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.

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

PubMed

Joosten, Robbie P; Salzemann, Jean; Bloch, Vincent; Stockinger, Heinz; Berglund, Ann-Charlott; Blanchet, Christophe; Bongcam-Rudloff, Erik; Combet, Christophe; Da Costa, Ana L; Deleage, Gilbert; Diarena, Matteo; Fabbretti, Roberto; Fettahi, Géraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco; Reichstadt, Matthieu; Breton, Vincent; Tickle, Ian J; Vriend, Gert

2009-06-01

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Synchrotron-based XAS on structure investigation of La0.99-xSrx(Na, K, Ba)0.01MnO3 nanoparticles: Evidence of magnetic properties

NASA Astrophysics Data System (ADS)

Daengsakul, Sujittra; Saengplot, Saowalak; Kidkhunthod, Pinit; Pimsawat, Adulphan; Maensiri, Santi

2018-04-01

This work presents the structural study of La0.99-xSrx(Na, K, Ba)0.01MnO3 or LSAM nanoparticles synthesized using thermal-hydro decomposition method where A denotes Na, K, Sr and Ba, respectively. The effect of ionic radii size of A dopants or rA from the substitution of A for La and Sr on the MnO6 octrahedral structure, where the average size of the cations occupying in A-site or 〈rA〉 is fixed at ∼ 1.24 Å, is focused. The LSAM nanoparticles are carefully studied using X-ray diffraction (XRD) including Rietveld refinement and X-ray Absorption Spectroscopy (XAS) including X-ray Absorption Near edge Structure (XANES) and X-ray Absorption Fine Structure (EXAFS). The Rietveld refinement shows all nano-powder samples have rhombohedral structure. By XANES technique we found that the effect of A substitutions at A-site causes a slight change of mean oxidation state of Mn between 3.54 and 3.60. Furthermore, the structural distortion of MnO6 octrahedral in samples is analysed and obtained from EXAFS. The observed trend of ferromagnetism for all LSAM samples can be clearly explained by evidences of A-site doping, structural distortion around Mn atoms and mixing Mn3+/Mn4+ valence states.

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

PubMed Central

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

2015-01-01

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophos­phodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis. PMID:26249347

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

DOE PAGES

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

2015-07-28

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

X-ray and neutron total scattering analysis of Hy·(Bi0.2Ca0.55Sr0.25)(Ag0.25Na0.75)Nb3O10·xH2O perovskite nanosheet booklets with stacking disorder

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

Metz, Peter; Koch, Robert; Cladek, Bernadette

Ion-exchanged Aurivillius materials form perovskite nanosheet booklets wherein well-defined bi-periodic sheets, with ~11.5 Å thickness, exhibit extensive stacking disorder. The perovskite layer contents were defined initially using combined synchrotron X-ray and neutron Rietveld refinement of the parent Aurivillius structure. The structure of the subsequently ion-exchanged material, which is disordered in its stacking sequence, is analyzed using both pair distribution function (PDF) analysis and recursive method simulations of the scattered intensity. Combined X-ray and neutron PDF refinement of supercell stacking models demonstrates sensitivity of the PDF to both perpendicular and transverse stacking vector components. Further, hierarchical ensembles of stacking models weightedmore » by a standard normal distribution are demonstrated to improve PDF fit over 1–25 Å. Recursive method simulations of the X-ray scattering profile demonstrate agreement between the real space stacking analysis and more conventional reciprocal space methods. The local structure of the perovskite sheet is demonstrated to relax only slightly from the Aurivillius structure after ion exchange.« less

Ion-pairing in aqueous CaCl 2 and RbBr solutions. Simultaneous structural refinement of XAFS and XRD data

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

Pham, Thai V.; Fulton, John L.

2013-01-22

We present a new methodology involving the simultaneous refinement of both x-ray absorption and x-ray diffraction spectra (X-ray Absorption/Diffraction Structural Refinement,XADSR), to study hydration and ion pair structure of CaCl 2 and RbBr salts in concentrated aqueous solutions. The XADSR analysis includes the XAFS spectra analysis of both the cation and anion as a probe of their short-range structure with an XRD spectral analysis as a probe of the global structural. Together they deliver a comprehensive picture of the cation and anion hydration, the contact ion pair (CIP) structure and the solvent-separated ion pair (SSIP) structure. XADSR analysis of 6.0more » m aqueous CaCl 2 reveals that there are an insignificant number of Ca 2+-Cl- CIP’s, but there are approximately 3.4 SSIP’s separated by about 4.99 Å. In contrast XADSR analysis of aqueous RbBr yields about 0.7 pair CIP at a bond length 3.51 Å. The present work demonstrates a new approach for a direct co-refinement of XRD and XAFS spectra in a simple and reliable fashion, opening new opportunities for analysis in various disordered and crystalline systems. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the U.S. Department of Energy by Battelle.« less

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

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.

Yes, one can obtain better quality structures from routine X-ray data collection.

PubMed

Sanjuan-Szklarz, W Fabiola; Hoser, Anna A; Gutmann, Matthias; Madsen, Anders Østergaard; Woźniak, Krzysztof

2016-01-01

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å(-1)). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also the results of translation-libration-screw (TLS) analysis and vibrational entropy values are more reliable for 2θmax > 65°.

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

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

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.

Advanced Computed-Tomography Inspection System

NASA Technical Reports Server (NTRS)

Harris, Lowell D.; Gupta, Nand K.; Smith, Charles R.; Bernardi, Richard T.; Moore, John F.; Hediger, Lisa

1993-01-01

Advanced Computed Tomography Inspection System (ACTIS) is computed-tomography x-ray apparatus revealing internal structures of objects in wide range of sizes and materials. Three x-ray sources and adjustable scan geometry gives system unprecedented versatility. Gantry contains translation and rotation mechanisms scanning x-ray beam through object inspected. Distance between source and detector towers varied to suit object. System used in such diverse applications as development of new materials, refinement of manufacturing processes, and inspection of components.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

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

Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I.

2014-05-01

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM)more » program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.« less

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

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

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.

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.

[Can the local energy minimization refine the PDB structures of different resolution universally?].

PubMed

Godzi, M G; Gromova, A P; Oferkin, I V; Mironov, P V

2009-01-01

The local energy minimization was statistically validated as the refinement strategy for PDB structure pairs of different resolution. Thirteen pairs of structures with the only difference in resolution were extracted from PDB, and the structures of 11 identical proteins obtained by different X-ray diffraction techniques were represented. The distribution of RMSD value was calculated for these pairs before and after the local energy minimization of each structure. The MMFF94 field was used for energy calculations, and the quasi-Newton method was used for local energy minimization. By comparison of these two RMSD distributions, the local energy minimization was proved to statistically increase the structural differences in pairs so that it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in a multidimensional space of atomic coordinates. For these randomized structures, the RMSD distribution was calculated and compared with that for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by X-ray diffraction for PDB. Some other results obtained by exploring the energy surface near these conformations are also presented. These results are expected to be very useful for the development of new protein refinement strategies based on energy minimization.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

PubMed

Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

2010-05-01

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy*

PubMed Central

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R.; Gerwert, Klaus; Kötting, Carsten

2015-01-01

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg2+ coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg2+ in GTPases. The Mg2+ coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. PMID:26272610

Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental, and theoretical IR spectroscopy.

PubMed

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R; Gerwert, Klaus; Kötting, Carsten

2015-10-02

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg(2+) coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg(2+) in GTPases. The Mg(2+) coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Coherent convergent-beam time-resolved X-ray diffraction

PubMed Central

Spence, John C. H.; Zatsepin, Nadia A.; Li, Chufeng

2014-01-01

The use of coherent X-ray lasers for structural biology allows the use of nanometre diameter X-ray beams with large beam divergence. Their application to the structure analysis of protein nanocrystals and single particles raises new challenges and opportunities. We discuss the form of these coherent convergent-beam (CCB) hard X-ray diffraction patterns and their potential use for time-resolved crystallography, normally achieved by Laue (polychromatic) diffraction, for which the monochromatic laser radiation of a free-electron X-ray laser is unsuitable. We discuss the possibility of obtaining single-shot, angle-integrated rocking curves from CCB patterns, and the dependence of the resulting patterns on the focused beam coordinate when the beam diameter is larger or smaller than a nanocrystal, or smaller than one unit cell. We show how structure factor phase information is provided at overlapping interfering orders and how a common phase origin between different shots may be obtained. Their use in refinement of the phase-sensitive intensity between overlapping orders is suggested. PMID:24914153

Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography.

PubMed

Weiss, Manfred S

2017-01-01

For many years, diffraction experiments in macromolecular crystallography at X-ray wavelengths longer than that of Cu-K α (1.54 Å) have been largely underappreciated. Effects caused by increased X-ray absorption result in the fact that these experiments are more difficult than the standard diffraction experiments at short wavelengths. However, due to the also increased anomalous scattering of many biologically relevant atoms, important additional structural information can be obtained. This information, in turn, can be used for phase determination, for substructure identification, in molecular replacement approaches, as well as in structure refinement. This chapter reviews the possibilities and the difficulties associated with such experiments, and it provides a short description of two macromolecular crystallography synchrotron beam lines dedicated to long-wavelength X-ray diffraction experiments.

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

Conformational Sampling of a Biomolecular Rugged Energy Landscape.

PubMed

Rydzewski, Jakub; Jakubowski, Rafal; Nicosia, Giuseppe; Nowak, Wieslaw

2018-01-01

The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

HPHT synthesis, structure and electrical properties of type-I clathrates Ba{sub 8}Al{sub x}Si{sub 46−x}

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

Liu, Binwu; Jia, Xiaopeng; Sun, Hairui

2016-01-15

Clathrate compounds Ba{sub 8}Al{sub x}Si{sub 46−x} were successfully synthesized using the method of high-pressure and high-temperature (HPHT). In this process, we used BaSi{sub 2} as one of the starting materials in place of Ba metals, which reduces the complexity of the program caused by the extremely high chemical reactivity. By using this method, the processing time was reduced from few days to an hour. X-ray diffraction and structural refinement indicated this composition crystallized in type-I clathrate phase. Bond length analysis showed the Ba atoms in small dodecahedron had spherical thermal ellipsoids while those in large tetrakaidecahedron displayed anisotropic thermal ellipsoids.more » The negative Seebeck coefficient indicated transport processes were dominated by electrons as carriers, and increased with the increasing temperature. The electrical properties, including Seebeck coefficient and Power factor, were greatly enhanced by Al substitution. - Graphical abstract: Left: The cavity structure diagram of a China-type large volume cubic high-pressure apparatus, and the Type-I clathrate structure of sample synthesized using HPHT. Middle: X-ray Rietveld refinement profile for Ba{sub 8}Si{sub 46} and element mapping for Ba{sub 8}Al{sub 16}Si{sub 30}. Right: Temperature dependence of Seebeck coefficient for Ba{sub 8}Al{sub x}Si{sub 46−x} prepared by HPHT. - Highlights: • HPHT is a simple and rapid synthetic approach. • We use BaSi{sub 2} as one of the starting materials replacing Ba metals. • The processing time reduces from few days to an hour. • Structure determination is refined by Rietveld analysis of XRD data. • Variable temperature electrical properties are characterized.« less

X-ray diffraction and infrared spectroscopy studies of Ba(Fe1/2Nb1/2)O3-(Na1/2Bi1/2)TiO3 ceramics

NASA Astrophysics Data System (ADS)

Chandra, K. P.; Yadav, Anjana; Prasad, K.

2018-05-01

Ceramics (1-x)Ba(Fe1/2Nb1/2)O3-x(Na1/2Bi1/2)TiO3; 0≤x≤1.0 were prepared by conventional ceramic synthesis technique. Rietveld refinements of X-ray diffraction data of these ceramics were carried out using FullProf software and determined their crystal symmetry, space group and unit cell dimensions. Rietveld refinement revealed that Ba(Fe1/2Nb1/2)O3 has cubic structure with space group Pm 3 ¯ m and Na1/2Bi1/2)TiO3 has rhombohedral structure with space group R3c. Addition of (Na1/2Bi1/2)TiO3 to Ba(Fe1/2Nb1/2)O3 resulted in the change of unit cell structure from cubic to tetragonal (P4/mmm) for x = 0.75 and the X-Ray diffraction peaks slightly shift towards higher Bragg's angle, suggesting slight decrease in unit cell volume. SEM studies were carried out in order to access the quality of the prepared ceramics which showed a change in grain shapes with the increase of (Na1/2Bi1/2)TiO3 content. FTIR spectra confirmed the formation of perovskite type solid solutions.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

2016-06-30

We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

Model-based Approaches for the Determination of Lipid Bilayer Structure from Small-Angle Neutron and X-ray Scattering Data

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

Heberle, Frederick A; Pan, Jianjun; Standaert, Robert F

2012-01-01

Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Ku erka et al. (Ku erka et al. 2012; Ku erka et al. 2008). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent in these models. In particular, it is recognized that standalone data do not contain enoughmore » information to fully resolve the structure of inherently disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structural parameters, including the much sought after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data sets, as well as the implementation of local volume conservation in the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.« less

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.

Neutron and X-ray total scattering study of hydrogen disorder in fully hydrated hydrogrossular, Ca3Al2(O4H4)3

NASA Astrophysics Data System (ADS)

Keen, David A.; Keeble, Dean S.; Bennett, Thomas D.

2018-04-01

The structure of fully hydrated grossular, or katoite, contains an unusual arrangement of four O-H bonds within each O4 tetrahedra. Neutron and X-ray total scattering from a powdered deuterated sample have been measured to investigate the local arrangement of this O4D4 cluster. The O-D bond length determined directly from the pair distribution function is 0.954 Å, although the Rietveld-refined distance between average O and D positions was slightly smaller. Reverse Monte Carlo refinement of supercell models to the total scattering data show that other than the consequences of this correctly determined O-D bond length, there is little to suggest that the O4D4 structure is locally significantly different from that expected based on the average structure determined solely from Bragg diffraction.

COMPUTATIONAL METHODOLOGIES for REAL-SPACE STRUCTURAL REFINEMENT of LARGE MACROMOLECULAR COMPLEXES

PubMed Central

Goh, Boon Chong; Hadden, Jodi A.; Bernardi, Rafael C.; Singharoy, Abhishek; McGreevy, Ryan; Rudack, Till; Cassidy, C. Keith; Schulten, Klaus

2017-01-01

The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. PMID:27145875

Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

DOE PAGES

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

2014-10-29

We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

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

Kiyota, Eduardo; Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP; Sousa, Sylvia Morais de

Preliminary X-ray diffraction studies of apo maize aldose reductase at 2.0 Å resolution are reported. Maize aldose reductase (AR) is a member of the aldo-keto reductase superfamily. In contrast to human AR, maize AR seems to prefer the conversion of sorbitol into glucose. The apoenzyme was crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 47.2, b = 54.5, c = 100.6 Å and one molecule in the asymmetric unit. Synchrotron X-ray diffraction data were collected and a final resolution limit of 2.0 Å was obtained after data reduction. Phasing was carried out by an automatedmore » molecular-replacement procedure and structural refinement is currently in progress. The refined structure is expected to shed light on the functional/enzymatic mechanism and the unusual activities of maize AR.« less

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

Na, K, Rb, and Cs Exchange in Heulandite Single-Crystals: X-Ray Structure Refinements at 100 K

NASA Astrophysics Data System (ADS)

Yang, Ping; Armbruster, Thomas

1996-04-01

The crystal structures of Na-, K-, Rb-, and Cs-exchanged varieties of the zeolite heulandite with the simplified compositionM+9Al9Si27O72·nH2O were studied by single-crystal X-ray diffraction at 100 K. The structure refinements of Na-, K-, and Rb-exchanged heulandite were performed in space groupC2/mwith resultantRvalues of 3.8, 3.0, and 4.9%, respectively. Cs-exchanged heulandite was refined in space groupC[formula], yielding anRvalue of 3.4%. X-ray single-crystal data of the Cs-exchanged variety indicated that many reflections of typeh k lwere not equivalent toh -k las expected for monoclinic symmetry. With increasing radius of the incorporated channel cations, thebaxis increases from 17.93 to 18.09 Å leading to a slight widening of the channels. The number of H2O molecules also decreases with increasing cation radius due to space limitations. Three general cation positions (II-1,C3, andB4) were found in the four exchanged heulandite samples. For Rb- and Cs-exchanged crystals, the additional cation siteA2 occurs. In Cs-exchanged heulandite symmetry lowering is due to partial Si, Al ordering in the framework accompanied with a more asymmetric arrangement of channel Cs. Only if heavy elements in the channels are present the symmetry information of the framework is enforced, thus partial Si, Al ordering can be resolved.

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.

Ba0.06(Na,Bi)0.94Ti1-x(Ni1/3Nb2/3)xO3 ceramics: X-ray diffraction and infrared spectroscopy studies

NASA Astrophysics Data System (ADS)

Mishra, R. K.; Prasad, Ashutosh; Chandra, K. P.; Prasad, K.

2018-05-01

Non-lead ceramic samples of Ba0.06(Na0.5Bi0.5)0.94Ti1-x(Ni1/3Nb2/3)xO3; 0 ≤ x ≤ 1.0 were prepared by standard high temperature ceramic synthesis method. Rietveld refinements of X-ray diffraction data of these ceramics were carried out using FullProf software and determined their crystal symmetry, space group and unit cell dimensions. Rietveld refinement revealed that Ba0.06(Na0.5Bi0.5)0.94TiO3 has a monoclinic structure with space group P4/m while B0.06(Na0.5Bi0.5)0.94(Ni1/3Nb2/3)O3 has tetragonal (pseudo-cubic) structure with space group P4/mmm. Partial replacement of Ti4+ ion by pseudo-cation (Ni1/33 +Nb2/3 5 +) 4 + resulted in the change of unit cell structure from monoclinic to tetragonal. SEM studies were carried out in order to access the quality of the prepared ceramics which showed a change in grain sizes with the increase of (Ni1/33 +Nb2/3 5 +) 4 + content. FTIR spectra confirmed the formation of perovskite type solid solutions.

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

DOE PAGES

Ginn, Helen Mary; Brewster, Aaron S.; Hattne, Johan; ...

2015-05-23

Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definitionmore » of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating theR splitvalue) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less

Simultaneous X-ray and neutron diffraction Rietveld refinements of nanophase iron substituted hydroxyapatite

NASA Astrophysics Data System (ADS)

Kyriacou, Andreas

The effect of Fe substitution on the crystal structure of hydroxyapatite (HAp) is studied by applying simultaneous Rietveld refinements of powder x-ray and neutron diffraction patterns. Fe is one of the trace elements replacing Ca in HAp, which is the major mineral phase in bones and teeth. The morphology and magnetic properties of the Fe-HAp system are also studied by transmission electron microscopy and magnetization measurements. Samples of Ca(5-x)Fex(PO4)3OH with 0 ≤ x ≤ 0.3 were prepared. Single phase HAp was identified in x-ray diffraction patterns (XRD) of samples with x < 0.1 inferring that the solubility limits are less than 0.1. Hematite (alpha-Fe2O3) is identified as a secondary phase for higher Fe content. The refined parameters show that Fe is incorporated in the HAp structure by replacing Ca in the two crystallographic sites with a preference at the Ca2 site. This preference explains the small effect of the Fe substitution on the lattice constants of HAp. The overall decrease of the lattice constants is explained by the ionic size difference of Ca and Fe. The increasing trend of the a-lattice constant with x in the Fe substituted samples is attributed to a lattice relaxation caused by the substitution of the 4- and 6-fold Fe at the 7- and 9-fold Ca1 and Ca2 sites. This Ca local geometry reduction is indicated by a slight increase of the Ca1-O3 and Ca2-O1 bond lengths. Above the solubility limit x = 0.05, the Fe is partitioned in and out of the HAp structure with increasing nominal Fe content x. The excess Fe is oxidized to hematite. The TEM analysis and magnetic measurements support the results of the simultaneous Rietveld refinements. The TEM images show no significant effect on the morphology and size of the HAp particles upon Fe incorporation. The particles are either spheres or short rods of dimensions 20--60 nm. Hematite particles are imaged in the samples with x exceeding the solubility limit. These particles are spheres, about 15 nm in diameter and are more resistant to electron beam damage. Magnetic measurements reveal a transition of the diamagnetic pure HAp to paramagnetic Fe substituted HAp.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of Mn K -edge XANES data

NASA Astrophysics Data System (ADS)

Monesi, C.; Meneghini, C.; Bardelli, F.; Benfatto, M.; Mobilio, S.; Manju, U.; Sarma, D. D.

2005-11-01

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K -edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3 . The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K -edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

First Results from a Microfocus X-Ray System for Macromolecular Crystallography

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

1999-01-01

The design and performance of a 40 Watt laboratory crystallography system optimized for the structure determination of small protein crystals are described. This system combines a microfocus x-ray generator (40 microns FWHM spot size at a power level of 40 Watts) and a short focal length (F = 2.6 mm) polycapillary collimating optic, and produces a small diameter quasi-parallel x-ray beam. Measurements of x-ray flux, divergence and spectral purity of the resulting x-ray beam are presented. The x-ray flux in a 250 microns diameter aperture produced by the microfocus system is 14.7 times higher .than that from a 3.15 kW rotating anode generator equipped with graphite monochromator. Crystallography data taken with the microfocus system are presented, and indicate that the divergence and spectral purity of the x-ray are sufficient to refine the diffraction data using a standard crystallographic software. Significant additional improvements in flux and beam divergence are possible, and plans for achieving these coals are discussed.

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.

On the release of cppxfel for processing X-ray free-electron laser images.

PubMed

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K; Stuart, David Ian

2016-06-01

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel , a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

On the release of cppxfel for processing X-ray free-electron laser images

DOE PAGES

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K.; ...

2016-05-11

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed formore » existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.« less

X-ray diffraction study of Penicillium Vitale catalase in the complex with aminotriazole

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

Borovik, A. A.; Grebenko, A. I.; Melik-Adamyan, V. R., E-mail: mawr@ns.crys.ras.ru

2011-07-15

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.

Synthesis and X-ray structural investigation of (5R*,6S*)-1-benzoyl-5-methylthio-6-methoxy-1-azapenam

NASA Astrophysics Data System (ADS)

Krajewski, J. W.; Gluziński, P.; Grochowski, E.; Pupek, K.; Mishnyov, A.; Kemme, A.

1992-08-01

The compound (5R*,6S*)-1-benzoyl-5-methylthio-6-methoxy-1-azapenam ( 3) has been synthesized and its structure investigated by X-ray diffraction. The compound crystallizes in a monoclinic system, space group Cc, Z = 4, a = 12.01(1), b = 16.51(1), c = 8.048(6) Å, β = 115.87(6)°. The structure was solved by direct methods and refined by a full-matrix, least-squares procedure to give R = 0.070, Rw = 0.046, w = 1.34/(σ 2F). The expected cis configuration around the β-lactam ring was fully confirmed.

Sharp chemical interface in epitaxial Fe{sub 3}O{sub 4} thin films

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

Gálvez, S.; Rubio-Zuazo, J., E-mail: rubio@esrf.fr; Salas-Colera, E.

Chemically sharp interface was obtained on single phase single oriented Fe{sub 3}O{sub 4} (001) thin film (7 nm) grown on NiO (001) substrate using oxygen assisted molecular beam epitaxy. Refinement of the atomic structure, stoichiometry, and oxygen vacancies were determined by soft and hard x-ray photoelectron spectroscopy, low energy electron diffraction and synchrotron based X-ray reflectivity, and X-ray diffraction. Our results demonstrate an epitaxial growth of the magnetite layer, perfect iron stoichiometry, absence of oxygen vacancies, and the existence of an intermixing free interface. Consistent magnetic and electrical characterizations are also shown.

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

Grain Refinement by Authigenic Inoculation Inherited from the Medium-Range Order Structure of Ni-Cr-W Superalloy

NASA Astrophysics Data System (ADS)

Gao, Zhongtang; Hu, Rui; Guo, Wei; Zhang, Chuanwei

2018-04-01

The combination of liquidus casting and thermal control solidification furnace was applied to obtain a fine-grained ingot. A rapid quenching method and x-ray diffraction measurement were used to investigate the effect of authigenic inoculation on grain refinement. The structure factor S(Q) of liquid Ni-Cr-W superalloy at 1400 °C (Liquidus temperature) and bright-field image of the microstructures quenched from 1400 °C have been measured by the high-temperature x-ray diffractometer and the transmission electron microscopy (TEM), respectively. The results show that a pre-peak exists on a S(Q) curve at the liquidus temperature. The clusters of atom in rapidly quenched microstructures obtained by isothermal heat treatment at 1400 °C were studied using TEM. Meanwhile, the effect of isothermal different temperatures on rapidly quenched microstructures was studied. The results also show that there are only the globular, equiaxed grains distributed in the solidification structure. These particles are inherited from the medium-range order structure, which is beneficial for grain refinement. The normalized work-hardening rate-strain curve indicates the work-hardening rate of fine grain is higher than that of conventional grain at the same temperature and the same deformation.

Grain Refinement by Authigenic Inoculation Inherited from the Medium-Range Order Structure of Ni-Cr-W Superalloy

NASA Astrophysics Data System (ADS)

Gao, Zhongtang; Hu, Rui; Guo, Wei; Zhang, Chuanwei

2018-05-01

The combination of liquidus casting and thermal control solidification furnace was applied to obtain a fine-grained ingot. A rapid quenching method and x-ray diffraction measurement were used to investigate the effect of authigenic inoculation on grain refinement. The structure factor S( Q) of liquid Ni -Cr-W superalloy at 1400 °C (Liquidus temperature) and bright-field image of the microstructures quenched from 1400 °C have been measured by the high-temperature x-ray diffractometer and the transmission electron microscopy (TEM), respectively. The results show that a pre-peak exists on a S( Q) curve at the liquidus temperature. The clusters of atom in rapidly quenched microstructures obtained by isothermal heat treatment at 1400 °C were studied using TEM. Meanwhile, the effect of isothermal different temperatures on rapidly quenched microstructures was studied. The results also show that there are only the globular, equiaxed grains distributed in the solidification structure. These particles are inherited from the medium-range order structure, which is beneficial for grain refinement. The normalized work-hardening rate-strain curve indicates the work-hardening rate of fine grain is higher than that of conventional grain at the same temperature and the same deformation.

X-ray Monitoring of eta Carinae: Variations on a Theme

NASA Technical Reports Server (NTRS)

Corcoran, M. F.

