induced infrared absorption (BLIRA) can reduce second harmonic generation (SHG) efficiency at high power, single-pass conversion efficiencies of 1%/W{center_dot}cm maymore » be achieved with incident fundamental powers of 10 W. The ability of KN to non-critically phasematch by temperature tuning provides blue-green wavelengths; together with critical angle-tuned phasematching, the entire visible spectrum may be accessed with efficient SHG conversion.« less

Optimization of the crystal growth of the superconductor CaKFe 4 As 4 from solution in the FeAs - CaFe 2 As 2 - KFe 2 As 2 system

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

Meier, W. R.; Kong, T.; Bud'ko, S. L.

Measurements of the anisotropic properties of single crystals play a crucial role in probing the physics of new materials. Determining a growth protocol that yields suitable high-quality single crystals can be particularly challenging for multicomponent compounds. Here we present a case study of how we refined a procedure to grow single crystals of CaKFe 4As 4 from a high temperature, quaternary liquid solution rich in iron and arsenic (“FeAs self-flux”). Temperature dependent resistance and magnetization measurements are emphasized, in addition to the x-ray diffraction, to detect intergrown CaKFe 4As 4, CaFe 2As 2, and KFe 2As 2 within what appearmore » to be single crystals. Guided by the rules of phase equilibria and these data, we adjusted growth parameters to suppress formation of the impurity phases. The resulting optimized procedure yielded phase-pure single crystals of CaKFe 4As 4. In conclusion, this optimization process offers insight into the growth of quaternary compounds and a glimpse of the four-component phase diagram in the pseudoternary FeAs–CaFe 2As 2–KFe 2As 2 system.« less

Optimization of the crystal growth of the superconductor CaKFe 4 As 4 from solution in the FeAs - CaFe 2 As 2 - KFe 2 As 2 system

DOE PAGES

Meier, W. R.; Kong, T.; Bud'ko, S. L.; ...

2017-06-19

Measurements of the anisotropic properties of single crystals play a crucial role in probing the physics of new materials. Determining a growth protocol that yields suitable high-quality single crystals can be particularly challenging for multicomponent compounds. Here we present a case study of how we refined a procedure to grow single crystals of CaKFe 4As 4 from a high temperature, quaternary liquid solution rich in iron and arsenic (“FeAs self-flux”). Temperature dependent resistance and magnetization measurements are emphasized, in addition to the x-ray diffraction, to detect intergrown CaKFe 4As 4, CaFe 2As 2, and KFe 2As 2 within what appearmore » to be single crystals. Guided by the rules of phase equilibria and these data, we adjusted growth parameters to suppress formation of the impurity phases. The resulting optimized procedure yielded phase-pure single crystals of CaKFe 4As 4. In conclusion, this optimization process offers insight into the growth of quaternary compounds and a glimpse of the four-component phase diagram in the pseudoternary FeAs–CaFe 2As 2–KFe 2As 2 system.« less

Naturally occurring 32Si and low-background silicon dark matter detectors

DOE PAGES

Orrell, John L.; Arnquist, Isaac J.; Bliss, Mary; ...

2018-02-10

Here, the naturally occurring radioisotope 32Si represents a potentially limiting background in future dark matter direct-detection experiments. We investigate sources of 32Si and the vectors by which it comes to reside in silicon crystals used for fabrication of radiation detectors. We infer that the 32Si concentration in commercial single-crystal silicon is likely variable, dependent upon the specific geologic and hydrologic history of the source (or sources) of silicon “ore” and the details of the silicon-refinement process. The silicon production industry is large, highly segmented by refining step, and multifaceted in terms of final product type, from which we conclude thatmore » production of 32Si-mitigated crystals requires both targeted silicon material selection and a dedicated refinement-through-crystal-production process. We review options for source material selection, including quartz from an underground source and silicon isotopically reduced in 32Si. To quantitatively evaluate the 32Si content in silicon metal and precursor materials, we propose analytic methods employing chemical processing and radiometric measurements. Ultimately, it appears feasible to produce silicon detectors with low levels of 32Si, though significant assay method development is required to validate this claim and thereby enable a quality assurance program during an actual controlled silicon-detector production cycle.« less

Naturally occurring 32Si and low-background silicon dark matter detectors

NASA Astrophysics Data System (ADS)

Orrell, John L.; Arnquist, Isaac J.; Bliss, Mary; Bunker, Raymond; Finch, Zachary S.

2018-05-01

The naturally occurring radioisotope 32Si represents a potentially limiting background in future dark matter direct-detection experiments. We investigate sources of 32Si and the vectors by which it comes to reside in silicon crystals used for fabrication of radiation detectors. We infer that the 32Si concentration in commercial single-crystal silicon is likely variable, dependent upon the specific geologic and hydrologic history of the source (or sources) of silicon "ore" and the details of the silicon-refinement process. The silicon production industry is large, highly segmented by refining step, and multifaceted in terms of final product type, from which we conclude that production of 32Si-mitigated crystals requires both targeted silicon material selection and a dedicated refinement-through-crystal-production process. We review options for source material selection, including quartz from an underground source and silicon isotopically reduced in 32Si. To quantitatively evaluate the 32Si content in silicon metal and precursor materials, we propose analytic methods employing chemical processing and radiometric measurements. Ultimately, it appears feasible to produce silicon detectors with low levels of 32Si, though significant assay method development is required to validate this claim and thereby enable a quality assurance program during an actual controlled silicon-detector production cycle.

Naturally occurring 32Si and low-background silicon dark matter detectors

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

Orrell, John L.; Arnquist, Isaac J.; Bliss, Mary

Here, the naturally occurring radioisotope 32Si represents a potentially limiting background in future dark matter direct-detection experiments. We investigate sources of 32Si and the vectors by which it comes to reside in silicon crystals used for fabrication of radiation detectors. We infer that the 32Si concentration in commercial single-crystal silicon is likely variable, dependent upon the specific geologic and hydrologic history of the source (or sources) of silicon “ore” and the details of the silicon-refinement process. The silicon production industry is large, highly segmented by refining step, and multifaceted in terms of final product type, from which we conclude thatmore » production of 32Si-mitigated crystals requires both targeted silicon material selection and a dedicated refinement-through-crystal-production process. We review options for source material selection, including quartz from an underground source and silicon isotopically reduced in 32Si. To quantitatively evaluate the 32Si content in silicon metal and precursor materials, we propose analytic methods employing chemical processing and radiometric measurements. Ultimately, it appears feasible to produce silicon detectors with low levels of 32Si, though significant assay method development is required to validate this claim and thereby enable a quality assurance program during an actual controlled silicon-detector production cycle.« less

Naturally occurring 32 Si and low-background silicon dark matter detectors

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

Orrell, John L.; Arnquist, Isaac J.; Bliss, Mary

The naturally occurring radioisotope Si-32 represents a potentially limiting background in future dark matter direct-detection experiments. We investigate sources of Si-32 and the vectors by which it comes to reside in silicon crystals used for fabrication of radiation detectors. We infer that the Si-32 concentration in commercial single-crystal silicon is likely variable, dependent upon the specific geologic and hydrologic history of the source (or sources) of silicon “ore” and the details of the silicon-refinement process. The silicon production industry is large, highly segmented by refining step, and multifaceted in terms of final product type, from which we conclude that productionmore » of Si-32-mitigated crystals requires both targeted silicon material selection and a dedicated refinement-through-crystal-production process. We review options for source material selection, including quartz from an underground source and silicon isotopically reduced in Si-32. To quantitatively evaluate the Si-32 content in silicon metal and precursor materials, we propose analytic methods employing chemical processing and radiometric measurements. Ultimately, it appears feasible to produce silicon-based detectors with low levels of Si-32, though significant assay method development is required to validate this claim and thereby enable a quality assurance program during an actual controlled silicon-detector production cycle.« less

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.

Effect of temperature on the formation of creep substructure in sodium chloride single crystals

NASA Technical Reports Server (NTRS)

Raj, Sai V.; Pharr, George M.

1992-01-01

The effect of temperature on the substructure morphology and the cell and subgrain size was investigated experimentally in NaCl single crystals under creep in the temperature range 573-873 K. It is found that the effect of temperature on the cell and subgrain sizes is weak in comparison with the effect of stress. However, there was a qualitative change in the substructure morphology with temperature, with the cells and subgrains better defined at higher temperatures. The volume fraction of the cell boundaries decreased with increasing temperature, thereby indicating a refinement of the microstructure at higher temperatures.

Structure and thermal expansion of Ca9Gd(VO4)7: A combined powder-diffraction and dilatometric study of a Czochralski-grown crystal

NASA Astrophysics Data System (ADS)

Paszkowicz, Wojciech; Shekhovtsov, Alexei; Kosmyna, Miron; Loiko, Pavel; Vilejshikova, Elena; Minikayev, Roman; Romanowski, Przemysław; Wierzchowski, Wojciech; Wieteska, Krzysztof; Paulmann, Carsten; Bryleva, Ekaterina; Belikov, Konstantin; Fitch, Andrew

2017-11-01

Materials of the Ca9RE(VO4)7 (CRVO) formula (RE = rare earth) and whitlockite-related structures are considered for applications in optoelectronics, e.g., in white-light emitting diodes and lasers. In the CRVO structure, the RE atoms are known to share the site occupation with Ca atoms at two or three among four Ca sites, with partial occupancy values depending on the choice of the RE atom. In this work, the structure and quality of a Czochralski-grown crystal of this family, Ca9Gd(VO4)7 (CGVO), are studied using X-ray diffraction methods. The room-temperature structure is refined using the powder diffraction data collected at a high-resolution synchrotron beamline ID22 (ESRF, Grenoble); for comparison purposes, a laboratory diffraction pattern was collected and analyzed, as well. The site occupancies are discussed on the basis of comparison with literature data of isostructural synthetic crystals of the CRVO series. The results confirm the previously reported site-occupation scheme and indicate a tendency of the CGVO compound to adopt a Gd-deficient composition. Moreover, the thermal expansion coefficient is determined for CGVO as a function of temperature in the 302-1023 K range using laboratory diffraction data. Additionally, for CGVO and six other single crystals of the same family, thermal expansion is studied in the 298-473 K range, using the dilatometric data. The magnitude and anisotropy of thermal expansion, being of importance for laser applications, are discussed for these materials.

Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).

PubMed Central

Webster, G D; Sanderson, M R; Skelly, J V; Neidle, S; Swann, P F; Li, B F; Tickle, I J

1990-01-01

The crystal structure of the dodecanucleotide d(CGCAAGCTGGCG) has been determined to a resolution of 2.5 A and refined to an R factor of 19.3% for 1710 reflections. The sequence crystallizes as a B-type double helix, with two G(anti).A(syn) base pairs. These are stabilized by three-center hydrogen bonds to pyrimidines that induce perturbations in base-pair geometry. The central AGCT region of the helix has a wide (greater than 6 A) minor groove. PMID:2395870

Molten salt flux synthesis and crystal structure of a new open-framework uranyl phosphate Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}: Spectroscopic characterization and cationic mobility studies

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

Yagoubi, S., E-mail: said.yagoubi@cea.fr; Renard, C.; Abraham, F.

2013-04-15

The reaction of triuranyl diphosphate tetrahydrate precursor (UO{sub 2}){sub 3}(PO{sub 4}){sub 2}(H{sub 2}O){sub 4} with a CsI flux at 750 °C yields a yellow single crystals of new compound Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}. The crystal structure (monoclinic, space group C2/c, a=13.6261 (13) Å, b=8.1081(8) Å, c=12.3983(12) Å, β=114.61(12)°, V=1245.41(20) Å{sup 3} with Z=4) has been solved using direct methods and Fourier difference techniques. A full-matrix least-squares refinement on the basis of F{sup 2} yielded R1=0.028 and wR2=0.071 for 79 parameters and 1352 independent reflections with I≥2σ(I) collected on a BRUKER AXS diffractometer with MoKα radiation and a charge-coupledmore » device detector. The crystal structure is built by two independent uranium atoms in square bipyramidal coordination, connected by two opposite corners to form infinite chains {sup 1}{sub ∞}[UO{sub 5}] and by one phosphorus atom in a tetrahedral environment PO{sub 4}. The two last entities {sup 1}{sub ∞}[UO{sub 5}] and PO{sub 4} are linked by sharing corners to form a three-dimensional structure presenting different types of channels occupied by Cs{sup +} alkaline cations. Their mobility within the tunnels were studied between 280 and 800 °C and compared with other tunneled uranyl minerals. The infrared spectrum shows a good agreement with the values inferred from the single crystal structure analysis of uranyl phosphate compound. - Graphical abstract: Arrhenius plot of the electrical conductivity of tunneled compounds Cs{sub 3}U{sub 2}PO{sub 10} and CsU{sub 2}Nb{sub 2}O{sub 11.5}. Highlights: ► The reaction of (UO{sub 2}){sub 3}(PO{sub 4}){sub 2}(H{sub 2}O){sub 4} in excess of molten CsI leads to single-crystals of new tunneled compound Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}. ► Ionic conductivity measurements and crystal structure analysis indicate a strong connection of the Cs{sup +} cations to the tunnels. ► A low symmetry in Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2} is the cause of IR activation and splitting of the bands in the IR spectrum.« less

Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

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

Pražnikar, Jure; University of Primorska,; Turk, Dušan, E-mail: dusan.turk@ijs.si

2014-12-01

The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. Theymore » utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.« less

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.

Temperature compensation effects of TiO2 on Ca[(Li1/3Nb2/3)0.8Sn0.2]O3-δ microwave dielectric ceramic

NASA Astrophysics Data System (ADS)

Hu, Mingzhe; Wei, Huanghe; Xiao, Lihua; Zhang, Kesheng; Hao, Yongde

2017-10-01

The crystal structure and dielectric properties of TiO2-modified Ca[(Li1/3Nb2/3)0.8Sn0.2]O3-δ microwave ceramics are investigated in the present paper. The crystal structure is probed by XRD patterns and their Rietveld refinement, results show that a single perovskite phase is formed in TiO2-modified Ca[(Li1/3Nb2/3)0.8Sn0.2]O3-δ ceramics with the crystal structure belonging to the orthorhombic Pbnm 62 space group. Raman spectra results indicate that the B-site order-disorder structure transition is a key point to the dielectric loss of TiO2-modified Ca[(Li1/3Nb2/3)0.8Sn0.2]O3-δ ceramics at microwave frequencies. After properly modified by TiO2, the large negative temperature coefficient of Ca[(Li1/3Nb2/3)0.8Sn0.2]O3-δ ceramic can be compensated and the optimal microwave dielectric properties can reach 𝜀r = 25.66, Qf = 18,894 GHz and TCF = -6.3 ppm/∘C when sintered at 1170∘C for 2.5 h, which manifests itself for potential use in microwave dielectric devices for modern wireless communication.

High-resolution crystal structure of Streptococcus pyogenes β-NAD⁺ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface.

PubMed

Yoon, Ji Young; An, Doo Ri; Yoon, Hye Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

2013-11-01

One of the virulence factors produced by Streptococcus pyogenes is β-NAD(+) glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38-451) and the full-length IFS (residues 1-161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPNct-IFS complex, which consists of the SPN C-terminal domain (SPNct; residues 193-451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPNct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution.

PubMed

Larson, Steven B; Day, John S; Nguyen, Chieugiang; Cudney, Robert; McPherson, Alexander

2010-02-01

Bovine pancreatic ribonuclease A (RNase A) was crystallized from a mixture of small molecules containing basic fuchsin, tobramycin and uridine 5'-monophosphate (U5P). Solution of the crystal structure revealed that the enzyme was selectively bound to U5P, with the pyrimidine ring of U5P residing in the pyrimidine-binding site at Thr45. The structure was refined to an R factor of 0.197 and an R(free) of 0.253.

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

PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

PubMed

Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

2008-11-01

The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.

Electronic structure of lead pyrophosphate

NASA Astrophysics Data System (ADS)

Suewattana, Malliga; Singh, David

2007-03-01

Lead Pyrophosphate Pb2P2O7 is of interest for potential radiation detection applications and use in long term waste storage. It forms in triclinic P1 crystals and can also be grown as glasses. We performed electronic structure calculations using the crystal structure which determined by Mullica et. al (J. Solid State Chem (1986)) using x-ray diffraction and found large forces on atoms suggesting that the refined atomic positions were not fully correct. Here we report first principles structure relaxation and a revised crystal structure for this compound. We analyze the resulting structure using pair distribution functions and discuss the implications for the electronic properties. This work was supported by DOE NA22 and the Office of Naval Research.

Overview of refinement procedures within REFMAC5: utilizing data from different sources.

PubMed

Kovalevskiy, Oleg; Nicholls, Robert A; Long, Fei; Carlon, Azzurra; Murshudov, Garib N

2018-03-01

Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.

Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Popov, V. O.

2017-11-01

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

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.

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.

Crystal Structure Analysis of Electromagnetic Wave Absorber Material BaFe12-xTix/2Znx/2O19Based

NASA Astrophysics Data System (ADS)

Delina, M.; Nenni, N.; Adi, W. A.

2018-04-01

The optimization of BaFe12-xTix/2Znx/2O19 (x=2.2; 2.4; 2.6; 2.8)single phase composition have been performed. The materials were synthesized by solid state reaction method through mechanical milling technique.The materials were made from the mixture of oxide materials, which are BaCO3, Fe2O3, TiO2 and ZnO. The mixture was milled for five hours using a High Energy Milling (HEM), was dried at 100°C in the Oven and then was sintered at 1000°C for five hours in the Furnace. The phase identification of BaFe12-xTix/2Znx/2O19 (x=2.2; 2.4; 2.6; 2.8) were carried out by using a Match Program while the crystal structure analysis were investigated by using a General Structure Analysis System (GSAS) program. The refinement results of x-ray diffraction pattern showed that the sample of x ≤ 2.4 have a BaFe12O19 single phase while the sample of x> 2.4 have two phases, which are BaFe12O19 and ZnFe2O4 phases. The surface morphology of sample and the element of sample were identified through an analysis of Scanning Electron Microscope (SEM) and Energy Dispersive Spectroscopy (EDS) data.

Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.

PubMed

Yarbrough, D; Wachter, R M; Kallio, K; Matz, M V; Remington, S J

2001-01-16

The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P2(1) and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low ( approximately 23%) amino acid sequence homology. The monomer consists of an 11-stranded beta barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a approximately 27 x 34-A rectangular array in two approximately antiparallel pairs. The geometry at the alpha carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp(2) hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90 degrees out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.

Diffraction-geometry refinement in the DIALS framework

DOE PAGES

Waterman, David G.; Winter, Graeme; Gildea, Richard J.; ...

2016-03-30

Rapid data collection and modern computing resources provide the opportunity to revisit the task of optimizing the model of diffraction geometry prior to integration. A comprehensive description is given of new software that builds upon established methods by performing a single global refinement procedure, utilizing a smoothly varying model of the crystal lattice where appropriate. This global refinement technique extends to multiple data sets, providing useful constraints to handle the problem of correlated parameters, particularly for small wedges of data. Examples of advanced uses of the software are given and the design is explained in detail, with particular emphasis onmore » the flexibility and extensibility it entails.« less

The crystal structures of Ni{sub 3+x}Sn{sub 4}Zn and Ni{sub 6+x}Sn{sub 8}Zn and their structural relations to Ni{sub 3+x}Sn{sub 4}, NiSn and Ni{sub 5−δ}ZnSn{sub 4}

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

Schmetterer, Clemens, E-mail: clemens.schmetterer@univie.ac.at; Effenberger, Herta Silvia; Rajamohan, Divakar

2016-06-15

The crystal structures of two new compounds were determined from single-crystal X-ray diffraction measurements: Ni{sub 3+x}Sn{sub 4}Zn, (x~1.35, a=7.110(2) Å, b=4.123(1) Å, c=10.346(3) Å, β=90.23(2)°, space group I2/m, Z=2. R1=0.025, wR2=0.059 for 748 unique reflections, 35 variable parameters) and Ni{sub 6+x}Sn{sub 8}Zn, x~1.35 (a=12.379(3) Å, b=4.095(1) Å, c=12.155(3) Å, β=116.25(3)°, space group C2/m, Z=2. R1=0.026, wR2=0.052 for 1346 unique reflections, 60 variable parameters). In addition, a structural refinement was performed for Ni{sub 3+x}Sn{sub 4}, x~0.13 (a=12.264(3) Å, b=4.066(1) Å, c=5.223(2) Å, β=104.85(3)°, space group C2/m, Z=2. R1=0.019, wR2=0.046 for 617 unique reflections, 29 variable parameters). The three compounds show pronouncedmore » similarities among each other as well as to the crystal structures of surrounding binary Ni–Sn and ternary Ni–Sn–Zn compounds. In particular, the two new compounds form a homologous series with Ni{sub 3+x}Sn{sub 4}, x~0.13. They contain “Ni{sub 4}Sn{sub 4}” and “Ni{sub 2}Sn{sub 4}” building blocks which by different interconnection build up the distinct structures. Topological relations with NiSn and Ni{sub 5−δ}Sn{sub 4}Zn, δ~0.25 are evident. - Graphical abstract: Projection of the structure of Ni{sub 6+x}ZnSn{sub 8}, x~1.35 and constituent building blocks. Display Omitted - Highlights: • The crystal structures of Ni{sub 6+x}Sn{sub 8}Zn and Ni{sub 3+x}Sn{sub 4}Zn were determined using single crystal XRD. • Topological relations to Ni–Sn and Ni–Sn–Zn compounds were established and discussed. • Common structural units were identified and their interconnection patterns described.« less

Synthesis, structure, and magnetic properties of LaTMg and CeTMg (T = Pd, Pt, Au)

NASA Astrophysics Data System (ADS)

Gibson, B. J.; Das, A.; Kremer, R. K.; Hoffmann, R.-D.; Pöttgen, R.

2002-05-01

The title compounds were prepared from the elements by reactions in sealed tantalum tubes in a water-cooled sample chamber of a high-frequency furnace. They crystallize with the ZrNiAl-type structure, space group P bar 6 2m. The structures of the cerium compounds were refined from single-crystal x-ray diffraction data: a = 767.3(1) pm, c = 410.37(4) pm, wR2 = 0.0324, 521 F2-values for CePdMg; a = 755.02(7) pm, c = 413.82(4) pm, wR2 = 0.0393, 514 F2-values for CePtMg; and a = 774.1(3) pm, c = 421.6(1) pm, wR2 = 0.0355, 395 F2-values for CeAuMg, with 14 variables for each refinement. The palladium compound shows a small homogeneity range: CePd1+xMg1-x. The structures contain two crystallographically different transition metal sites T1 and T2 which are located in tri-capped trigonal prisms: [T1 Mg6Ce3] and [T2 Ce6Mg3]. Magnetic susceptibility and heat capacity measurements reveal long-range magnetic ordering at 2.1(2) K for CePdMg, 3.6(2) K for CePtMg, and 2.0(2) K for CeAuMg. Curie-Weiss behaviour at higher temperatures shows that the cerium ions are in the 3+ oxidation state. The isotypic LaTMg compounds are Pauli paramagnetic down to lowest temperatures (T = 0.3 K). All the compounds, RETMg (RE = La, Ce; T = Pd, Pt, Au) show metallic behaviour.

Observation of high-spin mixed oxidation state of cobalt in ceramic Co3TeO6

NASA Astrophysics Data System (ADS)

Singh, Harishchandra; Ghosh, Haranath; Chandrasekhar Rao, T. V.; Sinha, A. K.; Rajput, Parasmani

2014-12-01

We report coexistence of high spin Co3+ and Co2+ in ceramic Co3TeO6 using X-ray Absorption Near Edge Structure (XANES), DC magnetization, and first principles ab-initio calculations. The main absorption line of cobalt Co K-edge XANES spectra, along with a linear combination fit, led us to estimate relative concentration of Co2+ and Co3+as 60:40. The pre edge feature of XANES spectrum shows crystal field splitting of ˜1.26 eV between eg and t2g states, suggesting a mixture of high spin states of both Co2+ and Co3+. Temperature dependent high field DC magnetization measurements reveal dominant antiferromagnetic order with two Neel temperatures (TN1 ˜ 29 K and TN2 ˜ 18 K), consistent with single crystal study. A larger effective magnetic moment is observed in comparison to that reported for single crystal (which contains only Co2+), supports our inference that Co3+ exists in high spin state. Furthermore, we show that both Co2+ and Co3+ being in high spin states constitute a favorable ground state through first principles ab-initio calculations, where Rietveld refined synchrotron X-ray diffraction data are used as input.

Coexistence of ferromagnetism and spin glass freezing in the site-disordered kagome ferrite SrSn2Fe4O11

NASA Astrophysics Data System (ADS)

Shlyk, Larysa; Strobel, S.; Farmer, B.; De Long, L. E.; Niewa, R.