2004-01-01

We present monitoring observations by the Rossi X-ray Timing Explorer of the 2-10 keV X-ray emission from the supermassive star eta Carinae from 1996 through late 2003. These data cover more than one of the stellar variability cycles in temporal detail and include especially detailed monitoring through two X-ray minima. We compare the current X-ray minimum which began on June 29, 2003 to the previous X-ray minimum which began on December 15, 1997, and refine the X-ray period to 2024 days. We examine the variations in the X-ray spectrum with phase and with time, and also refine our understanding of the X-ray peaks which have a quasi-period of 84 days, with significant variation. Cycle-to-cycle differences are seen in the level of X-ray intensity and in the detailed variations of the X-ray flux on the rise to maximum just prior to the X-ray minimum. Despite these differences the similarities between the decline to minimum, the duration of the minimum, and correlated variations of the X-ray flux and other measures throughout the electromagnetic spectrum leave little doubt that that the X-ray variation is strictly periodic and produced by orbital motion as the wind from eta Carinae collides with the wind of an otherwise unseen companion.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Crystal structure and europium luminescence of NaMgH3-xFx

NASA Astrophysics Data System (ADS)

Pflug, Christian; Franz, Alexandra; Kohlmann, Holger

2018-02-01

The solid solution series NaMgH3-xFx (x = 0, 0.5, 1, 1.5, 2, 2.5, 3) was synthesized by solid-state reactions under hydrogen gas pressure from binary ionic hydrides, fluorides and magnesium. Rietveld refinement based on X-ray powder diffraction data revealed the GdFeO3-structure type for all compounds and a trend of lattice parameters according to Vegard's law. The anion distribution in NaMgD2F and NaMgD1.5F1.5 was found to be statistical by Rietveld refinement based on neutron powder diffraction data. Photoluminescence measurements on europium(II) substituted NaMgH3-xFx revealed a strong red shift of the emission wavelength (λem = 665 nm for NaMgH2F:Eu) in comparison to violet emitting NaMgF3:Eu.

Application of micro X-ray diffraction to investigate the reaction products formed by the alkali silica reaction in concrete structures

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

Dähn, R.; Arakcheeva, A.; Schaub, Ph.

Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This particular high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating themore » sample. Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. Furthermore, it is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.« less

Application of micro X-ray diffraction to investigate the reaction products formed by the alkali–silica reaction in concrete structures

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

Dähn, R., E-mail: rainer.daehn@psi.ch; Arakcheeva, A.; Schaub, Ph.

Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating the sample.more » Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. It is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.« less

Crystal structure and X-ray photoemission spectroscopic study of A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta

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

Dutta, Alo, E-mail: alo_dutta@yahoo.com; Saha, Sujoy; Kumari, Premlata

2015-09-15

The X-ray photoemission spectroscopic (XPS) study of the double perovskite oxides A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta] synthesized by the solid-state reaction technique has been carried out to investigate the nature of the chemical state of the constituent ions and the bonding between them. The Rietveld refinement of the X-ray diffraction patterns suggests the monoclinic crystal structure of all the materials at room temperature. The negative and positive chemical shifts of the core level XPS spectrum of O-1s and Nb-3d{sub 3/2}/Ta-4f{sub 5/2} respectively suggest the covalent bonding between Nb/Ta cations and O ion. The change of the bonding strengthmore » between the anion and the cations from one material to another has been analyzed. The vibrational property of the materials is investigated using the room temperature Raman spectra. A large covalency of Ta-based compound than Nb compound is confirmed from the relative shifting of the Raman modes of the materials. - Graphical abstract: Crystal structure of two perovskite oxides CLN and CLT is investigated. XPS study confirms the two different co-ordination environments of Ca and covalent bonding between B-site cations and O-ion. - Highlights: • Ordered perovskite structure obtained by Rietveld refinement of XRD patterns. • Study of nature of chemical bonding by X-ray photoemission spectroscopy. • Opposite chemical shift of d-states of Nb/Ta with respect to O. • Covalent bonding between d-states of Nb/Ta and O. • Relative Raman shifts of CLN and CLT substantiate the more covalent character of Ta than Nb.« less

Role of Molecular Structure on X-ray Diffraction in Thermotropic Uniaxial and Biaxial Nematic Liquid Crystal Phases

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

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-08-27

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Role of Molecular Structure on X-ray Diffraction in Uniaxial and Biaxial Phases of Thermotropic Liquid Crystals

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

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-04-29

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

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 pentasodium hydrogen dicitrate from synchrotron X-ray powder diffraction data and DFT comparison

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

Rammohan, Alagappa; Kaduk, James A.

2017-01-27

The crystal structure of pentasodium hydrogen dicitrate, Na 5H(C 6H 5O 7) 2, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Each of the two independent citrate anions is joined into a dimer by very strong centrosymmetric O—H...O hydrogen bonds, with O...O distances of 2.419 and 2.409 Å. Four octahedrally coordinated Na +ions share edges to form open layers parallel to theabplane. A fifth Na +ion in trigonal–bipyramidal coordination shares faces with NaO 6octahedra on both sides of these layers.

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.

TOPICAL REVIEW: Digital x-ray tomosynthesis: current state of the art and clinical potential

NASA Astrophysics Data System (ADS)

Dobbins, James T., III; Godfrey, Devon J.

2003-10-01

Digital x-ray tomosynthesis is a technique for producing slice images using conventional x-ray systems. It is a refinement of conventional geometric tomography, which has been known since the 1930s. In conventional geometric tomography, the x-ray tube and image receptor move in synchrony on opposite sides of the patient to produce a plane of structures in sharp focus at the plane containing the fulcrum of the motion; all other structures above and below the fulcrum plane are blurred and thus less visible in the resulting image. Tomosynthesis improves upon conventional geometric tomography in that it allows an arbitrary number of in-focus planes to be generated retrospectively from a sequence of projection radiographs that are acquired during a single motion of the x-ray tube. By shifting and adding these projection radiographs, specific planes may be reconstructed. This topical review describes the various reconstruction algorithms used to produce tomosynthesis images, as well as approaches used to minimize the residual blur from out-of-plane structures. Historical background and mathematical details are given for the various approaches described. Approaches for optimizing the tomosynthesis image are given. Applications of tomosynthesis to various clinical tasks, including angiography, chest imaging, mammography, dental imaging and orthopaedic imaging, are also described.

Raman effect, structural and dielectric properties of sol-gel synthesized polycrystalline GaFe{sub 1-x}Zr{sub x}O{sub 3} (0≤x≤0.15)

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

Kumar, Rajeev, E-mail: rajeevgiitk@gmail.com; Mall, Ashish Kumar; Gupta, Rajeev

2016-05-23

Polycrystalline ceramic samples of Zirconium (Zr)-doped GaFeO{sub 3} (GaFe{sub 1-x}Zr{sub x}O{sub 3}) were studied using powder X-ray diffraction, complex impedance spectroscopy and Raman spectroscopic measurements to understand the effect of Zr doping on the structural and dielectric properties. The samples with varying Zr content were prepared by Sol-Gel method. X-ray data analysis confirmed the formation of single phase material without formation of any secondary phases and all are crystallized in Pc2{sub 1}n orthorhombic symmetry. Rietveld refinement of the X-ray data suggested an increase in the lattice constants due to size effect and decreases on x = 0.15 due to themore » effect of change in interplanner spacing. Impedance studies on the samples showed that the dielectric constant increases while loss tangent decrease as the Zr content increases. Raman scattering on GaFe{sub 1-x}Zr{sub x}O{sub 3} (x = 0, 0.05, 0.10, & 0.15) used to understand the composition dependence on phonon modes at room temperature. On Zr doping, Raman modes frequencies shifts to lower energies consistent with the X-ray data.« less

Incorporation of Cadmium and Nickel into Ferrite Spinel Solid Solution: X-ray Diffraction and X-ray Absorption Fine Structure Analyses.

PubMed

Su, Minhua; Liao, Changzhong; Chan, Tingshan; Shih, Kaimin; Xiao, Tangfu; Chen, Diyun; Kong, Lingjun; Song, Gang

2018-01-16

The feasibility of incorporating Cd and Ni in hematite was studied by investigating the interaction mechanism for the formation of Cd x Ni 1-x Fe 2 O 4 solid solutions (CNFs) from CdO, NiO, and α-Fe 2 O 3 . X-ray diffraction results showed that the CNFs crystallized into spinel structures with increasing lattice parameters as the Cd content in the precursors was increased. Cd 2+ ions were found to occupy the tetrahedral sites, as evidenced by Rietveld refinement and extended X-ray absorption fine structure analyses. The incorporation of Cd and Ni into ferrite spinel solid solution strongly relied on the processing parameters. The incorporation of Cd and Ni into the CNFs was greater at high x values (0.7 < x ≤ 1.0) than at low x values (0.0 ≤ x ≤ 0.7). A feasible treatment technique based on the investigated mechanism of CNF formation was developed, involving thermal treatment of waste sludge containing Cd and Ni. Both of these metals in the waste sludge were successfully incorporated into a ferrite spinel solid solution, and the concentrations of leached Cd and Ni from this solid solution were substantially reduced, stabilizing at low levels. This research offers a highly promising approach for treating the Cd and Ni content frequently encountered in electronic waste and its treatment residues.

Three-dimensional-printed gas dynamic virtual nozzles for x-ray laser sample delivery

PubMed Central

Nelson, Garrett; Kirian, Richard A.; Weierstall, Uwe; Zatsepin, Nadia A.; Faragó, Tomáš; Baumbach, Tilo; Wilde, Fabian; Niesler, Fabian B. P.; Zimmer, Benjamin; Ishigami, Izumi; Hikita, Masahide; Bajt, Saša; Yeh, Syun-Ru; Rousseau, Denis L.; Chapman, Henry N.; Spence, John C. H.; Heymann, Michael

2016-01-01

Reliable sample delivery is essential to biological imaging using X-ray Free Electron Lasers (XFELs). Continuous injection using the Gas Dynamic Virtual Nozzle (GDVN) has proven valuable, particularly for time-resolved studies. However, many important aspects of GDVN functionality have yet to be thoroughly understood and/or refined due to fabrication limitations. We report the application of 2-photon polymerization as a form of high-resolution 3D printing to fabricate high-fidelity GDVNs with submicron resolution. This technique allows rapid prototyping of a wide range of different types of nozzles from standard CAD drawings and optimization of crucial dimensions for optimal performance. Three nozzles were tested with pure water to determine general nozzle performance and reproducibility, with nearly reproducible off-axis jetting being the result. X-ray tomography and index matching were successfully used to evaluate the interior nozzle structures and identify the cause of off-axis jetting. Subsequent refinements to fabrication resulted in straight jetting. A performance test of printed nozzles at an XFEL provided high quality femtosecond diffraction patterns. PMID:27410079

Investigation on the structural, magnetic and magnetocaloric properties of nanocrystalline Pr-deficient Pr1-xSrxMnO3-δ manganites

NASA Astrophysics Data System (ADS)

Arun, B.; Athira, M.; Akshay, V. R.; Sudakshina, B.; Mutta, Geeta R.; Vasundhara, M.

2018-02-01

We have investigated the structural, magnetic and magnetocaloric properties of nanocrystalline Pr-deficient Pr1-xSrxMnO3-δ Perovskite manganites. Rietveld refinement of the X-ray powder diffraction patterns confirms that all the studied compounds have crystallized into an orthorhombic structure with Pbnm space group. Transmission electron microscopy analysis reveals nanocrystalline compounds with crystallite size less than 50 nm. The selected area electron diffraction patterns reveal the highly crystalline nature of the compounds and energy dispersive X-ray spectroscopic analysis shows that the obtained compositions are nearly identical with the nominal one. The oxygen stoichiometry is estimated by iodometric titration method and stoichiometric compositions are confirmed by X-ray Fluorescence Spectrometry analysis. A large bifurcation is observed in the ZFC/FC curves and Arrott plots not show a linear relation but have a convex curvature nature. The temperature dependence of inverse magnetic susceptibility at higher temperature confirms the existence of ferromagnetic clusters. The experimental results reveal that the reduction of crystallite size to nano metric scale in Pr-deficient manganites adversely influences structural, magnetic and magnetocaloric properties as compared to its bulk counterparts reported earlier.

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

Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

PubMed

DiMaio, Frank

2017-01-01

Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

Electronic structure modifications and band gap narrowing in Zn0.95V0.05O

NASA Astrophysics Data System (ADS)

Ahad, Abdul; Majid, S. S.; Rahman, F.; Shukla, D. K.; Phase, D. M.

2018-04-01

We present here, structural, optical and electronic structure studies on Zn0.95V0.05O, synthesized using solid state method. Rietveld refinement of x-ray diffraction pattern indicates no considerable change in the lattice of doped ZnO. The band gap of doped sample, as calculated by Kubelka-Munk transformed reflectance spectra, has been found reduced compared to pure ZnO. Considerable changes in absorbance in UV-Vis range is observed in doped sample. V doping induced decrease in band gap is supported by x-ray absorption spectroscopy measurements. It is experimentally confirmed that conduction band edge in Zn0.95V0.05O has shifted towards Fermi level than in pure ZnO.

Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

DOE PAGES

Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; ...

2015-09-21

In this paper, we review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach producesmore » robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). Finally, from model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.).« less

Direct Observations of a Dynamically Driven Phase Transition with in situ X-Ray Diffraction in a Simple Ionic Crystal

NASA Astrophysics Data System (ADS)

Kalita, Patricia; Specht, Paul; Root, Seth; Sinclair, Nicholas; Schuman, Adam; White, Melanie; Cornelius, Andrew L.; Smith, Jesse; Sinogeikin, Stanislav

2017-12-01

We report real-time observations of a phase transition in the ionic solid CaF2 , a model A B2 structure in high-pressure physics. Synchrotron x-ray diffraction coupled with dynamic loading to 27.7 GPa, and separately with static compression, follows, in situ, the fluorite to cotunnite structural phase transition, both on nanosecond and on minute time scales. Using Rietveld refinement techniques, we examine the kinetics and hysteresis of the transition. Our results give insight into the kinetic time scale of the fluorite-cotunnite phase transition under shock compression, which is relevant to a number of isomorphic compounds.

Direct Observations of a Dynamically Driven Phase Transition with in situ X-Ray Diffraction in a Simple Ionic Crystal

DOE PAGES

Kalita, Patricia E.; Specht, Paul Elliot; Root, Seth; ...

2017-12-21

Here, we report real-time observations of a phase transition in the ionic solid CaF 2, a model AB 2 structure in high-pressure physics. Synchrotron x-ray diffraction coupled with dynamic loading to 27.7 GPa, and separately with static compression, follows, in situ, the fluorite to cotunnite structural phase transition, both on nanosecond and on minute time scales. Using Rietveld refinement techniques, we examine the kinetics and hysteresis of the transition. Our results give insight into the kinetic time scale of the fluorite-cotunnite phase transition under shock compression, which is relevant to a number of isomorphic compounds.

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

PubMed

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

PubMed

Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

2016-01-01

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

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.

NMR crystallography of α-poly(L-lactide).

PubMed

Pawlak, Tomasz; Jaworska, Magdalena; Potrzebowski, Marek J

2013-03-07

A complementary approach that combines NMR measurements, analysis of X-ray and neutron powder diffraction data and advanced quantum mechanical calculations was employed to study the α-polymorph of L-polylactide. Such a strategy, which is known as NMR crystallography, to the best of our knowledge, is used here for the first time for the fine refinement of the crystal structure of a synthetic polymer. The GIPAW method was used to compute the NMR shielding parameters for the different models, which included the α-PLLA structure obtained by 2-dimensional wide-angle X-ray diffraction (WAXD) at -150 °C (model M1) and at 25 °C (model M2), neutron diffraction (WAND) measurements (model M3) and the fully optimized geometry of the PLLA chains in the unit cell with defined size (model M4). The influence of changes in the chain conformation on the (13)C σ(ii) NMR shielding parameters is shown. The correlation between the σ(ii) and δ(ii) values for the M1-M4 models revealed that the M4 model provided the best fit. Moreover, a comparison of the experimental (13)C NMR spectra with the spectra calculated using the M1-M4 models strongly supports the data for the M4 model. The GIPAW method, via verification using NMR measurements, was shown to be capable of the fine refinement of the crystal structures of polymers when coarse X-ray diffraction data for powdered samples are available.

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.

Accessing protein conformational ensembles using room-temperature X-ray crystallography

PubMed Central

Fraser, James S.; van den Bedem, Henry; Samelson, Avi J.; Lang, P. Therese; Holton, James M.; Echols, Nathaniel; Alber, Tom

2011-01-01

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation. PMID:21918110

Small Angle X-Ray Scattering from Lipid-Bound Myelin Basic Protein in Solution

PubMed Central

Haas, H.; Oliveira, C. L. P.; Torriani, I. L.; Polverini, E.; Fasano, A.; Carlone, G.; Cavatorta, P.; Riccio, P.

2004-01-01

The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution. PMID:14695288

Structural investigations of Pu{sup III} phosphate by X-ray diffraction, MAS-NMR and XANES spectroscopy

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

Popa, Karin; Raison, Philippe E., E-mail: philippe.raison@ec.europa.eu; Martel, Laura

2015-10-15

PuPO{sub 4} was prepared by a solid state reaction method and its crystal structure at room temperature was solved by powder X-ray diffraction combined with Rietveld refinement. High resolution XANES measurements confirm the +III valence state of plutonium, in agreement with valence bond derivation. The presence of the americium (as β{sup −} decay product of plutonium) in the +III oxidation state was determined based on XANES spectroscopy. High resolution solid state {sup 31}P NMR agrees with the XANES results and the presence of a solid-solution. - Graphical abstract: A full structural analysis of PuPO{sub 4} based on Rietveld analysis ofmore » room temperature X-ray diffraction data, XANES and MAS NMR measurements was performed. - Highlights: • The crystal structure of PuPO{sub 4} monazite is solved. • In PuPO{sub 4} plutonium is strictly trivalent. • The presence of a minute amount of Am{sup III} is highlighted. • We propose PuPO{sub 4} as a potential reference material for spectroscopic and microscopic studies.« less

Measuring and modeling diffuse scattering in protein X-ray crystallography

PubMed Central

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Wall, Michael E.

2016-01-01

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering. PMID:27035972

Measuring and modeling diffuse scattering in protein X-ray crystallography

DOE PAGES

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; ...

2016-03-28

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practicesmore » for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. In conclusion, these results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.« less

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

The period history of the X-ray pulsar in MSH 15-52

NASA Technical Reports Server (NTRS)

Weisskopf, M. C.; Elsner, R. F.; Darbo, W.; Leahy, D.; Naranan, S.; Harnden, F. R.; Seward, F. D.; Sutherland, P. G.; Grindlay, J. E.

1983-01-01

New and refined mesurements of the pulse period of the X-ray pulsar in the supernova remnant MSH 15-52 are presented. The data were obtained with the Monitor proportional Counter on board the HEAO 2 observatory. The period measurements were obtained by analyzing pulse arrival times determined by cross-correlating sample pulse profiles with a master template. The period history for the source and a representative 0.15 s X-ray light curve are shown. The X-ray measurements alone lead to a refined value of the period derivative of (1.5382 + or -0.0024) x 10 to the -12th s/s, while including the results of more recent radio observations leads to a value of (1.54029 + or -0.00095) x 10 to the -12th s/s. These results indicate a hard-point source surrounded by diffuse nebular emission.

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

Probing the structure of heterogeneous diluted materials by diffraction tomography.

PubMed

Bleuet, Pierre; Welcomme, Eléonore; Dooryhée, Eric; Susini, Jean; Hodeau, Jean-Louis; Walter, Philippe

2008-06-01

The advent of nanosciences calls for the development of local structural probes, in particular to characterize ill-ordered or heterogeneous materials. Furthermore, because materials properties are often related to their heterogeneity and the hierarchical arrangement of their structure, different structural probes covering a wide range of scales are required. X-ray diffraction is one of the prime structural methods but suffers from a relatively poor detection limit, whereas transmission electron analysis involves destructive sample preparation. Here we show the potential of coupling pencil-beam tomography with X-ray diffraction to examine unidentified phases in nanomaterials and polycrystalline materials. The demonstration is carried out on a high-pressure pellet containing several carbon phases and on a heterogeneous powder containing chalcedony and iron pigments. The present method enables a non-invasive structural refinement with a weight sensitivity of one part per thousand. It enables the extraction of the scattering patterns of amorphous and crystalline compounds with similar atomic densities and compositions. Furthermore, such a diffraction-tomography experiment can be carried out simultaneously with X-ray fluorescence, Compton and absorption tomographies, enabling a multimodal analysis of prime importance in materials science, chemistry, geology, environmental science, medical science, palaeontology and cultural heritage.

Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2.

PubMed

Fugel, Malte; Jayatilaka, Dylan; Hupf, Emanuel; Overgaard, Jacob; Hathwar, Venkatesha R; Macchi, Piero; Turner, Michael J; Howard, Judith A K; Dolomanov, Oleg V; Puschmann, Horst; Iversen, Bo B; Bürgi, Hans-Beat; Grabowsky, Simon

2018-01-01

Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element-hydrogen distances, r ( X -H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r ( X -H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro-carbon rubrene (orthorhombic 5,6,11,12-tetra-phenyl-tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element-hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.

Using neutrons, X-rays and nuclear magnetism to determine the role of transition metal oxide inclusions on both glass structure and stability in automotive glass enamels.

PubMed

Bowron, Daniel T; Booth, Jonathan; Barrow, Nathan S; Sutton, Patricia; Johnson, Simon R

2018-05-23

Low levels of transition metal oxides in alkali borosilicate glass systems can drastically influence crystallisation and phase separation properties. We investigated the non-monotonic effect of manganese doping on suppressing crystallisation, and the influence on optical properties by iron oxide doping, in terms of local atomic structure. Structural models based on empirical potential structure refinement were generated from neutron and X-ray scattering data, and compared against multinuclear solid-state NMR. This revealed that a 2.5% manganese doping had a disruptive effect on the entire glass network, supressing crystallisation of an undesired bismuth silicate phase, and that iron species preferentially locate near borate tetrahedra. Preventing phase separation and controlling crystallisation behaviour of glass are critical to the ultimate properties of automotive glass enamels.

Structure-phase state and mechanical properties of surface layers in titanium nikelide single crystals after shock mechanical treatment

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

Surikova, N., E-mail: surikova@ispms.tsc.ru; Panin, V., E-mail: paninve@ispms.tsc.ru; Vlasov, I.

2015-10-27

The influence of ultrasonic shock surface treatment (USST) on refine structure and mechanical characteristics of surface layers and deformation behaviour of volume samples of TiNi(Fe, Mo) shape memory effect alloy single crystals is studied using optical and transmission electron microscope, X-ray diffraction, nanoindentation, mechanical attrition testing and experiments on uniaxial tension.

Structure-phase state and mechanical properties of surface layers in titanium nikelide single crystals after shock mechanical treatment

NASA Astrophysics Data System (ADS)

Surikova, N.; Panin, V.; Vlasov, I.; Narkevich, N.; Surikov, N.; Tolmachev, A.

2015-10-01

The influence of ultrasonic shock surface treatment (USST) on refine structure and mechanical characteristics of surface layers and deformation behaviour of volume samples of TiNi(Fe, Mo) shape memory effect alloy single crystals is studied using optical and transmission electron microscope, X-ray diffraction, nanoindentation, mechanical attrition testing and experiments on uniaxial tension.

X-ray and dielectric characterization of Co doped tetragonal BaTiO3 ceramics

NASA Astrophysics Data System (ADS)

Bujakiewicz-Koronska, R.; Vasylechko, L.; Markiewicz, E.; Nalecz, D. M.; Kalvane, A.

2017-01-01

The crystal structure modifications of BaTiO3 induced by cobalt doping were studied. The polycrystalline (1 - x)BaTiO3 + xCo2O3 samples, with x ≤ 10 wt.%, were prepared by high temperature sintering conventional method. According to X-ray phase and structural characterization, performed by full-profile Rietveld refinement technique, all synthesized samples showed tetragonal symmetry perovskite structure with minor amount of parasitic phases. Pure single-phase composition has been detected only in the low level of doping BaTiO3. It was indicated that substitution of Co for the Ti sites in the (1 - x)BaTiO3 + xCo2O3 series led to decrease of tetragonality (c/a) of the BaTiO3 perovskite structure. This effect almost vanished in the (1 - x)BaTiO3 + xCo2O3 samples with nominal Co content higher than ∼1 wt.%, in which precipitation of parasitic Co-containing phases CoO and Co2TiO4 has been observed. Based on the results, the solubility limit of Co in Ti sub-lattice in the (1 - x)BaTiO3 + xCo2O3 series is estimated as x = 0.75 wt.%.

Correlation between the structural distortions and thermoelectric characteristics in La(1-x)A(x)CoO(3) (A = Ca and Sr).

PubMed

Wang, Yang; Sui, Yu; Ren, Peng; Wang, Lan; Wang, Xianjie; Su, Wenhui; Fan, Hong Jin

2010-04-05

Detailed structures and thermoelectric (TE) properties are investigated for the perovskite La(1-x)Ca(x)CoO(3) and La(1-x)Sr(x)CoO(3) with 0

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26)

USDA-ARS?s Scientific Manuscript database

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods, and to date has only been computationally examined using empirical force fi...

Constraints on Biogenic Emplacement of Crystalline Calcium Carbonate and Dolomite

NASA Astrophysics Data System (ADS)

Colas, B.; Clark, S. M.; Jacob, D. E.

2015-12-01

Amorphous calcium carbonate (ACC) is a biogenic precursor of calcium carbonates forming shells and skeletons of marine organisms, which are key components of the whole marine environment. Understanding carbonate formation is an essential prerequisite to quantify the effect climate change and pollution have on marine population. Water is a critical component of the structure of ACC and the key component controlling the stability of the amorphous state. Addition of small amounts of magnesium (1-5% of the calcium content) is known to promote the stability of ACC presumably through stabilization of the hydrogen bonding network. Understanding the hydrogen bonding network in ACC is fundamental to understand the stability of ACC. Our approach is to use Monte-Carlo simulations constrained by X-ray and neutron scattering data to determine hydrogen bonding networks in ACC as a function of magnesium doping. We have already successfully developed a synthesis protocol to make ACC, and have collected X-ray data, which is suitable for determining Ca, Mg and O correlations, and have collected neutron data, which gives information on the hydrogen/deuterium (as the interaction of X-rays with hydrogen is too low for us to be able to constrain hydrogen atom positions with only X-rays). The X-ray and neutron data are used to constrain reverse Monte-Carlo modelling of the ACC structure using the Empirical Potential Structure Refinement program, in order to yield a complete structural model for ACC including water molecule positions. We will present details of our sample synthesis and characterization methods, X-ray and neutron scattering data, and reverse Monte-Carlo simulations results, together with a discussion of the role of hydrogen bonding in ACC stability.