2018-05-01

Single-crystal x-ray diffraction refinements indicate SrSn2Fe4O11 crystallizes in the hexagonal R-type ferrite structure with non-centrosymmetric space group P63mc and lattice parameters a = 5.9541(2) Å, c = 13.5761(5) Å, Z = 2 (R(F) = 0.034). Octahedrally coordinated sites are randomly occupied by Sn and Fe; whereas tetrahedrally coordinated sites are exclusively occupied by Fe, whose displacement from ideal trigonal-bipyramidal coordination causes the loss of inversion symmetry. DC magnetization data indicate SrSn2Fe4O11 single crystals undergo ferro- or ferri-magnetic order below a transition temperature TC = 630 K with very low coercive fields Hc ⊥ = 0.27 Oe and Hc// = 1.5 Oe at 300 K, for applied fields perpendicular and parallel to the c-axis, respectively. The value for TC is exceptionally high, and the coercive fields exceptionally low, among the known R-type ferrites. Enhanced coercivity and thermomagnetic hysteresis suggest the onset of short-range, spin glass order occurs below Tf = 35 K. Optical measurements indicate a band gap of 0.8 eV, consistent with wide-gap semiconducting behavior and a previously established empirical correlation between the semiconducting gap and TC for R-type ferrites based upon Ru.

Three-dimensional structure of Erwinia carotovora L-asparaginase

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

Kislitsyn, Yu. A.; Kravchenko, O. V.; Nikonov, S. V.

2006-10-15

Three-dimensional structure of Erwinia carotovora L-asparaginase, which has antitumor activity and is used for the treatment of acute lymphoblastic leukemia, was solved at 3 A resolution and refined to R{sub cryst} = 20% and R{sub free} = 28%. Crystals of recombinant Erwinia carotovora L-asparaginase were grown by the hanging-drop vapor-diffusion method from protein solutions in a HEPES buffer (pH 6.5) and PEG MME 5000 solutions in a cacodylate buffer (pH 6.5) as the precipitant. Three-dimensional X-ray diffraction data were collected up to 3 A resolution from one crystal at room temperature. The structure was solved by the molecular replacement methodmore » using the coordinates of Erwinia chrysanthemi L-asparaginase as the starting model. The coordinates refined with the use of the CNS program package were deposited in the Protein Data Bank (PDB code 1ZCF)« less

The High Resolution Powder Diffraction Beam Line at ESRF.

PubMed

Fitch, A N

2004-01-01

The optical design and performance of the high-resolution powder diffraction beam line BM16 at ESRF are discussed and illustrated. Some recent studies carried out on BM16 are described, including crystal structure solution and refinement, anomalous scattering, in situ measurements, residual strain in engineering components, investigation of microstructure, and grazing-incidence diffraction from surface layers. The beam line is built on a bending magnet, and operates in the energy range from 5 keV to 40 keV. After the move to an undulator source in 2002, it will benefit from an extented energy range up to 60 keV and increased flux and resolution. It is anticipated that enhancements to the data quality will be achieved, leading to the solution of larger crystal structures, and improvements in the accuracy of refined structures. The systematic exploitation of anisotropic thermal expansion will help reduce the effects of peak overlap in the analysis of powder diffraction data.

Application of δ recycling to electron automated diffraction tomography data from inorganic crystalline nanovolumes.

PubMed

Rius, Jordi; Mugnaioli, Enrico; Vallcorba, Oriol; Kolb, Ute

2013-07-01

δ Recycling is a simple procedure for directly extracting phase information from Patterson-type functions [Rius (2012). Acta Cryst. A68, 399-400]. This new phasing method has a clear theoretical basis and was developed with ideal single-crystal X-ray diffraction data. On the other hand, introduction of the automated diffraction tomography (ADT) technique has represented a significant advance in electron diffraction data collection [Kolb et al. (2007). Ultramicroscopy, 107, 507-513]. When combined with precession electron diffraction, it delivers quasi-kinematical intensity data even for complex inorganic compounds, so that single-crystal diffraction data of nanometric volumes are now available for structure determination by direct methods. To check the tolerance of δ recycling to missing data-collection corrections and to deviations from kinematical behaviour of ADT intensities, δ recycling has been applied to differently shaped nanocrystals of various inorganic materials. The results confirm that it can phase ADT data very efficiently. In some cases even more complete structure models than those derived from conventional direct methods and least-squares refinement have been found. During this study it has been demonstrated that the Wilson-plot scaling procedure is largely insensitive to sample thickness variations and missing absorption corrections affecting electron ADT intensities.

Crystal structures of the new ternary stannides La3Mg4-xSn2+x and LaMg3-xSn2

NASA Astrophysics Data System (ADS)

Solokha, P.; De Negri, S.; Minetti, R.; Proserpio, D. M.; Saccone, A.

2016-01-01

Synthesis and structural characterization of the two new lanthanum-magnesium-stannides La3Mg4-xSn2+x (0.12≤x≤0.40) and LaMg3-xSn2 (0.33≤x≤0.78) are reported. The crystal structures of these intermetallics were determined by single crystal X-ray diffraction analysis and confirmed by Rietveld refinement of powder X-ray diffraction patterns of the corresponding samples. The La3Mg4-xSn2+x phase crystallizes in the hexagonal Zr3Cu4Si2 structure type (P6bar2m, hP9, Z=3, x=0.12(1), a=7.7974(7), c=4.8384(4) Å), which represents an ordered derivative of the hP9-ZrNiAl prototype, ubiquitous among equiatomic intermetallics. The LaMg3-xSn2 phase is the second representative of the trigonal LaMg3-xGe2 type, which is a superstructure of the LaLi3Sb2 structure type (P3bar1c, hP34-0.12, Z=6, x=0.35(1), a=8.3222(9), c=14.9546(16) Å). The scheme describing the symmetry reduction/coloring with respect to the parent type is reported here with the purpose to discuss the LaMg3-xSn2 off-stoichiometry from the geometrical point of view. Structural relationships between the La-Mg-Sn ternary phases, including the already known equiatomic LaMgSn compound (oP12-TiNiSi), are presented in the framework of the AlB2-related compounds family and discussed with the aid of group-subgroup relations in the Bärnighausen formalism.

A dynamic structural model of expanded RNA CAG repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

PubMed Central

Yildirim, Ilyas; Park, Hajeung; Disney, Matthew D.; Schatz, George C.

2013-01-01

One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded r(CAG) repeats can cause Huntington’s and other disease through translation of toxic proteins. Herein, crystal structure of r[5ʹUUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that show both anti-anti and syn-anti orientations for 1×1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using Amber force field in explicit solvent were run for over 500 ns on model systems r(5ʹGCGCAGCGC)2 (MS1) and r(5ʹCCGCAGCGG)2 (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti↔anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, over 800 ns explicit solvent MD simulation was run on r[5ʹGGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1×1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and develop small molecules that target RNA dynamic ensembles. PMID:23441937

Magnetic spherical cores partly coated with periodic mesoporous organosilica single crystals.

PubMed

Li, Jing; Wei, Yong; Li, Wei; Deng, Yonghui; Zhao, Dongyuan

2012-03-07

Core-shell structured materials are of special significance in various applications. Until now, most reported core-shell structures have polycrystalline or amorphous coatings as their shell layers, with popular morphologies of microspheres or quasi-spheres. However, the single crystals, either mesoscale or atomic ones, are still rarely reported as shell layers. If single crystals can be coated on core materials, it would result in a range of new type core-shell structures with various morphologies, and probably more potential applications. In this work, we demonstrate that periodic mesoporous organosilica (PMO) single crystals can partly grow on magnetic microspheres to form incomplete Fe(3)O(4)@nSiO(2)@PMO core-shell materials in aqueous solution, which indeed is the first illustration that mesoporous single-crystal materials can be used as shell layers for preparation of core-shell materials. The achieved materials have advantages of high specific surface areas, good magnetic responses, embedded functional groups and cubic mesopore channels, which might provide them with various application conveniences. We suppose the partial growth is largely decided by the competition between growing tendency of single crystals and the resistances to this tendency. In principle, other single crystals, including a range of atomic single crystals, such as zeolites, are able to be developed into such core-shell structures.

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

Crystal structure, thermal expansivity, and elasticity of OH-chondrodite: Trends among dense hydrous magnesium silicates

DOE PAGES

Ye, Yu; Jacobsen, Steven D.; Mao, Zhu; ...

2015-04-01

Here, we report the structure and thermoelastic properties of OH-chondrodite. The sample was synthesized at 12 GPa and 1523 K, coexisting with hydroxyl-clinohumite and hydrous olivine. The Fe content Fe/(Fe+Mg) is 1.1 mol%, and the monoclinic unit-cell parameters are: a = 4.7459(2) Å, b = 10.3480(7) Å, c = 7.9002(6) Å, α = 108.702(7)°, and V = 367.50(4) Å3. At ambient conditions the crystal structure was refined in space group P 21/b from 1915 unique reflection intensities measured by single-crystal x-ray diffraction. The volume thermal expansion coefficient was measured between 150 and 800 K, resulting in α V = 2.8(5)×10more » -9(K -2) × T + 40.9(7) × 10 -6(K -1) – 0.81(3)(K)/T 2, with an average value of 38.0(9)×10 -6 K -1. Brillouin spectroscopy was used to measure a set of acoustic velocities from which all thirteen components (C ij) of the elastic tensor were determined. The Voigt-Reuss-Hill average of the moduli yield for the adiabatic bulk modulus, K S0 = 117.9(12) GPa, and for shear modulus, G 0 = 70.1(5) GPa. The Reuss bound on the isothermal bulk modulus (K T0) is 114.2(14) GPa. From the measured thermodynamic properties, the Grüneisen parameter (γ) is calculated to be 1.66(4). Fitting previous static compression data using our independently measured bulk modulus (isothermal Reuss bound) as a fixed parameter, we refined the first pressure derivative of the bulk modulus, K T’ = 5.5(1). Systematic trends between H 2O content and physical properties are evaluated among dense hydrous magnesium silicate (DHMS) phases along the forsterite-brucite join.« less

Structure-Guided, Single-Point Modifications in the Phosphinic Dipeptide Structure Yield Highly Potent and Selective Inhibitors of Neutral Aminopeptidases

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

Vassiliou, Stamatia; Węglarz-Tomczak, Ewelina; Berlicki, Łukasz

Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor–enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extendedmore » structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH 2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. In conclusion, another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π–π stacking interaction between a pyridine ring and Tyr372.« less

Structure-Guided, Single-Point Modifications in the Phosphinic Dipeptide Structure Yield Highly Potent and Selective Inhibitors of Neutral Aminopeptidases

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

Vassiliou, Stamatia; Węglarz-Tomczak, Ewelina; Berlicki, Łukasz

2014-10-09

Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor-enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extendedmore » structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. Another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π-π stacking interaction between a pyridine ring and Tyr372.« less

Structure-Guided, Single-Point Modifications in the Phosphinic Dipeptide Structure Yield Highly Potent and Selective Inhibitors of Neutral Aminopeptidases

DOE PAGES

Vassiliou, Stamatia; Węglarz-Tomczak, Ewelina; Berlicki, Łukasz; ...

2014-10-09

Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor–enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extendedmore » structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH 2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. In conclusion, another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π–π stacking interaction between a pyridine ring and Tyr372.« less

Intrinsic Josephson junctions in mesas and ultrathin BSCCO single crystals: Ultimate control of shape and dimensions

NASA Astrophysics Data System (ADS)

Yurgens, A.; You, L. X.; Torstensson, M.; Winkler, D.

2007-09-01

We describe experiments which are only possible through an ultimate control of sample shape and dimensions down to nanometer scale whereby transport measurements can be done in various restricted geometries. We use photolithography patterning together with a flip-chip technique to isolate very thin (d ∼ 100 nm) pieces of Bi2Sr2CaCu2O8+δ (BSCCO) single crystals. Ar-ion milling allows us to further thin these crystals down to a few nanometers in a controlled way. With decreasing thickness below two to three unit cells, the superconducting transition temperature gradually decreases to zero and the in-plane resistivity increases to large values indicating the existence of a superconductor-insulator transition in these ultrathin single crystals. In a refined technique, a precise control of the etching depth from both sides of the crystal makes it possible to form stacks of intrinsic Josephson junctions (IJJs) inside the ultrathin single crystals. The stacks can be tailor-made to any microscopic height (0-9 nm < d), i.e. enclosing a specific number of IJJs (0-6). In certain geometries, by feeding current into the topmost Cu2O4-layer of a mesa on the surface of a BSCCO single crystal, we measured the critical value of this current by detecting a sharp upturn or break in the current-voltage characteristics. From this, we estimate the sheet critical current density of a single Cu2O4 plane to be ∼0.3-0.7 A/cm at 4.5 K, corresponding to a bulk current density of ∼2-5 MA/cm2. These values are among the largest ever reported for BSCCO single crystals, thin-films and tapes.

Crystal growth, crystal structure of new polymorphic modification, β-Bi 2B 8O 15 and thermal expansion of α-Bi 2B 8O 15

NASA Astrophysics Data System (ADS)

Bubnova, R. S.; Alexandrova, J. V.; Krivovichev, S. V.; Filatov, S. K.; Egorysheva, A. V.

2010-02-01

Single crystals of α- and β-polymorphs of Bi 2B 8O 15 were grown by Czochralski method from a charge of the stoichiometric composition. The crystal structure of β-Bi 2B 8O 15 was solved by direct methods from a twinned crystal and refined to R1=0.081 (w R=0.198) on the basis of 1584 unique observed reflections ( I>2 σ( I)). The compound is triclinic, space group P1¯, a=4.3159(8), b=6. 4604(12), c=22.485(4) Å, α=87.094(15)°, β=86.538(15)°, γ=74.420(14)°, V=602.40(19) Å 3, Z=2. The B-O layered anion of β-Bi 2B 8O 15 is topologically identical to the anion of α-Bi 2B 8O 15 but the orientation of neighboring layers is different. Thermal expansion of α-Bi 2B 8O 15 has been investigated by X-ray powder diffraction in air in temperature range from 20 to 700 °C. It is strongly anisotropic, which can be explained by the hinge mechanism applied to chains of Bi-O polyhedra. While the anisotropy of thermal expansion is rather high, the volume thermal expansion coefficient α V=40×10 6 °C -1 for α-Bi 2B 8O 15 is close to those of other bismuth borates.

Fe-Al alloy single-crystal thin film preparation for basic magnetic measurements

NASA Astrophysics Data System (ADS)

Abe, Tatsuya; Kawai, Tetsuroh; Futamoto, Masaaki; Ohtake, Mitsuru; Inaba, Nobuyuki

2018-04-01

Fe100-xAlx (x = 0, 4, 10, 20, 30 at. %) alloy films of 40 nm thickness are prepared on MgO(001) single-crystal substrates by varying substrate temperature from room temperature to 600 °C. Single-crystal films of (001) orientation with bcc-based disordered A2 structure are obtained for the Al content range of x = 0 - 20 at. %. An ordered phase of DO3 structure is observed in Fe70Al30 films prepared at temperatures higher than 200 °C, whereas (001) oriented single-crystal films of A2 structure are obtained when prepared at room temperature. The film surface profile does not depend much on the film composition, while the surface roughness increases with increasing substrate temperature. Island-like crystals are observed for films prepared at 600°C for all compositions. Difference in lattice spacing measured parallel and perpendicular to the substrate is noted for the single-crystal thin films and it increases with increasing Al content. The lattice strain in single-crystal film is caused possibly to accommodate the lattice mismatch with the MgO substrate. The (001)-oriented single-crystal films with A2 structure show four-fold symmetries in in-plane magnetic anisotropy with the easy magnetization axis A2[100] and the hard magnetization axis A2[110], whereas the films with DO3 ordered structure show almost isotropic magnetic properties.

Expression, purification, crystallization and preliminary X-ray crystallographic studies of Deinococcus radiodurans thioredoxin reductase

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

Obiero, Josiah; Bonderoff, Sara A.; Goertzen, Meghan M.

2006-08-01

Recombinant D. radiodurans TrxR with a His tag at the N-terminus was expressed in Escherichia coli and purified by metal-affinity chromatography. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of 35% PEG 4000, 0.2 M ammonium acetate and citric acid buffer pH 5.1 at 293 K. Deinococcus radiodurans, a Gram-positive bacterium capable of withstanding extreme ionizing radiation, contains two thioredoxins (Trx and Trx1) and a single thioredoxin reductase (TrxR) as part of its response to oxidative stress. Thioredoxin reductase is a member of the family of pyridine nucleotide-disulfide oxidoreductase flavoenzymes. Recombinant D. radiodurans TrxR with amore » His tag at the N-terminus was expressed in Escherichia coli and purified by metal-affinity chromatography. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of 35% PEG 4000, 0.2 M ammonium acetate and citric acid buffer pH 5.1 at 293 K. X-ray diffraction data were collected on a cryocooled crystal to a resolution of 1.9 Å using a synchrotron-radiation source. The space group was determined to be P3{sub 2}21, with unit-cell parameters a = b = 84.33, c = 159.88 Å. The structure of the enzyme has been solved by molecular-replacement methods and structure refinement is in progress.« less

Crystal structure of the formal 20 electron zirconocene penta-fulvene complex Cp2Zr(η5,η1-adamantyl-idene-penta-fulvene):toluene:n-hexane = 1:0.125:0.125.

PubMed

Fischer, Malte; Schmidtmann, Marc; Beckhaus, Rüdiger

2017-12-01

The crystal structure of a solvated zirconocene penta-fulvene complex with a bulky adamantyl-idene substitution pattern, namely (η 5 ,η 1 -adamantyl-idene-penta-fulvene)bis-(η 5 -cyclo-penta-dien-yl)zirconium(IV)-toluene- n -hexane (8/1/1), [Zr(C 15 H 18 )(C 5 H 5 ) 2 ]·0.125C 7 H 8 ·0.125C 6 H 14 , is reported. Reducing zirconocene dichloride with magnesium results in the formation of a low-valent zirconocene reagent that reacts readily with adamantyl-idene-penta-fulvene to give the aforementioned complex. Single crystal X-ray diffraction proves the dianion-like η 5 :η 1 binding mode of the fulvene ligand to the central Zr IV atom. The asymmetric unit contains four independent mol-ecules of [η 5 :η 1 -adamantyl-idene-penta-fulvene]bis-[(η 5 )-cyclo-penta-dien-yl]zirconium(IV), together with half a mol-ecule of toluene disordered with half a mol-ecule of n -hexane (the solvent mol-ecules have no direct influence on the complex). In each of the four complex mol-ecules, the central Zr IV atom has a distorted tetra-hedral coordination environment. The measured crystal consisted of two domains with a refined ratio of 0.77:0.23.

Performance Comparison of Al-Ti Master Alloys with Different Microstructures in Grain Refinement of Commercial Purity Aluminum.

PubMed

Ding, Wanwu; Xia, Tiandong; Zhao, Wenjun

2014-05-07

Three types of Al-5Ti master alloys were synthesized by a method of thermal explosion reaction in pure molten aluminum. Performance comparison of Al-5Ti master alloy in grain refinement of commercial purity Al with different additions (0.6%, 1.0%, 1.6%, 2.0%, and 3.0%) and holding time (10, 30, 60 and 120 min) were investigated. The results show that Al-5Ti master alloy with blocky TiAl₃ particles clearly has better refining efficiency than the master alloy with mixed TiAl₃ particles and the master alloy with needle-like TiAl₃ particles. The structures of master alloys, differing by sizes, morphologies and quantities of TiAl₃ crystals, were found to affect the pattern of the grain refining properties with the holding time. The grain refinement effect was revealed to reduce markedly for master alloys with needle-like TiAl₃ crystals and to show the further significant improvement at a longer holding time for the master alloy containing both larger needle-like and blocky TiAl₃ particles. For the master alloy with finer blocky particles, the grain refining effect did not obviously decrease during the whole studied range of the holding time.

Ferroelectric properties of oxalate and phenanthroline based 1-D single chain molecular magnet [{FeII(Δ)FeII(Λ)}0.5{CrII(Δ)CrII(Λ)}0.5(ox)2(phen)2

NASA Astrophysics Data System (ADS)

Bhatt, Pramod; Mukadam, M. D.; Mandal, B. P.; Yusuf, S. M.

2018-04-01

The one-dimensional (1-D) single chain molecular magnet [{FeII(Δ)FeII(Λ)}0.5{CrII(Δ)CrII(Λ)}0.5(ox)2(phen)2] is hydrothermally synthesized using oxalate (ox) and phenanthroline (phen) ligands with transition metal ions (Fe and Cr). The compound is characterized using x-ray diffraction, dc magnetization measurements and P-E ferroelectric loop measurements. The diffraction analysis using Rietveld refinement confirms a single phase formation of the compound in monoclinic structure with space group of P21. The compound crystallizes in 1-D chain like structure containing two different crystallographic sites of metal ions (Δ- and Λ-), which are bridged by the ox ligand and Phen ligand. These two metals site are different in bond length and bond angles results lattice distortions. The lattice distortion induces ferroelectric behavior in the compound which is discussed in terms of lattice distortion induced dipole moments.

Polarizable atomic multipole X-ray refinement: application to peptide crystals

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

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

[La(UO{sub 2})V{sub 2}O{sub 7}][(UO{sub 2})(VO{sub 4})] the first lanthanum uranyl-vanadate with structure built from two types of sheets based upon the uranophane anion-topology

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

Mer, A.; Obbade, S.; Rivenet, M.

2012-01-15

The new lanthanum uranyl vanadate divanadate, [La(UO{sub 2})V{sub 2}O{sub 7}][(UO{sub 2})(VO{sub 4})] was obtained by reaction at 800 Degree-Sign C between lanthanum chloride, uranium oxide (U{sub 3}O{sub 8}) and vanadium oxide (V{sub 2}O{sub 5}) and the structure was determined from single-crystal X-ray diffraction data. This compound crystallizes in the orthorhombic system with space group P2{sub 1}2{sub 1}2{sub 1} and unit-cell parameters a=6.9470(2) A, b=7.0934(2) A, c=25.7464(6) A, V=1268.73(5) A{sup 3}, Z=4. A full matrix least-squares refinement yielded R{sub 1}=0.0219 for 5493 independent reflections. The crystal structure is characterized by the stacking of uranophane-type sheets {sup 2}{sub {infinity}}[(UO{sub 2})(VO{sub 4})]{sup -}more » and double layers {sup 2}{sub {infinity}}[La(UO{sub 2})(V{sub 2}O{sub 7})]{sup +} connected through La-O bonds involving the uranyl oxygen of the uranyl-vanadate sheets. The double layers result from the connection of two {sup 2}{sub {infinity}}[La(UO{sub 2})(VO{sub 4}){sub 2}]{sup -} sheets derived from the uranophane anion-topology by replacing half of the uranyl ions by lanthanum atoms and connected through the formation of divanadate entities. - Graphical abstract: A view of the three-dimensional structure of [La(UO{sub 2})V{sub 2}O{sub 7}][(UO{sub 2})(VO{sub 4})]. Highlights: Black-Right-Pointing-Pointer New lanthanum uranyl vanadate divanadate has been synthesized. Black-Right-Pointing-Pointer Structure was determined from single-crystal X-ray diffraction data. Black-Right-Pointing-Pointer Structure is characterized by uranophane-type sheets and double layers {sup 2}{sub {infinity}}[La(UO{sub 2})(V{sub 2}O{sub 7})]{sup +}.« less

Transition metals in the transition zone: Crystal chemistry of minor element substitution in wadsleyite

DOE PAGES

Zhang, Li; Smyth, Joseph R.; Allaz, Julien; ...

2016-10-01

As the most abundant solid phase at depths of 410 to 525 km, wadsleyite constitutes a large geochemical reservoir in the Earth. In order to better understand the implications of minor element substitution and cation ordering in wadsleyite, we have synthesized wadsleyites coexisting with pyroxenes with about 3 wt% of either TiO 2, Cr 2O 3, V 2O 3, CoO, NiO, or ZnO under hydrous conditions in separate experiments at 1300 °C and 15 GPa. We have refined the crystal structures of these wadsleyites by single-crystal X-ray diffraction, analyzed the compositions by electron microprobe, and estimated M3 vacancy concentration frommore » b/a cell-parameter ratios. According to the crystal structure refinements, trivalent cations Fe 3+, Cr 3+ and V 3+, show a strong preference for M3 over M1 and M2 and significant substitution up to 2.7 % (atomic percent) at the tetrahedral site (T site). Divalent cations, Ni 2+, Co 2+, and Zn 2+ show site preferences similar to those of Fe2+ with M1≈ M3 > M2 > T. Transition metal site preferences appear to correlate with crystal field stabilization energies (CFSE) and are inconsistent with cation radius effects. The avoidance of Ni 2+, Co 2+ and Fe 2+ for the M2 site in both wadsleyite and olivine can be influenced by CFSE, which has a positive correlation with site preferences at octahedral sites, indicating that avoidance of the lower-symmetry M2 site is stronger for cations having lower (greater absolute value) CFSE. Ti 4+ substitutes primarily into the M3 octahedron, rather than M1, M2, or T sites. Electron microprobe analysis reveals that Ti 4+, Cr 3+, and V 3+ have greater solubility in wadsleyite than in olivine. Furthermore these transition metal cations may be enriched in a melt or an accessory phase if hydrous melting occurs on upward convection across the wadsleyite-olivine boundary and may be useful as indicators of high pressure origin.« less

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.