X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

PubMed

Genoni, Alessandro

2013-07-09

Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP{sup +}

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

Wan, Qun, E-mail: wqun@yzu.edu.cn; Kovalevsky, Andrey Y.; Wilson, Mark A.

2014-05-25

A 2.0 Å resolution neutron data set and a 1.6 Å resolution X-ray data set were collected for joint X-ray/neutron refinement of the ecDHFR–folate–NADP{sup +} complex in order to study the reaction mechanism of dihydrofolate reductase.

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%.

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

Assessing the Chemical Accuracy of Protein Structures via Peptide Acidity

PubMed Central

Anderson, Janet S.; Hernández, Griselda; LeMaster, David M.

2012-01-01

Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses. PMID:23182463

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.

A CPU benchmark for protein crystallographic refinement.

PubMed

Bourne, P E; Hendrickson, W A

1990-01-01

The CPU time required to complete a cycle of restrained least-squares refinement of a protein structure from X-ray crystallographic data using the FORTRAN codes PROTIN and PROLSQ are reported for 48 different processors, ranging from single-user workstations to supercomputers. Sequential, vector, VLIW, multiprocessor, and RISC hardware architectures are compared using both a small and a large protein structure. Representative compile times for each hardware type are also given, and the improvement in run-time when coding for a specific hardware architecture considered. The benchmarks involve scalar integer and vector floating point arithmetic and are representative of the calculations performed in many scientific disciplines.

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.

PubMed

Smart, Oliver S; Womack, Thomas O; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-04-01

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct 'target' structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

The effects of rigid motions on elastic network model force constants

PubMed Central

Lezon, Timothy R.

2012-01-01

Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model’s single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here we investigate the differences between calculated values of force constants _t to data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. PMID:22228562

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

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

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

DOE PAGES

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.; ...

2016-11-11

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less

Ginga observations of the dipping low-mass X-ray binaries XB 1916-053 and EXO 1748-676

NASA Technical Reports Server (NTRS)

Smale, Alan P.; Mukai, Koji; Williams, O. R.; Jones, Mark H.; Corbet, Robin H. D.

1992-01-01

Ginga observations of XB 1916-053 and EXO 0748-676, low-mass X-ray binaries with pronounced dips of variable depth and duration in their X-ray light curves, are reported. Periodicity studies of XB-1916-053 show results consistent with those from previous Ginga observations, specifically, that the derived X-ray period is shorter than the optical period by about 1 percent. This problem is discussed, and a more refined model for the system is described. Three bursts were detected during the observation of XB 1916-053, the second of which occurred during a dip. Spectral analysis suggests that the second burst caused an almost instantaneous ionization of the absorbing medium in the line of sight. This material then returned to its equilibrium state on the same time scale as the burst decay. Loose limits are placed upon the possible clumpiness of the material responsible for the accretion disk structure in XB 1916-053 and EXO 0748-676.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

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

Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.

2016-01-01

In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

Tomographic image via background subtraction using an x-ray projection image and a priori computed tomography

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

Zhang Jin; Yi Byongyong; Lasio, Giovanni

Kilovoltage x-ray projection images (kV images for brevity) are increasingly available in image guided radiotherapy (IGRT) for patient positioning. These images are two-dimensional (2D) projections of a three-dimensional (3D) object along the x-ray beam direction. Projecting a 3D object onto a plane may lead to ambiguities in the identification of anatomical structures and to poor contrast in kV images. Therefore, the use of kV images in IGRT is mainly limited to bony landmark alignments. This work proposes a novel subtraction technique that isolates a slice of interest (SOI) from a kV image with the assistance of a priori information frommore » a previous CT scan. The method separates structural information within a preselected SOI by suppressing contributions to the unprocessed projection from out-of-SOI-plane structures. Up to a five-fold increase in the contrast-to-noise ratios (CNRs) was observed in selected regions of the isolated SOI, when compared to the original unprocessed kV image. The tomographic image via background subtraction (TIBS) technique aims to provide a quick snapshot of the slice of interest with greatly enhanced image contrast over conventional kV x-ray projections for fast and accurate image guidance of radiation therapy. With further refinements, TIBS could, in principle, provide real-time tumor localization using gantry-mounted x-ray imaging systems without the need for implanted markers.« less

Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

2009-01-01

Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association

Structure Evolution of BaTiO3 on Co Doping: X-ray diffraction and Raman study

NASA Astrophysics Data System (ADS)

Mansuri, Amantulla; Mishra, Ashutosh

2016-10-01

In the present study, we have synthesize polycrystalline samples of BaTi1-xCoxO3 (x = 0, 0.05 and 0.1) with standard solid state reaction technique. The obtained samples are characterized by X-ray diffraction (XRD) and Raman spectroscopy. The detail structural analysis has been performed by Rietveld refinement using Fullprof program. The structural analysis reveal the samples are chemical pure and crystallize in tetragonal phase with space group Pm3m. We observe an increase in lattice parameters which results due to substitution of Co2+ with large ionic radii (0.9) for smaller ionic radii (0.6) Ti4+. Moreover peak at 45.5° shift to 45° on Co doping, which is due to structure phase transition from tetragonal to cubic. Raman study infers that the intensity of characteristic peaks decreases and linewidth increases with Co doping. The bands linked with the tetragonal structure (307 cm1) decreased due to the tetragonal-towards-cubic phase transition with Co doping. Our structural study reveals the expansion of BTO unit cell and tetragonal-to-cubic phase transformation takes place, results from different characterization techniques are conclusive and show structural evolution with Co doping.

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

Low-temperature synthesis and structural properties of ferroelectric K 3WO 3F 3 elpasolite

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Gavrilova, T. A.; Kesler, V. G.; Molokeev, M. S.; Aleksandrov, K. S.

2010-06-01

Low-temperature ferroelectric G2 polymorph of K 3WO 3F 3 has been prepared by chemical synthesis. Structural and chemical properties of the final product have been evaluated with X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). Structure parameters of G2-K 3WO 3F 3 are refined by the Rietveld method from XRD data measured at room temperature (space group Cm, Z = 2, a = 8.7350(3) Å, b = 8.6808(5) Å, c = 6.1581(3) Å, β = 135.124(3) Å, V = 329.46(3) Å 3; RB = 2.47%). Partial ordering of oxygen and fluorine atoms has been found over anion positions. Mechanism of ferroelectric phase transition in A 2BMO 3F 3 oxyfluorides is discussed.

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.

Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70

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

Worrall, Liam; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk

Crystals of the C-terminal 10 kDa lid subdomain from the C. elegans chaperone Hsp70 have been obtained that diffract X-rays to ∼3.5 Å and belong to space group I2{sub 1}2{sub 1}2{sub 1}. Analysis of X-ray data and initial heavy-atom phasing reveals 24 monomers in the asymmetric unit related by 432 non-crystallographic symmetry. Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542–640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to ∼3.4 Å. Crystals belong to space group I2{sub 1}2{sub 1}2{sub 1},more » with unit-cell parameters a = b = 197, c = 200 Å. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein–solvent boundary. Further density-modification, model-building and refinement are currently under way.« less

Structure refinement for tantalum nitrides nanocrystals with various morphologies

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

Liu, Lianyun; School of Science, Beijing Jiaotong University, 3 Shang Yuan Cun, Haidian District, Beijing 100044; Huang, Kai

2012-07-15

Graphical abstract: Tantalum nitrides nanocrystals with various phases and morphologies for the first time have been synthesized through homogenous sodium reduction under low temperature with the subsequent annealing process under high vacuum. Highlights: ► The spherical TaN, cuboidal TaN{sub 0.83} and TaN{sub 0.5} nanocrystals have been synthesized through homogenous sodium reduction under low temperature with the subsequent annealing process under high vacuum. ► The crystal structures of different tantalum nitrides were determined by Rietveld refinement on the X-ray diffraction data and the examinations of electron microcopies. ► The specific surface area of the tantalum nitrides powders was around 10 m{supmore » 2} g{sup −1}. ► Tantalum nitrides powders could be suitable for capacitor with high specific capacitance. -- Abstract: Tantalum nitrides (TaN{sub x}) nanocrystals with different phase and morphology have been synthesized through homogenous sodium reduction under low temperature with the subsequent annealing process under high vacuum. The crystal structures of tantalum nitrides were determined by Rietveld refinement based on the X-ray diffraction data. The morphologies of various tantalum nitrides nanocrystals in high quality were analyzed through the electron microcopies examinations. The spherical TaN nanoparticles, cuboidal TaN{sub 0.83} and TaN{sub 0.5} nanocrystals have been selectively prepared at different annealing temperatures. In addition, the specific surface areas of the tantalum nitrides nanocrystals measured by BET method were around 9.87–11.64 m{sup 2} g{sup −1}, indicating that such nano-sized tantalum nitrides could be suitable for capacitor with high specific capacitance.« less

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Combined Approach for the Structural Characterization of Alkali Fluoroscandates: Solid-State NMR, Powder X-ray Diffraction, and Density Functional Theory Calculations.

PubMed

Rakhmatullin, Aydar; Polovov, Ilya B; Maltsev, Dmitry; Allix, Mathieu; Volkovich, Vladimir; Chukin, Andrey V; Boča, Miroslav; Bessada, Catherine

2018-02-05

The structures of several fluoroscandate compounds are presented here using a characterization approach combining powder X-ray diffraction and solid-state NMR. The structure of K 5 Sc 3 F 14 was fully determined from Rietveld refinement performed on powder X-ray diffraction data. Moreover, the local structures of NaScF 4 , Li 3 ScF 6 , KSc 2 F 7 , and Na 3 ScF 6 compounds were studied in detail from solid-state 19 F and 45 Sc NMR experiments. The 45 Sc chemical shift ranges for six- and seven-coordinated scandium environments were defined. The 19 F chemical shift ranges for bridging and terminal fluorine atoms were also determined. First-principles calculations of the 19 F and 45 Sc NMR parameters were carried out using plane-wave basis sets and periodic boundary conditions (CASTEP), and the results were compared with the experimental data. A good agreement between the calculated shielding constants and experimental chemical shifts was obtained. This demonstrates the good potential of computational methods in spectroscopic assignments of solid-state 45 Sc NMR spectroscopy.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

PubMed

Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

2014-05-01

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Covalent Incorporation of Selenium into Oligonucleotides for X-ray Crystal Structure Determination via MAD: Proof of Principle

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

Teplova, M.; Wilds, C.J.; Wawrzak, Z.

2010-03-08

Selenium was incorporated into an oligodeoxynucleotide in the form of 2'-methylseleno-uridine (U{sub Se}). The X-ray crystal structure of the duplex d(GCGTA)U{sub Se}d(ACGC){sub 2} was determined by the multiwavelength anomalous dispersion (MAD) technique and refined to a resolution of 1.3 {angstrom}, demonstrating that selenium can selectively substitute oxygen in DNA and that the resulting compounds are chemically stable. Since derivatization at the 2'-{alpha}-position with selenium does not affect the preference of the sugar for the C3'-endo conformation, this strategy is suitable for incorporating selenium into RNA. The availability of selenium-containing nucleic acids for crystallographic phasing offers an attractive alternative to themore » commonly used halogenated pyrimidines.« less

Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jay Min

1990-08-01

The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the course of this study, we refine knowledge of intermediate range order structural configurations and the bistabilities related to these configurations. The importance of the lone-pair orbital interactions in the chalcogenide glassy network is underscored.

Evaluation of partial coherence correction in X-ray ptychography

DOE PAGES

Burdet, Nicolas; Shi, Xiaowen; Parks, Daniel; ...

2015-02-23

Coherent X-ray Diffraction Imaging (CDI) and X-ray ptychography both heavily rely on the high degree of spatial coherence of the X-ray illumination for sufficient experimental data quality for reconstruction convergence. Nevertheless, the majority of the available synchrotron undulator sources have a limited degree of partial coherence, leading to reduced data quality and a lower speckle contrast in the coherent diffraction patterns. It is still an open question whether experimentalists should compromise the coherence properties of an X-ray source in exchange for a higher flux density at a sample, especially when some materials of scientific interest are relatively weak scatterers. Amore » previous study has suggested that in CDI, the best strategy for the study of strong phase objects is to maintain a high degree of coherence of the illuminating X-rays because of the broadening of solution space resulting from the strong phase structures. In this article, we demonstrate the first systematic analysis of the effectiveness of partial coherence correction in ptychography as a function of the coherence properties, degree of complexity of illumination (degree of phase diversity of the probe) and sample phase complexity. We have also performed analysis of how well ptychographic algorithms refine X-ray probe and complex coherence functions when those variables are unknown at the start of reconstructions, for noise-free simulated data, in the case of both real-valued and highly-complex objects.« less

Structural, vibrational and dielectric studies of (0.95)Pb(Zr{sub x}Ti{sub 1−x})O{sub 3}-(0.05)BiFeO{sub 3} nanoceramics

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

Sharma, Subhash, E-mail: rk.dwivedi@jiit.ac.in; Singh, Vikash, E-mail: rk.dwivedi@jiit.ac.in; Dwivedi, R. K., E-mail: rk.dwivedi@jiit.ac.in

2014-04-24

(0.95)Pb(Zr{sub x}Ti{sub 1−x})O{sub 3}-(0.05)BiFeO{sub 3} nanoceramics with x=0.51, 0.53 and 0.55 were synthesized by sol-gel route. Rietveld refined X-ray powder diffraction pattern of the samples confirm the single phase formation of compounds with tetragonal structure (P4mm). FT-IR studies revealed that slight shift of phonon modes towards the lower wave number and increase in the bond length with increasing Zr{sup 4+} concentration. Room temperature dielectric properties of system revealed that relaxor characteristics of these samples. Ferroelectric hysteresis curve shows the decrease in polarization values with Zr concentration.

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

PubMed Central

Uervirojnangkoorn, Monarin; Zeldin, Oliver B; Lyubimov, Artem Y; Hattne, Johan; Brewster, Aaron S; Sauter, Nicholas K; Brunger, Axel T; Weis, William I

2015-01-01

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited. DOI: http://dx.doi.org/10.7554/eLife.05421.001 PMID:25781634

Structure, microstructure and infrared studies of Ba{sub 0.06}(Na{sub 1/2}Bi{sub 1/2}){sub 0.94}TiO{sub 3}-NaNbO{sub 3} ceramics

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

Roy, Sumit K., E-mail: sumit.sxc13@gmail.com; Singh, S. N., E-mail: snsphyru@gmail.com; Prasad, K., E-mail: k.prasad65@gmail.com

2016-05-06

Lead-free solid solutions (1-x)Ba{sub 0.06}(Na{sub 1/2}Bi{sub 1/2}){sub 0.94}TiO{sub 3}-xNaNbO{sub 3} (0 ≤ x ≤ 1.0) were prepared by conventional ceramic fabrication technique. X-ray diffraction and Rietveld refinement analyses of these ceramics were carried out using X’Pert HighScore Plus software to determine the crystal symmetry, space group and unit cell dimensions. Rietveld refinement revealed that NaNbO{sub 3} with orthorhombic structure was completely diffused into Ba{sub 0.06}(Na{sub 1/2}Bi{sub 1/2}){sub 0.94}TiO{sub 3} lattice having the rhombohedral-tetragonal symmetry. EDS and SEM studies were carried out in order to evaluate the quality and purity of the compounds. SEM images showed a change in grain shapemore » with the increase of NaNbO{sub 3} content. FTIR spectra confirmed the formation of solid solution.« less

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

PubMed Central

Smart, Oliver S.; Womack, Thomas O.; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-01-01

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -­target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand. PMID:22505257

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.

Synchrotron powder X-ray diffraction and structural analysis of Eu0.5La0.5FBiS2-x Se x

NASA Astrophysics Data System (ADS)

Nagasaka, K.; Jinno, G.; Miura, O.; Miura, A.; Moriyoshi, C.; Kuroiwa, Y.; Mizuguchi, Y.

2017-07-01

Eu0.5La0.5FBiS2-x Se x is a new BiS2-based superconductor system. In Eu0.5La0.5FBiS2-x Se x , electron carriers are doped to the BiS2 layer by the substitution of Eu by La. Bulk superconductivity in this system is induced by increasing the in-plane chemical pressure, which is controlled by the Se concentration (x). In this study, we have analysed the crystal structure of Eu0.5La0.5FBiS2-x Se x using synchrotron powder diffraction and the Rietveld refinement. The precise determination of the structural parameters and thermal factors suggest that the emergence of bulk superconductivity in Eu0.5La0.5FBiS2-x Se x is achieved by the enhanced in-plane chemical pressure and the decrease in in-plane disorder.

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

A New Look at the Structural and Magnetic Properties of Potassium Neptunate K2NpO4 Combining XRD, XANES Spectroscopy, and Low-Temperature Heat Capacity.

PubMed

Smith, Anna L; Colineau, Eric; Griveau, Jean-Christophe; Popa, Karin; Kauric, Guilhem; Martin, Philippe; Scheinost, Andreas C; Cheetham, Anthony K; Konings, Rudy J M

2017-05-15

The physicochemical properties of the potassium neptunate K 2 NpO 4 have been investigated in this work using X-ray diffraction, X-ray absorption near edge structure (XANES) spectroscopy at the Np-L 3 edge, and low-temperature heat capacity measurements. A Rietveld refinement of the crystal structure is reported for the first time. The Np(VI) valence state has been confirmed by the XANES data, and the absorption edge threshold of the XANES spectrum has been correlated to the Mössbauer isomer shift value reported in the literature. The standard entropy and heat capacity of K 2 NpO 4 have been derived at 298.15 K from the low-temperature heat capacity data. The latter suggest the existence of a magnetic ordering transition around 25.9 K, most probably of the ferromagnetic type.

Study of the mechanical behavior of the hydride blister/rim structure in Zircaloy-4 using in-situ synchrotron X-ray diffraction

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

Lin, Jun-li; Han, Xiaochun; Heuser, Brent J.

2016-04-01

High-energy synchrotron X-ray diffraction was utilized to study the mechanical response of the f.c.c delta hydride phase, the intermetallic precipitation with hexagonal C14 lave phase and the alpha-Zr phase in the Zircaloy-4 materials with a hydride rim/blister structure near one surface of the material during in-situ uniaxial tension experiment at 200 degrees C. The f.c.c delta was the only hydride phase observed in the rim/blister structure. The conventional Rietveld refinement was applied to measure the macro-strain equivalent response of the three phases. Two regions were delineated in the applied load versus lattice strain measurement: a linear elastic strain region andmore » region that exhibited load partitioning. Load partitioning was quantified by von Mises analysis. The three phases were observed to have similar elastic modulus at 200 degrees C.« less

Structural and magnetic behavior of (Ni, Cu) substituted Nd0.67Sr0.33MnO3 perovskite compounds

NASA Astrophysics Data System (ADS)

Arun, B.; Sudakshina, B.; Akshay, V. R.; Chandrasekhar, K. Devi; Yang, H. D.; Vasundhara, M.

2018-05-01

Structural and magnetic phase transition of Ni and Cu substituted Nd0.67Sr0.33MnO3 perovskite compounds have been investigated. The Rietveld refinement of X-ray powder diffraction patterns confirms that both compounds have crystallized into an orthorhombic structure with Pbnm space group same as that of Nd0.67Sr0.33MnO3 compound. X-ray absorption spectra studies completely ruled out the possibility of existence of any impurities. Both compounds do not obey the Curie-Weiss law indicates the presence of some ferromagnetic clusters within the paramagnetic matrix. Ni substituted compound shows a lower value of TC and Cu substituted compound shows a higher value of TC than that of the parent. Non-saturating tendency of magnetization is more prominently seen in the case of Cu substituted compound, indicating an increase in the AFM component.

Study of structural and magnetic characterization of polycrystalline Y0.5Ho0.5CrO3

NASA Astrophysics Data System (ADS)

Mall, Ashish Kumar; Garg, Ashish; Gupta, Rajeev

2018-05-01

A polycrystalline ceramic sample of Y0.5Ho0.5CrO3 was studied using powder X-ray diffraction, Raman spectroscopic and dc magnetometry measurement to understand the structural and magnetic properties. The Rietveld refinement of X-ray data suggests sample crystallized in Pnma orthorhombic structure without formation of any secondary phases confirming their phase-pure nature. However, Raman study shows a prominent effect of Ho doping in low wavenumber Raman active phonon modes. Further, M-T measurement shows magnetic phase transition (TN) at 141 K and a negative value of Curie-Weiss temperature suggesting an antiferromagnetic system. Subsequent, the appearance of the clear opening in the M-H loop below TN is an evidence of the appearance of a weak ferromagnetic component in the low- temperature regime while the magnetization increases linearly in the high magnetic field regime suggest antiferromagnetic component.

Ultra-high-resolution X-ray structure of proteins.

PubMed

Lecomte, C; Guillot, B; Muzet, N; Pichon-Pesme, V; Jelsch, C

2004-04-01

The constant advances in synchrotron radiation sources and crystallogenesis methods and the impulse of structural genomics projects have brought biocrystallography to a context favorable to subatomic resolution protein and nucleic acid structures. Thus, as soon as such precision can be frequently obtained, the amount of information available in the precise electron density should also be easily and naturally exploited, similarly to the field of small molecule charge density studies. Indeed, the use of a nonspherical model for the atomic electron density in the refinement of subatomic resolution protein structures allows the experimental description of their electrostatic properties. Some methods we have developed and implemented in our multipolar refinement program MoPro for this purpose are presented. Examples of successful applications to several subatomic resolution protein structures, including the 0.66 angstrom resolution human aldose reductase, are described.

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.

Prediction of Cavitation Depth in an Al-Cu Alloy Melt with Bubble Characteristics Based on Synchrotron X-ray Radiography

NASA Astrophysics Data System (ADS)

Huang, Haijun; Shu, Da; Fu, Yanan; Zhu, Guoliang; Wang, Donghong; Dong, Anping; Sun, Baode

2018-06-01

The size of cavitation region is a key parameter to estimate the metallurgical effect of ultrasonic melt treatment (UST) on preferential structure refinement. We present a simple numerical model to predict the characteristic length of the cavitation region, termed cavitation depth, in a metal melt. The model is based on wave propagation with acoustic attenuation caused by cavitation bubbles which are dependent on bubble characteristics and ultrasonic intensity. In situ synchrotron X-ray imaging of cavitation bubbles has been made to quantitatively measure the size of cavitation region and volume fraction and size distribution of cavitation bubbles in an Al-Cu melt. The results show that cavitation bubbles maintain a log-normal size distribution, and the volume fraction of cavitation bubbles obeys a tanh function with the applied ultrasonic intensity. Using the experimental values of bubble characteristics as input, the predicted cavitation depth agrees well with observations except for a slight deviation at higher acoustic intensities. Further analysis shows that the increase of bubble volume and bubble size both leads to higher attenuation by cavitation bubbles, and hence, smaller cavitation depth. The current model offers a guideline to implement UST, especially for structural refinement.

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.

Prediction of Cavitation Depth in an Al-Cu Alloy Melt with Bubble Characteristics Based on Synchrotron X-ray Radiography

NASA Astrophysics Data System (ADS)

Huang, Haijun; Shu, Da; Fu, Yanan; Zhu, Guoliang; Wang, Donghong; Dong, Anping; Sun, Baode

2018-04-01

The size of cavitation region is a key parameter to estimate the metallurgical effect of ultrasonic melt treatment (UST) on preferential structure refinement. We present a simple numerical model to predict the characteristic length of the cavitation region, termed cavitation depth, in a metal melt. The model is based on wave propagation with acoustic attenuation caused by cavitation bubbles which are dependent on bubble characteristics and ultrasonic intensity. In situ synchrotron X-ray imaging of cavitation bubbles has been made to quantitatively measure the size of cavitation region and volume fraction and size distribution of cavitation bubbles in an Al-Cu melt. The results show that cavitation bubbles maintain a log-normal size distribution, and the volume fraction of cavitation bubbles obeys a tanh function with the applied ultrasonic intensity. Using the experimental values of bubble characteristics as input, the predicted cavitation depth agrees well with observations except for a slight deviation at higher acoustic intensities. Further analysis shows that the increase of bubble volume and bubble size both leads to higher attenuation by cavitation bubbles, and hence, smaller cavitation depth. The current model offers a guideline to implement UST, especially for structural refinement.

Structural and microstructural description of the glacial state in triphenyl phosphite from powder synchrotron X-ray diffraction data and Raman scattering investigations

NASA Astrophysics Data System (ADS)

Derollez, P.; Hernandez, O.; Hédoux, A.; Guinet, Y.; Masson, O.; Lefebvre, J.; Descamps, M.

2004-06-01

The structure and microstructure (refinement of the isotropic size and microstrain parameters) of the glacial state in triphenyl phosphite (TPP, P(OC 6H 5) 3) transformed at 222K have been determined from powder synchrotron X-ray diffraction data through a Rietveld and a Le Bail refinement, respectively. It is shown that the glacial state is composed of crystallites of the stable crystal phase coexisting with non-transformed supercooled liquid, the apparent size of the crystallites—depending on the aging temperature at which the glacial state is isothermally formed, [Phys. Rev. B 60 (1999) 9390]—being equal to 329.2(2) Å at 222K. The molecular conformation is slightly less mirror-symmetric than the one in the crystal state, and correlatively only one of the two unusual weak intermolecular C-H⋯O hydrogen bonds already observed in the latter state is encountered in the glacial one. Additional Raman scattering investigations confirm the previous result and reveal in addition that no hydrogen bonding interaction is observed neither in the glass nor in the liquid states.

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

Magnetism in La{sub 0.7}Sr{sub 0.3}Mn{sub 1-x}Co{sub x}O{sub 3} (0 ≤ x ≤ 1)

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

Kumar, Ashutosh, E-mail: ashutosh.pph13@iitp.ac.in; Sharma, Himanshu; Tomy, C. V.

2016-05-23

We study the structural and magnetic properties of La{sub 0.7}Sr{sub 0.3}Mn{sub 1-x}Co{sub x}O{sub 3} (0 ≤ x ≤ 1). Rietveld refinement of X-ray Diffraction (XRD) pattern suggests phase purity of the polycrystalline samples with R-3c space group. Interplay of Ferromagnetic (FM) and Antiferromagnetic (AFM) interaction upon Co substitution at Mn site in La{sub 0.7}Sr{sub 0.3}MnO{sub 3} is evident from magnetic measurements. There is an optimal cobalt substitution at which the coercive field is maximum.

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.

Preparation, electronic structure, and chemical bonding of lead-free (1 - x)(K0.5Bi0.5)TiO3- xBaTiO3 solid solution

NASA Astrophysics Data System (ADS)

Sasikumar, S.; Saravanan, R.; Saravanakumar, S.; Robert, M. Charles

2018-01-01

Polycrystalline lead-free (1 - x)(K0.5Bi0.5)TiO3- xBaTiO3, ((1 - x)KBT- xBT) ( x = 0.00, 0.08, 0.12) ceramics were synthesized via solid-state reaction method. The powder X-ray diffraction (PXRD) and structural refinement results confirm that a single-phase tetragonal structure with space group P4mm. Charge density distribution inside the unit cell of (1 - x)KBT- xBT was investigated by the maximum entropy method. Charge density analysis reveals the reduction in ionic nature along K/Bi-O bond and enhancement of covalent nature along Ti-O bond with the addition of BaTiO3. The charge density distribution studies done using maximum entropy method for (1 - x)KBT- xBT have not been done so far. The surface morphology study was done using scanning electron microscopy (SEM). Energy dispersive X-rays spectra (EDS) were used to investigate the elemental compositions present in the system. The dielectric constant and loss tangent were studied as a function of frequency. The dielectric constant and loss were decreased with increase of frequency. Room temperature dielectric constant ( ɛ) and loss (tan δ) were measured for x = 0.00 about 511 and 0.51, respectively, at a frequency of 10 kHz.

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

The effects of rigid motions on elastic network model force constants.

PubMed

Lezon, Timothy R

2012-04-01

Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model's single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here, we investigate the differences between calculated values of force constants and data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. Copyright © 2011 Wiley Periodicals, Inc.

Static and Dynamical Structural Investigations of Metal-Oxide Nanocrystals by Powder X-ray Diffraction: Colloidal Tungsten Oxide as a Case Study

DOE PAGES

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo; ...

2016-02-02

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

High-resolution Measurement of Contact Ion-pair Structures in Aqueous RbCl Solutions from the Simultaneous Corefinement of their Rb and Cl K-edge XAFS and XRD Spectra

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

Pham, Van-Thai; Fulton, John L.

2016-06-21

In concentrated solutions of aqueous RbCl, all of the Rb+ and Cl- ions exist as contact ion pairs. This full structural assessment is derived from the refinement of three independent experimental measurements: the Rb and Cl K-edge x-ray absorption fine structure (XAFS) and the x-ray diffraction spectra (XRD). This simultaneous refinement of the XAFS and XRD data provides high accuracy since each method probes the structure of different local regions about the ions with high sensitivity. At high RbCl concentration (6 m (mol/kg )) the solution is dominated by Rb+ - Cl- contact ion pairs yielding an average of 1.5more » pairs at an Rb-Cl distance of 3.24 Å. Upon formation of these ion pairs, approximately 1.1 waters molecules are displaced from the Rb+ and 1.4 water molecules from Cl-. The hydration shells about both the cation and anion are also determined. These results greatly improve the understanding of monovalent ions and provide a basis for testing the Rb+-Cl- interaction potentials used in molecular dynamics (MD) simulation. This research was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

Crystal structure refinement and Mössbauer spectroscopy of an ordered, triclinic clinochlore

USGS Publications Warehouse

Smyth, Joseph R.; Dyar, M. Darby; May, Howard M.; Bricker, Owen P.; Acker, James G.

1997-01-01

The crystal structure of a natural, ordered IIb-4 triclinic clinochlore has been refined in space group C1¯ from 4282 unique X-ray intensity measurements of which 3833 are greater than 3 times the statistical counting error (3σ). Unit cell parameters are a = 5.3262(6) Å; b = 9.226(1) Å; c = 14.334(3) Å; α = 90.56(2)°; β = 97.47(2)°; and γ = 89.979(9)°, which represents the greatest deviation from monoclinic symmetry yet recorded for a triclinic chlorite. The final weighted R is 0.059 for reflections with I > 3σ and 0.064 for all reflections. The chemical formula is (Mg0.966Fe0.034)M1(Mg0.962Fe0.038)M22(Si2.96Al1.04)O10 (OH)2(Mg0.996Fe0.004)M32(Al0.841FeIII0.102Cr0.004Ti0.004)M4(OH)6, which is consistent with electron microprobe (EMP), wet chemical analyses, Mössbauer spectroscopy and X-ray structure refinement. The high degree of ordering of the divalent versus trivalent octahedral cations in the interlayer is noteworthy, with FeIII and Al in M4 and virtually no Fe in M3. In the 2:1 layer, M1 and M2 each contain similar amounts of Fe. The 2 tetrahedral sites have nearly identical mean oxygen distances and volumes, and thus show no evidence of long-range cation ordering.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography.

PubMed

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-05-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

PubMed Central

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M.; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-01-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors. PMID:27386545

Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

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

Gabdulkhakov, A. G., E-mail: azat@vega.protes.ru; Dontsova, M. V.; Saenger, W.

Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of themore » refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.« less

Quantitative Phase Analysis of Plasma-Treated High-Silica Materials

NASA Astrophysics Data System (ADS)

Kosmachev, P. V.; Abzaev, Yu. A.; Vlasov, V. A.

2018-06-01

The paper presents the X-ray diffraction (XRD) analysis of the crystal structure of SiO2 in two modifications, namely quartzite and quartz sand before and after plasma treatment. Plasma treatment enables the raw material to melt and evaporate after which the material quenches and condenses to form nanoparticles. The Rietveld refinement method is used to identify the lattice parameters of SiO2 phases. It is found that after plasma treatment SiO2 oxides are in the amorphous state, which are modeled within the microcanonical ensemble. Experiments show that amorphous phases are stable, and model X-ray reflection intensities approximate the experimental XRD patterns with fine precision. Within the modeling, full information is obtained for SiO2 crystalline and amorphous phases, which includes atom arrangement, structural parameters, atomic population of silicon and oxygen atoms in lattice sites.

Oxidative addition of allylic halides to ruthenium(II) compounds. Preparation, reactions, and X-ray crystallographic structure of ruthenium(IV)-allyl complexes

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

Nagashima, Hideo; Mukai, Katsunori; Shiota, Yusuke

1990-03-01

The oxidative addition of allylic halides to (C{sub 5}R{sub 5})RuL{sub 2}X (R = H, Me; L = CO, PPh{sub 3}) gave new Ru(IV)-{eta}{sup 3}-allyl complexes, (C{sub 5}R{sub 5})RuX{sub 2}({eta}{sup 3}-allyl). An X-ray structure determination was carried out on (C{sub 5}Me{sub 5})RuBr{sub 2}({eta}{sup 3}-C{sub 3}H{sub 5}), indicating a pseudo-piano-stool structure having two Br atoms and two terminal carbons of the endo-{eta}{sup 3}-allyl ligand located at the basal positions. There is a crystal mirror plane bisecting the pentamethylcyclopentadienyl and the {pi}-allyl ligands. Crystal data: orthorhombic, space group P2{sub 1}2{sub 1}2{sub 1}, a = 22.738 (1) {angstrom}, b = 13.367 (7) {angstrom}, cmore » = 9.383 (1) {angstrom}, Z = 4., data refined to R = 0.0695. Its {sup 1}H and {sup 13}C NMR spectra showed symmetric allyl signals, supporting that the above-described piano-stool structure is maintained even in solution.« less

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates.

PubMed

Masson, Olivier; Berghout, Abid; Béchade, Emilie; Jouin, Jenny; Thomas, Philippe; Asaka, Toru; Fukuda, Koichiro

2017-01-01

The local structure of apatite-type lanthanum silicates of general formula La 9.33+x (SiO 4 ) 6 O 2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO 4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions.

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates

PubMed Central

Masson, Olivier; Berghout, Abid; Béchade, Emilie; Jouin, Jenny; Thomas, Philippe; Asaka, Toru; Fukuda, Koichiro

2017-01-01

Abstract The local structure of apatite-type lanthanum silicates of general formula La9.33+x(SiO4)6O2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions. PMID:28970872

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates

NASA Astrophysics Data System (ADS)

Masson, Olivier; Berghout, Abid; Béchade, Emilie; Jouin, Jenny; Thomas, Philippe; Asaka, Toru; Fukuda, Koichiro

2017-12-01

The local structure of apatite-type lanthanum silicates of general formula La9.33+x(SiO4)6O2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions.

Rietveld analysis of the effect of annealing atmosphere on phase evolution of nanocrystalline TiO2 powders.

PubMed

Salari, M; Rezaee, M; Chidembo, A T; Konstantinov, K; Liu, H K

2012-06-01

The structural evolution of nanocrystalline TiO2 was studied by X-ray diffraction (XRD) and the Rietveld refinement method (RRM). TiO2 powders were prepared by the sol-gel technique. Post annealing of as-synthesized powders in the temperature range from 500 degrees C to 800 degrees C under air and argon atmospheres led to the formation of TiO2 nanoparticles with mean crystallite size in the range of 37-165 nm, based on the Rietveld refinement results. It was found that the phase structure, composition, and crystallite size of the resulting particles were dependent on not only the annealing temperature, but also the annealing atmosphere. Rietveld refinement of the XRD data showed that annealing the powders under argon atmosphere promoted the polymorphic phase transformation from anatase to rutile. Field emission scanning electron microscopy (FESEM) was employed to investigate the morphology and size of the annealed powders.

X-Ray Imaging System

NASA Technical Reports Server (NTRS)

1986-01-01

The FluoroScan Imaging System is a high resolution, low radiation device for viewing stationary or moving objects. It resulted from NASA technology developed for x-ray astronomy and Goddard application to a low intensity x-ray imaging scope. FlouroScan Imaging Systems, Inc, (formerly HealthMate, Inc.), a NASA licensee, further refined the FluoroScan System. It is used for examining fractures, placement of catheters, and in veterinary medicine. Its major components include an x-ray generator, scintillator, visible light image intensifier and video display. It is small, light and maneuverable.

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.

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

Effect of cobalt doping on structural and dielectric properties of nanocrystalline LaCrO3

NASA Astrophysics Data System (ADS)

Zarrin, Naima; Husain, Shahid

2018-05-01

Pure and Co doped Lanthanum chromite (LaCrO3) nanoparticles, LaCr1-xCoxO3 (0≤x≤0.3), have been synthesized through sol-gel process and their structural, morphological and dielectric properties have been studied. X ray diffraction patterns reveal that the samples are in single phase having orthorhombic structure with Pnma space group. Structural parameters are refined by Rietveld refinement using Fullprof software. Lattice parameters and unit cell volume are found to decrease with increase in Co doping. Crystallite size is calculated using Scherrer equation and is also found to decrease with increase in Co concentration. Surface morphology is examined using SEM-EDX analysis, which confirms the formation of regular and homogeneous samples without any impurities. The value of dielectric constant (ɛ') decreases with the increase in frequency while it enhances with the increase in Co concentration. The log (ɛ'×f) versus log (f) graphs have been plotted to verify the universal dielectric response (UDR) model. All the samples follow UDR model in the low frequency range.

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.

Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2

PubMed Central

Fugel, Malte; Hathwar, Venkatesha R.; Turner, Michael J.; Howard, Judith A. K.

2018-01-01

Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element–hydrogen distances, r(X—H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X—H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro­carbon rubrene (orthorhombic 5,6,11,12-tetra­phenyl­tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element–hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM. PMID:29354269

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

Synchrotron X-ray diffraction study of the Ba{sub 1−x}SrSnO{sub 3} solid solution

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

Prodjosantoso, Anti K., E-mail: Prodjosantoso@yahoo.com; Zhou, Qingdi; Kennedy, Brendan J.

At room temperature the sequence of phases with increasing amounts of strontium in the stannate perovskite system Ba{sub 1−x}SrSnO{sub 3} has been established from high resolution synchrotron X-ray powder diffraction. The observed sequence orthorhombic (Pbnm), orthorhombic (Ibmm), tetragonal (I4/mcm), and cubic (Pm3-bar m) is a consequence of the sequential introduction of cooperative tilting of the corner sharing SnO{sub 6} octahedra. The cell volume changes smoothly across the series with no obvious discontinuities associated with the phase transitions. - Graphical abstract: Portions of the synchrotron X-ray diffraction profiles (λ=0.82453 Å) from selected Ba{sub 1−x}Sr{sub x}SnO{sub 3} samples together with the resultsmore » of fitting by the Rietveld method. Highlights: ► Structures of the stannate perovskites Ba{sub 1−x}SrSnO{sub 3} refined from synchrotron XRD. ► The sequence Pm3-bar m→I4/mcm→Ibmm→Pbnm results from tilting of the octahedra. ► The tilting maintains optimal bonding of the cations seen from the BVS analysis.« less

Combined PDF and Rietveld studies of ADORable zeolites and the disordered intermediate IPC-1P.

PubMed

Morris, Samuel A; Wheatley, Paul S; Položij, Miroslav; Nachtigall, Petr; Eliášová, Pavla; Čejka, Jiří; Lucas, Tim C; Hriljac, Joseph A; Pinar, Ana B; Morris, Russell E

2016-09-28

The disordered intermediate of the ADORable zeolite UTL has been structurally confirmed using the pair distribution function (PDF) technique. The intermediate, IPC-1P, is a disordered layered compound formed by the hydrolysis of UTL in 0.1 M hydrochloric acid solution. Its structure is unsolvable by traditional X-ray diffraction techniques. The PDF technique was first benchmarked against high-quality synchrotron Rietveld refinements of IPC-2 (OKO) and IPC-4 (PCR) - two end products of IPC-1P condensation that share very similar structural features. An IPC-1P starting model derived from density functional theory was used for the PDF refinement, which yielded a final fit of Rw = 18% and a geometrically reasonable structure. This confirms the layers do stay intact throughout the ADOR process and shows PDF is a viable technique for layered zeolite structure determination.

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.

Thermal expansion in UO 2 determined by high-energy X-ray diffraction

DOE PAGES

Guthrie, M.; Benmore, C. J.; Skinner, L. B.; ...

2016-06-24

In this study, we present crystallographic analyses of high-energy X-ray diffraction data on polycrystalline UO 2 up to the melting temperature. The Rietveld refinements of our X-ray data are in agreement with previous measurements, but are systematically located around the upper bound of their uncertainty, indicating a slightly steeper trend of thermal expansion compared to established values. This observation is consistent with recent first principles calculations.

Structural studies of the HIV-1 accessory protein Vpu in langmuir monolayers: synchrotron X-ray reflectivity.

PubMed Central

Zheng, S; Strzalka, J; Ma, C; Opella, S J; Ocko, B M; Blasie, J K

2001-01-01

Vpu is an 81 amino acid integral membrane protein encoded by the HIV-1 genome with a N-terminal hydrophobic domain and a C-terminal hydrophilic domain. It enhances the release of virus from the infected cell and triggers degradation of the virus receptor CD4. Langmuir monolayers of mixtures of Vpu and the phospholipid 1,2-dilignoceroyl-sn-glycero-3-phosphocholine (DLgPC) at the water-air interface were studied by synchrotron radiation-based x-ray reflectivity over a range of mole ratios at constant surface pressure and for several surface pressures at a maximal mole ratio of Vpu/DLgPC. Analysis of the x-ray reflectivity data by both slab model-refinement and model-independent box-refinement methods firmly establish the monolayer electron density profiles. The electron density profiles as a function of increasing Vpu/DLgPC mole ratio at a constant, relatively high surface pressure indicated that the amphipathic helices of the cytoplasmic domain lie on the surface of the phospholipid headgroups and the hydrophobic transmembrane helix is oriented approximately normal to the plane of monolayer within the phospholipid hydrocarbon chain layer. At maximal Vpu/DLgPC mole ratio, the tilt of the transmembrane helix with respect to the monolayer normal decreases with increasing surface pressure and the conformation of the cytoplasmic domain varies substantially with surface pressure. PMID:11259297

Rietveld refinement and FTIR analysis of bulk ceramic Co3-xMnxO4 compositions

NASA Astrophysics Data System (ADS)

Meena, P. L.; Kumar, Ravi; Sreenivas, K.

2013-02-01

Co3-xMnxO4 (x = 0.0, 0.6, 1.2) prepared by solid state reaction method and characterized by powder X-ray diffraction (XRD) and Fourier transform infrared (FTIR). Lattice parameters (a), oxygen parameter (u), and ionic radii of cations have been determined through Rietveld analysis. Both a and u parameters are related to expansion of octahedral site as Mn content in Co3O4. Analysis of XRD data show that Mn (x ≤ 1.2) is accommodated at the octahedral site, while retaining the cubic spinel structure. FTIR results also confirm the same and signify strong interactions due to overlapping of Co and Mn octahedra.

From average to local structure: a Rietveld and an atomic pair distribution function (PDF) study of selenium clusters in zeolite-NdY.

PubMed

Abeykoon, A M Milinda; Donner, Wolfgang; Brunelli, Michela; Castro-Colin, Miguel; Jacobson, Allan J; Moss, Simon C

2009-09-23

The structure of Se particles in the approximately 13 A diameter alpha-cages of zeolite NdY has been determined by Rietveld refinement and pair distribution function (PDF) analysis of X-ray data. With the diffuse scattering subtracted an average structure comprised of an undistorted framework containing nanoclusters of 20 Se atoms is observed. The intracluster correlations and the cluster-framework correlations which give rise to diffuse scattering were modeled by using PDF analysis.

Toward Active X-ray Telescopes II

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Aldroft, Thomas L.; Atkins, Carolyn; Button, Timothy W.; Cotroneo, Vincenzo; Davis, William N.; Doel, Peter; Feldman, Charlotte H.; Freeman, Mark D.; Gubarev, Mikhail V.;

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

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

Smart, Oliver S., E-mail: osmart@globalphasing.com; Womack, Thomas O.; Flensburg, Claus

2012-04-01

Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled. Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less thanmore » 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and @@target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -target enables the correct ligand-binding structure to be found, and http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.« less

Influence of Mn doping on structural, dielectric and optical properties of neodymium orthoferrite

NASA Astrophysics Data System (ADS)

Somvanshi, Anand; Manzoor, Samiya; Husain, Shahid

2018-05-01

We report the study of structural, dielectric and optical properties of nanocrystalline samples of NdFe1-xMnxO3 (x=0, 0.1 and 0.2) synthesized using solid state reaction route. X-ray diffraction (XRD) patterns are recorded to confirm phase purity. These samples conform in orthorhombic crystal symmetry with Pbnm space group. The lattice parameters are determined using Rietveld refinement. The crystallite size is calculated using Scherrer formula and that is found to lie in the range of 40-50 nm. The dielectric constant (ɛ') decreases with the increase in frequency as well as Mn doping concentration. Energy bandgap (Eg) as determined using UV-Vis. absorption spectra, is found to decrease with the increase in Mn doping.

Quantum many-body effects in x-ray spectra efficiently computed using a basic graph algorithm

NASA Astrophysics Data System (ADS)

Liang, Yufeng; Prendergast, David

2018-05-01

The growing interest in using x-ray spectroscopy for refined materials characterization calls for an accurate electronic-structure theory to interpret the x-ray near-edge fine structure. In this work, we propose an efficient and unified framework to describe all the many-electron processes in a Fermi liquid after a sudden perturbation (such as a core hole). This problem has been visited by the Mahan-Noziéres-De Dominicis (MND) theory, but it is intractable to implement various Feynman diagrams within first-principles calculations. Here, we adopt a nondiagrammatic approach and treat all the many-electron processes in the MND theory on an equal footing. Starting from a recently introduced determinant formalism [Phys. Rev. Lett. 118, 096402 (2017), 10.1103/PhysRevLett.118.096402], we exploit the linear dependence of determinants describing different final states involved in the spectral calculations. An elementary graph algorithm, breadth-first search, can be used to quickly identify the important determinants for shaping the spectrum, which avoids the need to evaluate a great number of vanishingly small terms. This search algorithm is performed over the tree-structure of the many-body expansion, which mimics a path-finding process. We demonstrate that the determinantal approach is computationally inexpensive even for obtaining x-ray spectra of extended systems. Using Kohn-Sham orbitals from two self-consistent fields (ground and core-excited state) as input for constructing the determinants, the calculated x-ray spectra for a number of transition metal oxides are in good agreement with experiments. Many-electron aspects beyond the Bethe-Salpeter equation, as captured by this approach, are also discussed, such as shakeup excitations and many-body wave function overlap considered in Anderson's orthogonality catastrophe.

Structural-electrochemical relations in the aqueous copper hexacyanoferrate-zinc system examined by synchrotron X-ray diffraction

NASA Astrophysics Data System (ADS)

Renman, Viktor; Ojwang, Dickson O.; Valvo, Mario; Gómez, Cesar Pay; Gustafsson, Torbjörn; Svensson, Gunnar

2017-11-01

The storage process of Zn2+ in the Prussian blue analogue (PBA) copper hexacyanoferrate (Cu[Fe(CN)6]2/3·nH2O - CuHCF) framework structure in a context of rechargeable aqueous batteries is examined by means of in operando synchrotron X-ray diffraction. Via sequential unit-cell parameter refinements of time-resolved diffraction data, it is revealed that the step-profile of the cell output voltage curves during repeated electrochemical insertion and removal of Zn2+ in the CuHCF host structure is associated with a non-linear contraction and expansion of the unit-cell in the range 0.36 < x < 1.32 for Znx/3Cu[Fe(CN)6]2/3·nH2O. For a high insertion cation content there is no apparent change in the unit-cell contraction. Furthermore, a structural analysis with respect to the occupancies of possible Zn2+ sites suggests that the Fe(CN)6 vacancies within the CuHCF framework play an important role in the structural-electrochemical behavior of this particular system. More specifically, it is observed that Zn2+ swaps position during electrochemical cycling, hopping between cavity sites to vacant ferricyanide sites.

X-ray K-edge absorption spectra of Fe minerals and model compounds: II. EXAFS

NASA Astrophysics Data System (ADS)

Waychunas, Glenn A.; Brown, Gordon E.; Apted, Michael J.

1986-01-01

K-edge extended X-ray absorption fine structure (EXAFS) spectra of Fe in varying environments in a suite of well-characterized silicate and oxide minerals were collected using synchrotron radiation and analyzed using single scattering approximation theory to yield nearest neighbor Fe-O distances and coordination numbers. The partial inverse character of synthetic hercynite spinal was verified in this way. Comparison of the results from all samples with structural data from X-ray diffraction crystal structure refinements indicates that EXAFS-derived first neighbor distances are generally accurate to ±0.02 Å using only theoretically generated phase information, and may be improved over this if similar model compounds are used to determine EXAFS phase functions. Coordination numbers are accurate to ±20 percent and can be similarly improved using model compound EXAFS amplitude information. However, in particular cases the EXAFS-derived distances may be shortened, and the coordination number reduced, by the effects of static and thermal disorder or by partial overlap of the longer Fe-O first neighbor distances with second neighbor distances in the EXAFS structure function. In the former case the total information available in the EXAFS is limited by the disorder, while in the latter case more accurate results can in principle be obtained by multiple neighbor EXAFS analysis. The EXAFS and XANES spectra of Fe in Nain, Labrador osumulite and Lakeview, Oregon plagioclase are also analyzed as an example of the application of X-ray absorption spectroscopy to metal ion site occupation determination in minerals.

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.

Prospects for AGN Science using the ART-XC on the SRG Mission

NASA Technical Reports Server (NTRS)

Swartz, Douglas A.; Elsner, Ronald F.; Gubarev, Mikhail V.; O'Dell, Stephen L.; Ramsey, Brian D.; Bonamente, Massimiliano

2012-01-01

The enhanced hard X-ray sensitivity provided by the Astronomical Roentgen Telescope to the Spectrum Roentgen Gamma mission facilitates the detection of heavily obscured and other hard-spectrum cosmic X-ray sources. The SRG all-sky survey will obtain large, statistically-well-defined samples of active galactic nuclei (AGN) including a significant population of local heavily-obscured AGN. In anticipation of the SRG all-sky survey, we investigate the prospects for refining the bright end of the AGN luminosity function and determination of the local black hole mass function and comparing the spatial distribution of AGN with large-scale structure defined by galaxy clusters and groups. Particular emphasis is placed on studies of the deep survey Ecliptic Pole regions.

Experimental determination of spin-dependent electron density by joint refinement of X-ray and polarized neutron diffraction data.

PubMed

Deutsch, Maxime; Claiser, Nicolas; Pillet, Sébastien; Chumakov, Yurii; Becker, Pierre; Gillet, Jean Michel; Gillon, Béatrice; Lecomte, Claude; Souhassou, Mohamed

2012-11-01

New crystallographic tools were developed to access a more precise description of the spin-dependent electron density of magnetic crystals. The method combines experimental information coming from high-resolution X-ray diffraction (XRD) and polarized neutron diffraction (PND) in a unified model. A new algorithm that allows for a simultaneous refinement of the charge- and spin-density parameters against XRD and PND data is described. The resulting software MOLLYNX is based on the well known Hansen-Coppens multipolar model, and makes it possible to differentiate the electron spins. This algorithm is validated and demonstrated with a molecular crystal formed by a bimetallic chain, MnCu(pba)(H(2)O)(3)·2H(2)O, for which XRD and PND data are available. The joint refinement provides a more detailed description of the spin density than the refinement from PND data alone.

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.

Evidence for weak ferromagnetism, isostructural phase transition, and linear magnetoelectric coupling in the multiferroic Bi0.8Pb0.2Fe0.9Nb0.1O3 solid solution

NASA Astrophysics Data System (ADS)

Patel, Jay Prakash; Senyshyn, Anatoliy; Fuess, Hartmut; Pandey, Dhananjai

2013-09-01

Magnetization, dielectric, and calorimetric studies on Bi0.8 Pb0.2 Fe0.9 Nb0.1O3 (BF-0.2PFN) reveal very weak ferromagnetism but strong dielectric anomaly at the antiferromagnetic transition temperature (TN) characteristic of magnetoelectric coupling. We correlate these results with nuclear and magnetic structure studies using x-ray and neutron powder diffraction techniques, respectively. Rietveld refinements using x-ray powder diffraction data in the temperature range 300 to 673 K reveal pronounced anomalies in the unit cell parameters at TN, indicating strong magnetoelastic coupling. The nuclear and magnetic structures of BF-0.2PFN were determined from neutron powder diffraction data using a representation theory approach. They show the occurrence of a first-order isostructural phase transition (IPT) accompanying the magnetic ordering below TN˜566 K, leading to significant discontinuous change in the ionic polarization (ΔPz˜1.6(3) μC/cm2) and octahedral tilt angle (˜0.3°) at TN. The ionic polarization obtained from refined positional coordinates of the nuclear structure and Born effective charges is shown to scale linearly with sublattice magnetization, confirming the presence of linear magnetoelectric coupling in BF-0.2PFN at the atomic level, despite the very low value of remanent magnetization (Mr).