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.

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.

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

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

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

DOE PAGES

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

2015-01-01

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Drastic effect of the Mn-substitution in the strongly correlated semiconductor FeSb2.

NASA Astrophysics Data System (ADS)

Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

2017-06-01

We report the effects of Mn substitution, corresponding to hole doping, on the electronic properties of the narrow gap semiconductor, FeSb2, using single crystals of Fe1- x Mn x Sb2 grown by the Sb flux method. The orthorhombic Pnnm structure was confirmed by powder X-ray diffraction (XRD) for the pure and Mn-substituted samples. Their crystal structure parameters were refined using the Rietveld method. The chemical composition was investigated by wavelength-dispersive X-ray spectroscopy (WDX). The solubility limit of Mn in FeSb2 is x max ˜ 0.05 and the lattice constants change monotonically with increasing the actual Mn concentration. A drastic change from semiconducting to metallic electronic transports was found at very low Mn concentration at x ˜ 0.01. Our experimental results and analysis indicate that the substitution of a small amount of Mn changes drastically the electronic state in FeSb2 as well as the Co-substitution does: closing of the narrow gap and emergence of the density of states (DOS) at the Fermi level.

Nanoscale building blocks in a novel lithium arsenotungsten bronze: Synthesis and characterization

DOE PAGES

Zhao, Pei; Mangir Murshed, M.; Huq, Ashfia; ...

2015-02-19

Here we report on a novel compound Li 3AsW 7O 25 obtained by solid-state reaction and characterized by diffraction and spectroscopic methods. The bronze-type compound crystallizes in the orthorhombic space group Pbca with a=724.38(3) pm, b=1008.15(4) pm, c=4906.16(17) pm and Z=8. The structure is built up by chains of WO 6 octahedra interconnected by AsO 4 tetrahedra and WO 6 octahedra forming a polyhedral arrangement as seen in intergrowth tungsten bronzes. The X-ray single crystal structure refinement allows solving the complex arsenotungstate framework. The powder neutron diffraction data analysis locates the lithium atoms. Thermal analysis showed that Li 3AsW 7Omore » 25 is stable up to its melting at 1135(3) K followed by a decomposition at 1182(5) K. Finally, the Kubelka-Munk treatment of the UV-vis spectrum revealed a wide band gap in the range of 2.84-3.40 eV depending on the presumed electron transition type.« less

Crystal structure of methylprednisolone acetate form II, C 24H 32O 6

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

Wheatley, Austin M.; Kaduk, James A.; Gindhart, Amy M.

The crystal structure of methylprednisolone acetate form II, C 24H 32O 6, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Methylprednisolone acetate crystallizes in space groupP2 12 12 1(#19) witha= 8.17608(2),b= 9.67944(3),c= 26.35176(6) Å,V= 2085.474(6) Å 3, andZ= 4. Both hydroxyl groups act as hydrogen bond donors, resulting in a two-dimensional hydrogen bond network in theabplane. C–H…O hydrogen bonds also contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1412.

H-bonding scheme and cation partitioning in axinite: a single-crystal neutron diffraction and Mössbauer spectroscopic study

NASA Astrophysics Data System (ADS)

Gatta, G. Diego; Redhammer, Günther J.; Guastoni, Alessandro; Guastella, Giorgio; Meven, Martin; Pavese, Alessandro

2016-05-01

The crystal chemistry of a ferroaxinite from Colebrook Hill, Rosebery district, Tasmania, Australia, was investigated by electron microprobe analysis in wavelength-dispersive mode, inductively coupled plasma-atomic emission spectroscopy (ICP-AES), 57Fe Mössbauer spectroscopy and single-crystal neutron diffraction at 293 K. The chemical formula obtained on the basis of the ICP-AES data is the following: ^{X1,X2} {{Ca}}_{4.03} Y ( {{{Mn}}_{0.42} {{Mg}}_{0.23} {{Fe}}^{2 + }_{1.39} } )_{Σ 2.04} ^{Z1,Z2} ( {{{Fe}}^{3 + }_{0.15} {{Al}}_{3.55} {{Ti}}_{0.12} } )_{Σ 3.82} ^{T1,T2,T3,T4} ( {{{Ti}}_{0.03} {{Si}}_{7.97} } )_{Σ 8} ^{T5} {{B}}_{1.96} {{O}}_{30} ( {{OH}} )_{2.18} . The 57Fe Mössbauer spectrum shows unambiguously the occurrence of Fe2+ and Fe3+ in octahedral coordination only, with Fe2+/Fe3+ = 9:1. The neutron structure refinement provides a structure model in general agreement with the previous experimental findings: the tetrahedral T1, T2, T3 and T4 sites are fully occupied by Si, whereas the T5 site is fully occupied by B, with no evidence of Si at the T5, or Al or Fe3+ at the T1- T5 sites. The structural and chemical data of this study suggest that the amount of B in ferroaxinite is that expected from the ideal stoichiometry: 2 a.p.f.u. (for 32 O). The atomic distribution among the X1, X2, Y, Z1 and Z2 sites obtained by neutron structure refinement is in good agreement with that based on the ICP-AES data. For the first time, an unambiguous localization of the H site is obtained, which forms a hydroxyl group with the oxygen atom at the O16 site as donor. The H-bonding scheme in axinite structure is now fully described: the O16- H distance (corrected for riding motion effect) is 0.991(1) Å and an asymmetric bifurcated bonding configuration occurs, with O5 and O13 as acceptors [i.e. with O16··· O5 = 3.096(1) Å, H··· O5 = 2.450(1) Å and O16- H··· O5 = 123.9(1)°; O16··· O13 = 2.777(1) Å, H··· O13 = 1.914(1) Å and O16- H··· O13 = 146.9(1)°].

Super-resolution biomolecular crystallography with low-resolution data.

PubMed

Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

2010-04-22

X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X-ray crystallography and cryo-electron microscopy: as optical imaging advances to subnanometre resolution, it can use similar tools.

Cu- and Mn-bearing tourmalines from Brazil and Mozambique: crystal structures, chemistry and correlations

NASA Astrophysics Data System (ADS)

Ertl, Andreas; Giester, Gerald; Schüssler, Ulrich; Brätz, Helene; Okrusch, Martin; Tillmanns, Ekkehart; Bank, Hermann

2013-04-01

Cu- and Mn-bearing tourmalines from Brazil and Mozambique were characterised chemically (EMPA and LA-ICP-MS) and by X-ray single-crystal structure refinement. All these samples are rich in Al, Li and F (fluor-elbaite) and contain significant amounts of CuO (up to ~1.8 wt%) and MnO (up to ~3.5 wt%). Structurally investigated samples show a pronounced positive correlation between the < Y-O> distances and the (Li + Mn2+ + Cu + Fe2+) content (apfu) at this site with R 2 = 0.90. An excellent negative correlation exists between the < Y-O> distances and the Al2O3 content ( R 2 = 0.94). The samples at each locality generally show a strong negative correlation between the X-site vacancies and the (MnO + FeO) content. The Mn content in these tourmalines depends on the availability of Mn, on the formation temperature, as well as on stereochemical constraints. Because of a very weak correlation between MnO and CuO we believe that the Cu content in tourmaline is essentially dependent on the availability of Cu and on stereochemical constraints.

Crystal structures and transition mechanism of VO{sub 2}(A)

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

Oka, Yoshio; Yao, Takeshi; Yamamoto, Naoichi

1998-12-01

Structures of VO{sub 2}(A) have been redetermined by single-crystal diffractometry for low- (LTP) and high-temperature (HTP) phases at 298 and 473 K, respectively. The LTP adopts the tetragonal system P4/ncc with a = 8.4403(9) {angstrom}, c = 7.666(1) {angstrom}, and Z = 16, whereas the HTP adopts the body-centered tetragonal system I4/m with a = 8.476(2) {angstrom}, c = 3.824(2) {angstrom}, and Z = 8. The refinements led to R/R{sub w} = 0.031/0.032 for LTP and 0.012/0.033 for HTP. The structures of both phases consist of edge-sharing VO{sub 6} octahedra and exhibit quite similar oxygen frameworks. Through the transition themore » V{sup 4+}-V{sup 4+} bonding in LTP with a distance of 2.7695(8) {angstrom} is dissociated in HTP to a distance of 3.0794(3) {angstrom}. The transition occurs with cooperative movements of the V atoms, namely, a rotation around the c axis and a shift along the c axis. Strangely, twinning is induced on the LTP to HTP transition but disappears on the reverse transition.« less

Design of high-performance cathode materials with single-phase pathway for sodium ion batteries: A study on P2-Nax(LiyMn1-y)O2 compounds

NASA Astrophysics Data System (ADS)

Yang, Lufeng; Li, Xiang; Ma, Xuetian; Xiong, Shan; Liu, Pan; Tang, Yuanzhi; Cheng, Shuang; Hu, Yan-Yan; Liu, Meilin; Chen, Hailong

2018-03-01

Sodium-ion batteries (SIBs) are an emerging electrochemical energy storage technology that has high promise for electrical grid level energy storage. High capacity, long cycle life, and low cost cathode materials are very much desired for the development of high performance SIB systems. Sodium manganese oxides with different compositions and crystal structures have attracted much attention because of their high capacity and low cost. Here we report our investigations into a group of promising lithium doped sodium manganese oxide cathode materials with exceptionally high initial capacity of ∼223 mAh g-1 and excellent capacity retentions, attributed primarily to the absence of phase transformation in a wide potential range of electrochemical cycling, as confirmed by in-operando X-ray diffraction (XRD), Rietveld refinement, and high-resolution 7Li solid-state NMR characterizations. The systematic study of structural evolution and the correlation with the electrochemical behavior of the doped cathode materials provides new insights into rational design of high-performance intercalation compounds by tailoring the composition and the crystal structure evolution in electrochemical cycling.

Au 2PbP 2, Au 2TlP 2, and Au 2HgP 2: Ternary Gold Polyphosphides with Lead, Thallium, and Mercury in the Oxidation State Zero

NASA Astrophysics Data System (ADS)

Eschen, Marcus; Jeitschko, Wolfgang

2002-05-01

The polyphosphide Au2PbP2 was prepared by reaction of the elemental components using liquid lead as a reaction medium. Well-developed crystals were obtained after dissolving the matrix in hydrochloric acid. Their crystal structure was determined from four-circle X-ray diffractometer data: Cmcm, a=323.6(1) pm, b=1137.1(2) pm, c=1121.8(1) pm, Z=4, R=0.023 for 478 structure factors and 20 variable parameters. The structure contains zigzag chains of phosphorus atoms with a typical single-bond distance of 219.4(2) pm. The two different kinds of gold atoms are both in linear phosphorus coordination with typical single-bond distances of 232.6(2) and 234.2(2) pm, and the lead atoms have only metal neighbors (7 Au and 2 Pb). Accordingly, chemical bonding of the compound may be expressed by the formula (Au+1)2Pb±0(P-1)2. The corresponding thallium and mercury polyphosphides Au2TlP2 (a=324.1(1) pm, b=1136.1(1) pm, c=1122.1(1) pm) and Au2HgP2 (a=322.1(1) pm, b=1131.4(2) pm, c=1122.6(1) pm) were found to be almost isotypic with Au2PbP2. Their crystal structures were refined from single-crystal X-ray data to R=0.036 (682 F values, 25 variables) and R=0.026 (539 F values, 35 variables), respectively. The structure of these compounds may also be described as consisting of a three-dimensional network of condensed 8- and 10-membered Au2P6 and Au4P6 rings forming parallel channels, which are filled by the lead, thallium, and mercury atoms. The lead atoms are well localized in these channels, while the thallium and even more the mercury atoms occupy additional positions within these channels. Freshly prepared samples of Au2HgP2 show reproducibly slightly different axial ratios and larger cell volumes (ΔV=0.5%) than those after exposure of the samples to air for several days.

Synthesis, purification and bulk crystal growth of radiation detector materials using melt growth technique

NASA Astrophysics Data System (ADS)

Surabhi, Raja Rahul Reddy

In the past decade, there has been new and increased usage of radiation-detection technologies for applications in homeland security, non-proliferation, and national defense. Most of these applications require a portable device with high gamma-ray energy resolution and detection efficiency, compact size, room-temperature operation, and low cost. Consequently, there is a renewed understanding of the material limitations for these technologies and a great demand to develop next-generation radiation-detection materials that can operate at room temperature. Mercuric iodide (HgI2), Lead iodide (PbI2), and CdZnTe (CZT) are the current leading candidates for radiation detector applications. This is because of their high atomic number and large band gap that makes them particularly well suited for fabrication of high resolution and high efficiency compact devices. PbI2 is a promising material for room temperature nuclear radiation detectors, characterized by its wide band gap (EG=2.32eV) and high-density (rho=6.2g/cm3). It has been reported that PbI2 crystal detectors are able to detect gamma-ray in the range of 1KeV-1MeV, with good energy resolution. However, PbI 2 detectors have not been studied in detail because of non-availability of high quality single crystals. This study presents the synthesis, purification, growth and characterization of PbI2 single crystals grown. In this research, solid-state synthesis technique has been utilized for obtaining PbI2 as a starting material. For the first time, a unique low-temperature purification technique has been developed to obtain high-purity starting material. The crystals were grown using 2-zone Bridgman-Stockbarger (B.S) technique wherein growth rate and temperature gradient at the solid-liquid interface were optimized. Single crystals of PbI2 were successfully grown in quartz glass ampoule under different growth conditions. Material purity was determined by measuring the elemental concentration using the Inductively coupled plasma-optical emission spectroscopy (ICP-OES). ICP-OES is utilized for estimating impurities present in the low-temperature purified material, zone refined material and melt grown PbI2 crystals. The zone-refined material contains no traceable amounts of impurities, whereas the low-temperature purified material and melt grown PbI2 crystals show very low concentration of K (potassium) and Na (sodium) impurities. Crystal characterization has been performed for determining optical properties by UV-VIS spectroscopy. The energy band gap (EG) is an important parameter for materials used for room temperature gamma-ray detector applications. The absorption peak at 530nm is a characteristic of PbI2 and corresponds to the onset of the transitions from the valence band to the exciton level. From this absorption spectrum the calculated indirect band gap of PbI 2 was 2.33+/-0.025 eV at room temperature. For measuring the electrical properties (Dielectric and I-V characteristics) of the crystal, Ag (silver) contacts are applied to both sides of the sample. Dielectric analysis on melt grown PbI2 showed that space charge polarization was dominant at lower frequencies but stabilizes at higher frequencies over different operating temperatures. On the other hand, dielectric analysis for zone-refined material space charge polarization was constant over the operating range resulting in fewer lattice defects. Therefore the low temperature purified material followed by zone-refined purification provides detector grade material with fewer lattice defects. The measured electrical resistivity for melt grown PbI2 and zone-refined material are 3.185 x 10 10 O-cm and 0.754 x 109 O-cm at room temperature along (001) plane respectively.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

Ordonezite from the Theodoso Soto Mine, Sapioris, Durango, Mexico: new data and structure refinement

USGS Publications Warehouse

Ercit, T.S.; Foord, E.E.; Fitzpatrick, J.J.

2002-01-01

A new occurrence of the rare mineral species ordonezite has been found at the Theodoso Soto tin mine, near Sapioris, Durango, Mexico. The average composition of the samples is (Zn0.98Fe0.02)Σ1.00Sb2.00O6; the core of the crystals is slightly richer in Fe than the rim. The mineral is uniaxial (+), with all n greater than 2.30 (ncalc is 2.38 at 589 nm); Dobs 6.66 g/cm3, Dcalc 6.67 g/cm3. It is isostructural with ferrotapiolite, with a 4.668(2), c 9.269(6) A (from powder-diffraction data), space group P42/mnm, and is twinned on {103}. Its crystal structure, refined to R=4.1, wR=4.3% using 163 observed reflections, is fully cation-ordered.

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

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

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.

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.

Structural analysis of β-prism lectin from Colocasia esculenta (L.) S chott.

PubMed

Vajravijayan, S; Pletnev, S; Pletnev, V Z; Nandhagopal, N; Gunasekaran, K

2016-10-01

The Mannose-binding β-Prism Colocasia esculenta lectin (β-PCL) was purified from tubers using ion exchange chromatography. The purified β-PCL appeared as a single band of ∼12kDa on SDS-PAGE. β-PCL crystallizes in trigonal space group P3121 and diffracted to a resolution of 2.1Å. The structure was solved using Molecular replacement using Crocus vernus lectin (PDB: 3MEZ) as a model. From the final refined model to an R-factor of 16.5% and an Rfree of 20.4%, it has been observed that the biological unit consists of two β-Prism domains augmented through C-terminals swap over to form one of faces for each domain. Cα superposition of individual domains of β-PCL with individual domains of other related structures and superposition of whole protein structures were carried out. The higher RMS deviation for the superposition of whole structures suggest that β-prism domains assume different orientation in each structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Electrostatic properties of the pyrimethamine-2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters.

PubMed

Faroque, Muhammad Umer; Noureen, Sajida; Ahmed, Maqsood; Tahir, Muhammad Nawaz

2018-01-01

The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C 12 H 14 ClN 4 + ·C 7 H 5 O 4 - ·CH 3 OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

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.

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.

Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures

PubMed Central

Koparde, Vishal N.; Scarsdale, J. Neel; Kellogg, Glen E.

2011-01-01

Background The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high-resolution is assured by the data itself. However, at low-resolution, >3.0 Å, additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery. Methodology An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology. Results The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the low-resolution limit, ≥4.0 Å, the new protocol generated models with Cα positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions ≥4.0 Å, these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool. PMID:21246043

First Protein Crystallization Experiments on The International Space Station: Sweet Success in Space With Thaumatin

NASA Technical Reports Server (NTRS)

Kundrot, Craig E.; Barnes, Cindy L.; Snell, Eddie H.; Achari, Aniruddha; Whitaker, Ann F. (Technical Monitor)

2001-01-01

We determined the room temperature 1.2 A structure of thaumatin using a crystal grown in the first protein crystallization experiment conducted aboard the International Space Station (ISS). The crystals were grown in the Enhanced Gaseous Nitrogen Dewar (EGN) developed by Alexander McPherson and co-workers. EGN transports frozen solutions contained in tygon tubing in a liquid nitrogen Dewar to ISS where the tubes then thaw. Batch, free interface diffusion (FID), or vapor diffusion crystallization occurs after thawing. EGN was flown to the ISS on STS-106 on September 8, 2000. This was a "risk mitigation" flight that tested EGN performance and the process of conducting experiments on ISS. We focused on how to map a hanging drop crystallization recipe to the EGN FID method. Thaumatin was chosen as the test system. Three series of crystallization recipes were set-up. Each series tested different volume ratios of protein-rich solution to precipitant-rich solution. The series differed from each other by fixing either the protein concentration or the amount of protein in the solutions. Upon return of the samples to Earth on October 24 by STS-92, bubbles that spanned the diameter of the tubing were observed in all tubes. Such bubbles interrupt liquid-liquid diffusion and force vapor diffusion equilibration to occur instead. Nonetheless, crystals grew in 9 of 30 tubes. Many large crystals were grown, the largest being 2.0 x 1.1 x 1.0 cubic mm. The largest crystal was used to collect data at room temperature on beamline 7-1 of the Stanford Synchrotron Radiation Source to a maximum resolution of 1.2 A. The structure was refined anisotropically using SHELX with a data to parameter ratio of 4.5 to give an R(sub factor) of 15.8% (R(sub free) = 18.2%) for ail reflections without generated hydrogens. This refinement is proceeding. Comparisons of this 1.2 A microgravity structure to previous reports of the thaumatin structure at 1.75 A and to ground control crystals will be presented.

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

Osiry, H.; Cano, A.; Lemus-Santana, A.A.

This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which wasmore » actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.« less

Crystal structure of Plasmodium falciparum phosphoglycerate kinase: Evidence for anion binding in the basic patch

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

Smith, Craig D.; Chattopadhyay, Debasish; Pal, Biswajit

2012-11-09

3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the open conformation is presented in two different groups, namely I222 and P6{sub 1}22. The structure in I222 space group is solved using MAD and refined at 3 {angstrom} whereas that in P6{sub 1}22A is solved using MR and refined at 2.7 {angstrom}. I222 form has three monomers in asymmetric unit whereas P6{sub 1}22 form has two monomers in the asymmetric unit. In both crystal formsmore » a sulphate ion is located at the active site where ATP binds, but no Mg{sup 2+} ion is observed. For the first time another sulphate ion is found at the basic patch where the 3-phosphate of 1,3-biphosphoglycerate normally binds. This was found in both chains of P6{sub 1}22 form but only in chain A of I222 form.« less

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.

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

Antao, S.M.

The crystal structure of a biogenic aragonite from the nacre of an ammonite shell was obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinement. The well-preserved ammonite sample is from Alberta, Canada, and is from the Cretaceous period. The aragonite structure was refined in space group Pmcn, Z = 4, and the cell parameters obtained are a = 4.96265(2), b = 7.97016(4), c = 5.74474(3) {angstrom}, and V = 227.222(2) {angstrom}{sup 3}. The chemical analyses indicate a formula of [Ca{sub 0.995}Sr{sub 0.004}Ba{sub 0.001}]{Sigma} = 1.0(CO{sub 3}). The average and distances are 2.5281(3) and 1.2871(6)more » {angstrom}, respectively, and the average angle is 119.94(8){sup o}. The CO{sub 3} groups are non-planar. Based on crystal-structure data for biogenic and non-biogenic aragonite samples, aragonite from ammonite nacre has minimal structural distortions and is very similar to non-biogenic aragonite, in particular, a sample from Spain.« less

CsSnI[subscript 3]: Semiconductor or Metal? High Electrical Conductivity and Strong Near-Infrared Photoluminescence from a Single Material. High Hole Mobility and Phase-Transitions

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

Chung, In; Song, Jung-Hwan; Im, Jino

CsSnI{sub 3} is an unusual perovskite that undergoes complex displacive and reconstructive phase transitions and exhibits near-infrared emission at room temperature. Experimental and theoretical studies of CsSnI{sub 3} have been limited by the lack of detailed crystal structure characterization and chemical instability. Here we describe the synthesis of pure polymorphic crystals, the preparation of large crack-/bubble-free ingots, the refined single-crystal structures, and temperature-dependent charge transport and optical properties of CsSnI{sub 3}, coupled with ab initio first-principles density functional theory (DFT) calculations. In situ temperature-dependent single-crystal and synchrotron powder X-ray diffraction studies reveal the origin of polymorphous phase transitions of CsSnI{submore » 3}. The black orthorhombic form of CsSnI{sub 3} demonstrates one of the largest volumetric thermal expansion coefficients for inorganic solids. Electrical conductivity, Hall effect, and thermopower measurements on it show p-type metallic behavior with low carrier density, despite the optical band gap of 1.3 eV. Hall effect measurements of the black orthorhombic perovskite phase of CsSnI{sub 3} indicate that it is a p-type direct band gap semiconductor with carrier concentration at room temperature of {approx} 10{sup 17} cm{sup -3} and a hole mobility of {approx} 585 cm{sup 2} V{sup -1} s{sup -1}. The hole mobility is one of the highest observed among p-type semiconductors with comparable band gaps. Its powders exhibit a strong room-temperature near-IR emission spectrum at 950 nm. Remarkably, the values of the electrical conductivity and photoluminescence intensity increase with heat treatment. The DFT calculations show that the screened-exchange local density approximation-derived band gap agrees well with the experimentally measured band gap. Calculations of the formation energy of defects strongly suggest that the electrical and light emission properties possibly result from Sn defects in the crystal structure, which arise intrinsically. Thus, although stoichiometric CsSnI{sub 3} is a semiconductor, the material is prone to intrinsic defects associated with Sn vacancies. This creates highly mobile holes which cause the materials to appear metallic.« less

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™.

Crystal structure of 1-meth-oxy-2,2,2-tris-(pyrazol-1-yl)ethane.

PubMed

Lyubartseva, Ganna; Parkin, Sean; Coleman, Morgan D; Mallik, Uma Prasad

2014-09-01

The title compound, C12H14N6O, consists of three pyrazole rings bound via nitro-gen to the distal ethane carbon of meth-oxy ethane. The dihedral angles between the three pyrazole rings are 67.62 (14), 73.74 (14), and 78.92 (12)°. In the crystal, mol-ecules are linked by bifurcated C-H,H⋯N hydrogen bonds, forming double-stranded chains along [001]. The chains are linked via C-H⋯O hydrogen bonds, forming a three-dimensional framework structure. The crystal was refined as a perfect (0.5:0.5) inversion twin.

Crystal Structure of Mistletoe Lectin I (ML-I) from Viscum album in Complex with 4-N-Furfurylcytosine at 2.85 Å Resolution.

PubMed

Ahmad, Malik Shoaib; Rasheed, Saima; Falke, Sven; Khaliq, Binish; Perbandt, Markus; Choudhary, M Iqbal; Markiewicz, Wojciech T; Barciszewski, Jan; Betzel, Christian

2018-05-23

Viscum album (the European mistletoe) is a semi-parasitic plant, which is of high medical interest. It is widely found in Europe, Asia and North America. It contains at least three distinct lectins (i.e. ML-I, II, and III), varying in molecular mass and specificity. Among them ML-I is in focus of medical research for various activities, including anti-cancer activities. To understand the molecular basis for such medical applications a few studies have already addressed the structural and functional analysis of ML-I in complex with ligands. In continuation of these efforts, we are reporting the crystal structure of ML from Viscum album in complex with the nucleic acid oxidation product 4-N-furfurylcytosine (FC) refined to 2.85 Å resolution. FC is known to be involved in different metabolic pathways related to oxidative stress and DNA modification. X-ray suitable hexagonal crystals of the ML-I/FC complex were grown within four days at 294 K using the hanging drop vapor diffusion method. Diffraction data were collected up to a resolution of 2.85 Å. The ligand affinity was verified via in-silico docking. The high-resolution structure was refined subsequently to analyze particularly the active site conformation and binding epitope of 4-N-furfurylcytosine. A distinct 2Fo-Fc electron density at the active site was interpreted as a single FC molecule. The specific binding of FC is achieved also through hydrophobic interactions involving Tyr76A, Tyr115A, Glu165A, and Leu157A of the ML-I A-chain. The binding energy of FC to the active site of ML-I was calculated as well to be -6.03 kcal mol-1. In comparison to other reported ML-I complexes we observed distinct differences in the vicinity of the nucleic acid base binding site upon interaction with FC. Therefore, data obtained will provide new insights in understanding the specificity, inhibition and cytotoxicity of the ML-I A-chain and related RIPs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Laser furnace and method for zone refining of semiconductor wafers

NASA Technical Reports Server (NTRS)

Griner, Donald B. (Inventor); zur Burg, Frederick W. (Inventor); Penn, Wayne M. (Inventor)

1988-01-01

A method of zone refining a crystal wafer (116 FIG. 1) comprising the steps of focusing a laser beam to a small spot (120) of selectable size on the surface of the crystal wafer (116) to melt a spot on the crystal wafer, scanning the small laser beam spot back and forth across the surface of the crystal wafer (116) at a constant velocity, and moving the scanning laser beam across a predetermined zone of the surface of the crystal wafer (116) in a direction normal to the laser beam scanning direction and at a selectible velocity to melt and refine the entire crystal wafer (116).

Ferri-magnetic order in Mn induced spinel Co3-xMnxO4 (0.1≤x≤1.0) ceramic compositions

NASA Astrophysics Data System (ADS)

Meena, P. L.; Sreenivas, K.; Singh, M. R.; Kumar, Ashok; Singh, S. P.; Kumar, Ravi

2016-04-01

We report structural and magnetic properties of spinel Co3-xMnxO4 (x=0.1-1.0) synthesized by solid state reaction technique. Rietveld refinement analysis of X-ray diffraction (XRD) data, revealed the formation of polycrystalline single phase Co3-xMnxO4 without any significant structural change in cubic crystal symmetry with Mn substitution, except change in lattice parameter. Temperature dependent magnetization data show changes in magnetic ordering temperature, indicating formation of antiferromagnetic (AFM) and ferrimagnetic (FM) phase at low Mn concentration (x≤0.3) and well-defined FM phase at high Mn concentration (x≥0.5). The isothermal magnetization records established an AFM/FM mixed phase for composition ranging 0.10.5.

Mono- and polynucleation, atomistic growth, and crystal phase of III-V nanowires under varying group V flow

NASA Astrophysics Data System (ADS)

Dubrovskii, V. G.

2015-05-01

We present a refined model for the vapor-liquid-solid growth and crystal structure of Au-catalyzed III-V nanowires, which revisits several assumptions used so far and is capable of describing the transition from mononuclear to polynuclear regime and ultimately to regular atomistic growth. We construct the crystal phase diagrams and calculate the wurtzite percentages, elongation rates, critical sizes, and polynucleation thresholds of Au-catalyzed GaAs nanowires depending on the As flow. We find a non-monotonic dependence of the crystal phase on the group V flow, with the zincblende structure being preferred at low and high group V flows and the wurtzite structure forming at intermediate group V flows. This correlates with most of the available experimental data. Finally, we discuss the atomistic growth picture which yields zincblende crystal structure and should be very advantageous for fabrication of ternary III-V nanowires with well-controlled composition and heterointerfaces.

Epitaxial Growth of an Organic p-n Heterojunction: C60 on Single-Crystal Pentacene.

PubMed

Nakayama, Yasuo; Mizuno, Yuta; Hosokai, Takuya; Koganezawa, Tomoyuki; Tsuruta, Ryohei; Hinderhofer, Alexander; Gerlach, Alexander; Broch, Katharina; Belova, Valentina; Frank, Heiko; Yamamoto, Masayuki; Niederhausen, Jens; Glowatzki, Hendrik; Rabe, Jürgen P; Koch, Norbert; Ishii, Hisao; Schreiber, Frank; Ueno, Nobuo

2016-06-01

Designing molecular p-n heterojunction structures, i.e., electron donor-acceptor contacts, is one of the central challenges for further development of organic electronic devices. In the present study, a well-defined p-n heterojunction of two representative molecular semiconductors, pentacene and C60, formed on the single-crystal surface of pentacene is precisely investigated in terms of its growth behavior and crystallographic structure. C60 assembles into a (111)-oriented face-centered-cubic crystal structure with a specific epitaxial orientation on the (001) surface of the pentacene single crystal. The present experimental findings provide molecular scale insights into the formation mechanisms of the organic p-n heterojunction through an accurate structural analysis of the single-crystalline molecular contact.

Abinitio powder x-ray diffraction and PIXEL energy calculations on thiophene derived 1,4 dihydropyridine

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

Karthikeyan, N., E-mail: karthin10@gmail.com; Sivakumar, K.; Pachamuthu, M. P.

We focus on the application of powder diffraction data to get abinitio crystal structure determination of thiophene derived 1,4 DHP prepared by cyclocondensation method using solid catalyst. Crystal structure of the compound has been solved by direct-space approach on Monte Carlo search in parallel tempering mode using FOX program. Initial atomic coordinates were derived using Gaussian 09W quantum chemistry software in semi-empirical approach and Rietveld refinement was carried out using GSAS program. The crystal structure of the compound is stabilized by one N-H…O and three C-H…O hydrogen bonds. PIXEL lattice energy calculation was carried out to understand the physical naturemore » of intermolecular interactions in the crystal packing, on which the total lattice energy is contributed into Columbic, polarization, dispersion, and repulsion energies.« less

Single-crystal X-ray diffraction study of Fe 2SiO 4 fayalite up to 31 GPa

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

Zhang, Jin S.; Hu, Yi; Shelton, Hannah

2016-10-03

Olivine is widely believed to be the most abundant mineral in the Earth’s upper mantle. Here, we report structural refinement results for the Fe-end-member olivine, Fe 2SiO 4 fayalite, up to 31 GPa in diamond-anvil cell, using single-crystal synchrotron X-ray diffraction. Unit-cell parameters a, b, c and V, average Si–O Fe–O bond lengths, as well as Si–O Fe–O polyhedral volumes continuously decrease with increasing pressure. The pressure derivative of isothermal bulk modulus K' T0 is determined to be 4.0 (2) using third-order Birch–Murnaghan equation of state with ambient isothermal bulk modulus fixed to 135 GPa on the basis of previousmore » Brillouin measurements. The Si–O tetrahedron is stiffer than the Fe–O octahedra, and the compression mechanism is dominated by Fe–O bond and Fe–O octahedral compression. Densities of olivine along 1600 and 900 K adiabats are calculated based on this study. The existence of metastable olivine inside the cold subduction slab could cause large positive buoyancy force against subduction, slow down the subduction and possibly affect the slab geometry.« less

Multidataset Refinement Resonant Diffraction, and Magnetic Structures

PubMed Central

Attfield, J. Paul

2004-01-01

The scope of Rietveld and other powder diffraction refinements continues to expand, driven by improvements in instrumentation, methodology and software. This will be illustrated by examples from our research in recent years. Multidataset refinement is now commonplace; the datasets may be from different detectors, e.g., in a time-of-flight experiment, or from separate experiments, such as at several x-ray energies giving resonant information. The complementary use of x rays and neutrons is exemplified by a recent combined refinement of the monoclinic superstructure of magnetite, Fe3O4, below the 122 K Verwey transition, which reveals evidence for Fe2+/Fe3+ charge ordering. Powder neutron diffraction data continue to be used for the solution and Rietveld refinement of magnetic structures. Time-of-flight instruments on cold neutron sources can produce data that have a high intensity and good resolution at high d-spacings. Such profiles have been used to study incommensurate magnetic structures such as FeAsO4 and β–CrPO4. A multiphase, multidataset refinement of the phase-separated perovskite (Pr0.35Y0.07Th0.04Ca0.04Sr0.5)MnO3 has been used to fit three components with different crystal and magnetic structures at low temperatures. PMID:27366599

The application and use of chemical space mapping to interpret crystallization screening results

PubMed Central

Snell, Edward H.; Nagel, Ray M.; Wojtaszcyk, Ann; O’Neill, Hugh; Wolfley, Jennifer L.; Luft, Joseph R.

2008-01-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually. PMID:19018100

The application and use of chemical space mapping to interpret crystallization screening results.

PubMed

Snell, Edward H; Nagel, Ray M; Wojtaszcyk, Ann; O'Neill, Hugh; Wolfley, Jennifer L; Luft, Joseph R

2008-12-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually.

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.

Electron paramagnetic resonance study of radiation-induced paramagnetic centers in succinic anhydride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz; Er, Emine

2017-09-01

Succinic anhydride single crystals were exposed to 60Co-gamma irradiation at room temperature. The irradiated single crystals were investigated at 125 K by Electron Paramagnetic Resonance (EPR) Spectroscopy. The investigation of EPR spectra of irradiated single crystals of succinic anhydride showed the presence of two succinic anhydride anion radicals. The anion radicals observed in gamma-irradiated succinic anhydride single crystal were created by the scission of the carbon-oxygen double bond. The structure of EPR spectra demonstrated that the hyperfine splittings arise from the same radical species. The reduction of succinic anhydride was identified which is formed by the addition of an electron to oxygen of the Csbnd O bond. The g values, the hyperfine structure constants and direction cosines of the radiation damage centers observed in succinic anhydride single crystal were obtained.

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

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.

Effect of cobalt doping on structural and optical properties of nanocrystalline La0.8Pb0.2CrO3 orthochromite

NASA Astrophysics Data System (ADS)

Zarrin, Naima; Shahidhusain

2018-04-01

We have synthesized nanocrystalline La0.8Pb0.2Cr1-xCoxO3 (0≤x≤0.3) through sol-gel process and studied their structural and optical properties. X-ray diffraction patterns reveal that the samples conform in the orthorhombic crystal symmetry with Pnma space group. Structural parameters are refined by Rietveld Refinement using Fullprof software. Lattice parameters and unit cell volume of doped samples are found to decrease with increase in Co doping. The optical energy band gapdecreases whereas Urbach energy increases with the increase in Co content.

6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

NASA Astrophysics Data System (ADS)

Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

2016-09-01

13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

Triclinic lysozyme at 0.65 angstrom resolution.

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

Wang, J.; Dauter, M.; Alkire, R.

The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been refined against diffraction data extending to 0.65 {angstrom} resolution measured at 100 K using synchrotron radiation. Refinement with anisotropic displacement parameters and with the removal of stereochemical restraints for the well ordered parts of the structure converged with a conventional R factor of 8.39% and an R{sub free} of 9.52%. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. In addition to the 129-residue protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and three ethylene glycol molecules weremore » located in the electron-density map. Eight sections of the main chain and many side chains were modeled with alternate conformations. The occupancies of the water sites were refined and this step is meaningful when assessed by use of the free R factor. A detailed description and comparison of the structure are made with reference to the previously reported triclinic HEWL structures refined at 0.925 {angstrom} (at the low temperature of 120 K) and at 0.95 {angstrom} resolution (at room temperature).« less

Numerical analysis of impurity separation from waste salt by investigating the change of concentration at the interface during zone refining process

NASA Astrophysics Data System (ADS)

Choi, Ho-Gil; Shim, Moonsoo; Lee, Jong-Hyeon; Yi, Kyung-Woo

2017-09-01

The waste salt treatment process is required for the reuse of purified salts, and for the disposal of the fission products contained in waste salt during pyroprocessing. As an alternative to existing fission product separation methods, the horizontal zone refining process is used in this study for the purification of waste salt. In order to evaluate the purification ability of the process, three-dimensional simulation is conducted, considering heat transfer, melt flow, and mass transfer. Impurity distributions and decontamination factors are calculated as a function of the heater traverse rate, by applying a subroutine and the equilibrium segregation coefficient derived from the effective segregation coefficients. For multipass cases, 1d solutions and the effective segregation coefficient obtained from three-dimensional simulation are used. In the present study, the topic is not dealing with crystal growth, but the numerical technique used is nearly the same since the zone refining technique was just introduced in the treatment of waste salt from nuclear power industry because of its merit of simplicity and refining ability. So this study can show a new application of single crystal growth techniques to other fields, by taking advantage of the zone refining multipass possibility. The final goal is to achieve the same high degree of decontamination in the waste salt as in zone freezing (or reverse Bridgman) method.

Lattice damage and Al-metal precipitation in 2.5 MeV-electron-irradiated AlH3

NASA Astrophysics Data System (ADS)

Zogal, O. J.; Vajda, P.; Beuneu, F.; Pietraszko, A.

1998-04-01

AlH3 powder was bombarded with energetic electrons at 20 K and at room temperature and investigated by EPR, NMR, X-ray diffractometry, and microwave dielectric-constant measurements. The EPR spectra of the irradiated powder and of a selected single crystal cuboid of ˜ {10^{ - 1}} mm edge show a complex asymmetric line centered at g = 2.009, with a Curie-like temperature dependence, attributed to radiation-induced color centers and/or their agglomerates. At the same time, the grains, which have become shiny black after irradiation, exhibit an increase of both the real and the imaginary part of ɛ. 27Al-NMR spectra of the irradiated powder present a Knight-shifted line at 1600(50) ppm, close to the position of bulk metallic Al, and corresponding to a concentration of c(Al) ˜ {10^{ - 1}}. In addition, the main hydride line differs from that before irradiation, demonstrating an alteration of environmental symmetry. The irradiation induces also a change in shape and width of the 1H-NMR line, another indication of symmetry change in the lattice. Finally, a refined X-ray single-crystal structure analysis of the irradiated cuboid indicates a change of structure from trigonal R -3 c to R -3, with a loss of mirror symmetry for the two Al sites caused by the introduction of Al-defects in the vicinity of one of them.

Neutron diffraction study and theoretical analysis of the antiferromagnetic order and the diffuse scattering in the layered kagome system CaBaCo2Fe2O7

NASA Astrophysics Data System (ADS)

Reim, J. D.; Rosén, E.; Zaharko, O.; Mostovoy, M.; Robert, J.; Valldor, M.; Schweika, W.

2018-04-01

The hexagonal swedenborgite, CaBaCo2Fe2O7 , is a chiral frustrated antiferromagnet, in which magnetic ions form alternating kagome and triangular layers. We observe a long-range √{3 }×√{3 } antiferromagnetic order setting in below TN=160 K by neutron diffraction on single crystals of CaBaCo2Fe2O7 . Both magnetization and polarized neutron single crystal diffraction measurements show that close to TN spins lie predominantly in the a b plane, while upon cooling the spin structure becomes increasingly canted due to Dzyaloshinskii-Moriya interactions. The ordered structure can be described and refined within the magnetic space group P 31 m' . Diffuse scattering between the magnetic peaks reveals that the spin order is partial. Monte Carlo simulations based on a Heisenberg model with two nearest-neighbor exchange interactions show a similar diffuse scattering and coexistence of the √{3 }×√{3 } order with disorder. The coexistence can be explained by the freedom to vary spins without affecting the long-range order, which gives rise to ground-state degeneracy. Polarization analysis of the magnetic peaks indicates the presence of long-period cycloidal spin correlations resulting from the broken inversion symmetry of the lattice, in agreement with our symmetry analysis.

Structure and Growth Control of Organic-Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals.

PubMed

Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong; Liang, Ziqi

2016-04-01

Recently, organic-inorganic halide perovskites have sparked tremendous research interest because of their ground-breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light-emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high-quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three-dimensional large sized single crystals, two-dimensional nanoplates, one-dimensional nanowires, to zero-dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high-performance (opto)electronic devices.

Deformation Mechanism and Recrystallization Relationships in Galfenol Single Crystals: On the Origin of Goss and Cube Orientations

NASA Astrophysics Data System (ADS)

Na, Suok-Min; Smith, Malcolm; Flatau, Alison B.

2018-06-01

In this work, deformation mechanism related to recrystallization behavior in single-crystal disks of Galfenol (Fe-Ga alloy) was investigated to gain insights into the influence of crystal orientations on structural changes and selective grain growth that take place during secondary recrystallization. We started with the three kinds of single-crystal samples with (011)[100], (001)[100], and (001)[110] orientations, which were rolled and annealed to promote the formation of different grain structures and texture evolutions. The initial Goss-oriented (011)[100] crystal mostly rotated into {111}<112> orientations with twofold symmetry and shear band structures by twinning resulted in the exposure of rolled surface along {001}<110> orientation during rolling. In contrast, the Cube-oriented (001)[100] single crystal had no change in texture during rolling with the thickness reduction up to 50 pct. The {123}<111> slip systems were preferentially activated in these single crystals during deformation as well as {112}<111> slip systems that are known to play a role in primary slip of body-centered cubic (BCC) materials such as α-iron and Fe-Si alloys. After annealing, the deformed Cube-oriented single crystal had a small fraction (<10 pct) of recrystallized Goss-oriented grains. The weak Goss component remained in the shear bands of the 50 pct rolled Goss-oriented single crystal, and it appeared to be associated with coalescence of subgrains inside shear band structures during primary recrystallization. Rolling of the (001)[110] single crystal led to the formation of a tilted (001)[100] component close to the <120> orientation, associated with {123}<111> slip systems as well. This was expected to provide potential sites of nucleation for secondary recrystallization; however, no Goss- and Cube-oriented components actually developed in this sample during secondary recrystallization. Those results illustrated how the recrystallization behavior can be influenced by deformed structure and the slip systems.

Single-Crystal X-Ray Diffraction of Pyrope Garnet to 84 GPa

NASA Astrophysics Data System (ADS)

Finkelstein, G. J.; Dera, P. K.; Duffy, T. S.

2012-12-01

Garnets are characteristic minerals of many metamorphic and igneous rocks, and are also important upper-mantle constituents. Mg-rich (pyrope) garnets occur in both peridotite and eclogite compositions in the upper mantle. At high temperatures and pressures above 25 GPa, garnets transform to the perovskite structure. The post-garnet transition kinetics are sluggish, and in cold subducting slabs garnets could persist metastably at temperatures as high as 1700 K on geological timescales. These phases could add positive buoyancy to a subducting slab, inhibiting subduction. There has been minimal previous work on the 300 K compression behavior of aluminosilicate garnets at pressures higher than 10 GPa. In this work, we have collected single-crystal X-ray diffraction data on near end-member natural pyrope (Dora Maira pyrope) to 84 GPa. By extending the compression of pyrope to much higher pressures, we can better constrain the equation of state while also characterizing the structural response to such extreme pressures for the first time. Crystals were polished to ~5-10 μm in thickness, and loaded in a diamond anvil cell with gold foil and ruby balls as pressure calibrants. Helium was used as a pressure-transmitting medium. High-pressure single-crystal X-ray diffraction experiments were performed at the GSECARS 13-ID-D beamline of the Advanced Photon Source and the 12.2.2 beamline of the Advanced Light Source. Structure refinements were carried out successfully to the highest pressure using Shelx-97, extending the range over which the compression behavior of this material has been characterized by a factor of nearly three. Pyrope exhibits smooth compression behavior and no phase transitions over the investigated pressure range. A preliminary 3rd order Birch-Murnaghan equation of state was successfully fit to data up to 52 GPa. If the bulk modulus is fixed to 170 GPa, a value consistent with previous Brillouin and Ultrasonic studies, our data yields a pressure derivative of the bulk modulus of 4.33(2). The equation of state fitting will be extended to include data up to 84 GPa. The compression mechanisms observed for pyrope are consistent with those reported at lower pressures by Zhang et al., 1998. A detailed description of the structural response of pyrope to high pressures will be reported.

Rietveld refined structural and room temperature vibrational properties of BaTiO3 doped La0.67Ba0.33MnO3 composites

NASA Astrophysics Data System (ADS)

Dar, M. A.; Sheikh, M. W.; Malla, M. S.; Varshney, Dinesh

2016-05-01

The composites of (1-x) La0.67Ba0.33MnO3 (LBMO) + xBaTiO3 (BTO) (x = 0, 0.25 and 1.0) were synthesized by conventional solid-state reaction method. Rietveld refinement was employed to characterize the structural information of the prepared ceramics. The result of the Rietveld refinement of X-ray powder diffraction of La0.67Ba0.33MnO3 and BaTiO3 shows that these compounds crystallize in rhombohedral (R3c) and tetragonal (P4mm), respectively. The structural parameters and the reliability factors for the LBMO-BTO composite ceramics were successfully determined by the Rietveld refinement. At room temperature, Raman active phonon modes predicted by the group theory were observed only in BaTiO3 and composite sample. Pure LBMO does not show any Raman active Phonon mode at room temperature.

The Quality and Validation of Structures from Structural Genomics

PubMed Central

Domagalski, Marcin J.; Zheng, Heping; Zimmerman, Matthew D.; Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein–ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement. PMID:24203341

Thermal response, catalytic activity, and color change of the first hybrid vanadate containing Bpe guest molecules.

PubMed

Fernández de Luis, Roberto; Urtiaga, M Karmele; Mesa, José L; Larrea, Edurne S; Iglesias, Marta; Rojo, Teófilo; Arriortua, María I

2013-03-04

Four isomorphic compounds with formula [{Co2(H2O)2(Bpe)2}(V4O12)]·4H2O·Bpe, CoBpe 1; [{CoNi(H2O)2(Bpe)2}(V4O12)]·4H2O·Bpe, CoNiBpe 2; [{Co0.6Ni1.4(H2O)2(Bpe)2}(V4O12)]·4H2O·Bpe, NiCoBpe 3; and [{Ni2(H2O)2(Bpe)2}(V4O12)]·4H2O·Bpe, NiBpe 4, have been obtained by hydrothermal synthesis. The crystal structures of CoBpe 1 and NiBpe 4 were determined by single-crystal X-ray diffraction (XRD). The Rietveld refinement of CoNiBpe 2 and NiCoBpe 3 XRD patterns confirms that those are isomorphic. The compounds crystallize in the P1̅ space group, exhibiting a crystal structure constructed from inorganic layers pillared by Bpe ligands. The crystal structure contains intralayer and interlayer channels, in which the crystallization water molecules and Bpe guest molecules, respectively, are located. The solvent molecules establish a hydrogen bonding network with the coordinated water molecules. Thermodiffractometric and thermogravimetric studies showed that the loss of crystallization and coordinated water molecules takes place at different temperatures, giving rise to crystal structure transformations that involve important reduction of the interlayer distance, and strong reduction of crystallinity. The IR, Raman, and UV-vis spectra of the as-synthesized and heated compounds confirm that the structural building blocks and octahedral coordination environment of the metal centers are maintained after the structural transformations. The color change and reversibility of the water molecules uptake/removal were tested showing that the initial color is not completely recovered when the compounds are heated at temperatures higher than 200 °C. The thermal evolution of the magnetic susceptibility indicates one-dimensional antiferromagnetic coupling of the metal centers at high temperatures. For NiCoBpe 3 and NiBpe 4 compounds magnetic ordering is established at low temperatures, as can be judged by the maxima observed in the magnetic susceptibilities. CoNiBpe 2 was proved as catalyst being active for cyanosilylation reactions of aldehydes.