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.

Boron monosulfide: Equation of state and pressure-induced phase transition

NASA Astrophysics Data System (ADS)

Cherednichenko, K. A.; Kruglov, I. A.; Oganov, A. R.; Le Godec, Y.; Mezouar, M.; Solozhenko, V. L.

2018-04-01

Quasi-hydrostatic compression of rhombohedral boron monosulfide (r-BS) has been studied up to 50 GPa at room temperature using diamond-anvil cells and angle-dispersive synchrotron X-ray diffraction. A fit of the experimental P-V data to the Vinet equation of state yields the bulk modulus B0 of 42.2(1.4) GPa and its first pressure derivative B0' of 7.6(2) that are in excellent agreement with our ab initio calculations. Formation of a new high-pressure phase of boron monosulfide (hp-BS) has been observed above 35 GPa. According to ab initio evolutionary crystal structure predictions combined with Rietveld refinement of high-pressure X-ray diffraction data, the structure of hp-BS has trigonal symmetry and belongs to the space group P-3m1. As it follows from the electron density of state calculations, the phase transformation is accompanied by an insulator-metal transition.

High-Pressure Polymorph of NaBiO3.

PubMed

Naa, Octavianti; Kumada, Nobuhiro; Miura, Akira; Takei, Takahiro; Azuma, Masaki; Kusano, Yoshihiro; Oka, Kengo

2016-06-20

A new high-pressure polymorph of NaBiO3 (hereafter β-NaBiO3) was synthesized under the conditions of 6 GPa and 600 °C. The powder X-ray diffraction pattern of this new phase was indexed with a hexagonal cell of a = 9.968(1) Å and c = 3.2933(4) Å. Crystal structure refinement using synchrotron powder X-ray diffraction data led to RWP = 8.53% and RP = 5.55%, and the crystal structure was closely related with that of Ba2SrY6O12. No photocatalytic activity for phenol decomposition was observed under visible-light irradiation in spite of a good performance for its mother compound, NaBiO3. The optical band-gap energy of β-NaBiO3 was narrower than that of NaBiO3, which was confirmed with density of states curves simulated by first-principles density functional theory calculation.

Superparamagnetic behavior in Sn0.95Mg0.05O2 nanoparticles

NASA Astrophysics Data System (ADS)

Ahmed, Ateeq; Siddique, M. Naseem; Ali, Tinku; Tripathi, P.

2018-04-01

We have studied structural, optical and magnetic properties of Sn0.95Mg0.05O2 nanoparticles synthesized by sol-gel process. Single phase tetragonal structure of Mg doped SnO2 nanoparticles (NPs) have been inferred by X-ray diffraction, which involves Rietveld refinement analysis and average crystallite size is found to be 20.4 nm. Energy dispersive X -ray analysis confirmed the presence of Mg into host SnO2 lattice. The energy band gap is found to be wider (Eg = 3.73 eV) compared to the bulk (3.6 eV) which is due to the quantum confinement effect. The observed defects due to oxygen vacancies are studied by the photoluminescence study. The SQUID magnetometer measurements shows superparamagnetic behavior of Mg-doped SnO2 NPs at room temperature and they are single domain NPs. Our results suggest that it is possible to control the superparamagnetic properties through chemical composition.

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.

Structural evolution in three and four-layer Aurivillius solid solutions: A comparative study versus relaxor properties

NASA Astrophysics Data System (ADS)

Tellier, Jenny; Boullay, Philippe; Ben Jennet, Dorra; Mercurio, Daniele

2008-02-01

Two solid solutions of three-layer Ba xBi 4- xNb xTi 3- xO 12 (0 ≤ x ≤ 1.2) and four-layer Aurivillius compounds (Na 0.5Bi 0.5) 1- xBa xBi 4Ti 4O 15 (0 ≤ x ≤ 1), which both present a ferroelectric to relaxor-like transition with increasing x, were synthesized by solid state reaction. The evolution of their crystal structures, as a function of x, was performed using Rietveld refinements from X-ray powder diffraction data. As x increases, the average crystal structures become less distorted with respect to the archetypal high temperature tetragonal one and the coordination number of Bi 3+ in M 2O 2 layers continuously changes from {4 + 2} to {4}. The relaxor behaviour which appears in samples for a tolerance factor t > 0.96 is associated with a general static disorder in A and M sites together with the presence of some Ba 2+ cations in M 2O 2 layers (less than 10%).

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.

Construction of a 3D model of nattokinase, a novel fibrinolytic enzyme from Bacillus natto. A novel nucleophilic catalytic mechanism for nattokinase.

PubMed

Zheng, Zhong-liang; Zuo, Zhen-yu; Liu, Zhi-gang; Tsai, Keng-chang; Liu, Ai-fu; Zou, Guo-lin

2005-01-01

A three-dimensional structural model of nattokinase (NK) from Bacillus natto was constructed by homology modeling. High-resolution X-ray structures of Subtilisin BPN' (SB), Subtilisin Carlsberg (SC), Subtilisin E (SE) and Subtilisin Savinase (SS), four proteins with sequential, structural and functional homology were used as templates. Initial models of NK were built by MODELLER and analyzed by the PROCHECK programs. The best quality model was chosen for further refinement by constrained molecular dynamics simulations. The overall quality of the refined model was evaluated. The refined model NKC1 was analyzed by different protein analysis programs including PROCHECK for the evaluation of Ramachandran plot quality, PROSA for testing interaction energies and WHATIF for the calculation of packing quality. This structure was found to be satisfactory and also stable at room temperature as demonstrated by a 300ps long unconstrained molecular dynamics (MD) simulation. Further docking analysis promoted the coming of a new nucleophilic catalytic mechanism for NK, which is induced by attacking of hydroxyl rich in catalytic environment and locating of S221.

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.

A Spin-Canted Antiferromagnetic Ground State in CeRu2Al10

NASA Astrophysics Data System (ADS)

Dean, Philip; Muro, Yuji; Takabatake, Toshiro; Hatton, Peter D.

2018-01-01

Resonant polarised soft x-ray scattering at the cerium M-edge has been used to refine the magnetic structure of CeRu2Al10. A strong resonant feature at the cerium MIV-edge was observed at the disallowed (0,1,0) Bragg position, consistent with previous neutron diffraction refinement of the moment pointing along the c-axis. The magnetic peak was found to have a temperature dependence expected for the paramagnetic-antiferromagnetic transition, disappearing above around 30 K. The polarisation dependence of the scattered x-rays conclusively shows that the low-temperature antiferromagnetic structure is non-collinear in nature. Fitting the polarisation dependence of the obtained Stokes parameters was undertaken with models for canting along either the a-axis or the b-axis. The experimental data agrees better with the model involving canting towards the a-axis. However, this is inconsistent with the Cmcm space group, suggestive of a symmetry lowering to either Pmnm or Cm2m. The resulting model is then achieved with a 9.6° ± 1.1 canting of the moments towards the a-axis. No resonance features were observed at the ruthenium L-edges. This suggests that the ruthenium atoms play no part in the antiferromagnetic ordering.

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.

The X-Ray Structure and Spectrum of the Pulsar Wind Nebula Surrounding PSR B1853+01 in W44

NASA Technical Reports Server (NTRS)

Petre, R.; Kuntz, K. D.; Shelton, R. L.; White, Nicholas E. (Technical Monitor)

2001-01-01

We present the result of a Chandra ACIS observation of the pulsar PSR B1853+01 and its associated pulsar wind nebula (PWN), embedded within the supernova remnant W44. A hard band ACIS map cleanly distinguishes the PWN from the thermal emission of W44. The nebula is extended in the north-south direction, with an extent about half that of the radio emission. Morphological differences between the X-ray and radio images are apparent. Spectral fitting reveals a clear difference in spectral index between the hard emission from PSR B1853+01 (Gamma approx. 1.4) and the extended nebula (Gamma approx. 2.2). The more accurate values for the X-ray flux and spectral index are used refine estimates for PWN parameters, including magnetic field strength, the average Lorentz factor gamma of the particles in the wind, the magnetization parameter sigma, and the ratio k of electrons to other particles.

Establishing nonlinearity thresholds with ultraintense X-ray pulses

NASA Astrophysics Data System (ADS)

Szlachetko, Jakub; Hoszowska, Joanna; Dousse, Jean-Claude; Nachtegaal, Maarten; Błachucki, Wojciech; Kayser, Yves; Sà, Jacinto; Messerschmidt, Marc; Boutet, Sebastien; Williams, Garth J.; David, Christian; Smolentsev, Grigory; van Bokhoven, Jeroen A.; Patterson, Bruce D.; Penfold, Thomas J.; Knopp, Gregor; Pajek, Marek; Abela, Rafael; Milne, Christopher J.

2016-09-01

X-ray techniques have evolved over decades to become highly refined tools for a broad range of investigations. Importantly, these approaches rely on X-ray measurements that depend linearly on the number of incident X-ray photons. The advent of X-ray free electron lasers (XFELs) is opening the ability to reach extremely high photon numbers within ultrashort X-ray pulse durations and is leading to a paradigm shift in our ability to explore nonlinear X-ray signals. However, the enormous increase in X-ray peak power is a double-edged sword with new and exciting methods being developed but at the same time well-established techniques proving unreliable. Consequently, accurate knowledge about the threshold for nonlinear X-ray signals is essential. Herein we report an X-ray spectroscopic study that reveals important details on the thresholds for nonlinear X-ray interactions. By varying both the incident X-ray intensity and photon energy, we establish the regimes at which the simplest nonlinear process, two-photon X-ray absorption (TPA), can be observed. From these measurements we can extract the probability of this process as a function of photon energy and confirm both the nature and sub-femtosecond lifetime of the virtual intermediate electronic state.

Structural analysis and characterization of layer perovskite oxynitrides made from Dion Jacobson oxide precursors

NASA Astrophysics Data System (ADS)

Schottenfeld, Joshua A.; Benesi, Alan J.; Stephens, Peter W.; Chen, Gugang; Eklund, Peter C.; Mallouk, Thomas E.

2005-07-01

A three-layer oxynitride Ruddlesden-Popper phase Rb 1+xCa 2Nb 3O 10-xN x· yH 2O ( x=0.7-0.8, y=0.4-0.6) was synthesized by ammonialysis at 800 °C from the Dion-Jacobson phase RbCa 2Nb 3O 10 in the presence of Rb 2CO 3. Incorporation of nitrogen into the layer perovskite structure was confirmed by XPS, combustion analysis, and MAS NMR. The water content was determined by thermal gravimetric analysis and the rubidium content by ICP-MS. A similar layered perovskite interconversion occurred in the two-layer Dion-Jacobson oxide RbLaNb 2O 7 to yield Rb 1+xLaNb 2O 7-xN x· yH 2O ( x=0.7-0.8, y=0.5-1.0). Both compounds were air- and moisture-sensitive, with rapid loss of nitrogen by oxidation and hydrolysis reactions. The structure of the three-layer oxynitride Rb 1.7Ca 2Nb 3O 9.3N 0.7·0.5H 2O was solved in space group P4 /mmm with a=3.887(3) and c=18.65(1) Å, by Rietveld refinement of X-ray powder diffraction data. The two-layer oxynitride structure Rb 1.8LaNb 2O 6.3N 0.7·1.0H 2O was also determined in space group P4 /mmm with a=3.934(2) and c=14.697(2) Å. GSAS refinement of synchrotron X-ray powder diffraction data showed that the water molecules were intercalated between a double layer of Rb+ ions in both the two- and three-layer Ruddlesden-Popper structures. Optical band gaps were measured by diffuse reflectance UV-vis for both materials. An indirect band gap of 2.51 eV and a direct band gap of 2.99 eV were found for the three-layer compound, while an indirect band gap of 2.29 eV and a direct band gap of 2.84 eV were measured for the two-layer compound. Photocatalytic activity tests of the three-layer compound under 380 nm pass filtered light with AgNO 3 as a sacrificial electron acceptor gave a quantum yield of 0.025% for oxygen evolution.

Fatigue of LiNi0.8Co0.15Al0.05O2 in commercial Li ion batteries

NASA Astrophysics Data System (ADS)

Kleiner, Karin; Dixon, Ditty; Jakes, Peter; Melke, Julia; Yavuz, Murat; Roth, Christina; Nikolowski, Kristian; Liebau, Verena; Ehrenberg, Helmut

2015-01-01

The degradation of LiNi0.8Co0.15Al0.05O2 (LNCAO), a cathode material in lithium-ion-batteries, was studied using in situ powder diffraction and in situ Ni K edge X-ray absorption spectroscopy (XAS). The fatigued material was taken from a 7 Ah battery which was cycled for 34 weeks under defined durability conditions. Meanwhile, a cell was stored, as reference, under controlled conditions without electrochemical treatment. The fatigued LNCAO used in this study showed a capacity loss of 26% ± 9% compared to the non-cycled material. During charge and discharge the local and the overall structure of LNCAO was investigated by X-ray near edge structure (XANES) analysis, the extended X-ray absorption fine structure (EXAFS) analysis and by using Rietveld refinement of in situ powder diffraction patterns. Both powder diffraction and XAS revealed additional, rhombohedral phases which do not change with electrochemical cycling. Moreover, a phase with the lattice parameters of fully lithiated LNCAO was still present in the fatigued material at high potentials, while it was absent in the non-fatigued reference material. The coexistence of these phases is described by domains within the LNCAO particles, in correlation with the observed fatigue.

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.

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.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography.

PubMed

Gicquel, Yannig; Schubert, Robin; Kapis, Svetlana; Bourenkov, Gleb; Schneider, Thomas; Perbandt, Markus; Betzel, Christian; Chapman, Henry N; Heymann, Michael

2018-04-24

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

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

Rodríguez Guilbe, María M.; Protein Research and Development Center, University of Puerto Rico; Alfaro Malavé, Elisa C.

The genetically encoded fluorescent calcium-indicator protein GCaMP2 was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution and the structure was solved by molecular replacement. Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, thismore » protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way.« less

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Identification of NpO2+x in the binary Np-O system

NASA Astrophysics Data System (ADS)

Tayal, Akhil; Conradson, Steven D.; Baldinozzi, Gianguido; Namdeo, Sonu; Roberts, Kevin E.; Allen, Patrick G.; Shuh, David K.

2017-07-01

In contrast to UO2 and PuO2, there is no consensus on the existence of mixed valence NpO2+x, resulting in a gap between NpO2 and Np2O5 (the highest binary oxide of Np) in the Np-O phase diagram. We now show NpO2+x via Np LIII Extended X-ray Absorption Fine Structure (EXAFS) spectra of three samples of NpO2 that, analogous to U and Pu, exhibit multisite Np-O distributions with varying numbers of oxygen atoms at 1.87-1.91 Å. This is supported by the diffraction pattern of the sample with the largest amount of this oxo-type species that can be refined with both the simple fluorite structure and a trigonal one related to α-U4O9. The implied Np(V)-bridging oxo moieties as well as possible indications of OHbar found by detailed EXAFS analysis suggest that NpO2+x more closely resembles PuO2+x than UO2+x. An additional common characteristic suggested by the EXAFS and X-Ray Diffraction (XRD) is the phase separation into NpO2 and what would be previously unreported Np4O9(-δ), indicative of O clustering.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

PubMed Central

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

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.

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.

Accurate determination of segmented X-ray detector geometry

PubMed Central

Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; White, Thomas A.; Chapman, Henry N.; Barty, Anton

2015-01-01

Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments. PMID:26561117

Structure and photoluminescence properties of Ba2-xSi4O10:2xSm3+

NASA Astrophysics Data System (ADS)

Ramteke, D. D.; Swart, H. C.

2018-04-01

We investigated the structure and photoluminescence properties of novel Ba2-xSi4O10:2xSm3+ phosphor prepared by the solid state reaction method. In the prepared phosphor the high temperature monoclinic phase was dominant over the low temperature orthorhombic phase. The shifting of the X-ray diffraction peaks with the Sm3+ ion addition was explained on the basis of the refinement results. The photoluminescence study showed that on excitation with 402 nm the phosphor emitted at 560 nm, 600 nm and 645 nm which corresponds to the 4G5/2→4H5/2, 4G5/2→4H7/2 and 4G5/2→4H9/2 transitions, respectively. Concentration quenching effect was also observed in the prepared phosphor. CIE chromaticity coordinates showed that the phosphor can be further developed for display applications.

Taguchi's technique: an effective method for improving X-ray medical radiographic screen performance.

PubMed

Vlachogiannis, J G

2003-01-01

Taguchi's technique is a helpful tool to achieve experimental optimization of a large number of decision variables with a small number of off-line experiments. The technique appears to be an ideal tool for improving the performance of X-ray medical radiographic screens under a noise source. Currently there are very many guides available for improving the efficiency of X-ray medical radiographic screens. These guides can be refined using a second-stage parameter optimization. based on Taguchi's technique, selecting the optimum levels of controllable X-ray radiographic screen factors. A real example of the proposed technique is presented giving certain performance criteria. The present research proposes the reinforcement of X-ray radiography by Taguchi's technique as a novel hardware mechanism.

Structural, spectroscopic, and magnetic properties of Eu3+-doped GdVO4 nanocrystals synthesized by a hydrothermal method.

PubMed

Szczeszak, Agata; Grzyb, Tomasz; Śniadecki, Zbigniew; Andrzejewska, Nina; Lis, Stefan; Matczak, Michał; Nowaczyk, Grzegorz; Jurga, Stefan; Idzikowski, Bogdan

2014-12-01

New interesting aspects of the spectroscopic properties, magnetism, and method of synthesis of gadolinium orthovanadates doped with Eu(3+) ions are discussed. Gd(1-x)Eu(x)VO4 (x = 0, 0.05, 0.2) bifunctional luminescent materials with complex magnetic properties were synthesized by a microwave-assisted hydrothermal method. Products were formed in situ without previous precipitation. The crystal structures and morphologies of the obtained nanomaterials were analyzed by X-ray diffraction and transmission and scanning electron microscopy. Crystallographic data were analyzed using Rietveld refinement. The products obtained were nanocrystalline with average grain sizes of 70-80 nm. The qualitative and quantitative elemental composition as well as mapping of the nanocrystals was proved using energy-dispersive X-ray spectroscopy. The spectroscopic properties of red-emitting nanophosphors were characterized by their excitation and emission spectra and luminescence decays. Magnetic measurements were performed by means of vibrating sample magnetometry. GdVO4 and Gd0.8Eu0.2VO4 exhibited paramagnetic behavior with a weak influence of antiferromagnetic couplings between rare-earth ions. In the substituted sample, an additional magnetic contribution connected with the population of low-lying excited states of europium was observed.

The X-Ray Lightcurve of Eta Carinae: Refinement of the Orbit and Evidence for Phase Dependent Mass Loss

NASA Technical Reports Server (NTRS)

Corcoran, M. F.; Ishibashi, K.; Swank, J. H.; Petre, R.; White, Nicholas E. (Technical Monitor)

2000-01-01

We solve the RXTE X-ray lightcurve of the extremely luminous and massive star eta Carinae with a colliding wind emission model to refine the ground-based orbital elements. The sharp decline to X-ray minimum at the end of 1997 fixes the date of the last periastron passage at 1997.95 +/- 0.05, not 1998.13 as derived from ground-based radial velocities. This helps resolve a discrepancy between the ground-based radial velocities and spatially-resolved velocity measures obtained by STIS. The X-ray data are consistent with a mass function f(M) approx. = 1.5, lower than the value f(M) approx. = 7.5 previously reported, so that the masses of eta Carinae and the companion are M(sub eta) greater than or = 80 solar mass and M(sub c) approx. 30 solar mass respectively. In addition the X-ray data suggest that the mass loss rate from eta Carinae is generally less than 3 x 10(exp -4) solar mass/yr, about a factor of 5 lower than that derived from some observations in other wavebands. We could not match the duration of the X-ray minimum with any standard colliding wind model in which the wind is spherically symmetric and the mass loss rate is constant. However we show that we can match the variations around X-ray minimum if we include an increase of a factor of approx. 20 in the mass loss rate from eta Carinae for approximately 80 days following periastron. If real, this excess in M would be the first evidence of enhanced mass flow off the primary when the two stars are close (presumably driven by tidal interactions). Our interpretation of the X-ray data suggest that the ASCA and RXTE X-ray spectra near the X-ray minimum are significantly contaminated by unresolved hard emission (E greater than or = 2 keV) from sonic other nearby source, probably associated with scattering of tile colliding wind emission by circumstellar dust. Based on the X-ray fluxes the distance to n Carinae is 2300 pc with formal uncertainties of only approx. 10%.

Rietveld refinement and electrical properties of Ni-Zn spinel ferrites

NASA Astrophysics Data System (ADS)

Hooda, Ashima; Sanghi, Sujata; Agarwal, Ashish; Khasa, Satish; Hooda, Bhawana

2017-05-01

NiFe2O4, ZnFe2O4, Ni0.5Zn0.5Fe2O4 spinel samples have been synthesized by conventional solid state reaction technique. Powder X-ray diffraction and Rietveld refinement revealed that the samples were single Spinel phase with space group fd3m. The average crystalline size (D), lattice constant (a), X-ray density (ρx), measured density (ρm) and Porosity (P) of prepared samples were determined from XRD data. The dc electrical resistivity (p) was measured as a function of temperature. The variations of ρ were explained on the basis of Verwey and de Bohr mechanism. The value of DC resistivity found to increase with increase Zn concentration.

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

Structural, magnetic, and Mössbauer spectroscopy of Cu substituted M-type hexaferrites

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

Awadallah, Ahmad, E-mail: ahmadmoh@yahoo.co; Mahmood, Sami H., E-mail: s.mahmood@ju.edu.jo; Maswadeh, Yazan, E-mail: nawabra251@gmail.com

2016-02-15

Highlights: • Single BaM hexaferrite structural phases with Cu substations were prepared. • The magnetocrystalline anisotropy decreased with Cu substitution. • The coercivity was significantly modified while the magnetization remained high. • Hexaferrites with 0.2–0.4 Cu possess properties suitable for magnetic recording. • Ionic distributions from structural refinement agreed with Mössbauer spectroscopy. - Abstract: BaFe{sub 12−x}Cu{sub x}O{sub 19} hexaferrites were prepared using ball milling and sintering at 1100 °C. Refinement of the X-ray diffraction patterns was carried out to determine the structural parameters and the ionic distribution over the crystallographic sites. The preferential site occupation and valence state of Cumore » was consistent with the results obtained from the analysis of Mössbauer spectra. Further, the magnetic parameters of the samples were discussed in light of the structural and Mössbauer analyses. The magnetic phase transition temperature was found to decrease with the level of Cu substitution, in accordance with the reduction of the superexchange interactions. Further, the magnetic softening of the hexaferrite and the significant reduction in magnetocrystalline anisotropy with Cu substitution was consistent with the ionic distribution in the lattice. This study clearly demonstrated the feasibility of using a simple method to fabricate hexaferrites with a modified coercivity, while maintain the saturation magnetization high enough for practical applications.« less

Structural analysis and ferroelectric properties of Fe doped BaTiO{sub 3}

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

Mishra, Ashutosh, E-mail: a.mansuri14@gmail.com, E-mail: amishra1960@yahoo.co.in; Mansuri, Amantulla, E-mail: a.mansuri14@gmail.com, E-mail: amishra1960@yahoo.co.in; Dwivedi, J. P.

2016-05-23

The polycrystalline samples of Fe doped BaTiO{sub 3} (BTO) with compositional formula BaTi{sub 1-x}Fe{sub x}O{sub 3} (x = 0, 0.03, 0.04 and 0.05) were prepared by solid-state reaction route. The influence of the Fe content on the structural, vibrational and electric properties of BaTiO{sub 3} was investigated using X-ray powder diffraction (XRD), Raman spectroscopy and Polarization techniques. XRD analysis indicates the formation of single-phase tetragonal structure for all the prepared samples. Tetragonal cubic structure with space group P4mm of all samples is further approved by Rietveld refinement. Room temperature Raman spectra of pure BaTiO{sub 3} show four active modes ofmore » vibration whose intensity decreases with increasing Fe doping. Small shift in Raman modes and increment in the line width has been observed with the doping ions. The hysteresis loop is very well performed with regular sharp characteristic of ferroelectric materials.« less

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

Extended investigation of intermartensitic transitions in Ni-Mn-Ga magnetic shape memory alloys: A detailed phase diagram determination

NASA Astrophysics Data System (ADS)

Ćakιr, Aslι; Righi, Lara; Albertini, Franca; Acet, Mehmet; Farle, Michael; Aktürk, Selçuk

2013-11-01

Martensitic transitions in shape memory Ni-Mn-Ga Heusler alloys take place between a high temperature austenite and a low temperature martensite phase. However, intermartensitic transformations have also been encountered that occur from one martensite phase to another. To examine intermartensitic transitions in magnetic shape memory alloys in detail, we carried out temperature dependent magnetization, resistivity, and x-ray diffraction measurements to investigate the intermartensitic transition in Ni50Mn50-xGax in the composition range 12≤x≤25 at. %. Rietveld refined x-ray diffraction results are found to be consistent with magnetization and resistivity data. Depending on composition, we observe that intermartensitic transitions occur in the sequences 7M→L10, 5M →7M, and 5M→7M→L10 with decreasing temperature. The L10 non-modulated structure is most stable at low temperature.

The reversal of the spontaneous exchange bias effect and zero-field-cooling magnetization in La1.5Sr0.5Co1-xFexMnO6: the effect of Fe doping.