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.

Development and photoelectric properties of In/p-Ag{sub 3}AsS{sub 3} surface-barrier structures

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

Rud', V. Yu., E-mail: rudvas@spbstu.ru; Rud', Yu. V.; Terukov, E. I.

2010-08-15

Homogeneous p-Ag{sub 3}AsS{sub 3} bulk single crystals with rhombic structure have been grown by planar crystallization from melts with atomic composition corresponding to this ternary compound. Photosensitive surface-barrier structures based on the interface between the surface of these crystals and thin films of pure indium are fabricated for the first time. The photosensitivity of fabricated structures is studied in natural and linearly polarized light. Photosensitivity spectra of In/p-Ag{sub 3}AsS{sub 3} structures are measured for the first time and used to determine the nature and energy of interband transitions in p-Ag{sub 3}AsS{sub 3} crystals. The phenomenon of natural photopleochroism is studiedmore » for surface-barrier structures grown on oriented p-Ag{sub 3}AsS{sub 3} single crystals. It is concluded that Ag{sub 3}AsS{sub 3} single crystals can be used in photoconverters of natural and linearly polarized light.« less

Synthesis, structural, thermal and Hirshfeld surface analysis of novel [1,2,4]triazolo[3,4-b][1,3,4] thiadiazine carrying 1,4-benzothiazine-3-one moiety

NASA Astrophysics Data System (ADS)

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

2018-05-01

Needle shaped single crystal of the title compound was grown by slow evaporation solution growth technique using ethanol as solvent. The grown single crystal was characterized using FT-IR, Single crystal XRD and Thermal analysis. The FT-IR spectrum confirms the molecular structure and identifies the different functional groups present in the compound. Single crystal XRD study reveals that the crystallized compound belongs to the monoclinic crystal system with P21/c space group and the corresponding cell parameters were identified. The thermal stability of the material was determined using both TGA and DTA analysis. The intermolecular interaction of each individual atom in the crystal lattice was estimated using Hirshfeld surface and finger print analysis.

Purification of organic nonlinear optical materials for bulk crystal growth from melt

NASA Astrophysics Data System (ADS)

Gebre, Tesfaye; Bhat, Kamala N.; Batra, Ashok K.; Lal, Ravindra B.; Aggarwal, Mohan D.; Penn, Benjamin G.; Frazier, Donald O.

2002-10-01

The techniques developed for purification of nonlinear optical organic materials, such as benzil, 2-methyl-4-nitroaniline (MNA), Dicyanovinyl anisole (DIVA) and its derivatives, nitrophenyl prolinol (NPP) and other Schiff's base compounds, include Kugelrohy method, physical vapor transport, zone refining and recrystallization from the solvent are described. Purity of the materials is tested using differential thermal analysis, gas chromatograph/Mass detector, Fourier Transform Infrared spectroscopy and melting point measurements. The purified materials were later used in the growth of single crystal by Bridgman-Stockbarger and Czochralski techniques.

Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

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

Machesky, Michael L.; Predota, M.; Wesolowski, David J

The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming thatmore » the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite ({alpha}-SnO{sub 2}) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.« less

Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework.

PubMed

Machesky, Michael L; Predota, Milan; Wesolowski, David J; Vlcek, Lukas; Cummings, Peter T; Rosenqvist, Jörgen; Ridley, Moira K; Kubicki, James D; Bandura, Andrei V; Kumar, Nitin; Sofo, Jorge O

2008-11-04

The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 A of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 degrees C that agrees quantitatively with the experimentally determined value (5.4+/-0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees C into quantitative agreement with the experimental value (4.8+/-0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 degrees C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite (alpha-SnO2) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.

Crystalline structure of Cu4SSe

NASA Astrophysics Data System (ADS)

Amiraslanov, I. R.; Alieva, N. A.; Guseinov, G. G.

2016-12-01

Ternary compound Cu4SSe has been first synthesized by alloying the Cu, S, and Se elements taken in stoichiometric ratios. An X-ray diffraction study of polycrystalline samples has revealed the synthesized material to be crystallized into the trigonal system with unit-cell parameters a = 4.021(1) Å, c = 6.838(1) Å, and V = 95.75(4) Å3; sp. gr. P bar 3 m1; Z = 1; D x = 6.333(3) g/cm3. The crystal structure has been solved and refined to the reliability factor R Bragg = 0.40%.

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.

First investigations on the quaternary system Na2O-K2O-CaO-SiO2: synthesis and crystal structure of the mixed alkali calcium silicate K1.08Na0.92Ca6Si4O15

NASA Astrophysics Data System (ADS)

Kahlenberg, Volker; Mayerl, Michael Jean-Philippe; Schmidmair, Daniela; Krüger, Hannes; Tribus, Martina

2018-04-01

In the course of an exploratory study on the quaternary system Na2O-K2O-CaO-SiO2 single crystals of the first anhydrous sodium potassium calcium silicate have been obtained from slow cooling of a melt in the range between 1250 and 1050 °C. Electron probe micro analysis suggested the following idealized molar ratios of the oxides for the novel compound: K2O:Na2O:CaO:SiO2 = 1:1:12:8 (or KNaCa6Si4O15). Single-crystal diffraction measurements on a crystal with chemical composition K1.08Na0.92Ca6Si4O15 resulted in the following basic crystallographic data: monoclinic symmetry, space group P 21/ c, a = 8.9618(9) Å, b = 7.3594(6) Å, c = 11.2453(11) Å, β= 107.54(1)°, V = 707.2(1) Å3, Z = 2. Structure solution was performed using direct methods. The final least-squares refinement converged at a residual of R(|F|) = 0.0346 for 1288 independent reflections and 125 parameters. From a structural point of view, K1.08Na0.92Ca6Si4O15 belongs to the group of mixed-anion silicates containing [Si2O7]- and [SiO4]-units in the ratio 1:2. The mono- and divalent cations occupy a total of four crystallographically independent positions located in voids between the tetrahedra. Three of these sites are exclusively occupied by calcium. The fourth site is occupied by 54(1)% K and 46%(1) Na, respectively. Alternatively, the structure can be described as a heteropolyhedral framework based on corner-sharing silicate tetrahedra and [CaO6]-octahedra. The network can build up from kröhnkite-like [Ca(SiO4)2O2]-chains running along [001]. A detailed comparison with other A2B6Si4O15-compounds including topological and group-theoretical aspects is presented.

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.

Life Prediction of Turbine Blade Nickel Base Superalloy Single Crystals.

DTIC Science & Technology

1986-08-01

mechanical properties between single crystals and the DS version of Mar-M200. Soon it was recognized again through the mechanical property - structure ... property achievements demonstrated by screening and simulated engine tests. 1 Single crystals are the results of extensive investigation on the mechanical ...behavior, (especially fatigue and creep) of, and the structure - property correlations in the equiaxed and directionally solidified (DS) nickel-base

How to tackle protein structural data from solution and solid state: An integrated approach.

PubMed

Carlon, Azzurra; Ravera, Enrico; Andrałojć, Witold; Parigi, Giacomo; Murshudov, Garib N; Luchinat, Claudio

2016-02-01

Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule. Copyright © 2016 Elsevier B.V. All rights reserved.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Structure of the catalytic domain of Plasmodium falciparum ARF GTPase-activating protein (ARFGAP)

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

Cook, William J.; Senkovich, Olga; Chattopadhyay, Debasish

2012-03-26

The crystal structure of the catalytic domain of the ADP ribosylation factor GTPase-activating protein (ARFGAP) from Plasmodium falciparum has been determined and refined to 2.4 {angstrom} resolution. Multiwavelength anomalous diffraction (MAD) data were collected utilizing the Zn{sup 2+} ion bound at the zinc-finger domain and were used to solve the structure. The overall structure of the domain is similar to those of mammalian ARFGAPs. However, several amino-acid residues in the area where GAP interacts with ARF1 differ in P. falciparum ARFGAP. Moreover, a number of residues that form the dimer interface in the crystal structure are unique in P. falciparummore » ARFGAP.« less

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Magnetic structure of the ferromagnetic new ternary silicide Nd5CoSi2.

PubMed

Mayer, C; Gaudin, E; Gorsse, S; Porcher, F; André, G; Chevalier, B

2012-04-04

Nd(5)CoSi(2) was obtained from the elements by arc-melting followed by annealing at 883 K. Its investigation by single-crystal x-ray and neutron powder diffraction shows that this ternary silicide crystallizes as Nd(5)Si(3) in a tetragonal structure deriving from the Cr(5)B(3)-type (I4/mcm space group; a = 7.7472(2) and c = 13.5981(5) Å as unit cell parameters). The structural refinements confirm the mixed occupancy on the 8h site between Si and Co atoms, as already observed for Gd(5)CoSi(2). Magnetization and specific heat measurements reveal a ferromagnetic behavior below T(C) = 55 K for Nd(5)CoSi(2). This magnetic ordering is further evidenced by neutron powder diffraction investigation revealing between 1.8 K and T(C) a canted ferromagnetic structure in the direction of the c-axis described by a propagation vector k = (0 0 0). At 1.8 K, the two Nd(3+) ions carry ordered magnetic moments equal respectively to 1.67(7) and 2.37(7) μ(B) for Nd1 and Nd2; these two moments exhibit a canting angle of θ = 4.3(6)°. This magnetic structure presents some similarities with that reported for Nd(5)Si(3). © 2012 IOP Publishing Ltd

Peptide crystal simulations reveal hidden dynamics

PubMed Central

Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

2013-01-01

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

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

Synthesis, Crystal Structure, and Physical Properties of New Layered Oxychalcogenide La2O2Bi3AgS6

NASA Astrophysics Data System (ADS)

Hijikata, Yudai; Abe, Tomohiro; Moriyoshi, Chikako; Kuroiwa, Yoshihiro; Goto, Yosuke; Miura, Akira; Tadanaga, Kiyoharu; Wang, Yongming; Miura, Osuke; Mizuguchi, Yoshikazu

2017-12-01

We have synthesized a new layered oxychalcogenide La2O2Bi3AgS6. From synchrotron X-ray diffraction and Rietveld refinement, the crystal structure of La2O2Bi3AgS6 was refined using a model of the P4/nmm space group with a = 4.0644(1) Å and c = 19.412(1) Å, which is similar to the related compound LaOBiPbS3, while the interlayer bonds (M2-S1 bonds) are apparently shorter in La2O2Bi3AgS6. The tunneling electron microscopy (TEM) image confirmed the lattice constant derived from Rietveld refinement (c ˜ 20 Å). The electrical resistivity and Seebeck coefficient suggested that the electronic states of La2O2Bi3AgS6 are more metallic than those of LaOBiS2 and LaOBiPbS3. The insertion of a rock-salt-type chalcogenide into the van der Waals gap of BiS2-based layered compounds, such as LaOBiS2, will be a useful strategy for designing new layered functional materials in the layered chalcogenide family.

Synthesis, Rietveld refinements, Infrared and Raman spectroscopy studies of the sodium diphosphate NaCryFe1-yP2O7 (0 ≤ y ≤ 1)

NASA Astrophysics Data System (ADS)

Bih, H.; Saadoune, I.; Bih, L.; Mansori, M.; ToufiK, H.; Fuess, H.; Ehrenberg, H.

2016-01-01

In the present study we report on the synthesis and crystal structure studies of NaCryFe1-yP2O7 sodium diphosphate solid solution (0 ≤ y ≤ 1). The X-ray diffraction shows that these compounds are isostructural with NaFeP2O7 and NaCrP2O7 (space group P21/c (C2h5) Z = 4). The Rietveld refinements based on the XRD patterns show the existence of a continuous solid solution over the whole composition range (0 ≤ y ≤ 1). A continuous evolution of the monoclinic unit cell parameters was obtained. The transition metal ions (Cr3+ and/or Fe3+) connect the diphosphate anions forming a three-dimensional network with cages filled by Na+ cations. IR and Raman spectra have been interpreted using factor group analysis. A small shift of the band frequencies is observed when Fe is substituted by Cr. The POP bridge angles are determined from Lazarev's relation and agree well with those deduced from the crystal structure refinement.

Precursor routes to quaternary intermetallics: Synthesis, crystal structure, and physical properties of clathrate-II Cs8Na16Al24Si112

NASA Astrophysics Data System (ADS)

Wei, Kaya; Dong, Yongkwan; Nolas, George S.

2016-05-01

A new quaternary clathrate-II composition, Cs8Na16Al24Si112, was synthesized by kinetically controlled thermal decomposition (KCTD) employing both NaSi and NaAlSi as the precursors and CsCl as a reactive flux. The crystal structure and composition of Cs8Na16Al24Si112 were investigated using both Rietveld refinement and elemental analysis, and the temperature dependent transport properties were investigated. Our results indicate that KCTD with multiple precursors is an effective method for the synthesis of multinary inorganic phases that are not easily accessible by traditional solid-state synthesis or crystal growth techniques.

Crystal Structure of 17α-Dihydroequilin, C18H22O2, from Synchrotron Powder Diffraction Data and Density Functional Theory

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

Kaduk, James; Gindhart, Amy; Blanton, Thomas

The crystal structure of 17α-dihydroequilin has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. 17α-dihydroequilin crystallizes in space group P212121 (#19) with a = 6.76849(1) Å, b = 8.96849(1) Å, c = 23.39031(5) Å, V = 1419.915(3) Å3, and Z = 4. Both hydroxyl groups form hydrogen bonds to each other, resulting in zig-zag chains along the b-axis. The powder diffraction pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ as the entry 00-066-1608.

X-ray diffraction studies of enkephalins. Crystal structure of [(4'-bromo) Phe4,Leu5]enkephalin.

PubMed Central

Ishida, T; Kenmotsu, M; Mino, Y; Inoue, M; Fujiwara, T; Tomita, K; Kimura, T; Sakakibara, S

1984-01-01

In order to investigate the structure-activity relationship of [Leu5]- and [Met5]enkephalins, [(4'-bromo)Phe4, Leu5]-, [(4'-bromo)Phe4, Met5]- and [Met5] enkephalins were synthesized and crystallized. The crystal structure of [(4'-bromo) Phe4, Leu5]- enkephalin was determined by X-ray diffraction method using the heavy atom method and refined to R = 0.092 by the least-squares method. The molecule in this crystal took essentially the same type I' beta-turn conformation found in [Leu5]enkephalin [Smith & Griffin (1978) Science 199, 1214-1216). On the other hand, the preliminary three-dimensional Patterson analyses showed that the most probable conformations of [(4'-bromo)Phe4,Met5]- and [Met5]enkephalins are both the dimeric extended forms. Based on these insights, the biologically active conformation of enkephalin was discussed in relation to the mu- and delta-receptors. PMID:6721829

Crystal structure of paliperidone palmitate (INVEGA SUSTENNA®), C39H57FN4O4

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

Kaduk, James A.; Dmitrienko, Artem O.; Gindhart, Amy M.

2017-08-29

The crystal structure of paliperidone palmitate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Paliperidone palmitate crystallizes in space groupP2 1/c(#14) witha= 34.415 40(35),b= 10.093 49(7),c= 10.904 92(9) Å,β= 94.3917(9)°,V= 3776.94(6) Å 3, andZ= 4. The conformation of the paliperidone fragment differs from that of the parent compound. The palmitate chain exhibits a slight twist close to the ester group. Several C–H•••O hydrogen bonds contribute to the crystal packing, which is dominated by van der Waals interactions. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1614.

Structure and Growth Control of Organic–Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals

PubMed Central

Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong

2016-01-01

Recently, organic–inorganic halide perovskites have sparked tremendous research interest because of their ground‐breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light‐emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high‐quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three‐dimensional large sized single crystals, two‐dimensional nanoplates, one‐dimensional nanowires, to zero‐dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high‐performance (opto)electronic devices. PMID:27812463

Design of Functional Layered Oxide Materials Through Understanding Structure-Property Relationships

NASA Astrophysics Data System (ADS)

Strayer, Megan E.

A fundamental understanding of structure-property relationships is imperative in the rational design of new materials for tailored applications. In this dissertation, structureproperty relationships are exploited in layered oxides and their composite materials. Recent advances in characterization techniques have allowed for more in-depth investigations into both the atomic level structure and properties of these materials. This dissertation focuses on understanding the structure-property relationships in supported catalytic systems and ferroelectric materials to aid in the rational design of functional materials. In Chapter 2, a correlation between the enthalpy of nanoparticle adsorption to oxide supports and the subsequent growth of these nanoparticles as a function of temperature is investigated. When deposited onto layered niobium oxide and tantalum oxide supports, rhodium hydroxide nanoparticles remain small and evenly dispersed upon heating to 750 °C. Using isothermal titration calorimetry, the bonding enthalpy of rhodium hydroxide nanoparticles to oxide supports is quantified for the first time under the wet synthetic conditions of catalyst preparation. Rh(OH)3 is concluded to have a strong, covalent interaction with the early transition metal oxide supports, and the interfacial bonding is hypothesized to occur through Rh - O - Nb bonding. Chapter 3 extends the studies in Chapter 2 to include supported metal, metal oxide, and metal hydroxide nanoparticles in the cobalt, nickel and copper triads. The data confirms a strong correlation between the heats of interaction and stability of the supported nanoparticles. Both experimental data and density functional theory calculations demonstrate that the support and nanoparticle compositions impact the heat of interaction and that the qualitative periodic trends of the metal bonding interaction are independent of the metal oxidation state. A strong bond is shown computationally to arise from the formation of mixed d-states between an adsorbed metal atom and a metal atom in the support. A preliminary investigation into the synthesis and stability of catalytically relevant ligand-free metal nanoparticles is presented in Chapter 4. The nanoparticles are synthesized via base hydrolysis and reduction with methanol. When deposited onto a niobium oxide support, the nanoparticles are thermally stable at temperatures up to 900 °C. The mechanism of platinum nanoparticle formation is still largely unknown, and a synthesis of rhodium and iridium ligand-free nanoparticles is reported. In Chapter 5, the n = 2 Dion Jacobson family A'LaB2O 7 (A': Rb, Cs; B: Nb, Ta) is reported as non-centrosymmetric and piezoelectric at room temperature for the first time. This non-centrosymmetry is predicted to arise from two nonpolar oxygen octahedral rotational modes condensing via the hybrid improper ferroelectricity mechanism. Rietveld refinement of synchrotron X-ray diffraction data is unable to confirm an acentric crystal structure as peak splitting is evident, revealing that multiple phases are likely present in these materials. Chapter 6 presents temperature-dependent synchrotron X-ray diffraction and neutron diffraction Rietveld refinement analysis of CsLaNb2O 7 to investigate the crystal structure and mechanism of non-centrosymmetry. The crystal structure is found to be in the centrosymmetric P4/mmm phase at 600 K and above. From 550 K to 350 K, the space group is assigned to the non-centrosymmetric Amm2 phase, as SHG signal is steadily increasing over this temperature range. Unfortunately, the 300 K and below crystal structure(s) have yet to be solved. Currently, both single-phase and dual-phase models are being refined in the synchrotron X-ray and neutron diffraction data.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

PubMed

Brunger, Axel T; Das, Debanu; Deacon, Ashley M; Grant, Joanna; Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Levitt, Michael; Schröder, Gunnar F

2012-04-01

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

PubMed Central

Brunger, Axel T.; Das, Debanu; Deacon, Ashley M.; Grant, Joanna; Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Levitt, Michael; Schröder, Gunnar F.

2012-01-01

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence. PMID:22505259

Design considerations for a Space Shuttle Main Engine turbine blade made of single crystal material

NASA Technical Reports Server (NTRS)

Abdul-Aziz, A.; August, R.; Nagpal, V.

1993-01-01

Nonlinear finite-element structural analyses were performed on the first stage high-pressure fuel turbopump blade of the Space Shuttle Main Engine. The analyses examined the structural response and the dynamic characteristics at typical operating conditions. Single crystal material PWA-1480 was considered for the analyses. Structural response and the blade natural frequencies with respect to the crystal orientation were investigated. The analyses were conducted based on typical test stand engine cycle. Influence of combined thermal, aerodynamic, and centrifugal loadings was considered. Results obtained showed that the single crystal secondary orientation effects on the maximum principal stresses are not highly significant.

Double-stranded helical twisted beta-sheet channels in crystals of gramicidin S grown in the presence of trifluoroacetic and hydrochloric acids.

PubMed

Llamas-Saiz, Antonio L; Grotenbreg, Gijsbert M; Overhand, Mark; van Raaij, Mark J

2007-03-01

Gramicidin S is a nonribosomally synthesized cyclic decapeptide antibiotic with twofold symmetry (Val-Orn-Leu-D-Phe-Pro)(2); a natural source is Bacillus brevis. Gramicidin S is active against Gram-positive and some Gram-negative bacteria. However, its haemolytic toxicity in humans limits its use as an antibiotic to certain topical applications. Synthetically obtained gramicidin S was crystallized from a solution containing water, methanol, trifluoroacetic acid and hydrochloric acid. The structure was solved and refined at 0.95 A resolution. The asymmetric unit contains 1.5 molecules of gramicidin S, two trifluoroacetic acid molecules and ten water molecules located and refined in 14 positions. One gramicidin S molecule has an exact twofold-symmetrical conformation; the other deviates from the molecular twofold symmetry. The cyclic peptide adopts an antiparallel beta-sheet secondary structure with two type II' beta-turns. These turns have the residues D-Phe and Pro at positions i + 1 and i + 2, respectively. In the crystals, the gramicidin S molecules line up into double-stranded helical channels that differ from those observed previously. The implications of the supramolecular structure for several models of gramicidin S conformation and assembly in the membrane are discussed.

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

Structure cristalline du composé Hg3-xSbx(S+Se)2+xI2-x (x ≃ 0.1)

PubMed Central

Kars, Mohammed; Herrero, Adrian Gómez; Roisnel, Thierry; Rebbah, Allaoua; Otero-Diáz, L. Carlos

2016-01-01

Single crystals of the mercury chalcohalide Hg3-xSbx(S+Se)2+xI2-x (x ≃ 0.1) (mercury anti­mony sulfide selenide iodide), were grown by a chemical transport reaction. The structure contains three independent A (Hg/Sb) atoms; each atom is strongly covalently bonded with two X (Se/S) atoms to form approximately linear X–A–X units. The X–A–X units link to form A 4 X 4 rings, which are combined into infinite crankshaft-type bands running along the [100] direction. Four equatorial E (I/X = Se,S) atoms at relatively long distances complete the distorted octa­hedral coordination of A (Hg/Sb). The crystal under investigation was twinned by non-merohedry with a refined twin domain fraction of 0.814 (6):0.186 (6). The structure is isotypic with Hg3Se2I2 [Beck & Hedderich (2000 ▸). J. Solid State Chem. 151, 73–76], but the current determination reveals a coupled substitution, with partial replacement of Hg+2 by Sb+3, balanced by the equivalent substitution of I−1 by S−2 and Se−2. Bond-valence calculations are consistent with this relative substitution model. PMID:27006793

New insights into the crystal chemistry of agardite-(Ce): refinement of the crystal structure, hydrogen bonding, and epitaxial intergrowths with the Sb-analogue of auriacusite

NASA Astrophysics Data System (ADS)

Aksenov, Sergey M.; Chukanov, Nikita V.; Göttlicher, Jörg; Möckel, Steffen; Varlamov, Dmitriy; Van, Konstantin V.; Rastsvetaeva, Ramiza K.