PubMed

Zhang, H G; Xie, L; Liu, X C; Xiong, M X; Cao, L L; Li, Y T

2017-09-20

The crystal structure, electronic structure and magnetic properties were systematically studied in a series of Fe-doped La 1.5 Sr 0.5 CoMnO 6 double perovskites. The X-ray diffraction patterns of the samples are all refined with a rhombohedral (R3[combining macron]c) structure. The parameters a and c continuously increase with increasing Fe doping concentration x. X-ray photoelectron spectroscopy (XPS) spectra of the Mn, Co, and Fe 2p core levels, consistent with the soft X-ray absorption spectroscopy (XAS) spectra of Mn, Co, and Fe L 2,3 edges, indicate that their valence states are Mn 3+ and Mn 4+ , Co 2+ and Co 3+ , and Fe 3+ , respectively. However, relative to samples with x ≤ 0.1, there is an abrupt change of photon energy in the Co- and Fe-2p XAS spectra for x ≥ 0.2, implying the spin state transition is from high to low. In addition, this is further confirmed by a comparison between the calculated effective spin moment from the paramagnetic data and the theoretical value. Interestingly, we demonstrate the reversal of both zero-field-cooling magnetization and the sign switching of the spontaneous exchange bias (SEB) with the doping concentration from magnetic measurements. The magnetization reverses from positive to negative with the temperature decreasing across the compensation temperature at the critical concentration x = 0.2. Meanwhile, the exchange bias field of the SEB reverses from large negative values to positive ones. Our findings allow us to propose that the spin state transition caused by inhomogeneity is considered to play an important role in the reversal of the magnetization and the SEB effect.

High-level expression and deuteration of sperm whale myoglobin: A study of its solvent structure by X-ray and neutron diffraction methods

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

Shu, F.; Ramakrishnan, V.; Schoenborn, B.P.

1994-12-31

Neutron diffraction has become one of the best ways to study light atoms, such as hydrogens. Hydrogen however has a negative coherent scattering factor, and a large incoherent scattering factor, while deuterium has virtually no incoherent scattering, but a large positive coherent scattering factor. Beside causing high background due to its incoherent scattering, the negative coherent scattering of hydrogen tends to cancel out the positive contribution from other atoms in a neutron density map. Therefore a fully deuterated sample will yield better diffraction data with stronger density in the hydrogen position. On this basis, a sperm whale myoglobin gene modifiedmore » to include part of the A cII protein gene has been cloned into the T7 expression system. Milligram amounts of fully deuterated holo-myoglobin have been obtained and used for crystallization. The synthetic sperm whale myoglobin crystallized in P2{sub 1} space group isomorphous with the native protein crystal. A complete X-ray diffraction dataset at 1.5{Angstrom} has been collected. This X-ray dataset, and a neutron data set collected previously on a protonated carbon-monoxymyoglobin crystal have been used for solvent structure studies. Both X-ray and neutron data have shown that there are ordered hydration layers around the protein surface. Solvent shell analysis on the neutron data further has shown that the first hydration layer behaves differently around polar and apolar regions of the protein surface. Finally, the structure of per-deuterated myoglobin has been refined using all reflections to a R factor of 17%.« less

An Improved X-ray Diffraction Method For Cellulose Crystallinity Measurement

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

Ju, Xiaohui; Bowden, Mark E.; Brown, Elvie E.

2015-06-01

We show in this work a modified X-ray diffraction method to determine cellulose crystallinity index (CrI). Nanocrystalline cellulose (NCC) dervided from bleached wood pulp was used as a model substrate. Rietveld refinement was applied with consideration of March-Dollase preferred orientation at the (001) plane. In contrast to most previous methods, three distinct amorphous peaks identified from new model samples which are used to calculate CrI. A 2 theta range from 10° to 75° was found to be more suitable to determine CrI and crystallite structural parameters such as d-spacing and crystallite size. This method enables a more reliable measurement ofmore » CrI of cellulose and may be applicable to other types of cellulose polymorphs.« less

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

Grain size dependent phase stabilities and presence of a monoclinic (Pm) phase in the morphotropic phase boundary region of (1-x)Bi(Mg1/2Ti1/2)O3-xPbTiO3 piezoceramics

NASA Astrophysics Data System (ADS)

Upadhyay, Ashutosh; Singh, Akhilesh Kumar

2015-04-01

Results of the room temperature structural studies on (1-x)Bi(Mg1/2Ti1/2)O3-xPbTiO3 ceramics using Rietveld analysis of the powder x-ray diffraction data in the composition range 0.28 ≤ x ≤ 0.45 are presented. The morphotropic phase boundary region exhibits coexistence of monoclinic (space group Pm) and tetragonal (space group P4 mm) phases in the composition range 0.33 ≤ x ≤ 0.40. The structure is nearly single phase monoclinic (space group Pm) in the composition range 0.28 ≤ x ≤ 0.32. The structure for the compositions with x ≥ 0.45 is found to be predominantly tetragonal with space group P4 mm. Rietveld refinement of the structure rules out the coexistence of rhombohedral and tetragonal phases in the morphotropic phase boundary region reported by earlier authors. The Rietveld structure analysis for the sample x = .35 calcined at various temperatures reveals that phase fraction of the coexisting phases in the morphotropic phase boundary region varies with grain size. The structural parameters of the two coexisting phases also change slightly with changing grain size.

X-ray characterization of solid small molecule organic materials

DOEpatents

Billinge, Simon; Shankland, Kenneth; Shankland, Norman; Florence, Alastair

2014-06-10

The present invention provides, inter alia, methods of characterizing a small molecule organic material, e.g., a drug or a drug product. This method includes subjecting the solid small molecule organic material to x-ray total scattering analysis at a short wavelength, collecting data generated thereby, and mathematically transforming the data to provide a refined set of data.

Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.

PubMed

Machado, Agnes Thiane Pereira; Fonseca, Emanuella Maria Barreto; Reis, Marcelo Augusto Dos; Saraiva, Antonio Marcos; Santos, Clelton Aparecido Dos; de Toledo, Marcelo Augusto Szymanski; Polikarpov, Igor; de Souza, Anete Pereira; Aparicio, Ricardo; Iulek, Jorge

2017-10-01

Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein. © 2017 Wiley Periodicals, Inc.

Ambient and high pressure single crystal x-ray studies of pyrope and synthetic ferric majorite

NASA Astrophysics Data System (ADS)

Smith, Henrietta Mercer

The mineral garnet is widely accepted as a major constituent of Earth's upper mantle and transition zone. As such, understanding of the state of the material at high pressures and temperatures will increase our ability to correlate seismic data with the mineralogy in these regions of Earth's interior. Studies of varied compositions of garnet at ambient conditions may enhance our understanding of solid-solution energetics, and yield predictive power concerning element partitioning among various minerals at different depths within Earth. This study began with structure refinements at ambient conditions of eighteen natural and two synthetic garnets, nominally in the pyrope-grossular-almandine ternary system. The natural, nearly-pure pyrope sample of this group was then used in developing the techniques necessary for high-pressure structure refinements. For high pressure work, a diamond anvil pressure cell (DAC) was loaded with the sample and mounted on an 18 kW rotating anode four-circle diffractometer. Unit cells and oxygen positional parameters of the pyrope sample were refined at five pressures to 9.9 GPa. The data were in agreement with those of other studies, and extended by 40% the pressure range achieved previously. The zero-pressure bulk modulus, K = 176 GPa, with Ksp' = dK/dP = 4. Following the high pressure pyrope study, synthetic samples of Fe-bearing majoritic garnet became available. These samples are of particular interest because they were grown at transition zone conditions and coexisted with a hydrous wadsleyite phase. The hydration state of earth's mantle is a topic of much current research, and samples such as these will provide information necessary to the placement of constraints on the degree of hydration actually present. The structures of five majorite samples from three different synthesis runs were refined at ambient conditions, and two of these samples were analyzed using Mossbauer spectroscopy. Fesp{3+}/SigmaFe ranged from 85-95%. One sample, for which there were both X-ray and Mossbauer data, was loaded into a DAC. The structure was refined at ten pressures to 12.9 GPa. K = 172.5 GPa with Ksp{''} = 4. The bulk compression is nearly identical to that of pyrope, but the compressions of the coordination polyhedra are quite different.

Establishing nonlinearity thresholds with ultraintense X-ray pulses

DOE PAGES

Szlachetko, Jakub; Hoszowska, Joanna; Dousse, Jean-Claude; ...

2016-09-13

X-ray techniques have evolved over decades to become highly refined tools for a broad range of investigations. Importantly, these approaches rely on X-ray measurements that depend linearly on the number of incident X-ray photons. The advent of X-ray free electron lasers (XFELs) is opening the ability to reach extremely high photon numbers within ultrashort X-ray pulse durations and is leading to a paradigm shift in our ability to explore nonlinear X-ray signals. However, the enormous increase in X-ray peak power is a double-edged sword with new and exciting methods being developed but at the same time well-established techniques proving unreliable.more » Consequently, accurate knowledge about the threshold for nonlinear X-ray signals is essential. Here in this paper we report an X-ray spectroscopic study that reveals important details on the thresholds for nonlinear X-ray interactions. By varying both the incident X-ray intensity and photon energy, we establish the regimes at which the simplest nonlinear process, two-photon X-ray absorption (TPA), can be observed. From these measurements we can extract the probability of this process as a function of photon energy and confirm both the nature and sub-femtosecond lifetime of the virtual intermediate electronic state.« less

High-resolution synchrotron x-ray powder diffraction study of the incommensurate modulation in the martensite phase of Ni2MnGa: Evidence for nearly 7M modulation and phason broadening

NASA Astrophysics Data System (ADS)

Singh, Sanjay; Petricek, V.; Rajput, Parasmani; Hill, Adrian H.; Suard, E.; Barman, S. R.; Pandey, Dhananjai

2014-07-01

The modulated structure of the martensite phase of Ni2MnGa is revisited using high-resolution synchrotron x-ray powder diffraction measurements, which reveal higher-order satellite reflections up to the third order and phason broadening of the satellite peaks. The structure refinement, using the (3+1) dimensional superspace group approach, shows that the modulated structure of Ni2MnGa can be described by orthorhombic superspace group Immm(00γ)s00 with lattice parameters a=4.218 61(2)Å,b=5.546 96(3)Å, and c=4.187 63(2) Å, and an incommensurate modulation wave vector q =0.43160(3)c*=(3/7+δ)c*, where δ =0.00303(3) is the degree of incommensuration of the modulated structure. Additional satellite peak broadening, which could not be accounted for in terms of the anisotropic strain broadening based on a lattice parameter distribution, has been modeled in terms of phasons using fourth-rank covariant strain-tensor representation for incommensurate structures. The simulation of single-crystal diffraction patterns from the refined structural parameters unambiguously reveals a rational approximant structure with 7M modulation. The inhomogeneous displacement of different atomic sites on account of incommensurate modulation and the presence of phason broadening clearly rule out the adaptive phase model proposed recently by Kaufmann et al. [S. Kaufmann, U. K. Rößler, O. Heczko, M. Wuttig, J. Buschbeck, L. Schultz, and S. Fähler, Phys. Rev. Lett. 104, 145702 (2010), 10.1103/PhysRevLett.104.145702] and suggest that the modulation in Ni2MnGa originates from soft-mode phonons.

Temperature Dependence of the Structural Parameters in the Transformation of Aragonite to Calcite, as Determined from In Situ Synchrotron Powder X-ray-Diffratction Data

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

Antao, Sytle M.; Hassan, Ishmael; West Indies)

The temperature dependency of the crystal structure and the polymorphic transition of CaCO{sub 3} from aragonite to calcite were studied using Rietveld structure refinement and high-temperature in situ synchrotron powder X-ray-diffraction data at ambient pressure, P. The orthorhombic metastable aragonite at room P, space group Pmcn, transforms to trigonal calcite, space group R{bar 3}c, at about T{sub c} = 468 C. This transformation occurs rapidly; it starts at about 420 C and is completed by 500 C, an 80 C interval that took about 10 minutes using a heating rate of 8 C/min. Structurally, from aragonite to calcite, the distributionmore » of the Ca atom changes from approximately hexagonal to cubic close-packing. A 5.76% discontinuous increase in volume accompanies the reconstructive first-order transition. Besides the change in coordination of the Ca atom from nine to six from aragonite to calcite, the CO{sub 3} groups change by a 30{sup o} rotation across the transition.« less

Structural studies of the rhombohedral and orthorhombic monouranates: CaUO{sub 4}, α-SrUO{sub 4}, β-SrUO{sub 4} and BaUO{sub 4}

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

Murphy, Gabriel; Kennedy, Brendan J., E-mail: kennedyb@chem.usyd.edu.au; Johannessen, Bernt

The structures of some AUO{sub 4} (A=Ca, Sr, or Ba) oxides have been determined using a combination of neutron and synchrotron X-ray diffraction, supported by X-ray absorption spectroscopic measurements at the U L{sub 3}-edge. The smaller Ca cation favours a rhombohedral AUO{sub 4} structure with 8-coordinate UO{sub 8} moieties whilst an orthorhombic structure based on UO{sub 6} groups is found for BaUO{sub 4}. Both the rhombohedral and orthorhombic structures can be stabilised for SrUO{sub 4}. The structural studies suggest that the bonding requirements of the A site cation play a significant role in determining which structure is favoured. In themore » rhombohedral structure, Bond Valence Sums demonstrate the A site is invariably overbonded, which, in the case of rhombohedral α-SrUO{sub 4}, is compensated for by the formation of vacancies in the oxygen sub-lattice. The uranium cation, with its flexible oxidation state, is able to accommodate this by inducing vacancies along its equatorial coordination site as demonstrated by neutron powder diffraction. - Graphical abstract: Diffraction studies of AUO{sub 4} (A = Ca, Sr, or Ba) oxides reveal the importance of the bonding requirements of the A site cation in determining whether the structure is rhombohedral or orthorhombic. - Highlights: • Structures of AUO{sub 4} ( A = Ca Sr, Ba) refined against X-ray and Neutron diffraction. • The alkali cations size has a dramatic effect on the crystal structure. • Smaller cations favouring a rhombohedral structure. • Oxygen vacancies to stabilise the rhombohedral structure in SrUO{sub 4}.« less

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.

Internal structure of InP/ZnS nanocrystals unraveled by high-resolution soft X-ray photoelectron spectroscopy.

PubMed

Huang, Kai; Demadrille, Renaud; Silly, Mathieu G; Sirotti, Fausto; Reiss, Peter; Renault, Olivier

2010-08-24

High-energy resolution photoelectron spectroscopy (DeltaE < 200 meV) is used to investigate the internal structure of semiconductor quantum dots containing low Z-contrast elements. In InP/ZnS core/shell nanocrystals synthesized using a single-step procedure (core and shell precursors added at the same time), a homogeneously alloyed InPZnS core structure is evidenced by quantitative analysis of their In3d(5/2) spectra recorded at variable excitation energy. When using a two-step method (core InP nanocrystal synthesis followed by subsequent ZnS shell growth), XPS analysis reveals a graded core/shell interface. We demonstrate the existence of In-S and S(x)-In-P(1-x) bonding states in both types of InP/ZnS nanocrystals, which allows a refined view on the underlying reaction mechanisms.

Rietveld refinement and dielectric properties of (Na{sub 0.5}Bi{sub 0.5}TiO{sub 3})-(Bi{sub 0.8}Ba{sub 0.2}FeO{sub 3}) ceramics

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

Kaswan, Kavita, E-mail: kaswan.kavita@gmail.com; Agarwal, Ashish; Sanghi, Sujata

2015-06-24

(1-x)(Na{sub 0.5}Bi{sub 0.5}TiO{sub 3})-x(Bi{sub 0.8}Ba{sub 0.2}FeO{sub 3}) lead free ceramics (NBT, NBT-BBFO; x = 0.0, 0.1 respectively) have been synthesized by conventional solid state reaction method. Crystalline phase of sintered ceramics was investigated at room temperature using X-ray diffraction. Rietveld refinement of XRD data performed by FullProf revealed that both the samples exhibited rhombohedral structure with R3c space group. Dielectric properties of these ceramics were studied at different temperatures in a wide frequency range using impedance analyzer. Dielectric constant and dielectric loss were found to be increase with increase of BBFO content. The prepared ceramics exhibit a broad maximum inmore » dielectric permittivity at 593K and dispersive permittivity at high temperatures. The NBT-BBFO sample shows a relaxor ferroelectric behavior at different frequencies.« less

Crystal structure, electrical transport and phase transition in 2-methoxyanilinium hexachlorido stannate(IV) dehydrate

NASA Astrophysics Data System (ADS)

Karoui, Sahel; Chouaib, Hassen; Kamoun, Slaheddine

2017-04-01

A new organic-inorganic (C7H10NO)2[SnCl6]2H2O compound was synthesized and characterized by X-ray diffraction, thermal analysis, NMR spectroscopy and dielectric measurements. The crystal structure refinement shows that this compound crystallizes at 298 K in the monoclinic system (P21/a space group (Z = 2)). The structure was solved by Patterson method and refined to a final value of R = 0.034 for 2207 independent observed reflections. The cohesion and stability of the atomic arrangement result from the establishment of Nsbnd H⋯Cl, O(W)sbnd H(W)⋯Cl and Nsbnd H⋯O(W) hydrogen bonds between (C7H10NO)+ cations, isolated (SnCl6)2- anions and water molecules. This compound exhibits a phase transition at 305 K which was characterized by differential scanning calorimetry (DSC), X-rays powder diffraction and dielectric measurements. At high frequency, the electrical σTot.(ω,T) conductivity obey to the Jonscher's power law σTot.(ω,T) = σDC(T) + B(T) ωS(T). DC and AC conductivity in (C7H10NO)2[SnCl6]2H2O was investigated revealing that the phase transition from the monoclinic P21/a (phase I) to the monoclinic C2/c (phase II) which occurs at 305 K is characterized by a change of the mechanism of the electric transport: SPT in phase I and CBH in phase II.

Influence of Ce Doping on Structural and Transport Properties of Ca1- x Ce x MnO3 ( x=0.2) Manganite

NASA Astrophysics Data System (ADS)

Varshney, Dinesh; Mansuri, Irfan

2011-01-01

We have investigated structural, electric, magnetic and thermal transport properties of electron doped Ca1- x Ce x MnO3 ( x=0.2) manganites. The Cerium substitution for Ca2+causes electron doping into insulating CaMnO3 without e g electron. At room temperature the polycrystalline Ca0.8Ce0.2MnO3 is in the crystallographic orthorhombic structure, with Pnma space group symmetry from the refinement of x-ray powder diffraction patterns. The electrical resistivity data infers that Ca0.8Ce0.2MnO3 manganite is in the semiconducting phase. A smooth linear behavior of log plot values is obtained and is well fitted with adiabatic small polaron conduction model. Nearest-neighbor hopping of a small polaron leads to a mobility with a thermally activated form. The negative values of thermopower infer electron as carriers in Ca0.8Ce0.2MnO3. From susceptibility measurements the Ce doped CaMnO3 shows a transition from antiferromagnetic (AFM) to paramagnetic (PM) phase.

Extended investigation of intermartensitic transitions in Ni-Mn-Ga magnetic shape memory alloys: A detailed phase diagram determination

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

Çakir, Asli; Aktürk, Selçuk; Righi, Lara

2013-11-14

Martensitic transitions in shape memory Ni-Mn-Ga Heusler alloys take place between a high temperature austenite and a low temperature martensite phase. However, intermartensitic transformations have also been encountered that occur from one martensite phase to another. To examine intermartensitic transitions in magnetic shape memory alloys in detail, we carried out temperature dependent magnetization, resistivity, and x-ray diffraction measurements to investigate the intermartensitic transition in Ni{sub 50}Mn{sub 50–x}Ga{sub x} in the composition range 12≤x≤25 at. %. Rietveld refined x-ray diffraction results are found to be consistent with magnetization and resistivity data. Depending on composition, we observe that intermartensitic transitions occur inmore » the sequences 7M→L1{sub 0}, 5M→7M, and 5M→7M→L1{sub 0} with decreasing temperature. The L1{sub 0} non-modulated structure is most stable at low temperature.« less

Synthesis and characterization of spinel type high-power cathode materials Li MxMn2-x O4 (M=Ni, Co, Cr)

NASA Astrophysics Data System (ADS)

Yoon, Y. K.; Park, C. W.; Ahn, H. Y.; Kim, D. H.; Lee, Y. S.; Kim, J.

2007-05-01

The transition metal-doped spinel cathode materials, LiM0.5Mn1.5O4 (M=Ni. Co, Cr) were prepared by solid-state reaction. The structure and morphology of the samples were investigated by X-ray diffraction, Rietveld refinement and scanning electron microscopy (SEM). The diffraction peaks of all the samples corresponded to a single phase of cubic spinel structure with a space group Fd3m. Field-emission SEM shows octahedron like shapes and the primary particles size was between 500 nm and 2 μm. Oxidation states of Ni, Co and Cr were found to be 2+, 2+ and 3+ as revealed by X-ray photoelectron spectroscopy. During discharging, LiNi0.5Mn1.5O4 and LiCo0.5Mn1.5O4 sample shows more than 130 mAh/g between 3.5 and 5.2 V at a current density of 0.65 mA/cm2 and well developed plateau around 5 V, respectively.

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.

Investigation of the structure of human dental tissue at multiple length scales using high energy synchrotron X-ray SAXS/WAXS

NASA Astrophysics Data System (ADS)

Sui, Tan; Landini, Gabriel; Korsunsky, Alexander M.

2011-10-01

High energy (>50keV) synchrotron X-ray scattering experiments were carried out on beamline I12 JEEP at the Diamond Light Source (DLS, Oxford, UK). Although a complete human tooth could be studied, in the present study attention was focused on coupons from the region of the Dentin-Enamel Junction (DEJ). Simultaneous high energy SAXS/WAXS measurements were carried out. Quantitative analysis of the results allows multiple length scale characterization of the nano-crystalline structure of dental tissues. SAXS patterns analysis provide insight into the mean thickness and orientation of hydroxyapatite particles, while WAXS (XRD) patterns allow the determination of the crystallographic unit cell parameters of the hydroxyapatite phase. It was found that the average particle thickness determined from SAXS interpretation varies as a function of position in the vicinity of the DEJ. Most mineral particles are randomly orientated within dentin, although preferred orientation emerges and becomes stronger on approach to the enamel. Within the enamel, texture is stronger than anywhere in the dentin, and the determination of lattice parameters can be accomplished by Pawley refinement of the multiple peak diffraction pattern. The results demonstrate the feasibility of using high energy synchrotron X-ray beams for the characterization of human dental tissues. This opens up the opportunity of studying thick samples (e.g., complete teeth) in complex sample environments (e.g., under saline solution). This opens new avenues for the application of high energy synchrotron X-ray scattering to dental research.

Crystallographic perturbations to valence charge density and hydrogen-surface interactions

NASA Astrophysics Data System (ADS)

Ciston, James W.

The subject of surfaces has been the epicenter of numerous studies in recent years, particularly with respect to applications in catalysis, thin films, and self-assembly of nanostructures where the surface-to-volume ratio is large. Understanding how the atomic structure of materials differs at surfaces where the atoms are far less constrained can yield fundamental insight into these interesting nanoscale phenomena. Quantum surface crystallography takes this one step further in an attempt to experimentally measure the structure of the electrons themselves, which is of greater importance than atomic positions in determining material properties. We report a procedure for obtaining a much better initial parameterization of the charge density than what is possible from a neutral atom model. This procedure involves the parameterization of a bulk charge density model in terms of simple variables such as bond lengths, which can then be transferred to the problem of interest, for instance a surface. Parameterization is accomplished through the fitting of Density Functional Theory calculations of a variety of crystal distortions to a bond-centered pseudoatom (BCPA) model. This parameterized model can then be applied to surfaces or for other problems where an initial higher-order model is needed without the addition of any extra fitted parameters. Through the use of the BCPA model, we report a three-dimensional charge density refinement from x-ray diffraction intensities of the Si (001) 2x1H surface. By properly accounting for the covalent bonding effects in the silicon structure, we were able to stably refine the positions of hydrogen atoms at this surface in three dimensions, which had never before been accomplished for any surface. In addition, we found experimentally an increased, slightly localized bond density of approximately 0.31 electrons between each Si atom pair at the surface. Both the atomic positions and the charge density were found to be in remarkably good agreement with density functional theory (DFT) calculations. The BCPA model was also applied to an experimental refinement of the local charge density at the Si (111) 7x7 surface utilizing a combination of x-ray and high energy electron diffraction. By perturbing about the bond-centered pseudoatom model, we found experimentally that the adatoms were in an anti-bonding state with the atoms directly below. We were also able to experimentally refine a charge transfer of 0.26+/-0.04 e- from each adatom site to the underlying layers. This was the first statistically significant refinement of site-specific bonding information at any surface utilizing x-ray diffraction data. Precession electron diffraction (PED) is a technique which is gaining increasing interest due to its ease of use and reduction of the dynamical scattering problem in electron diffraction. To further investigate the usefulness of this technique, we performed a systematic study of the effect of precession angle on the mineral andalusite where the semiangle was varied from 6.5 to 32 mrad in five discrete steps. We have shown that the intensities of kinematically forbidden reflections decayed exponentially as the precession semiangle (ϕ) was increased. Additionally, we have determined that charge density effects were best observed at moderately low angles (6.5-13 mrad) even though PED patterns became more kinematical in nature as the precession angle was increased further. We have also shown that the amount of interpretable information provided by direct methods phase inversion of the diffraction data increases monotonically but non-systematically as ϕ increases. We report an experimental and theoretical analysis of the ✓3x✓3-R30° and 2x2 reconstructions on the MgO (111) surface combining transmission electron microscopy, x-ray photoelectron spectroscopy, and reasonably accurate density functional calculations using the meta-GGA functional TPSS. We have not only conclusively solved the atomic structures of these reconstructions, but have developed a kinetic model for an evolutionary pathway between structures driven entirely by exchange of water molecules between the surface and the environment that does not require the cations to move when the structure transforms. This is the first time an experimentally and theoretically supported kinetic model has described not only all of the structures in a series on a single oxide surface, but also describes why none of the structures pass through the thermodynamically most stable configuration. Lastly, we have investigated the observability of valence bonding effects in aberration-corrected high resolution electron microscopy (HREM) images along the [010] projection of the mineral Forsterite (Mg2SiO 4). Direct observability of bonding effects would be both faster and less ambiguous than the refinement of similar features against diffraction data. Through analysis of simulated high resolution electron microscopy images, we have determined that bonding effects should be observable at levels approaching 20% of the total contrast. Initial experimental results for this material system have also been presented.