2018-01-01

Agardite-(Ce) from Clara Mine, Schwarzwald, Germany, has been investigated by means of electron microprobe analysis, single-crystal X-ray analysis, XANES spectroscopy and IR spectroscopy. Hexagonal unit-cell parameters are: a = 13.598(6), c = 5.954(3) Å; V = 953.5(2) Å3; space group P63/ m. The structure has been solved and refined to final R 1 = 3.87%, w R 2 = 5.02 for 786 I > 3 σ( I). Hydrogen atoms have been localized. The crystal-chemical formula is ( Z = 2): A(1)(Ce0.82Ca0.14Sr0.04)Σ1.00 A(2)(Ca0.03Ce0.02)Σ0.05 [Cu5.75(Fe3+, Mn)0.20]Σ5.95 [ T(1)(AsO4) 2.96 T(2) (SbO4)0.04)]Σ3.00 (OH)5.96O0.04·3H2O. Hydrogen bonding in agardite-series minerals has been characterized for the first time. IR spectra of agardite-(Ce) and agardite-(Nd) from Lavrion used for comparison, as well as structural data indicate the presence of isolated H+ cations that do not form strong covalent bonds with coordinating O atoms. Agardite-(Ce) from Clara Mine forms epitaxial growths with the Sb-analogue of auriacusite. The latter mineral was characterized by EDS analyses; its typical empirical formulae are {Ca}_{0.0 6} {Ce}_{0.0 4} {Fe}^{ 3+ }{}_{ 1.0 6} {Cu}_{0. 8 9}[(SbO4)0.58(AsO4)0.38(SiO4)0.04]Σ1.00(O,OH) and {Ca}_{0.0 7 5} {Ce}_{0.0 4} {Fe}^{ 3+ }{}_{0. 9 3} {Cu}_{0. 9 7}[(SbO4)0.59(AsO4)0.35(SiO4)0.06]Σ1.00(O,OH). The formation of uniaxial growths of the Sb-analogue of auriacusite and agardite-(Ce) is caused by the close values of their c parameters (for auriacusite s.s. c = 5.9501(5) Å). Three-valence state of iron and five-valence of antimony in both minerals has been validated by means of Fe K- and Sb L 2,3-edge XANES spectroscopy.

Phase diagram of the relaxor ferroelectric (1- x )Pb(Mg 1/3Nb 2/3)O 3+ x PbTiO 3 revisited: a neutron powder diffraction study of the relaxor skin effect

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

Phelan, D.; Rodriguez, E. E.; Gao, J.

2014-11-17

We revisit the phase diagram of the relaxor ferroelectric PMN- xPT using neutron powder diffraction to test suggestions that residual oxygen vacancies and/or strain affect the ground state crystal structure. Powdered samples of PMN- xPT were prepared with nominal compositions of x = 0:10, 0.20, 0.30, and 0.40 and divided into two identical sets, one of which was annealed in air to relieve grinding-induced strain and to promote an ideal oxygen stoichiometry. For a given composition and temperature the same structural phase is observed for each specimen. However, the distortions in all of the annealed samples are smaller than thosemore » in the as-grown samples. Further, the diffraction patterns for x = 0:10, 0.20, and 0.30 are best refined using the monoclinic Cm space group. By comparing our neutron diffraction results to those obtained on single crystals having similar compositions, we conclude that the relaxor skin effect in PMN- xPT vanishes on the Ti-rich side of the morphotropic phase boundary.« less

Crystal structure and phase transition of thermoelectric SnSe.

PubMed

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

2016-06-01

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

Synthesis and structure determination of La{sub 8}Ti{sub 10}S{sub 24}O{sub 4}

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

Cario, L.; Deudon, C.; Meerschaut, A.

1998-02-15

The new compound La{sub 8}Ti{sub 10}S{sub 24}O{sub 4} has been prepared from a mixture of La{sub 2}Ti{sub 2}O{sub 7} and La{sub 2}O{sub 3} (in a 5:1 ratio) heated at 1,200 C under a H{sub 2}S gas flow. This new quaternary phase was obtained due to an incomplete sulfidizing process. Single-crystal X-ray diffraction studies show that La{sub 8}Ti{sub 10}S{sub 24}O{sub 4} crystallizes in space group P4/mmm, with Z = 1, in a cell of dimensions a = b = 10.421 {angstrom} and c = 8.384 {angstrom}. Least-squares refinement converged to values of R - 0.045 and R{sub w} = 0.048. Themore » structure can be viewed as a stacking of two types of layers along the {rvec c} axis. These layers are built up from infinite rutile-like chains (Ti octahedra) that cross perpendicularly. La atoms, in a tricapped prismatic coordination, are located in tunnels that develop parallel to the {rvec c} direction.« less

Novel Electronically Conducting Tellurium Oxides

NASA Astrophysics Data System (ADS)

Subramanian, Mas; Siritanon, Theerunan; Sleight, Arthur

2010-03-01

Tellurium oxides seldom show measurable electronic conductivity. Tellurium oxides that appear to have Te^5+ contain Te^4+ and Te^6+ in two distinct crystallographic sites and are electronic insulators. Here we report on the synthesis and characterization of several new tellurium rich oxides of the general formula, CsMxTe2-xO6, crystallizing in modified pyrochlore structure. Most of the compounds reported here are black in color with some exhibiting good electronic conductivities (2 S/cm) and Seebeck measurements indicate all are n-type. The observation of high electronic conductivities in compounds like CsGe0.5Te1.5O6, CsAl0.33Te1.67O6 confirms that observed conductivity is arising from doping of electrons into the empty 5s orbitals of Te^6+. This reduction is apparently accompanied with some small deviation from the ideal formula: oxygen content and/or ratio of cations on octahedral sites. This is in consistent with single-crystal X-ray as well as powder neutron diffraction structure refinements and the observed sign of the Seebeck coefficient. To our knowledge, this is a first observance of high electrical conductivity in mixed valent tellurium oxides.

The Crystal and Molecular Structure of an Asymmetric Diacetylene Monomer, 6-(2-methyl-4-nitroanilino)-2,4-hexadiyne-1-ol

NASA Technical Reports Server (NTRS)

Vlasse, Marcus; Paley, Mark S.

1993-01-01

The crystal and molecular structure of an asymmetric diacetylene monomer has been determined from x-ray diffraction data. The crystals, obtained from an acetone/pentane solution, are orthorhombic, Fdd2 with Z = 16 in a unit cell having dimensions of a = 42.815(6) A, b = 22.224(5) A, c = 4.996(l) A. The structure was solved by direct methods and refined by least- squares techniques to an R(sub F) of 6.4% for 988 reflections and 171 variables. The diacetylene chains are disposed in the unit cell in a complex manner in order to satisfy the hydrogen- bonding, crystal packing, and symmetry requirements of the system. The solid state polymerization mechanism is discussed with respect to the geometric disposition of the diacetylene chains. These chains are far apart and incorrectly oriented with respect to each other to permit polymerization in the crystal by means of 1,4-addition, consistent with the Baughman mechanistic model.

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

DOE PAGES

Lyubimov, Artem Y.; Murray, Thomas D.; Koehl, Antoine; ...

2015-03-27

X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat formore » conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.« less

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

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

Lyubimov, Artem Y.; Murray, Thomas D.; Koehl, Antoine

X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat formore » conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.« less

Structural, mechanical, electrical and optical properties of a new lithium boro phthalate NLO crystal synthesized by a slow evaporation method

NASA Astrophysics Data System (ADS)

Mohanraj, K.; Balasubramanian, D.; Jhansi, N.

2017-11-01

A new non-linear optical (NLO) single crystal of lithium boro phthalate (LiBP) was grown by slow solvent evaporation technique. The powder sample was subjected to powder X-ray diffraction (PXRD) to find its crystalline nature and the crystal structure of the grown crystal was determined using single crystal X-ray (SXRD) diffraction analysis. The Fourier Transform Infrared (FTIR) spectrum was recorded for grown crystal to identify the various functional groups present in the compound. The mechanical property of the LiBP single crystal was studied using Vickers microhardness tester. The dielectric constant and dielectric loss measurements were carried out for the grown crystal at various temperatures. The grown crystal was subjected to UV-Visible Spectral Studies to analyze the linear optical behavior of the grown crystal. The Kurtz-Perry Powder technique was employed to measure the Second Harmonic Generation efficiency of the grown crystal.

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.

The comparison of approaches to the solid-state NMR-based structural refinement of vitamin B1 hydrochloride and of its monohydrate

NASA Astrophysics Data System (ADS)

Czernek, Jiří; Pawlak, Tomasz; Potrzebowski, Marek J.; Brus, Jiří

2013-01-01

The 13C and 15N CPMAS SSNMR measurements were accompanied by the proper theoretical description of the solid-phase environment, as provided by the density functional theory in the pseudopotential plane-wave scheme, and employed in refining the atomic coordinates of the crystal structures of thiamine chloride hydrochloride and of its monohydrate. Thus, using the DFT functionals PBE, PW91 and RPBE, the SSNMR-consistent solid-phase structures of these compounds are derived from the geometrical optimization, which is followed by an assessment of the fits of the GIPAW-predicted values of the chemical shielding parameters to their experimental counterparts.

Phase equilibria and crystal structure of the complex oxides in the Sr Fe Co O system

NASA Astrophysics Data System (ADS)

Aksenova, T. V.; Gavrilova, L. Ya.; Cherepanov, V. A.

2008-06-01

Phase relations in the Sr-Fe-Co-O system have been investigated at 1100 °C in air by X-ray powder diffraction on quenched samples. Solid solutions of the form SrFe 1-xCo xO 3-δ (0⩽ x⩽0.7), Sr 3Fe 2-yCo yO 7-δ (0⩽ y⩽0.4) and Sr 4Fe 6-zCo zO 13±δ (0⩽ z⩽1.6) were prepared by solid-state reaction and by the sol-gel method. The structural parameters of single-phase samples were refined by the Rietveld profile method. The variation of the lattice parameters with composition has been determined for each solid solution and a cross-section of the phase diagram at 1100 °C in air for the entire Sr-Fe-Co-O system has been constructed.

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Structured laser gain-medium by new bonding for power micro-laser

NASA Astrophysics Data System (ADS)

Kausas, Arvydas; Zheng, Lihe; Taira, Takunori

2017-02-01

In this work, we have compared the Q-switched performance of single rod crystal to a newly developed distributed face cooling structure. This structure was made by surface activated bonding technology and allowed to combine transparent heatsink to a gain crystal at room temperature. The Sapphire and Nd3+:YAG crystal plates were combined in this fashion to produce eight crystal chip which was further used to obtain Q-switch pulses with Cr4+:YAG crystal as saturable absorber. Energy of 9 mJ and pulse duration of 815 ps were achieved. Although the energy obtained with single rod system was 10 mJ, the degradation of the beam prevents such crystal to be used in further applications. This is the first demonstration of distributed face cooling system outperformed conventionally single rod system.

Crystal structure of carnidazole form II from synchrotron X-ray powder diffraction: structural comparison with form I, the hydrated form and the low energy conformations in vacuo.

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van den Mooter, Guy; De Ridder, Dirk J A; Schenk, Henk

2006-10-01

The crystal structure of carnidazole form II, O-methyl [2-(2-methyl-5-nitro-1H-imidazole-1-yl)ethyl]thiocarbamate, has been determined using synchrotron X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined by the Rietveld method. For structure solution, 12 degrees of freedom were defined: one motion group and six torsions. Form II crystallizes in space group P2(1)/n, Z=4, with unit cell parameters after Rietveld refinement: a=13.915(4), b=8.095(2), c=10.649(3) A, beta=110.83(1) degrees, and V=1121.1(5) A3. The two polymorphic forms, as well as the hydrate, crystallize in the monoclinic space group P2(1)/n having four molecules in the cell. In form II, the molecules are held together by forming two infinite zig-zag chains via hydrogen bonds of the type N--H...N, the same pattern as in form I. A conformational study of carnidazole, at semiempirical PM3 level, was performed using stochastic approaches based on modification of the flexible torsion angles. The values of the torsion angles for the molecules of the two polymorphic forms and the hydrate of carnidazole are compared to those obtained from the conformational search. Form I and form II are enantiotropic polymorphic pairs this agrees with the fact that the two forms are conformational polymorphs. Copyright (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association

The effect of Fe 3+ doping in Potassium Hydrogen Phthalate single crystals on structural and optical properties

NASA Astrophysics Data System (ADS)

Kumar, R. Ashok; Sivakumar, N.; Vizhi, R. Ezhil; Babu, D. Rajan

2011-02-01

This work investigates the influence of iron doping on Potassium Hydrogen Phthalate (KHP) single crystals by the slow evaporation solution growth technique. Factors such as evaporation rate, solution pH, solute concentration, super saturation limit, etc. are very important in order to have optically transparent single crystals. As part of the work, the effects of metallic salt FeCl 3 in different concentrations were analyzed with pure KHP. Powder X-ray diffraction suggests that the grown crystals are crystallized in the orthorhombic structure. The functional groups and the effect of moisture on the doped crystals can be analyzed with the help of a FTIR spectrum. The pure and doped KHP single crystal shows good transparency in the entire visible region, which is suitable for optical device applications. The refractive indices along b axis of pure and doped KHP single crystals were analyzed by the prism coupling technique. The emission of green light with the use of a Nd:YAG laser ( λ=1064 nm) confirmed the second harmonic generation properties of the grown crystals.

Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr{sub 5}Fe{sub 6}O{sub 15.4}

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

Lepoittevin, Christophe, E-mail: christophe.lepoittevin@neel.cnrs.fr

2016-10-15

The crystal structure of the strontium ferrite Sr{sub 5}Fe{sub 6}O{sub 15.4}, was solved by direct methods on electron diffraction tomography data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern. - Highlights: • Complex structure of Sr{submore » 5}Fe{sub 6}O{sub 15.4} solved by electron diffraction tomography. • Observed Fourier maps allow determining missing oxygen atoms in the structure. • Structural model refined from powder X-ray diffraction data. • Intergrowth between quadruple perovskite layer with double rock-salt-type layer.« less

Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

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

Post,J.; Bish, D.; Heaney, P.

2007-01-01

Rietveld refinements using synchrotron powder X-ray diffraction data were used to study the crystal structure and dehydration behavior of sepiolite from Durango, Mexico. The room-temperature (RT) sepiolite structure in air compares well with previous models but reveals an additional zeolitic H{sub 2}O site. The RT structure under vacuum retained only {approx}1/8 of the zeolitic H{sub 2}O and the volume decreased by 1.3%. Real-time, temperature-resolved synchrotron powder X-ray diffraction data and Rietveld refinements were used to investigate the behavior of the sepiolite structure from 300 to 925 K. Rietveld refinements revealed that most of the zeolitic H{sub 2}O is lost bymore » {approx}390 K, accompanied by a decrease in the a and c unit-cell parameters. Above {approx}600 K the sepiolite structure folds as one-half of the crystallographically bound H{sub 2}O is lost. Rietveld refinements of the 'anhydrous' sepiolite structure reveal that, in general, unit-cell parameters a and b and volume steadily decrease with increasing temperature; there is an obvious change in slope at {approx}820 K suggesting a phase transformation coinciding with the loss of the remaining bound H{sub 2}O molecule.« less

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.

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

Crystallization in lactose refining-a review.

PubMed

Wong, Shin Yee; Hartel, Richard W

2014-03-01

In the dairy industry, crystallization is an important separation process used in the refining of lactose from whey solutions. In the refining operation, lactose crystals are separated from the whey solution through nucleation, growth, and/or aggregation. The rate of crystallization is determined by the combined effect of crystallizer design, processing parameters, and impurities on the kinetics of the process. This review summarizes studies on lactose crystallization, including the mechanism, theory of crystallization, and the impact of various factors affecting the crystallization kinetics. In addition, an overview of the industrial crystallization operation highlights the problems faced by the lactose manufacturer. The approaches that are beneficial to the lactose manufacturer for process optimization or improvement are summarized in this review. Over the years, much knowledge has been acquired through extensive research. However, the industrial crystallization process is still far from optimized. Therefore, future effort should focus on transferring the new knowledge and technology to the dairy industry. © 2014 Institute of Food Technologists®

Structure of Cs{sub 4}(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}) single crystals

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

Makarova, I. P., E-mail: makarova@crys.ras.ru; Grebenev, V. V.; Vasil’ev, I. I.

2016-01-15

Single crystals of Cs{sub 4}(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}) are synthesized and studied for the first time. The new compound is found in the course of studies of the phase diagram of the CsHSO{sub 4}–CsH{sub 2}PO{sub 4}–H{sub 2}O triple system. Data on the atomic crystal structure of single-crystalline and powder specimens, as well as on structural phase transitions, are obtained.

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

Light emission from organic single crystals operated by electrolyte doping

NASA Astrophysics Data System (ADS)

Matsuki, Keiichiro; Sakanoue, Tomo; Yomogida, Yohei; Hotta, Shu; Takenobu, Taishi

2018-03-01

Light-emitting devices based on electrolytes, such as light-emitting electrochemical cells (LECs) and electric double-layer transistors (EDLTs), are solution-processable devices with a very simple structure. Therefore, it is necessary to apply this device structure into highly fluorescent organic materials for future printed applications. However, owing to compatibility problems between electrolytes and organic crystals, electrolyte-based single-crystal light-emitting devices have not yet been demonstrated. Here, we report on light-emitting devices based on organic single crystals and electrolytes. As the fluorescent materials, α,ω-bis(biphenylyl)terthiophene (BP3T) and 5,6,11,12-tetraphenylnaphthacene (rubrene) single crystals were selected. Using ionic liquids as electrolytes, we observed clear light emission from BP3T LECs and rubrene EDLTs.

Solid state parameters, structure elucidation, High Resolution X-Ray Diffraction (HRXRD), phase matching, thermal and impedance analysis on L-Proline trichloroacetate (L-PTCA) NLO single crystals.

PubMed

Kalaiselvi, P; Raj, S Alfred Cecil; Jagannathan, K; Vijayan, N; Bhagavannarayana, G; Kalainathan, S

2014-11-11

Nonlinear optical single crystal of L-Proline trichloroacetate (L-PTCA) was successfully grown by Slow Evaporation Solution Technique (SEST). The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm the structure. From the single crystal XRD data, solid state parameters were determined for the grown crystal. The crystalline perfection has been evaluated using high resolution X-ray diffractometer. The frequencies of various functional groups were identified from FTIR spectral analysis. The percentage of transmittance was obtained from UV Visible spectral analysis. TGA-DSC measurements indicate the thermal stability of the crystal. The dielectric constant, dielectric loss and ac conductivity were measured by the impedance analyzer. The DC conductivity was calculated by the cole-cole plot method. Copyright © 2014 Elsevier B.V. All rights reserved.

The effect of aluminum alloying on strength properties and deformation mechanisms of the <123> Hadfield steel single crystals

NASA Astrophysics Data System (ADS)

Astafurova, E. G.; Tukeev, M. S.; Chumlyakov, Yu. I.

2007-10-01

The role of aluminum alloying on strength properties and deformation mechanisms (slip, twinning) of <123> single crystals of Hadfield steel under tensile loading at T = 300 K is demonstrated. It is found out that aluminum alloying suppresses twinning deformation in the <123> single crystals and, during slip, results in a dislocation structure change from a uniform dislocation distribution to a planar dislocation structure.

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

PubMed Central

van Beusekom, Bart; Touw, Wouter G.; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L.; Perrakis, Anastassis

2017-01-01

Abstract The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H‐bond) distances as a source of information. However, H‐bond restraints can improve structures at low resolution where diffraction data are limited. To improve low‐resolution structure refinement, we present methods for deriving H‐bond information either globally from well‐refined high‐resolution structures from the PDB‐REDO databank, or specifically from on‐the‐fly constructed sets of homologous high‐resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low‐resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB‐REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. PMID:29168245

Homology-based hydrogen bond information improves crystallographic structures in the PDB.

PubMed

van Beusekom, Bart; Touw, Wouter G; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L; Perrakis, Anastassis; Joosten, Robbie P

2018-03-01

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. © 2017 The Protein Society.

Ge 3P 6Si 2O 25: A cage structure closely related to the intersecting tunnel structure KMo 3P 6Si 2O 25

NASA Astrophysics Data System (ADS)

Leclaire, A.; Raveau, B.

1988-08-01

A germanosilicophosphate Ge 3P 6Si 2O 25 has been isolated. Its structure was solved from a single-crystal study in the space group P overline31c . Its cell parameters are a = b = 7.994(1) Å, c = 16.513(2) Å, Z = 2. The refinement by full-matrix least-squares calculations leads to R = 0.043 with 686 independent reflections. The structure of this oxide is built up from corner-sharing PO 4 and SiO 4 tetrahedra and GeO 6 octahedra. One observes a feature common to several silicophosphates: the presence of the structural unit P 6Si 2O 25 built up from a disilicate group sharing its corners with six PO 4 tetrahedra. The structural relationships between this oxide and the silicophosphates AMo 3P 6Si 2O 25 and Si 3P 6Si 2O 25 (or Ge 3P 6 Ge 2O 25) are described.

The crystal structure of galgenbergite-(Ce), CaCe2(CO3)4•H2O

NASA Astrophysics Data System (ADS)

Walter, Franz; Bojar, Hans-Peter; Hollerer, Christine E.; Mereiter, Kurt

2013-04-01

Galgenbergite-(Ce) from the type locality, the railroad tunnel Galgenberg between Leoben and St. Michael, Styria, Austria, was investigated. There it occurs in small fissures of an albite-chlorite schist as very thin tabular crystals building rosette-shaped aggregates associated with siderite, ancylite-(Ce), pyrite and calcite. Electron microprobe analyses gave CaO 9.49, Ce2O3 28.95, La2O3 11.70, Nd2O3 11.86, Pr2O3 3.48, CO2 30.00, H2O 3.07, total 98.55 wt.%. CO2 and H2O calculated by stoichiometry. The empirical formula (based on Ca + REE ∑3.0) is C{{a}_{1.00 }}{{( {C{{e}_{1.04 }}L{{a}_{0.42 }}N{{d}_{0.42 }}P{{r}_{0.12 }}} )}_{2.00 }}{{( {C{{O}_3}} )}_4}\\cdot {{H}_2}O , and the simplified formula is CaC{{e}_2}{{( {C{{O}_3}} )}_4}\\cdot {{H}_2}O . According to X-ray single crystal diffraction galgenbergite-(Ce) is triclinic, space group Poverline{1},a=6.3916(5) , b = 6.4005(4), c = 12.3898(9) Å, α = 100.884(4), β = 96.525(4), γ = 100.492(4)°, V = 483.64(6) Å3, Z = 2. The eight strongest lines in the powder X-ray diffraction pattern are [ d calc in Å/( I)/ hkl]: 5.052/(100)/011; 3.011/(70)/0-22; 3.006/(66)/004; 5.899/(59)/-101; 3.900/(51)/1-12; 3.125/(46)/-201; 2.526/(42)/022; 4.694/(38)/-102. The infrared absorption spectrum reveals H2O (OH-stretching mode at 3,489 cm-1, HOH bending mode at 1,607 cm-1) and indicates the presence of distinctly non-equivalent CO3-groups by double and quadruple peaks of their ν1, ν2, ν3 and ν4 modes. The crystal structure of galgenbergite-(Ce) was refined with X-ray single crystal data to R1 = 0.019 for 2,448 unique reflections ( I > 2 σ( I)) and 193 parameters. The three cation sites of the structure Ca(1), Ce(2) and Ce(3) have a modest mixed site occupation by Ca and small amount of REE (Ce, La, Pr, Nd) and vice versa. The structure is based on double layers parallel to (001), which are composed of Ca(1)Ce(2)(CO3)2 single layers with an ordered chessboard like arrangement of Ca and Ce, and with a roof tile-like stacking of the CO3 groups. Perpendicular to (001) the double layers are connected to a triclinic framework structure with good cleavage parallel to (001) by a differently organized and more open part of the structure formed by Ce(3)(CO3)2(H2O). Based on the topology of the CaCe(CO3)2 single layer in galgenbergite-(Ce), structural relationships to rutherfordine, to aragonite and ancylite type minerals, and to lanthanite are outlined.

Low-resolution structure of Drosophila translin

PubMed Central

Kumar, Vinay; Gupta, Gagan D.

2012-01-01

Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to Rwork (Rfree) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin–TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers. PMID:23650579

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.