Impedance spectroscopy studies on lead free Ba1-xMgx(Ti0.9Zr0.1)O3 ceramics

NASA Astrophysics Data System (ADS)

Ben Moumen, S.; Neqali, A.; Asbani, B.; Mezzane, D.; Amjoud, M.; Choukri, E.; Gagou, Y.; El Marssi, M.; Luk'yanchuk, Igor A.

2018-06-01

Ba1-xMgx(Ti0.9Zr0.1)O3 (x = 0.01 and 0.02) ceramics were prepared using the conventional solid state reaction. Rietveld refinement performed on X-ray diffraction patterns indicates that the samples are tetragonal crystal structure with P4mm space group. By increasing Mg content from 1 to 2% the unit cell volume decreased. Likewise, the grains size is greatly reduced from 10 μm to 4 μm. The temperature dependence of dielectric constants at different frequencies exhibited typical relaxor ferroelectric characteristic, with sensitive dependence in frequency and temperature for ac conductivity. The obtained activation energy values were correlated to the proposed conduction mechanisms.

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

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

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.

Accurate determination of segmented X-ray detector geometry

DOE PAGES

Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; ...

2015-10-22

Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical formore » many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. Furthermore, we show that the refined detector geometry greatly improves the results of experiments.« less

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.

Structure Evolution and Reactivity of the Sc(2- x)V xO3+δ (0 ≤ x ≤ 2.0) System.

PubMed

Lussier, Joey A; Simon, Fabian J; Whitfield, Pamela S; Singh, Kalpana; Thangadurai, Venkataraman; Bieringer, Mario

2018-05-07

Solid oxide fuel cells (SOFCs) are solid-state electrochemical devices that directly convert chemical energy of fuels into electricity with high efficiency. Because of their fuel flexibility, low emissions, high conversion efficiency, no moving parts, and quiet operation, they are considered as a promising energy conversion technology for low carbon future needs. Solid-state oxide and proton conducting electrolytes play a crucial role in improving the performance and market acceptability of SOFCs. Defect fluorite phases are some of the most promising fast oxide ion conductors for use as electrolytes in SOFCs. We report the synthesis, structure, phase diagram, and high-temperature reactivity of the Sc (2- x) V x O 3+δ (0 ≤ x ≤ 2.00) oxide defect model system. For all Sc (2- x) V x O 3.0 phases with x ≤ 1.08 phase-pure bixbyite-type structures are found, whereas for x ≥ 1.68 phase-pure corundum structures are reported, with a miscibility gap found for 1.08 < x < 1.68. Structural details obtained from the simultaneous Rietveld refinements using powder neutron and X-ray diffraction data are reported for the bixbyite phases, demonstrating a slight V 3+ preference toward the 8b site. In situ X-ray diffraction experiments were used to explore the oxidation of the Sc (2- x) V x O 3.0 phases. In all cases ScVO 4 was found as a final product, accompanied by Sc 2 O 3 for x < 1.0 and V 2 O 5 when x > 1.0; however, the oxidative pathway varied greatly throughout the series. Comments are made on different synthesis strategies, including the effect on crystallinity, reaction times, rate-limiting steps, and reaction pathways. This work provides insight into the mechanisms of solid-state reactions and strategic guidelines for targeted materials synthesis.

Titanium doped LSCM anode for hydrocarbon fuelled SOFCs

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

Azad, Abul K.; Hakem, Afizul; Petra, Pg. M. Iskandar

2015-05-15

La{sub 0.75}Sr{sub 0.25}Cr{sub 0.5-x}Mn{sub 0.5}Ti{sub x}O{sub 3} (x = 0.1, 0.2) has been synthesized in solid state reaction method and tested as a potential anode material for solid oxide fuel cells. Rietveld refinement of X-ray powder diffraction data using Fullprof software shows that the materials crystallize in the rhombohedral symmetry in the R-3C space group. The cell parameters are: a = b = 5.5286 (4) Å, c = 13.408(1) Å, α = β = 90°, γ = 120°. Particle size distribution measurements show that the average particle size for x = 0.1 and 0.2 was 232.66 nm and 176.63 nm, respectively. Themore » potential on particles were found to be −22.86 mV and −27.73 mV, for x = 0.1 and x = 0.2, respectively. Thermal expansion measurement using thermo-mechanical analyzer shows that the thermal expansion coefficient is 13.96 × 10{sup −6}/°C which is close to the thermal expansion of the state-of–the art YSZ electrolyte. Microstructure has been observed from scanning electron microscopy which shows a porous structure. Energy dispersive X-ray shows that the percentage of the different cations and anions in the structure are close to the chemical occupancies.« less

Charge Density Wave and Narrow Energy Gap at Room Temperature in 2D Pb 3–xSb 1+xS 4Te 2-δ with Square Te Sheets

DOE PAGES

Chen, Haijie; Malliakas, Christos D.; Narayan, Awadhesh; ...

2017-07-17

We report a new two-dimensional compound Pb 3–xSb 1+xS 4Te 2-δ has a charge density wave (CDW) at room temperature. The CDW is incommensurate with q-vector of 0.248(6)a* + 0.246(8)b* + 0.387(9)c* for x = 0.29(2) and d = 0.37(3) due to positional and occupational long range ordering of Te atoms in the sheets. The modulated structure was refined from the single crystal X-ray diffraction data with a superspace group Pmore » $$\\bar{1}$$(αβγ)0 using (3 + 1)-dimensional crystallography. The resistivity increases with decreasing temperature, suggesting semiconducting behavior. The transition temperature (T CDW) of the CDW is ~ 345 K above which the Te square sheets become disordered with no q-vector. Lastly, first-principles density functional theory calculations on the undistorted structure and an approximate commensurate supercell reveal that the gap is due to the structure modulation.« less

Charge Density Wave and Narrow Energy Gap at Room Temperature in 2D Pb 3–xSb 1+xS 4Te 2-δ with Square Te Sheets

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

Chen, Haijie; Malliakas, Christos D.; Narayan, Awadhesh

We report a new two-dimensional compound Pb 3–xSb 1+xS 4Te 2-δ has a charge density wave (CDW) at room temperature. The CDW is incommensurate with q-vector of 0.248(6)a* + 0.246(8)b* + 0.387(9)c* for x = 0.29(2) and d = 0.37(3) due to positional and occupational long range ordering of Te atoms in the sheets. The modulated structure was refined from the single crystal X-ray diffraction data with a superspace group Pmore » $$\\bar{1}$$(αβγ)0 using (3 + 1)-dimensional crystallography. The resistivity increases with decreasing temperature, suggesting semiconducting behavior. The transition temperature (T CDW) of the CDW is ~ 345 K above which the Te square sheets become disordered with no q-vector. Lastly, first-principles density functional theory calculations on the undistorted structure and an approximate commensurate supercell reveal that the gap is due to the structure modulation.« less

Charge Density Wave and Narrow Energy Gap at Room Temperature in 2D Pb3-xSb1+xS4Te2-δ with Square Te Sheets.

PubMed

Chen, Haijie; Malliakas, Christos D; Narayan, Awadhesh; Fang, Lei; Chung, Duck Young; Wagner, Lucas K; Kwok, Wai-Kwong; Kanatzidis, Mercouri G

2017-08-16

We report a new two-dimensional compound, Pb 3-x Sb 1+x S 4 Te 2-δ , that has a charge density wave (CDW) at room temperature. The CDW is incommensurate with q-vector of 0.248(6)a* + 0.246(8)b* + 0.387(9)c* for x = 0.29(2) and δ = 0.37(3) due to positional and occupational long-range ordering of Te atoms in the sheets. The modulated structure was refined from the single-crystal X-ray diffraction data with a superspace group P1̅(αβγ)0 using (3 + 1)-dimensional crystallography. The resistivity increases with decreasing temperature, suggesting semiconducting behavior. The transition temperature (T CDW ) of the CDW is ∼345 K, above which the Te square sheets become disordered with no q-vector. First-principles density functional theory calculations on the undistorted structure and an approximate commensurate supercell reveal that the gap is due to the structure modulation.

Facile one-pot synthesis of hexagons of NaSrB5O9:Tb3+ phosphor for solid-state lighting

NASA Astrophysics Data System (ADS)

Ramesh, B.; Dillip, G. R.; Deva Prasad Raju, B.; Somasundaram, K.; Prasad Peddi, Siva; de Carvalho dos Anjos, Virgilio; Joo, S. W.

2017-04-01

NaSrB5O9:Tb3+ hexagons were synthesized by a facile solid-state reaction method. The synthesized powders were structurally examined by x-ray diffraction analysis (XRD), and Rietveld refinement was performed using the XRD data and Fullprof software. Hexagon-like morphology was observed using field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). The elemental composition of the phosphors was investigated qualitatively by energy dispersive x-ray analysis (EDS) and quantitatively by x-ray photoelectron spectroscopy (XPS). The phosphor has a strong green emission at 545 nm under excitation of 379 nm, which is due to the 5{{\\text{D}}4}{{\\to}7}{{\\text{F}}5} transition of the Tb3+ ion. A lifetime of 3.48 ms was obtained for the phosphor. The important parameters of the light source were determined, such as the thermal quenching, critical distance, the nature of the dopant ion interaction, color coordinates, and quantum yield values. Other reported properties include the site occupancy of the dopant, surface properties, morphological properties, and optical properties.

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

Effects of Al(3+) doping on the structure and properties of goethite and its adsorption behavior towards phosphate.

PubMed

Li, Wei; Wang, Longjun; Liu, Fan; Liang, Xiaoliang; Feng, Xionghan; Tan, Wenfeng; Zheng, Lirong; Yin, Hui

2016-07-01

Al substitution in goethite is common in soils, and has strong influence on the structure and physicochemical properties of goethite. In this research, a series of Al-doped goethites were synthesized, and characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FT-IR) and extended X-ray absorption fine structure (EXAFS) spectroscopy. The adsorption behavior of these samples towards PO4(3-) was also investigated. Characterization results demonstrated that increasing Al content in goethite led to a reduction in crystallinity, increase in specific surface area (SSA), and morphology change from needle-like to granular. Rietveld structure refinement revealed that the lattice parameter a remained almost constant and b slightly decreased, but c was significantly reduced, and the calculated crystal density increased. EXAFS analysis demonstrated that the Fe(Al)-O distance in the structure of the doped goethites was almost the same, but the Fe-Fe(Al) distance decreased with increasing Al content. Surface analysis showed that, with increasing Al content, the content of OH groups on the mineral surface increased. The adsorption of phosphate per unit mass of Al-doped goethite increased, while adsorption per unit area decreased owing to the decrease of the relative proportion of (110) facets in the total surface area of the minerals. The results of this research facilitate better understanding of the effect of Al substitution on the structure and properties of goethite and the cycling of phosphate in the environment. Copyright © 2016. Published by Elsevier B.V.

Equations of state of anhydrous AlF3 and AlI3: Modeling of extreme condition halide chemistry

NASA Astrophysics Data System (ADS)

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; Crowhurst, Jonathan C.; Goncharov, Alexander F.; Radousky, Harry B.; Armstrong, Michael R.; Roberts, Sarah K.; Plaue, Jonathan W.

2015-06-01

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF3) and separately, aluminum triiodide (AlI3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF3 and AlI3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: applied stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.

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

Quantifying point defects in Cu 2 ZnSn(S,Se) 4 thin films using resonant x-ray diffraction

DOE PAGES

Stone, Kevin H.; Christensen, Steven T.; Harvey, Steven P.; ...

2016-10-17

Cu 2ZnSn(S,Se)4 is an interesting, earth abundant photovoltaic material, but has suffered from low open circuit voltage. To better understand the film structure, we have measured resonant x-ray diffraction across the Cu and Zn K-edges for the device quality thin films of Cu 2ZnSnS4 (8.6% efficiency) and Cu 2ZnSn(S,Se)4 (3.5% efficiency). This approach allows for the confirmation of the underlying kesterite structure and quantification of the concentration of point defects and vacancies on the Cu, Zn, and Sn sublattices. Rietveld refinement of powder diffraction data collected at multiple energies is used to determine that there exists a high level ofmore » Cu Zn and Zn Cu defects on the 2c and 2d Wyckoff positions. We observe a significantly lower concentration of Zn Sn defects and Cu or Zn vacancies.« less

Crystallization and initial crystallographic characterization of the Corynebacterium glutamicum nitrilotriacetate monooxygenase component A

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

Kim, Kyung-Jin, E-mail: kkj@postech.ac.kr; Kim, Sujin; Lee, Sujin

2006-11-01

The Corynebacterium glutamicum NTA monooxygenase component A protein, which plays the central role in NTA biodegradation, was crystallized. The initial X-ray crystallographic characterization is reported. Safety and environmental concerns have recently dictated the proper disposal of nitrilotriacetate (NTA). Biodegradation of NTA is initiated by NTA monooxygenase, which is composed of two proteins: component A and component B. The NTA monooxygenase component A protein from Corynebacterium glutamicum was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate as the precipitant. X-ray diffraction data were collected to a maximum resolution of 2.5 Å on a synchrotron beamline. The crystalmore » belongs to the monoclinic space group C2, with unit-cell parameters a = 111.04, b = 98.51, c = 171.61 Å, β = 101.94°. The asymmetric unit consists of four molecules, corresponding to a packing density of 2.3 Å{sup 3} Da{sup −1}. The structure was solved by molecular replacement. Structure refinement is in progress.« less

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the pectin methylesterase from the sugar cane weevil Sphenophorus levis.

PubMed

Evangelista, Danilo Elton; Schutzer de Godoy, Andre; Fonseca Pereira de Paula, Fernando; Henrique-Silva, Flavio; Polikarpov, Igor

2014-03-01

Pectin methylesterase removes the methyl groups from the main chain of pectin, the major component of the middle lamella of the plant cell wall. The enzyme is involved in plant cell-wall development, is part of the enzymatic arsenal used by microorganisms to attack plants and also has a wide range of applications in the industrial sector. Therefore, there is a considerable interest in studies of the structure and function of this enzyme. In this work, the pectin methylesterase from Sphenophorus levis was produced in Pichia pastoris and purified. Crystals belonging to the monoclinic space group C2, with unit-cell parameters a = 122.181, b = 82.213, c = 41.176 Å, β = 97.48°, were obtained by the sitting-drop vapour-diffusion method and an X-ray diffraction data set was collected to 2.1 Å resolution. Structure refinement and model building are in progress.

The sequence and X-ray structure of the trypsin from Fusarium oxysporum.

PubMed

Rypniewski, W R; Hastrup, S; Betzel, C; Dauter, M; Dauter, Z; Papendorf, G; Branner, S; Wilson, K S

1993-06-01

The trypsin from Fusarium oxysporum is equally homologous to trypsins from Streptomyces griseus, Streptomyces erythraeus and to bovine trypsin. A DFP (diisopropylfluorophosphate) inhibited form of the enzyme has been crystallized from 1.4 M Na2SO4, buffered with citrate at pH 5.0-5.5. The crystals belong to space group P2(1) with cell parameters a = 33.43 A, b = 67.65 A, c = 39.85 A and beta = 107.6 degrees. There is one protein molecule in the asymmetric unit. X-ray diffraction data to a resolution of 1.8 A were collected on film using synchrotron radiation. The structure was solved by molecular replacement using models of bovine and S. griseus trypsins and refined to an R-factor of 0.141. The overall fold is similar to other trypsins, with some insertions and deletions. There is no evidence of the divalent cation binding sites seen in other trypsins. The covalently bound inhibitor molecule is clearly visible.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1

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

Miller, Edward B.; Gurda-Whitaker, Brittney; Govindasamy, Lakshmanan

2006-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. The diffraction data were subsequently processed and reduced with an overall R{sub sym} of 12.3% and a completeness of 89.0%. Based on the unit-cellmore » volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 Å resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.« less

When combined X-ray and polarized neutron diffraction data challenge high-level calculations: spin-resolved electron density of an organic radical.

PubMed

Voufack, Ariste Bolivard; Claiser, Nicolas; Lecomte, Claude; Pillet, Sébastien; Pontillon, Yves; Gillon, Béatrice; Yan, Zeyin; Gillet, Jean Michel; Marazzi, Marco; Genoni, Alessandro; Souhassou, Mohamed

2017-08-01

Joint refinement of X-ray and polarized neutron diffraction data has been carried out in order to determine charge and spin density distributions simultaneously in the nitronyl nitroxide (NN) free radical Nit(SMe)Ph. For comparison purposes, density functional theory (DFT) and complete active-space self-consistent field (CASSCF) theoretical calculations were also performed. Experimentally derived charge and spin densities show significant differences between the two NO groups of the NN function that are not observed from DFT theoretical calculations. On the contrary, CASSCF calculations exhibit the same fine details as observed in spin-resolved joint refinement and a clear asymmetry between the two NO groups.

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.

Role of Short-Range Chemical Ordering in (GaN) 1–x (ZnO) x for Photodriven Oxygen Evolution

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

Chen, Dennis P.; Neuefeind, Joerg C.; Koczkur, Kallum M.

(GaN)1–x(ZnO)x (GZNO) is capable of visible-light driven water splitting, but its bandgap at x ≤ 0.15 (>2.7 eV) results in poor visible-light absorption. Unfortunately, methods to narrow its bandgap by incorporating higher ZnO concentrations are accompanied by extensive Urbach tailing near the absorption-edge, which is indicative of structural disorder or chemical inhomogeneities. We evaluated whether this disorder is intrinsic to the bond-length distribution in GZNO or is a result of defects introduced from the loss of Zn during nitridation. Here, the synthesis of GZNO derived from layered double hydroxide (LDH) precursors is described which minimizes Zn loss and chemical inhomogeneitiesmore » and enhances visible-light absorption. The average and local atomic structures of LDH-derived GZNO were investigated using X-ray and neutron scattering and are correlated with their oxygen evolution rates. An isotope-contrasted neutron-scattering experiment was conducted in conjunction with reverse Monte Carlo (RMC) simulations. We showed that a bond-valence bias in the RMC refinements reproduces the short-range ordering (SRO) observed in structure refinements using isotope-contrasted neutron data. The findings suggest that positional disorder of cation–anion pairs in GZNO partially arises from SRO and influences local bond relaxations. Furthermore, particle-based oxygen evolution reactions (OERs) in AgNO3 solution reveal that the crystallite size of GZNO correlates more than positional disorder with oxygen evolution rate. These findings illustrate the importance of examining the local structure of multinary photocatalysts to identify dominant factors in particulate-based photodriven oxygen evolution.« less

Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography.

PubMed

Yefanov, Oleksandr; Gati, Cornelius; Bourenkov, Gleb; Kirian, Richard A; White, Thomas A; Spence, John C H; Chapman, Henry N; Barty, Anton

2014-07-17

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure 'three-dimensional merging'. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.

X-ray powder diffraction, spectroscopic study, dielectric properties and thermal analysis of new doped compound TiGa0.67Te2.33O8

NASA Astrophysics Data System (ADS)

Smaoui, S.; Ben Aribia, W.; Kabadou, A.; Abdelmouleh, M.

2017-04-01

A novel mixed valence tellurium oxide, TiGa0.67Te2.33O8, was synthesized and its crystal structure determined using the X-ray powder diffraction technique. The obtained oxide was found to crystallize in a cubic unit-cell, Ia 3 bar space group, with the lattice parameter a = 10.9557(1) Å. Rietveld refinement of the structure led to ultimate confidence factors Rp = 7.63 and Rwp = 6.71. This structure was based on slabs containing groups of (Te/Ga)O4 joined by the metal cations Ti4+. The structure analysis showed a cation ordering of Te4+ and Te6+ yielding a TiGa2/3Te7/3O8 formula. The IR and RAMAN spectra confirmed the presence of the TiO6 and (Te/Ga)O4 groups. The dielectric anomalies observed at 500 K were attributed to the mixed valence structure, arising from the mixed-valence Te6+/Te4+. We detected only one peak in thermal behavior by the DTA/TG analysis; which implied a melting reaction.

Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling.

PubMed

Filip, Xenia; Borodi, Gheorghe; Filip, Claudiu

2011-10-28

A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data. This journal is © the Owner Societies 2011

Structural and magnetic properties of Nd0.67Ba0.33MnO3 manganites with partial replacement of Fe and Cu at Mn-site

NASA Astrophysics Data System (ADS)

Sudakshina, B.; Arun, B.; Chandrasekhar, K. Devi; Yang, H. D.; Vasundhara, M.

2018-06-01

We have investigated the structural and magnetic properties of Nd0.67Ba0.33MnO3 manganite and partial replacement of Mn with Fe and Cu compounds followed by X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS) and vibrating sample magnetometer (VSM). The Rietveld refinement of XRD indicates orthorhombic crystal structure with I-mma space group for all the compounds and thus obtained lattice parameters confirm the presence of co-operative Jahn-Teller effect. XRD and XAS spectra results suggests the existence of Fe3+ in Fe-substituted compound where as a mixed state of Cu2+ and Cu3+ ions in the Cu-substituted compound. The ferromagnetic (FM) to paramagnetic (PM) transition and magnetic moment is found to decrease upon the substitution of Fe and Cu atoms because of the suppression of double exchange interaction. The theoretically obtained and experimentally determined values of effective PM moment and saturation magnetic moment confirms the presence of inhomogeneous magnetic states containing FM and antiferromagnetic clusters in all the studied compounds.

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

Crystal structures of (Mg1-x,Fe(x))SiO3 postperovskite at high pressures.

PubMed

Yamanaka, Takamitsu; Hirose, Kei; Mao, Wendy L; Meng, Yue; Ganesh, P; Shulenburger, Luke; Shen, Guoyin; Hemley, Russell J

2012-01-24

X-ray diffraction experiments on postperovskite (ppv) with compositions (Mg(0.9)Fe(0.1))SiO(3) and (Mg(0.6)Fe(0.4))SiO(3) at Earth core-mantle boundary pressures reveal different crystal structures. The former adopts the CaIrO(3)-type structure with space group Cmcm, whereas the latter crystallizes in a structure with the Pmcm (Pmma) space group. The latter has a significantly higher density (ρ = 6.119(1) g/cm(3)) than the former (ρ = 5.694(8) g/cm(3)) due to both the larger amount of iron and the smaller ionic radius of Fe(2+) as a result of an electronic spin transition observed by X-ray emission spectroscopy (XES). The smaller ionic radius for low-spin compared to high-spin Fe(2+) also leads to an ordered cation distribution in the M1 and M2 crystallographic sites of the higher density ppv structure. Rietveld structure refinement indicates that approximately 70% of the total Fe(2+) in that phase occupies the M2 site. XES results indicate a loss of 70% of the unpaired electronic spins consistent with a low spin M2 site and high spin M1 site. First-principles calculations of the magnetic ordering confirm that Pmcm with a two-site model is energetically more favorable at high pressure, and predict that the ordered structure is anisotropic in its electrical and elastic properties. These results suggest that interpretations of seismic structure in the deep mantle need to treat a broader range of mineral structures than previously considered.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: from protein structure to nanodisk assemblies.

PubMed

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

2010-11-07

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

NASA Astrophysics Data System (ADS)

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

2010-11-01

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

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

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.

2010-11-07

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on themore » basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.« less

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

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.

Reversal magnetization dependence with the Cr and Fe oxidation states in YFe1-xCrxO3 (0≤x≤1) perovskites

NASA Astrophysics Data System (ADS)

Fabian, F. A.; Pedra, P. P.; Moura, K. O.; Duque, J. G. S.; Meneses, C. T.

2016-06-01

In this work, we have carried out a detailed study of the magnetic and structural properties of YFe1-xCrxO3 (0≤x≤1) samples with orthorhombic structure obtained by co-precipitation method. Analysis of X-ray diffraction data using Rietveld refinement show that all samples present an orthorhombic crystal system with space group Pnma. Besides, we have observed a reduction of unit cell volume with increasing of the Cr concentration. SEM images show the formation of grains of micrometer order. X-ray Absorption near edge spectroscopy (XANES) measurements show a shift of absorption edge which can be indicate there is (i) different oxidation states to Fe and Cr ions and/or (ii) a changing in the point symmetry of Fe and Cr ions to the compounds. The magnetization measurements indicate a continuous decreasing of the magnetic transition temperature as function of chromium doping. The reversal magnetization effect was observed to concentrations around x=0.5. Besides, the deviation of the Curie-Weiss law and a weak ferromagnetic behavior observed at room temperature in the M vs H curves can be attributed to the strong magnetic interactions between the transition metals with different oxidation states.

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

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

Liu, Jue; Olds, Daniel; Peng, Rui

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. It is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

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

Liu, Jue; Olds, Daniel; Peng, Rui

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. As a result, it is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

DOE PAGES

Liu, Jue; Olds, Daniel; Peng, Rui; ...

2017-06-14

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. As a result, it is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Structural studies of TiC{sub 1−x}O{sub x} solid solution by Rietveld refinement and first-principles calculations

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

Jiang, Bo, E-mail: youqin5912@yahoo.com.cn; Hou, Na; Huang, Shanyan

2013-08-15

The lattice parameters, structural stability and electronic structure of titanium oxycarbides (TiC{sub 1−x}O{sub x}, 0≤x≤1) solid solution were investigated by Rietveld refinement and first-principles calculations. Series of TiC{sub 1−x}O{sub x} were precisely synthesized by sintering process under the vacuum. Rietveld refinement results of XRD patterns show the properties of continuous solid solution in TiC{sub 1−x}O{sub x} over the whole composition range. The lattice parameters vary from 0.4324 nm to 0.4194 nm decreasing with increasing oxygen concentration. Results of first-principles calculations reveal that the disorder C/O structure is stable than the order C/O structure. Further investigations of the vacancy in Ti{submore » 1−Va}(C{sub 1−x}O{sub x}){sub 1−Va} solid solution present that the structure of vacancy segregated in TiO-part is more stable than the disorder C/O structure, which can be ascribed to the Ti–Ti bond across O-vacancy and the charge redistributed around Ti-vacancy via the analysis of the electron density difference plots and PDOS. - Graphical abstract: XRD of series of titanium oxycarbides (TiC{sub 1−x}O{sub x}, 0≤x≤1) solid solution prepared by adjusting the proportion of TiO in the starting material. Highlights: • Titanium oxycarbides were obtained by sintering TiO and TiC under carefully controlled conditions. • Rietveld refinement results show continuous solid solution with FCC structure in TiC{sub 1−x}O{sub x}. • The disorder C/O structure is stable than the order C/O structure. • Introduction of vacancy segregated in TiO-part is more stable than disorder C/O structure. • Ti–Ti bond across O-vacancy and the charge redistributed around Ti-vacancy enhance structural stability.« less

Development of microchannel plate x-ray optics

NASA Technical Reports Server (NTRS)

Kaaret, Philip

1995-01-01

The goal of this research program was to develop a novel technique for focusing x-rays based on the optical system of a lobster's eye. A lobster eye employs many closely packed reflecting surfaces arranged within a spherical or cylindrical shell. These optics have two unique properties: they have unlimited fields of view and can be manufactured via replication of identical structures. Because the angular resolution is given by the ratio of the size of the individual optical elements to the focal length, optical elements with size on the order of one hundred microns are required to achieve good angular resolution with a compact telescope. We employed anisotropic etching of single crystal silicon wafers for the fabrication of micron-scale optical elements. This technique, commonly referred to as silicon micromachining, is based on silicon fabrication techniques developed by the microelectronics industry. We have succeeded in producing silicon lenses with a geometry suitable for a 1-d focusing x-ray optics. These lenses have an aspect ratio (40:1) suitable for x-ray reflection and have very good optical surface alignment. We have developed a number of process refinements which improved the quality of the lens geometry and the repeatability of the etch process. In addition to the silicon fabrication, an x-ray beam line was constructed at Columbia for testing the optics. Most recently, we have done several experiments to find the fundamental limits that the anisotropic etch process placed on the etched surface roughness.