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

Aliev, Ziya S., E-mail: ziyasaliev@gmail.com; Institute of Physics, ANAS, H.Javid ave. 131, AZ1143 Baku; Donostia International Physics Center

Single crystals of the ternary copper compounds CuTlS and CuTlSe have been successfully grown from stoichiometric melt by using vertical Bridgman-Stockbarger method. The crystal structure of the both compounds has been determined by powder and single crystal X-Ray diffraction. They crystallize in the PbFCl structure type with two formula units in the tetragonal system, space group P4/nmm, a=3.922(2); c=8.123(6); Z=2 and a=4.087(6); c=8.195(19) Å; Z=2, respectively. The band structure of the reported compounds has been analyzed by means of full-potential linearized augmented plane-wave (FLAPW) method based on the density functional theory (DFT). Both compounds have similar band structures and aremore » narrow-gap semiconductors with indirect band gap. The resistivity measurements agree with a semiconductor behavior although anomalies are observed at low temperature. - Graphical abstract: The crystal structures of CuTl and CuTlSe are isostructural with the PbFCl-type and the superconductor LiFeAs-type tetragonal structure. The band structure calculations confirmed that they are narrow-gap semiconductors with indirect band gaps of 0.326 and 0.083 eV. The resistivity measurements, although confirming the semiconducting behavior of both compounds exhibit unusual anomalies at low temperatures. - Highlights: • Single crystals of CuTlS and CuTlSe have been successfully grown by Bridgman-Stockbarger method. • The crystal structure of the both compounds has been determined by single crystal XRD. • The band structure of the both compounds has been analyzed based on the density functional theory (DFT). • The resistivity measurements have been carried out from room temperature down to 10 K.« less

High-pressure/high-temperature synthesis and characterization of the first palladium or platinum containing lithium transition-metal sulfides Li2M3S4 (M=Pd, Pt)

NASA Astrophysics Data System (ADS)

Heymann, Gunter; Niehaus, Oliver; Krüger, Hannes; Selter, Philipp; Brunklaus, Gunther; Pöttgen, Rainer

2016-10-01

The new lithium transition-metal sulfides Li2M3S4 (M=Pd, Pt) were obtained via multianvil high-pressure/high-temperature syntheses at 8 GPa and 1150 °C starting from a stoichiometric mixture of lithium nitride, sulfur, and palladium or platinum. Single crystal structure analyses indicated the space group P21/c (no. 14) with the following lattice parameters and refinement results: a=492.9(1), b=1005.9(2), c=614.9(2) pm, β=110.9 (1)°, R1=0.0165, wR2=0.0308 (all data) for Li2Pd3S4 and a=498.2(1), b=1005.5(2), c=613.0(2) pm, β=110.8(1)°, R1=0.0215, wR2=0.0450 (all data) for Li2Pt3S4. The crystal structures are built up from two distinct Pd/Pt sites, one of which is a special position (0,0,0), two sulfur sites, and one lithium site. The atoms Pd2/Pt2 form isolated square planar PdS4/PtS4 units, whereas the Pd1/Pt1 atoms form pairs of square planar PdS4/PtS4 units, which are connected via a common edge. These two structural motives built up a three-dimensional network structure by linking through common corners. The lithium atoms are positioned inside of the so formed channels. Li2M3S4 (M=Pd, Pt) are isostructural to the minerals jaguéite, Cu2Pd3Se4 and chrisstanleyite, Ag2Pd3Se4, which are up to now the only representatives of this structure type. Both compounds were studied with respect to their magnetic properties and can be classified as Pauli paramagnetic or diamagnetic. Regarding the possibility of lithium mobility inside the channels, of the structure, solid state 7Li NMR and high-temperature single crystal investigations revealed localization of the lithium atoms on their crystallographic sites.

Sponge-like nanoporous single crystals of gold

PubMed Central

Khristosov, Maria Koifman; Bloch, Leonid; Burghammer, Manfred; Kauffmann, Yaron; Katsman, Alex; Pokroy, Boaz

2015-01-01

Single crystals in nature often demonstrate fascinating intricate porous morphologies rather than classical faceted surfaces. We attempt to grow such crystals, drawing inspiration from biogenic porous single crystals. Here we show that nanoporous single crystals of gold can be grown with no need for any elaborate fabrication steps. These crystals are found to grow following solidification of a eutectic composition melt that forms as a result of the dewetting of nanometric thin films. We also present a kinetic model that shows how this nano-porous single-crystalline structure can be obtained, and which allows the potential size of the porous single crystal to be predicted. Retaining their single-crystalline nature is due to the fact that the full crystallization process is faster than the average period between two subsequent nucleation events. Our findings clearly demonstrate that it is possible to form single-crystalline nano porous metal crystals in a controlled manner. PMID:26554856

2D photonic crystal complete band gap search using a cyclic cellular automaton refination

NASA Astrophysics Data System (ADS)

González-García, R.; Castañón, G.; Hernández-Figueroa, H. E.

2014-11-01

We present a refination method based on a cyclic cellular automaton (CCA) that simulates a crystallization-like process, aided with a heuristic evolutionary method called differential evolution (DE) used to perform an ordered search of full photonic band gaps (FPBGs) in a 2D photonic crystal (PC). The solution is proposed as a combinatorial optimization of the elements in a binary array. These elements represent the existence or absence of a dielectric material surrounded by air, thus representing a general geometry whose search space is defined by the number of elements in such array. A block-iterative frequency-domain method was used to compute the FPBGs on a PC, when present. DE has proved to be useful in combinatorial problems and we also present an implementation feature that takes advantage of the periodic nature of PCs to enhance the convergence of this algorithm. Finally, we used this methodology to find a PC structure with a 19% bandgap-to-midgap ratio without requiring previous information of suboptimal configurations and we made a statistical study of how it is affected by disorder in the borders of the structure compared with a previous work that uses a genetic algorithm.

Photomagnetic switching of heterometallic complexes [M(dmf)4(H2O)3(mu-CN)Fe(CN)5].H2O (M=Nd, La, Gd, Y) analyzed by single-crystal X-ray diffraction and ab initio theory.

PubMed

Svendsen, Helle; Overgaard, Jacob; Chevallier, Marie A; Collet, Eric; Chen, Yu-Sheng; Jensen, Frank; Iversen, Bo B

2010-06-25

Single-crystal X-ray diffraction measurements have been carried out on [Nd(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (1; dmf=dimethylformamide), [Nd(dmf)(4)(H(2)O)(3)(mu-CN)Co(CN)(5)].H(2)O (2), [La(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (3), [Gd(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (4), and [Y(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (5), at 15(2) K with and without UV illumination of the crystals. Significant changes in unit-cell parameters were observed for all the iron-containing complexes, whereas 2 showed no response to UV illumination. Photoexcited crystal structures have been determined for 1, 3, and 4 based on refinements of two-conformer models, and excited-state occupancies of 78.6(1), 84(6), and 86.6(7)% were reached, respectively. Significant bond-length changes were observed for the Fe-ligand bonds (up to 0.19 A), the cyano bonds (up to 0.09 A), and the lanthanide-ligand bonds (up to 0.10 A). Ab initio theoretical calculations were carried out for the experimental ground-state geometry of 1 to understand the electronic structure changes upon UV illumination. The calculations suggest that UV illumination gives a charge transfer from the cyano groups on the iron atom to the lanthanide ion moiety, {Nd(dmf)(4)(H(2)O)(3)}, with a distance of approximately 6 A from the iron atom. The charge transfer is accompanied by a reorganization of the spin state on the {Fe(CN)(6)} complex, and a change in geometry that produces a metastable charge-transfer state with an increased number of unpaired electrons, thus accounting for the observed photomagnetic effect.

An Excel Spreadsheet for a One-Dimensional Fourier Map in X-ray Crystallography

ERIC Educational Resources Information Center

Clegg, William

2004-01-01

The teaching of crystal structure determination with single-crystal X-ray diffraction at undergraduate level faces numerous challenges. Single-crystal X-ray diffraction is used in a vast range of chemical research projects and forms the basis for a high proportion of structural results that are presented to high-school, undergraduate, and graduate…

Growth and microtopographic study of CuInSe{sub 2} single crystals

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

Chauhan, Sanjaysinh M.; Chaki, Sunil, E-mail: sunilchaki@yahoo.co.in; Deshpande, M. P.

2016-05-23

The CuInSe{sub 2} single crystals were grown by chemical vapour transport (CVT) technique using iodine as transporting agent. The elemental composition of the as-grown CuInSe{sub 2} single crystals was determined by energy dispersive analysis of X-ray (EDAX). The unit cell crystal structure and lattice parameters were determined by X-ray diffraction (XRD) technique. The surface microtopographic study of the as-grown CuInSe{sub 2} single crystals surfaces were done to study the defects, growth mechanism, etc. of the CVT grown crystals.

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

Structure cristalline de NaLiYb/sub 2/F/sub 8/: composes isotypes

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

Dib, A.; Gorius, M.F.; Aleonard, S.

1986-11-15

NaLiYb/sub 2/F/sub 8/ crystallizes in the monoclinic system, space group C2/c, with a = 10.3516(9), b = 8.2069(9), c = 6,9674(7) A, ..beta.. = 90/sup 0/, Z = 4. The crystal structure has been solved from single crystal diffractometer measurements (AgK..cap alpha.. radiation) using Patterson and Fourier syntheses and refined by a least-squares method. The final R value is 0.021 for 1756 independent observed reflections. Two YbF/sub 8/ polyhedra share one of their edges to form Yb/sub 2/F/sub 14/ groups which are three-dimensionally linked and create cavities in which Na and Li are located. Yb/sub 2/F/sub 14/ groups share twomore » of their edges with these of one NaF/sub 7/ (or NaF/sub 9/ polyhedron to form Y/sub 2/NaF/sub 20/ blocks. As well, the structure may be described by the packing of planes formed by these two-dimensionally linked blocks. The description of this structure is compared with that ascribed to NaLiY/sub 2/F/sub 8/, which has been described in the monoclinic system, space group P2/sub 1//m, with a' = (a + b)/2, b' = c,c' = (b - a)/2, Z = 2. It is shown that positions of the atoms confer pseudoorthorhombic symmetry on the cell. Lattice parameters of isotypic compounds are given in the pseudoorthorhombic lattice and they are compared with those recently published with the structure described in the monoclinic system, space group P2/sub 1//m.« less

Three NiAs-Ni 2In Type Structures in the Mn-Sn System

NASA Astrophysics Data System (ADS)

Elding-Pontén, Margareta; Stenberg, Lars; Larsson, Ann-Kristin; Lidin, Sven; Ståhl, Kenny

1997-03-01

TheB8-type structure field of the Mn-Sn system has been investigated. Two high temperature phases (HTP1 and HTP2) and one low temperature phase (Mn3Sn2) were found. They all crystallize with the NiAs structure type with part of the trigonal bipyramidal interstices filled by manganese atoms in an ordered manner. The ordering as well as the manganese content is different for the three phases, giving rise to three different orthorhombic superstructures. Mn3Sn2seems to have the lowest manganese content, since the corresponding basal unit cell is smaller than for HTP1-2. Structural models of the phases are based on selected area electron diffraction, X-ray powder diffraction, and preliminary single crystal X-ray measurements. The ideal cell parameters found are (a=7ahex,b=3ahex,c=chex), (a=5ahex,b=3ahex,c=chex), and (a=2ahex,b=3ahex,c=chex) for HTP1, HTP2, and Mn3Sn2, respectively. The crystal structure of Mn3Sn2has been refined by means of the Rietveld method from X-ray powder diffraction data. Mn3Sn2is orthorhombic,Pnma,a=7.5547(2),b=5.4994(2),c=8.5842(2) Å,Z=4. (Pbnmin the setting above.) The compound is isostructural with Ni3Sn2andγ‧-Co3Sn2(H. Fjellvåg and A. Kjekshus,Acta Chem. Scand.A40, 23-30 (1986)). FinalRp=8.97%,Rwp=11.44%, GOF=2.86, andRBragg=4.11% using 43 parameters and 5701 observations and 330 Bragg reflections.

Structural Mineral Physics at Extreme Conditions

NASA Astrophysics Data System (ADS)

Chariton, S.; Dubrovinsky, L. S.; Dubrovinskaia, N.

2017-12-01

Laser heating techniques in diamond anvil cells (DACs) cover a wide pressure-temperature range - above 300 GPa and up to 5000 K. Recent advantages in on-line laser heating techniques resulted in a significant improvement of reliability of in situ X-ray powder diffraction studies in laser-heated DACs, which have become routine at a number of synchrotron facilities including specialized beam-lines at the 3rd generation synchrotrons. However, until recently, existing DAC laser-heating systems could not be used for structural X-ray diffraction studies aimed at structural refinements, i.e. measuring of the diffraction intensities, and not only at determining of lattice parameters. The reason is that in existing DAC laser-heating facilities the laser beam enters the cell at a fixed angle, and a partial rotation of the DAC, as required in monochromatic structural X-ray diffraction experiments, results in a loss of the target crystal and may be even dangerous if the powerful laser light starts to scatter in arbitrary directions by the diamond anvils. In order to overcome this problem we have develop a portable laser heating system and implement it at different diffraction beam lines. We demonstrate the application of this system for simultaneous high-pressure and high-temperature powder and single crystal diffraction studies using examples of studies of chemical and phase relations in the Fe-O system, transition metals carbonates, and silicate perovskites.

Magnetic and magnetostrictive behavior of Dy 3+ doped CoFe 2O 4 single crystals grown by flux method

NASA Astrophysics Data System (ADS)

Kambale, Rahul C.; Song, K. M.; Won, C. J.; Lee, K. D.; Hur, N.

2012-02-01

We studied the effect of Dy 3+ content on the magnetic properties of cobalt ferrite single crystal. The single crystals of CoFe 1.9Dy 0.1O 4 were grown by the flux method using Na 2B 4O 7.10 H 2O (Borax) as a solvent (flux). The black and shiny single crystals were obtained as a product. The X-ray diffraction analysis at room temperature confirmed the spinel cubic structure with lattice constant a=8.42 Å of the single crystals. The compositional analysis endorses the presence of constituents Co, Fe and Dy elements after sintering at 1300 °C within the final structure. The magnetic hysteresis measurements at various temperatures viz. 10 K, 100 K, 200 K and 300 K reveal the soft ferrimagnetic nature of the single crystal than that of for pure CoFe 2O 4. The observed saturation magnetization ( Ms) and coercivity ( Hc) are found to be lower than that of pure CoFe 2O 4 single crystal. The magnetostriction ( λ) measurement was carried out along the [001] direction. The magnetic measurements lead to conclude that the present single crystals can be used for magneto-optic recording media.

Hirshfeld atom refinement.

PubMed

Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-09-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

Hirshfeld atom refinement

PubMed Central

Capelli, Silvia C.; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-01-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å. PMID:25295177

A Layered Solution Crystal Growth Technique and the Crystal Structure of (C 6H 5C 2H 4NH 3) 2PbCl 4

NASA Astrophysics Data System (ADS)

Mitzi, D. B.

1999-07-01

Single crystals of the organic-inorganic perovskite (C6H5C2H4NH3)2PbCl4 have been grown at room temperature using a layered solution approach. The bottom solution layer, contained within a long straight tube, consists of PbCl2 dissolved in concentrated aqueous HCl. A less dense layer of methanol is carefully placed on top of the HCl/PbCl2 solution using a syringe. Finally, a stoichiometric quantity of C6H5C2H4NH2 (relative to the PbCl2) is added to the top of the column. As the layers slowly diffuse together, well-formed crystals of (C6H5C2H4NH3)2PbCl4 appear near the interface between the HCl/PbCl2 and C6H5C2H4NH2 solutions. The thick, plate-like crystals are well suited for X-ray crystallography studies. Room temperature intensity data were refined using a triclinic (Poverline1) cell (a=11.1463(3) Å, b=11.2181(3) Å, c=17.6966(5) Å, α= 99.173(1)°, β=104.634(1)°, γ=89.999(1)°, V=2111.8(1) Å3, Z=4, Rf/Rw=0.031/0.044). The organic-inorganic layered perovskite structure features well-ordered sheets of corner-sharing distorted PbCl6 octahedra separated by bilayers of phenethylammonium cations. Tilting and rotation of the PbCl6 octahedra within the perovskite sheets, coupled with organic cation ordering, leads to the unusual in-sheet 2ap×2ap superstructure, where ap is the lattice constant for the ideal cubic perovskite.

Intrinsic crystal phase separation in the antiferromagnetic superconductor Rb(y)Fe(2-x)Se2: a diffraction study.

PubMed

Yu Pomjakushin, V; Krzton-Maziopa, A; Pomjakushina, E V; Conder, K; Chernyshov, D; Svitlyk, V; Bosak, A

2012-10-31

The crystal and magnetic structures of the superconducting iron-based chalcogenides Rb(y)Fe(2-x)Se(2) have been studied by means of single-crystal synchrotron x-ray and high-resolution neutron powder diffraction in the temperature range 2-570 K. The ground state of the crystal is an intrinsically phase-separated state with two distinct-by-symmetry phases. The main phase has the iron vacancy ordered √5 × √5 superstructure (I4/m space group) with AFM ordered Fe spins. The minority phase does not have √5 × √5-type of ordering and has a smaller in-plane lattice constant a and larger tetragonal c-axis and can be well described by assuming the parent average vacancy disordered structure (I4/mmm space group) with the refined stoichiometry Rb(0.60(5))(Fe(1.10(5))Se)(2). The minority phase amounts to 8-10% mass fraction. The unit cell volume of the minority phase is 3.2% smaller than the one of the main phase at T = 2 K and has quite different temperature dependence. The minority phase merges with the main vacancy ordered phase on heating above the phase separation temperature T(P) = 475 K. The spatial dimensions of the phase domains strongly increase above T(P) from 1000 to >2500 Å due to the integration of the regions of the main phase that were separated by the second phase at low temperatures. Additional annealing of the crystals at a temperature T = 488 K, close to T(P), for a long time drastically reduces the amount of the minority phase.

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.

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.

Growth of single crystals of BaFe12O19 by solid state crystal growth

NASA Astrophysics Data System (ADS)

Fisher, John G.; Sun, Hengyang; Kook, Young-Geun; Kim, Joon-Seong; Le, Phan Gia

2016-10-01

Single crystals of BaFe12O19 are grown for the first time by solid state crystal growth. Seed crystals of BaFe12O19 are buried in BaFe12O19+1 wt% BaCO3 powder, which are then pressed into pellets containing the seed crystals. During sintering, single crystals of BaFe12O19 up to ∼130 μm thick in the c-axis direction grow on the seed crystals by consuming grains from the surrounding polycrystalline matrix. Scanning electron microscopy-energy dispersive spectroscopy analysis shows that the single crystal and the surrounding polycrystalline matrix have the same chemical composition. Micro-Raman scattering shows the single crystal to have the BaFe12O19 structure. The optimum growth temperature is found to be 1200 °C. The single crystal growth behavior is explained using the mixed control theory of grain growth.

Phase equilibria in the NaF-CdO-NaPO{sub 3} system at 873 K and crystal structure and physico-chemical characterizations of the new Na{sub 2}CdPO{sub 4}F fluorophosphate

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

Aboussatar, Mohamed; Laboratoire de Physico-Chimie de l’État Solide, Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax; Mbarek, Aïcha

Isothermal sections of the diagram representing phase relationships in the NaF-CdO-NaPO{sub 3} system have been investigated by solid state reactions and powder X-ray diffraction. This phase diagram investigation confirms the polymorphism of the NaCdPO{sub 4} side component and the structure of the ß high temperature polymorph (orthorhombic, space group Pnma and unit cell parameters a=9.3118(2), b=7.0459(1), c=5.1849(1) Å has been refined. A new fluorophosphate, Na{sub 2}CdPO{sub 4}F, has been discovered and its crystal structure determined and refined from powder X-ray diffraction data. It exhibits a new 3D structure with orthorhombic symmetry, space group Pnma and unit cell parameters a=5.3731(1), b=6.8530(1),more » c=12.2691(2) Å. The structure is closely related to those of the high temperature polymorph of the nacaphite Na{sub 2}CaPO{sub 4}F and the fluorosilicate Ca{sub 2}NaSiO{sub 4}F but differs essentially in the cationic repartition since the structure is fully ordered with one Na site (8d) and one Cd site (4c). Relationships with other Na{sub 2}M{sup II}PO{sub 4}F (M{sup II}=Mg, Ca, Mn, Fe, Co, Ni) have been examined and the crystal-chemical and topographical analysis of these fluorophosphates is briefly reviewed. IR, Raman, optical and {sup 19}F, {sup 23}Na, {sup 31}P MAS NMR characterizations of Na{sub 2}CdPO{sub 4}F have been investigated. - Graphical abstract: The structure of the compound Na{sub 2}CdPO{sub 4}F, discovered during the study of the phase relationships in the NaF-CdO-NaPO{sub 3} system, has been determined and compared with other Na{sub 2}M{sup II}PO{sub 4}F fluorophosphates. - Highlights: • XRD analysis of the isothermal section of the NaF-CdO-NaPO{sub 3} system at 923 K. • Rietveld refinement of the high temperature polymorph β-NaCdPO{sub 4}. • Crystal structure of the new Na{sub 2}CdPO{sub 4}F fluorophosphate determined from powder XRD. • Crystal structure - composition relationships of Na{sub 2}M{sup II}PO{sub 4}F compounds are reviewed. • IR, Raman, optical and {sup 19}F, {sup 23}Na, {sup 31}P MAS NMR characterizations of Na{sub 2}CdPO{sub 4}F.« less

Single crystalline growth of a soluble organic semiconductor in a parallel aligned liquid crystal solvent using rubbing-treated polyimide films

NASA Astrophysics Data System (ADS)

Matsuzaki, Tomoya; Shibata, Yosei; Takeda, Risa; Ishinabe, Takahiro; Fujikake, Hideo

2017-01-01

For directional control of organic single crystals, we propose a crystal growth method using liquid crystal as the solvent. In this study, we examined the formation of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) single crystals using a parallel aligned liquid crystal (LC) cell and rubbing-treated polyimide films in order to clarify the effects of LC alignment on anisotropic C8-BTBT crystal growth. Based on the results, we found that the crystal growth direction of C8-BTBT single crystals was related to the direction of the aligned LC molecules because of rubbing treatment. Moreover, by optical evaluation, we found that the C8-BTBT single crystals have a aligned molecular structure.

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

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

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka

2015-09-08

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.« less

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

DOE PAGES

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; ...

2015-09-08

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σ A dissociation.« less

Molecular structure and charge density analysis of p-methoxybenzoic acid (anisic acid)

NASA Astrophysics Data System (ADS)

Fausto, R.; Matos-Beja, A.; Paixão, J. A.

1997-12-01

A concerted X-ray and ab initio SCF-MO study of the structure and charge density of p-methoxybenzoic acid (anisic acid) is reported. An extensive X-ray data set (7401 reflections) was measured on a single crystal using Mo K α radiation and the structure refined with 2121 unique reflections, leading to a final R( F)-factor of 0.047 calculated for reflections with I>2 σ. The molecular geometry of crystalline anisic acid, where the molecules dimerize via a moderately strong CO-H⋯O hydrogen bond, is compared with that of the isolated molecule, resulting from SCF-MO ab initio calculations. A topological analysis of the molecular charge density was performed using Bader's method to gain insight into the dominant intra- and intermolecular interactions in this compound. In particular, the effects of the substituents on the observed distortions of the benzene ring were investigated as well as the internal rotation of the methyl group.

Synthesis, Structure and bonding Analysis of the Polar Intermetallic Phase Ca2Pt2Cd

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

Samal, Saroj L.; Corbett, John D.

The polar intermetallic phase Ca2Pt2Cd was discovered during explorations of the Ca-Pt-Cd system. The compound was synthesized by high temperature reactions, and its structure refined by single-crystal X-ray diffraction as orthorhombic, Immm, a = 4.4514(5), b = 5.8415(6), c = 8.5976(9) Å, Z = 2. The structure formally contains infinite, planar networks of [Pt2Cd]4– along the ab plane, which can be described as tessellation of six and four-member rings of the anions, with cations stuffed between the anion layers. The infinite condensed platinum chains show a substantial long–short distortion of 0.52 Å, an appreciable difference between Ca2Pt2Cd (26 valence electrons)more » and the isotypic but regular Ca2Cu2Ga (29 VE). The relatively large cation proportion diminishes the usual dominance of polar (Pt–Cd) and 5d–5d (Pt–Pt) contributions to the total Hamilton populations.« less

Neutron diffraction study of the in situ oxidation of UO(2).

PubMed

Desgranges, Lionel; Baldinozzi, Gianguido; Rousseau, Gurvan; Nièpce, Jean-Claude; Calvarin, Gilbert

2009-08-17

This paper discusses uranium oxide crystal structure modifications that are observed during the low-temperature oxidation which transforms UO(2) into U(3)O(8). The symmetries and the structural parameters of UO(2), beta-U(4)O(9), beta-U(3)O(7), and U(3)O(8) were determined by refining neutron diffraction patterns on pure single-phase samples. Neutron diffraction patterns were also collected during the in situ oxidation of powder samples at 483 K. The lattice parameters and relative ratios of the four pure phases were measured during the progression of the isothermal oxidation. The transformation of UO(2) into U(3)O(8) involves a complex modification of the oxygen sublattice and the onset of complex superstructures for U(4)O(9) and U(3)O(7), associated with regular stacks of complex defects known as cuboctahedra, which consist of 13 oxygen atoms. The kinetics of the oxidation process are discussed on the basis of the results of the structural analysis.

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.

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

PubMed

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

2015-06-15

Organic nonlinear optical material, pyrrolidinium-2-carboxylate-4-nitrophenol (PCN) was synthesized and single crystals were grown by slow evaporation solution growth method. Single crystal X-ray diffraction analysis confirmed the structure and lattice parameters of PCN crystals. Infrared, Raman and NMR spectral analyses were used to elucidate the functional groups present in the compound. The thermal behavior of synthesized compound was studied by thermogravimetric and differential scanning calorimetry (TG-DSC) analyses. The photoluminescence property was studied by exciting the crystal at 360 nm. The relative second harmonic generation (SHG) efficiency of grown crystal was estimated by using Nd:YAG laser with fundamental wavelength of 1,064 nm. Copyright © 2015 Elsevier B.V. All rights reserved.

Surface Modification and Nanojunction Fabrication with Molecular Metal Wires

DTIC Science & Technology

2012-12-21

single - crystal X-ray diffraction studies of 2 and 3. Both the single - crystal structural data of 2 and 3 and the spectroscopic/voltammetric data...structure, magnetic properties, and single -molecule conductance of two new trinuclear metal string complexes, [Ni3(dzp)4(NCS)2] (2) and [ Co3 (dzp)4(NCS...modifying the crystallization conditions. The [s- Co3 (dpa)4(Cl)2] contains a symmetrical tricobalt framework with identical Co–Co bond lengths (2.34 Å

High Temperature Stability of Binary Microstructures Derived from Liquid Precursors

DTIC Science & Technology

1994-06-30

isopropoxide , Ti(OC3H7 )4 was stirred into the solution under nitrogen to produce a composition with a 1:1 Pb:Ti ratio. The solution was then boiled and...This program has emphasized two topics: 1) the crystallization of metastable, solid- solution structures, their partitioning into equilibrium structures...structural ceramics and their composites, and 2) the formation of single crystal thin films via spin coating single crystal substrates with solution

Redetermination of the crystal structure of the 2D heterometallic framework prepared from [Ni(cyclam)]2+ and [Re(CN)7]3-

NASA Astrophysics Data System (ADS)

Sukhikh, Taisiya S.; Vostrikova, Kira E.

2018-02-01

A new XRD experiment and crystal structure refinement was performed for the earlier published compound in the paper "Heterobimetallic coordination polymers involving 3d metal complexes and heavier transition metals cyanometallates" by Peresypkina et al. (2015) [1]. A choice of a crystal cell taking in consideration the superstructural reflections allowed to obtain more reliable data about the symmetry and bond distances in the heterometallic 2D framework {[Ni(cyclam)]2[ReO(OH)0.5(MeOH)0.5(CN)4]}2.5+. Additionally, doubling of the parameter c permitted to get more details about interlayer space. As a result, disordered perchlorate anions and solvate molecules were located.

Crystal structure of choline fenofibrate (Trilipix®), (C5H14NO) (C17H14ClO4)

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

Kaduk, James A.; Zhong, Kai; Gindhart, Amy M.

2016-04-04

The crystal structure of choline fenofibrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Choline fenofibrate crystallizes in space groupPbca(#61) witha= 12.341 03(2),b= 28.568 70(6),c= 12.025 62(2) Å,V= 4239.84(1) Å 3, andZ= 8. The hydroxyl group of the choline anion makes a strong hydrogen bond to the ionized carboxylate group of the fenofibrate anion. Together with C–H···O hydrogen bonds, these link the cations and anions into layers parallel to theac-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

A model of insulin fibrils derived from the x-ray crystal structure of a monomeric insulin (despentapeptide insulin).

PubMed

Brange, J; Dodson, G G; Edwards, D J; Holden, P H; Whittingham, J L

1997-04-01

The crystal structure of despentapeptide insulin, a monomeric insulin, has been refined at 1.3 A spacing and subsequently used to predict and model the organization in the insulin fibril. The model makes use of the contacts in the densely packed despentapeptide insulin crystal, and takes into account other experimental evidence, including binding studies with Congo red. The dimensions of this model fibril correspond well with those measured experimentally, and the monomer-monomer contacts within the fibril are in accordance with the known physical chemistry of insulin fibrils. Using this model, it may be possible to predict mutations in insulin that might alleviate problems associated with fibril formation during insulin therapy.

Grain refinement of 7075Al alloy microstructures by inoculation with Al-Ti-B master alloy

NASA Astrophysics Data System (ADS)

Hotea, V.; Juhasz, J.; Cadar, F.

2017-05-01

This paper aims to bring some clarification on grain refinement and modification of high strength alloys used in aerospace technique. In this work it was taken into account 7075 Al alloy, and the melt treatment was carried out by placing in the form of master alloy wire ternary AlTiB the casting trough at 730°C. The morphology of the resulting microstructures was characterized by optical microscopy. Micrographs unfinished and finished with pre-alloy containing ternary Al5Ti1B evidence fine crystals, crystal containing no columnar structure and highlights the size of the dendrites, and intermetallic phases occurring at grain boundaries in Al-Zn-Mg-Cu alloy. It has been found that these intermetallic compounds are MgZn2 type. AlTiB master alloys finishing ensures a fine eutectic structure, which determines the properties of hardware and improving the mechanical properties of aluminum alloys used in aeronautical engineering.

Purification and Crystal Growth of Lead Iodide by Physical Vapor Transport Method

NASA Technical Reports Server (NTRS)

Wright, G. W.; Cole, M.; Chen, Y.-F.; Chen, K.-T.; Chen, H.; Chattopadhyay, K.; Burger, A.

1998-01-01

Lead iodide (PbI2) is a layered compound semiconductor being developed as room temperature x- and gamma-ray detector. Compared to the more studied material, mercuric iodide, PbI2 has a higher melting temperature and no phase transition until liquid phase which are indications of better mechanical properties. In this study, the source material was purified by the zone-refining process, and the purest section was extracted from center of the the zone-refined ingot to be grown by physical vapor transport (PVT) method. The zone-refined material and as-grown crystals were characterized by optical microscopy and differential scanning calorimetry (DSC) to reveal the surface morphology, purity and stoichiometry. The results shows that both materials are near-stoichiometric composition, with the purity of the as-grown crystals higher than zone-refined materials. The resistivity of the as-grown crystal (10" Omega-cm) was derived from current-voltage (I-V) measurement, and is 10 times higher than the zone-refined materials. Detail results will be presented and discussed.

Conversion of broadband IR radiation and structural disorder in lithium niobate single crystals with low photorefractive effect

NASA Astrophysics Data System (ADS)

Litvinova, Man Nen; Syuy, Alexander V.; Krishtop, Victor V.; Pogodina, Veronika A.; Ponomarchuk, Yulia V.; Sidorov, Nikolay V.; Gabain, Aleksei A.; Palatnikov, Mikhail N.; Litvinov, Vladimir A.

2016-11-01

The conversion of broadband IR radiation when the noncritical phase matching condition is fulfilled in lithium niobate (LiNbO3) single crystals with stoichiometric (R = Li/Nb = 1) and congruent (R = 0.946) compositions, as well as in congruent single crystals doped with zinc has been investigated. It is shown that the spectrum parameters of converted radiation, such as the conversion efficiency, spectral width and position of maximum, depend on the ordering degree of structural units of the cation sublattice along the polar axis of crystal.

Incommensurate structure of a lillianite-type samarium chromium sulfide Sm{sub 2/3}Cr{sub 2}S{sub 4}

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

Lafond, A.; Cario, L.; Meerschaut, A.

1996-12-01

The structure of Sm{sub 2/3}Cr{sub 2}S{sub 4} has been solved from single-crystal X-ray diffraction data. This compound presents a 3 X a superstructure along a and an incommensurate superstructure along b close to 3 x b. The basic structure is described in the space group Pmnb with a = 3.5030(3) {Angstrom}, b = 10.9199(8) {Angstrom}, c = 12.7987(8) {Angstrom}, Z = 4, R = 0.046 for 916 observed reflections. The modulated structure refinement, taking into account the two superstructures, was carried out in a (3 + 2)D superspace group and leads to R = 0.063 for 1706 reflections. This structuremore » consists of staggered double columns of [CrS{sub 6}] octahedra connected by samarium atoms in a trigonal prismatic bicapped environment. This structure is reminiscent of that found in the lillianite mineral family. The statistical occupancy of samarium atoms (1/3), in agreement with the charge equilibrium (Sm{sup 3+}, Cr{sup 3+}, S{sup 2-}), is related to the superstructure.« less

Synthesis and crystal structure of bis(di- n-butyldithiocarbamato)(1,10-phenanthroline)cadmium(II)

NASA Astrophysics Data System (ADS)

Ivanchenko, A. V.; Gromilov, S. A.; Zemskova, S. M.; Baidina, I. A.; Glinskaya, L. A.

2002-02-01

A new mixed-ligand complex, Cd(S2CN(C4H9)2)2Phen, is synthesized and investigated by thermal, element, and IR analyses and by diffractometry of polycrystals (DRON-3M, CuKα radiation, Ni filter). The crystal structure was determined on a CAD-4 Enraf-Nonius automatic diffractometer (MoKα radiation, θ from 1.5 to 25‡, 2325 nonzero independent reflections, 190 refined parameters, R = 0.036 for I > 2Σ(I)). Crystal data for C30H44CdN4S4 : a = 15.592(3), b = 22.724(5), c = 9.922(2) å, space group Pbcn, V = 3515.5(12) å3, Z = 4, M = 701.33, dcalc = 1.325 g/cm3. The structure involves monomeric molecules in which the cadmium atom has a distorted octahedral environment.

Subsurface Stress Fields in FCC Single Crystal Anisotropic Contacts

NASA Technical Reports Server (NTRS)

Arakere, Nagaraj K.; Knudsen, Erik; Swanson, Gregory R.; Duke, Gregory; Ham-Battista, Gilda

2004-01-01

Single crystal superalloy turbine blades used in high pressure turbomachinery are subject to conditions of high temperature, triaxial steady and alternating stresses, fretting stresses in the blade attachment and damper contact locations, and exposure to high-pressure hydrogen. The blades are also subjected to extreme variations in temperature during start-up and shutdown transients. The most prevalent high cycle fatigue (HCF) failure modes observed in these blades during operation include crystallographic crack initiation/propagation on octahedral planes, and non-crystallographic initiation with crystallographic growth. Numerous cases of crack initiation and crack propagation at the blade leading edge tip, blade attachment regions, and damper contact locations have been documented. Understanding crack initiation/propagation under mixed-mode loading conditions is critical for establishing a systematic procedure for evaluating HCF life of single crystal turbine blades. This paper presents analytical and numerical techniques for evaluating two and three dimensional subsurface stress fields in anisotropic contacts. The subsurface stress results are required for evaluating contact fatigue life at damper contacts and dovetail attachment regions in single crystal nickel-base superalloy turbine blades. An analytical procedure is presented for evaluating the subsurface stresses in the elastic half-space, based on the adaptation of a stress function method outlined by Lekhnitskii. Numerical results are presented for cylindrical and spherical anisotropic contacts, using finite element analysis (FEA). Effects of crystal orientation on stress response and fatigue life are examined. Obtaining accurate subsurface stress results for anisotropic single crystal contact problems require extremely refined three-dimensional (3-D) finite element grids, especially in the edge of contact region. Obtaining resolved shear stresses (RSS) on the principal slip planes also involves considerable post-processing work. For these reasons it is very advantageous to develop analytical solution schemes for subsurface stresses, whenever possible.

Synthesis, growth, structural, optical, luminescence, surface and HOMO LUMO analysis of 2-[2-(4-cholro-phenyl)-vinyl]-1-methylquinolinium naphthalene-2-sulfonate organic single crystals grown by a slow evaporation technique

NASA Astrophysics Data System (ADS)

Karthigha, S.; Kalainathan, S.; Maheswara Rao, Kunda Uma; Hamada, Fumio; Yamada, Manabu; Kondo, Yoshihiko

2016-02-01

Single crystals of 2-[2-(4-cholro-phenyl)-vinyl]-1-methylquinolinium naphthalene-2-sulfonate (4CLNS) were grown by a slow evaporation technique. The formation of molecule was confirmed from 1H NMR and FTIR analysis. The confirmation of crystal structure was done by single crystal XRD and atomic packing of grown crystal was identified. The grown single crystal crystallized in triclinic structure with centrosymmetric space group P-1. The crystalline nature of the synthesised material was recorded by powder XRD. The optical absorption properties of the grown crystals were analyzed by UV-vis spectral studies. The thermal behaviour of the title material has been studied by TG/DTA analysis which revealed the stability of the compound till its melting point 276.7 °C. The third order nonlinear optical property of 4CLNS was investigated in detail by Z scan technique and it confirms that the title crystal is suitable for photonic devices and NLO optical applications. Emissions at 519 nm in green region of the EM spectrum were found by photoluminescence studies. The charge transfer occurring within the molecule is explained by the calculated HOMO and LUMO energies.

Structure disordering and thermal decomposition of manganese oxalate dihydrate, MnC2O4·2H2O

NASA Astrophysics Data System (ADS)

Puzan, Anna N.; Baumer, Vyacheslav N.; Lisovytskiy, Dmytro V.; Mateychenko, Pavel V.

2018-04-01

It is found that the known regular structures of MnC2O4·2H2O (I) do not allow to refine the powder X-ray pattern of (I) properly using the Rietveld method. Implementation of order-disorder scheme [28] via the including of appropriate displacement vector improves the refinement results. Also it is found that in the case of (I) the similar improvement may be achieved using the data on two phases of (I) obtained as result of decomposition MnC2O4·3H2O single crystal in the mother solution after growth. Thermal decomposition of (I) produce the anhydrous γ-MnC2O4 (II) the structure of which is differ from the known α- and β-modifications of VIIIb transition metal oxalates. The solved ab initio from the powder pattern structure (II) (space group Pmna, a = 7.1333 (1), b = 5.8787 (1), c = 9.0186 (2) Å, V = 378.19 (1) Å3, Z = 4 and Dx = 2.511 Mg m-3) contains seven-coordinated Mn atoms with Mn-O distances of 2.110-2.358 Å, and is not close-packed. Thermal decomposition of (II) in air flows via forming of amorphous MnO, the heating of which up to 723 K is accompanied by oxidation of MnO to Mn2O3 and further recrystallization of the latter.

Structure guided design of a series of selective pyrrolopyrimidinone MARK inhibitors

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

Katz, Jason D.; Haidle, Andrew; Childers, Kaleen K.

2017-01-01

The initial structure activity relationships around an isoindoline uHTS hit will be described. Information gleaned from ligand co-crystal structures allowed for rapid refinements in both MARK potency and kinase selectivity. These efforts allowed for the identification of a compound with properties suitable for use as an in vitro tool compound for validation studies on MARK as a viable target for Alzheimer’s disease.

Co2+-doped diopside: crystal structure and optical properties

NASA Astrophysics Data System (ADS)

Gori, C.; Tribaudino, M.; Mezzadri, F.; Skogby, H.; Hålenius, U.

2018-05-01

Synthetic clinopyroxenes along the CaMgSi2O6-CaCoSi2O6 join were investigated by a combined chemical-structural-spectroscopic approach. Single crystals were synthesized by flux growth methods, both from Ca-saturated and Ca-deficient starting compositions. Single crystal structure refinements show that the incorporation of Co2+ at the octahedrally coordinated cation sites of diopside, increases the unit-cell as well as the M1 and the M2 polyhedral volumes. Spectroscopic investigations (UV-VIS-NIR) of the Ca-rich samples reveal three main optical absorption bands, i.e. 4 T 1g → 4 T 2g( F), 4 T 1g → 4 A 2g( F) and 4 T 1g → 4 T 1g( P) as expected for Co2+ at a six-coordinated site. The bands arising from the 4 T 1g → 4 T 2g( F) and the 4 T 1g → 4 T 1g( P) electronic transitions, are each split into two components, due to the distortions of the M1 polyhedron from ideal Oh-symmetry. In spectra of both types, a band in the NIR range at ca 5000 cm-1 is caused by the 4 A 2g → 4 T 1g( F) electronic transition in Co2+ in a cubic field in the M2 site. Furthermore, an additional component to a band system at 14,000 cm-1, due to electronic transitions in Co2+ at the M2 site, is recorded in absorption spectra of Ca-deficient samples. No variations in Dq and Racah B parameters for Co2+ at the M1 site in response to compositional changes, were demonstrated, suggesting complete relaxation of the M1 polyhedron within the CaMgSi2O6-CaCoSi2O6 solid solution.

Co2+-doped diopside: crystal structure and optical properties

NASA Astrophysics Data System (ADS)

Gori, C.; Tribaudino, M.; Mezzadri, F.; Skogby, H.; Hålenius, U.

2017-12-01

Synthetic clinopyroxenes along the CaMgSi2O6-CaCoSi2O6 join were investigated by a combined chemical-structural-spectroscopic approach. Single crystals were synthesized by flux growth methods, both from Ca-saturated and Ca-deficient starting compositions. Single crystal structure refinements show that the incorporation of Co2+ at the octahedrally coordinated cation sites of diopside, increases the unit-cell as well as the M1 and the M2 polyhedral volumes. Spectroscopic investigations (UV-VIS-NIR) of the Ca-rich samples reveal three main optical absorption bands, i.e. 4 T 1g → 4 T 2g(F), 4 T 1g → 4 A 2g(F) and 4 T 1g → 4 T 1g(P) as expected for Co2+ at a six-coordinated site. The bands arising from the 4 T 1g → 4 T 2g(F) and the 4 T 1g → 4 T 1g(P) electronic transitions, are each split into two components, due to the distortions of the M1 polyhedron from ideal Oh-symmetry. In spectra of both types, a band in the NIR range at ca 5000 cm-1 is caused by the 4 A 2g → 4 T 1g(F) electronic transition in Co2+ in a cubic field in the M2 site. Furthermore, an additional component to a band system at 14,000 cm-1, due to electronic transitions in Co2+ at the M2 site, is recorded in absorption spectra of Ca-deficient samples. No variations in Dq and Racah B parameters for Co2+ at the M1 site in response to compositional changes, were demonstrated, suggesting complete relaxation of the M1 polyhedron within the CaMgSi2O6-CaCoSi2O6 solid solution.

Phase equilibria in the NaF-CdO-NaPO3 system at 873 K and crystal structure and physico-chemical characterizations of the new Na2CdPO4F fluorophosphate

NASA Astrophysics Data System (ADS)

Aboussatar, Mohamed; Mbarek, Aïcha; Naili, Houcine; El-Ghozzi, Malika; Chadeyron, Geneviève; Avignant, Daniel; Zambon, Daniel

2017-04-01

Isothermal sections of the diagram representing phase relationships in the NaF-CdO-NaPO3 system have been investigated by solid state reactions and powder X-ray diffraction. This phase diagram investigation confirms the polymorphism of the NaCdPO4 side component and the structure of the ß high temperature polymorph (orthorhombic, space group Pnma and unit cell parameters a=9.3118(2), b=7.0459(1), c=5.1849(1) Å has been refined. A new fluorophosphate, Na2CdPO4F, has been discovered and its crystal structure determined and refined from powder X-ray diffraction data. It exhibits a new 3D structure with orthorhombic symmetry, space group Pnma and unit cell parameters a=5.3731(1), b=6.8530(1), c=12.2691(2) Å. The structure is closely related to those of the high temperature polymorph of the nacaphite Na2CaPO4F and the fluorosilicate Ca2NaSiO4F but differs essentially in the cationic repartition since the structure is fully ordered with one Na site (8d) and one Cd site (4c). Relationships with other Na2MIIPO4F (MII=Mg, Ca, Mn, Fe, Co, Ni) have been examined and the crystal-chemical and topographical analysis of these fluorophosphates is briefly reviewed. IR, Raman, optical and 19F, 23Na, 31P MAS NMR characterizations of Na2CdPO4F have been investigated.

The role of the cubic structure in freezing of a supercooled water droplet on an ice substrate

NASA Astrophysics Data System (ADS)

Takahashi, T.; Kobayashi, T.

1983-12-01

The possibility of the formation of a metastable cubic (diamond) structure and its role in freezing of a supercooled water droplet on an ice substrate are discussed in terms of two-dimensional nucleation. The mode of stacking sequence of new layers formed by two-dimensional nucleation is divided into single and multi-nucleation according to the degree of supercooling and to the size of the supercooled droplet. In the case of single nucleation a frozen droplet develops into a complete hexagonal single crystal or an optically single crystal (containing discontinuous stacking faults). In the case of multi-nucleation attention is paid to the size effect and the stacking direction of the nucleus to calculate the waiting time in the nucleation. Then the frozen droplets are crystallographically divided into three categories: completely single crystals, optically single crystals (containing a small cubic structure, i.e. stacking faults) and polycrystals with a misorientation of 70.53° between the c-axes.

Influence of valence electron concentration on Laves phases: Structures and phase stability of pseudo-binary MgZn 2-xPd x

DOE PAGES

Thimmaiah, Srinivasa; Miller, Gordon J.

2015-06-03

A series of pseudo-binary compounds MgZn 2-xPd x (0.15 ≤ x ≤ 1.0) were synthesized and structurally characterized to understand the role of valence electron concentration (vec) on the prototype Laves phase MgZn 2 with Pd-substitution. Three distinctive phase regions were observed with respect to Pd content, all exhibiting fundamental Laves phase structures: 0.1 ≤ x ≤ 0.3 (MgNi 2-type, hP24; MgZn 1.80Pd 0.20(2)), 0.4 ≤ x ≤ 0.6 (MgCu 2-type, cF24; MgZn 1.59Pd 0.41(2)), and 0.62 ≤ x ≤ 0.8 (MgZn 2-type, hP12: MgZn 1.37Pd 0.63(2)). Refinements from single-crystal X-ray diffraction indicated nearly statistical distributions of Pd and Znmore » atoms among the majority atom sites in these structures. Interestingly, the MgZn 2-type structure re-emerges in MgZn 2–xPd x at x ≈ 0.7 with the refined composition MgZn 1.37(2)Pd 0.63 and a c/a ratio of 1.59 compared to 1.64 for binary MgZn 2. Electronic structure calculations on a model “MgZn 1.25Pd 0.75” yielded a density of states (DOS) curve showing enhancement of a pseudogap at the Fermi level as a result of electronic stabilization due to the Pd addition. Moreover, integrated crystal orbital Hamilton population values show significant increases of orbital interactions for (Zn,Pd)–(Zn,Pd) atom pairs within the majority atom substructure, i.e., within the Kagomé nets as well as between a Kagomé net and an apical site, from binary MgZn 2 to the ternary “MgZn 1.25Pd 0.75”. Multi-centered bonding is evident from electron localization function plots for “MgZn 1.25Pd 0.75”, an outcome which is in accordance with analysis of other Laves phases.« less

Recrystallization and grain growth in NiAl

NASA Technical Reports Server (NTRS)

Haff, G. R.; Schulson, E. M.

1982-01-01

Aluminide intermetallics, because of their strength, microstructural stability, and oxidation resistance at elevated temperatures, represent potential structural materials for use in advanced energy conversion systems. This inherent potential of the intermetallics can currently not be realized in connection with the general brittleness of the materials under ambient conditions. It is pointed out, however, that brittleness is not an inherent characteristic. Single crystals are ductile and polycrystals may be, too, if their grains are fine enough. The present investigation is concerned with an approach for reducing material brittleness, taking into account thermal-mechanically induced grain refinement in NiAl, a B2 aluminide which melts at 1638 C and which retains complete order to its melting point. Attention is given to the kinetics of recrystallization and grain growth of warm-worked, nickel-rich material.

Effect of Al–5Ti–C Master Alloy on the Microstructure and Mechanical Properties of Hypereutectic Al–20%Si Alloy

PubMed Central

Ding, Wanwu; Xia, Tiandong; Zhao, Wenjun; Xu, Yangtao

2014-01-01

Al–5Ti–C master alloy was prepared and used to modify hypereutectic Al–20%Si alloy. The microstructure evolution and mechanical properties of hypereutectic Al–20%Si alloy with Al–5Ti–C master alloy additions (0, 0.4, 0.6, 1.0, 1.6 and 2.0 wt%) were investigated. The results show that, Al–5Ti–C master alloy (0.6 wt%, 10 min) can significantly refine both eutectic and primary Si of hypereutectic Al–20%Si alloy. The morphology of the primary Si crystals was significantly refined from a coarse polygonal and star-like shape to a fine polyhedral shape and the grain size of the primary Si was refined from roughly 90–120 μm to 20–50 μm. The eutectic Si phases were modified from a coarse platelet-like/needle-like structure to a fine fibrous structure with discrete particles. The Al–5Ti–C master alloy (0.6 wt%, 30 min) still has a good refinement effect. The ultimate tensile strength (UTS), elongation (El) and Brinell hardness (HB) of Al–20%Si alloy modified by the Al–5Ti–C master alloy (0.6 wt%, 10 min) increased by roughly 65%, 70% and 51%, respectively, due to decreasing the size and changing the morphology on the primary and eutectic Si crystals. The change in mechanical properties corresponds to evolution of the microstructure. PMID:28788509

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.