Discovery of a Highly Selective JAK2 Inhibitor, BMS-911543, for the Treatment of Myeloproliferative Neoplasms

PubMed Central

2015-01-01

JAK2 kinase inhibitors are a promising new class of agents for the treatment of myeloproliferative neoplasms and have potential for the treatment of other diseases possessing a deregulated JAK2-STAT pathway. X-ray structure and ADME guided refinement of C-4 heterocycles to address metabolic liability present in dialkylthiazole 1 led to the discovery of a clinical candidate, BMS-911543 (11), with excellent kinome selectivity, in vivo PD activity, and safety profile. PMID:26288683

Correction of Hydrostatic Cluster Masses through Power Ratios and Weak Lensing

NASA Astrophysics Data System (ADS)

Mahdavi, Andisheh

2009-09-01

The evolution of rich, X-ray emitting clusters of galaxies has given us precise measurements of the cosmological parameters, with dramatic constraints on the dark energy equation of state. Built into these measurements are wholesale corrections for the infamous "X-ray mass underestimate"---the fact that X-ray masses are systematically low due to the incomplete thermalization of the intracluster plasma. We seek to refine the mass correction for cosmological use through morphological power ratios. Power ratios deliver more accurate correction factors because they take into account variations in substructure from cluster to cluster. We will test their ability to correct X-ray masses by comparing hydrostatic and weak lensing mass profiles for a sample of 44 rich clusters of galaxies.

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.

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.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

Structural, magnetic and magnetoreactance studies in NiFe2-xRxO4 (x = 0, 0.05; R = Y, Yb and Lu)

NASA Astrophysics Data System (ADS)

Ugendar, Kodam; Chunchu, Venkatrao; Rani, G. Neeraja; Markaneyulu, G.

2018-04-01

Structural, magnetic and magnetoreactance (mr) properties of NiFe2-xRxO4 (x = 0, 0.05; R = Y, Yb and Lu) compounds were investigated and the results are discussed and presented in this paper. Rietveld refined X-ray diffraction (XRD) patterns and Raman spectroscopy revealed the cubic inverse spinel phase for all the compounds investigated. The former also identified small amounts of RFeO3 as the secondary phase. Lattice constant values were increased upon partial substitution of Fe3+ by R3+ (R = Y, Yb and Lu). Magnetization measurements revealed that the magnetic moment of R3+ (R = Y, Yb and Lu) substituted compounds decreased compared with NiFe2O4. mr was measured at 3 kHz and 3 MHz both longitudinal (LT) and transverse (TR) configuration. A maximum mr of 54 % was observed in Y3+ substituted NiFe2O4 in TR mode.

Accurate solid solution range of BiMnxFe3-xO6 and low temperature magnetism

NASA Astrophysics Data System (ADS)

Jiang, Pengfei; Yue, Mufei; Cong, Rihong; Gao, Wenliang; Yang, Tao

2017-11-01

BiMnxFe3-xO6 (x = 1) represents a new type of oxide structure containing Bi3+ and competing magnetic super-exchanges. In literature, multiple magnetic states were realized at low temperatures in BiMnFe2O6, and the hypothetical parent compounds (BiMn3O6, BiFe3O6) were predicted to be different in magnetism. Herein, we performed a careful study on the syntheses of BiMnxFe3-xO6 at ambient pressure, and the solid solution range was determined to be 0.9 ≤ x ≤ 1.3 by Rietveld refinements on high-quality powder X-ray diffraction data. Due to the very similar cationic size of Mn3+ and Fe3+, and possibly the structural rigidity, there was no significant structure change in the whole range of solid solution. The magnetic behavior of BiMnxFe3-xO6 (x = 1.2, 1.22, 1.26, 1.28 and 1.3) was generally similar to BiMnFe2O6, while the relative higher concentration of Mn3+ led to the decreasing of the antiferromagnetic ordering temperature.

Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

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

Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

2010-05-15

The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

Doping effect on the structural properties of Cu1-x(Ni, Zn, Al and Fe)xO samples (0

NASA Astrophysics Data System (ADS)

Amaral, J. B.; Araujo, R. M.; Pedra, P. P.; Meneses, C. T.; Duque, J. G. S.; dos S. Rezende, M. V.

2016-09-01

In this work, the effect of insertion of transition metal, TM (=Ni, Zn, Al and Fe), ions in Cu1-xTMxO samples (0

Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling.

PubMed Central

Thanki, N.; Rao, J. K.; Foundling, S. I.; Howe, W. J.; Moon, J. B.; Hui, J. O.; Tomasselli, A. G.; Heinrikson, R. L.; Thaisrivongs, S.; Wlodawer, A.

1992-01-01

The structure of a crystal complex of recombinant human immunodeficiency virus type 1 (HIV-1) protease with a peptide-mimetic inhibitor containing a dihydroxyethylene isostere insert replacing the scissile bond has been determined. The inhibitor is Noa-His-Hch psi [CH(OH)CH(OH)]Vam-Ile-Amp (U-75875), and its Ki for inhibition of the HIV-1 protease is < 1.0 nM (Noa = 1-naphthoxyacetyl, Hch = a hydroxy-modified form of cyclohexylalanine, Vam = a hydroxy-modified form of valine, Amp = 2-pyridylmethylamine). The structure of the complex has been refined to a crystallographic R factor of 0.169 at 2.0 A resolution by using restrained least-squares procedures. Root mean square deviations from ideality are 0.02 A and 2.4 degrees, for bond lengths and angles, respectively. The bound inhibitor diastereomer has the R configurations at both of the hydroxyl chiral carbon atoms. One of the diol hydroxyl groups is positioned such that it forms hydrogen bonds with both the active site aspartates, whereas the other interacts with only one of them. Comparison of this X-ray structure with a model-built structure of the inhibitor, published earlier, reveals similar positioning of the backbone atoms and of the side-chain atoms in the P2-P2' region, where the interaction with the protein is strongest. However, the X-ray structure and the model differ considerably in the location of the P3 and P3' end groups, and also in the positioning of the second of the two central hydroxyl groups. Reconstruction of the central portion of the model revealed the source of the hydroxyl discrepancy, which, when corrected, provided a P1-P1' geometry very close to that seen in the X-ray structure. PMID:1304383

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.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

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.

Experimental conformational energy maps of proteins and peptides.

PubMed

Balaji, Govardhan A; Nagendra, H G; Balaji, Vitukudi N; Rao, Shashidhar N

2017-06-01

We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol -1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A Deep Pulse Search in 11 Low Mass X-Ray Binaries

NASA Astrophysics Data System (ADS)

Patruno, A.; Wette, K.; Messenger, C.

2018-06-01

We present a systematic coherent X-ray pulsation search in 11 low mass X-ray binaries (LMXBs). We select a relatively broad variety of LMXBs, including persistent and transient sources, spanning orbital periods between 0.3 and 17 hr. We use about 3.6 Ms of data collected by the Rossi X-Ray Timing Explorer and XMM-Newton and apply a semi-coherent search strategy to look for weak and persistent pulses in a wide spin frequency range. We find no evidence for X-ray pulsations in these systems and consequently set upper limits on the pulsed sinusoidal semi-amplitude below 1.6% for ten outbursting/persistent LMXBs and 6% for a quiescent system; the upper limits are further refined, by searching a narrower parameter space around the outliers, down to 0.14%–0.78% and 2.9%, respectively. These results suggest that weak pulsations might not form in (most) non pulsating LMXBs.

New Insight into the Local Structure of Hydrous Ferric Arsenate Using Full-Potential Multiple Scattering Analysis, Density Functional Theory Calculations, and Vibrational Spectroscopy.

PubMed

Wang, Shaofeng; Ma, Xu; Zhang, Guoqing; Jia, Yongfeng; Hatada, Keisuke

2016-11-15

Hydrous ferric arsenate (HFA) is an important arsenic-bearing precipitate in the mining-impacted environment and hydrometallurgical tailings. However, there is no agreement on its local atomic structure. The local structure of HFA was reprobed by employing a full-potential multiple scattering (FPMS) analysis, density functional theory (DFT) calculations, and vibrational spectroscopy. The FPMS simulations indicated that the coordination number of the As-Fe, Fe-As, or both in HFA was approximately two. The DFT calculations constructed a structure of HFA with the formula of Fe(HAsO 4 ) x (H 2 AsO 4 ) 1-x (OH) y ·zH 2 O. The presence of protonated arsenate in HFA was also evidenced by vibrational spectroscopy. The As and Fe K-edge X-ray absorption near-edge structure spectra of HFA were accurately reproduced by FPMS simulations using the chain structure, which was also a reasonable model for extended X-Ray absorption fine structure fitting. The FPMS refinements indicated that the interatomic Fe-Fe distance was approximately 5.2 Å, consistent with that obtained by Mikutta et al. (Environ. Sci. Technol. 2013, 47 (7), 3122-3131) using wavelet analysis. All of the results suggested that HFA was more likely to occur as a chain with AsO 4 tetrahedra and FeO 6 octahedra connecting alternately in an isolated bidentate-type fashion. This finding is of significance for understanding the fate of arsenic and the formation of ferric arsenate minerals in an acidic environment.

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

DOE PAGES

Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; ...

2015-06-11

Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data revealmore » the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.« less

Structural modeling of djenkolic acid with sulfur replaced by selenium and tellurium.

PubMed

Melnikov, Petr; Nascimento, Valter A; Silva, Anderson F; Consolo, Lourdes Z Z

2014-04-17

The comparative structural modeling of djenkolic acid and its derivatives containing selenium and tellurium in chalcogen sites (Ch=Se, Te) has provided detailed information about the bond lengths and bond angles, filling the gap in what we know about the structural characteristics of these aminoacids. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds methionine and selenomethionine, as well as for an estimate made earlier for telluromethionine. It was shown that the Ch-C(3) and Ch-C(4) bond lengths grow in parallel with the increasing anionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of conformers is quite different owing to the possibility of rotation about four carbon atoms, hence the remarkable variability observed in dihedral angles. It was shown that the compounds contain a rigid block with two Ch atoms connected through a methylene group. The standard program Gaussian 03 with graphical interface Gaussview 4.1.2 has proved to be satisfactory tool for the structural description of less-common bioactive compositions when direct X-ray results are absent.

Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

X-ray diffraction investigations of structural modifications in In-doped tin pyrophosphates

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

Botez, Cristian E.; Martinez, Heber; Morris, Joshua L.

2017-08-01

Laboratory and synchrotron x-ray powder diffraction were used to investigate the structural modifications that occur upon indium doping of tin pyrophosphate. The data collected under air, vacuum, and inert gas sample environments at temperatures (T) from 50 °C to 300 °C show that regardless of the In-doping level (0 ≤ x ≤ 0.18) all InxSn1-xP2O7 samples are isomorphic (have the same P a -3 cubic crystal structure) at all temperatures and under all the conditions investigated. The cubic lattice parameter (a) increases linearly with T at all doping levels, but the “a vs. x|T“ isotherms exhibit a robust peak atmore » x = 0.1 when data are collected on samples measured in air. On the other hand, Rietveld refinements against data collected on InxSn1-xP2O7 samples yield values of OO bond lengths and POP bond angles that show no major changes at x = 0.1 at any temperature. This is significant, as the Sn0.9In0.1P2O7 (x = 0.1) compound is known to exhibit the highest proton conductivity within the series, but the microscopic details responsible for the increased proton conductivity are not understood. Finally, the peak observed in the “a vs. x|T“ curves vanishes if the measurements are taken on samples kept either under vacuum or in an inert gas environment. This is a remarkable behavior as it lends further support to our hypothesis that a key microscopic feature responsible for the large proton conductivity of the Sn0.9In0.1P2O7 compound is the enlargement of the lattice constant at x = 0.1.« less

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.

X-Ray Optics at NASA Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Atkins, Carolyn; Broadway, David M.; Elsner, Ronald F.; Gaskin, Jessica A.; Gubarev, Mikhail V.; Kilaru, Kiranmayee; Kolodziejczak, Jeffery J.; Ramsey, Brian D.; Roche, Jacqueline M.;

Nitroxoline Molecule: Planar or Not? A Story of Battle between π-π Conjugation and Interatomic Repulsion.

PubMed

Tikhonov, Denis S; Sharapa, Dmitry I; Otlyotov, Arseniy A; Solyankin, Peter M; Rykov, Anatolii N; Shkurinov, Alexander P; Grikina, Olga E; Khaikin, Leonid S

2018-02-15

The conformational properties of the nitro group in nitroxoline (8-hydroxy-5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO 2 group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO 2 group from the closest hydrogen, which overcomes the energy gain from the π-π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO 2 group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds.

Strategies for carbohydrate model building, refinement and validation

PubMed Central

2017-01-01

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein–sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade. PMID:28177313

Strategies for carbohydrate model building, refinement and validation.

PubMed

Agirre, Jon

2017-02-01

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.

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

Synthesis, crystal structure, and electrical and magnetic properties of BaMo{sub 6}Te{sub 6}: A novel reduced molybdenum telluride containing infinite chains of trans-face shared Mo{sub 6} octahedra

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

Gall, Philippe; Guizouarn, Thierry; Potel, Michel

Powder samples and single crystals of the new ternary compound BaMo{sub 6}Te{sub 6} were obtained by solid state reaction. The structure was determined by single-crystal X-ray diffraction. BaMo{sub 6}Te{sub 6} crystallizes in the hexagonal space group P6{sub 3}/m (No. 176) with unit-cell parameters a=9.3941(2) Å, c=4.5848(1) Å and Z=1. Full-matrix least-squares refinement on F{sup 2} using 452 independent reflections for 17 refinable parameters resulted in R1=0.0208 and wR2=0.0539. The structure consists of one-dimensional infinite chains of trans-face shared Mo{sub 6} octahedra capped by Se atoms. These chains that are running along the c axis are separated from each other bymore » nine-coordinate Ba atoms. Resistivity measurements on a single crystal indicated that the BaMo{sub 6}Te{sub 6} compound is metallic down to 160 K and semiconductor below. Magnetic susceptibility measurements showed that BaMo{sub 6}Te{sub 6} is weakly diamagnetic with no anomaly at the metal–semiconductor transition. - Graphical abstract: We present here the synthesis, the crystal structure, and the electrical and magnetic properties of the new compound BaMo{sub 6}Te{sub 6} containing infinite chains of trans-face shared Mo{sub 6} octahedra. - Highlights: • BaMo{sub 6}Te{sub 6} contains infinite chains of trans-face-sharing Mo{sub 6} octahedra |Mo{sub 6/2}|{sub ∞}{sup 1}. • Synthesis by solid state reaction. • Single-crystal X-ray study. • Continuous metal–nonmetal transition. • Anderson localization.« less

Evolution of ferroelectric SrBi2Nb2O9 phase embedded in tellurite glass

NASA Astrophysics Data System (ADS)

Mohamed, E. A.

2017-12-01

Glasses with the composition, [(100-x)TeO2- x(SrO-Bi2O3-Nb2O5)] with x = 20, 30 and 40 (in mol %) were prepared. The X-ray diffraction (XRD) pattern and differential thermal analysis (DTA) for the as-prepared samples confirmed the amorphous and glassy characteristics, respectively. The SrBi2Nb2O9 phase in tellurite glass for HT773 sample at x = 40 mol % is formed and confirmed by the Rietveld refinement. DTA curves for all glass samples exhibit two endothermic dips while the two broad exothermic peaks at lower x reduced to one at higher x. Infrared (IR) results revealed that the glassy matrix are composed of TeO3, TeO3+1, TeO4, BiO6 and NbO6 structural units. The changes in the density (ρ), molar volume (Vm), oxygen molar volume (V0) and oxygen packing fraction (OPD) have correlated with structural changes in the glass network. The optical studies show an absorption bands below the absorption edge in the glass samples.

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

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.

Bragg projection ptychography on niobium phase domains

NASA Astrophysics Data System (ADS)

Burdet, Nicolas; Shi, Xiaowen; Clark, Jesse N.; Huang, Xiaojing; Harder, Ross; Robinson, Ian

2017-07-01

Bragg projection ptychography (BPP) is a coherent x-ray diffraction imaging technique which combines the strengths of scanning microscopy with the phase contrast of x-ray ptychography. Here we apply it for high resolution imaging of the phase-shifted crystalline domains associated with epitaxial growth. The advantages of BPP are that the spatial extent of the sample is arbitrary, it is nondestructive, and it gives potentially diffraction limited spatial resolution. Here we demonstrate the application of BPP for revealing the domain structure caused by epitaxial misfit in a nanostructured metallic thin film. Experimental coherent diffraction data were collected from a niobium thin film, epitaxially grown on a sapphire substrate as the beam was scanned across the sample. The data were analyzed by BPP using a carefully selected combination of refinement procedures. The resulting image shows a close packed array of epitaxial domains, shifted with respect to each other due to misfit between the film and its substrate.

Structure, microstructure, and size dependent catalytic properties of nanostructured ruthenium dioxide

NASA Astrophysics Data System (ADS)

Nowakowski, Pawel; Dallas, Jean-Pierre; Villain, Sylvie; Kopia, Agnieszka; Gavarri, Jean-Raymond

2008-05-01

Nanostructured powders of ruthenium dioxide RuO 2 were synthesized via a sol gel route involving acidic solutions with pH varying between 0.4 and 4.5. The RuO 2 nanopowders were characterized by X-ray diffraction, scanning and transmission electron microscopy (SEM and TEM). Rietveld refinement of mean crystal structure was performed on RuO 2 nanopowders and crystallized standard RuO 2 sample. Crystallite sizes measured from X-ray diffraction profiles and TEM analysis varied in the range of 4-10 nm, with a minimum of crystallite dimension for pH=1.5. A good agreement between crystallite sizes calculated from Williamson Hall approach of X-ray data and from direct TEM observations was obtained. The tetragonal crystal cell parameter (a) and cell volumes of nanostructured samples were characterized by values greater than the values of standard RuO 2 sample. In addition, the [Ru-O 6] oxygen octahedrons of rutile structure also depended on crystal size. Catalytic conversion of methane by these RuO 2 nanostructured catalysts was studied as a function of pH, catalytic interaction time, air methane composition, and catalysis temperature, by the way of Fourier transform infrared (FTIR) spectroscopy coupled to homemade catalytic cell. The catalytic efficiency defined as FTIR absorption band intensities I(CO 2) was maximum for sample prepared at pH=1.5, and mainly correlated to crystallite dimensions. No significant catalytic effect was observed from sintered RuO 2 samples.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Low-temperature x-ray crystal structure analysis of the cage-structured compounds M Be13 (M =La,Sm, and U)

NASA Astrophysics Data System (ADS)

Hidaka, Hiroyuki; Nagata, Ryoma; Tabata, Chihiro; Shimizu, Yusei; Miura, Naoyuki; Yanagisawa, Tatsuya; Amitsuka, Hiroshi

2018-05-01

The beryllides M Be13 (M = rare earths and actinides) crystallize in a NaZn13-type cubic structure, which can be categorized as a cage-structured compound. In this study, powder x-ray diffraction measurements have been performed on LaBe13,SmBe13, and UBe13 in the temperature range between 7 and 300 K in order to investigate their crystallographic characteristics systematically. They keep the NaZn13-type cubic structure down to the lowest temperature. We estimated their Debye temperature to be 600-750 K from analyses of the temperature dependence of a lattice parameter, being in good agreement with the values reported previously. Rietveld refinements on the obtained powder patterns revealed that the M atom in the 8 a site is located in an almost ideal snub cube formed by 24 BeII atoms in the 96 i site, whose caged structure is unchanged even at the low temperatures. In addition, it is argued from the temperature variation of an isotropic mean-square displacement parameter that the M Be13 compounds commonly have a low-energy phonon mode, which can be described by a model assuming an Einstein oscillation of the M atom with a characteristic temperature of ˜160 K.

Insights into the effect of iron and cobalt doping on the structure of nanosized ZnO.

PubMed

Giuli, Gabriele; Trapananti, Angela; Mueller, Franziska; Bresser, Dominic; d'Acapito, Francesco; Passerini, Stefano

2015-10-05

Here we report an in-depth structural characterization of transition metal-doped zinc oxide nanoparticles that have recently been used as anode materials for Li-ion batteries. Structural refinement of powder X-ray diffraction (XRD) data allowed the determination of small though reproducible changes in the unit cell dimensions of four ZnO samples (wurtzite structure) prepared with different dopants or different synthesis conditions. Moreover, large variations of the full width at half-maximum of the XRD reflections indicate that the crystallinity of the samples decreases in the order ZnO, Zn0.9Co0.1O, Zn0.9Fe0.1O/C, and Zn0.9Fe0.1O (the crystallite sizes as determined by Williamson-Hall plots are 42, 29, 15, and 13 nm, respectively). X-ray absorption spectroscopy data indicate that Co is divalent, whereas Fe is purely trivalent in Zn0.9Fe0.1O and 95% trivalent (Fe(3+)/(Fe(3+) + Fe(2+)) ratio = 0.95) in Zn0.9Fe0.1O/C. The aliovalent substitution of Fe(3+) for Zn(2+) implies the formation of local defects around Fe(3+) such as cationic vacancies or interstitial oxygen for charge balance. The EXAFS (extended X-ray absorption fine structure) data, besides providing local Fe-O and Co-O bond distances, are consistent with a large amount of charge-compensating defects. The Co-doped sample displays similar EXAFS features to those of pure ZnO, suggesting the absence of a large concentration of defects as found in the Fe-doped samples. These results are of substantial importance for understanding and elucidating the modified electrochemical lithiation mechanism by introducing transition metal dopants into the ZnO structure for the application as lithium-ion anode material.

Probing high-redshift clusters with HST/ACS gravitational weak-lensing and Chandra x-ray observations

NASA Astrophysics Data System (ADS)

Jee, Myungkook James

2006-06-01

Clusters of galaxies, the largest gravitationally bound objects in the Universe, are useful tracers of cosmic evolution, and particularly detailed studies of still-forming clusters at high-redshifts can considerably enhance our understanding of the structure formation. We use two powerful methods that have become recently available for the study of these distant clusters: spaced- based gravitational weak-lensing and high-resolution X-ray observations. Detailed analyses of five high-redshift (0.8 < z < 1.3) clusters are presented based on the deep Advanced Camera for Surveys (ACS) and Chandra X-ray images. We show that, when the instrumental characteristics are properly understood, the newly installed ACS on the Hubble Space Telescope (HST) can detect subtle shape distortions of background galaxies down to the limiting magnitudes of the observations, which enables the mapping of the cluster dark matter in unprecedented high-resolution. The cluster masses derived from this HST /ACS weak-lensing study have been compared with those from the re-analyses of the archival Chandra X-ray data. We find that there are interesting offsets between the cluster galaxy, intracluster medium (ICM), and dark matter centroids, and possible scenarios are discussed. If the offset is confirmed to be uniquitous in other clusters, the explanation may necessitate major refinements in our current understanding of the nature of dark matter, as well as the cluster galaxy dynamics. CL0848+4452, the highest-redshift ( z = 1.27) cluster yet detected in weak-lensing, has a significant discrepancy between the weak- lensing and X-ray masses. If this trend is found to be severe and common also for other X-ray weak clusters at redshifts beyond the unity, the conventional X-ray determination of cluster mass functions, often inferred from their immediate X-ray properties such as the X-ray luminosity and temperature via the so-called mass-luminosity (M-L) and mass-temperature (M-T) relations, will become highly unstable in this redshift regime. Therefore, the relatively unbiased weak-lensing measurements of the cluster mass properties can be used to adequately calibrate the scaling relations in future high-redshift cluster investigations.

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.

Electronic structure and bonding interactions in Ba1- x Sr x Zr0.1Ti0.9O3 ceramics

NASA Astrophysics Data System (ADS)

Mangaiyarkkarasi, Jegannathan; Sasikumar, Subramanian; Saravanan, Olai Vasu; Saravanan, Ramachandran

2017-06-01

An investigation on the precise electronic structure and bonding interactions has been carried out on Ba1- x Sr x Zr0.1Ti0.9O3 (short for BSZT, x = 0, 0.05, 0.07 and 0.14) ceramic systems prepared via high-temperature solid state reaction technique. The influence of Sr doping on the BSZT structure has been examined by characterizing the prepared samples using PXRD, UV-visible spectrophotometry, SEM and EDS. Powder profile refinement of X-ray data confirms that all the synthesized samples have been crystallized in cubic perovskite structure with single phase. Charge density distribution of the BSZT systems has been completely analyzed by the maximum entropy method (MEM). Co-substitution of Sr at the Ba site and Zr at the Ti site into the BaTiO3 structure presents the ionic nature between Ba and O ions and the covalent nature between Ti and O ions, revealed from MEM calculations. Optical band gap values have been evaluated from UV-visible absorption spectra. Particles with irregular shapes and well defined grain boundaries are clearly visualized from SEM images. The phase purity of the prepared samples is further confirmed by EDS qualitative spectral analysis.

Advanced Computational Methods for High-accuracy Refinement of Protein Low-quality Models

NASA Astrophysics Data System (ADS)

Zang, Tianwu

Predicting the 3-dimentional structure of protein has been a major interest in the modern computational biology. While lots of successful methods can generate models with 3˜5A root-mean-square deviation (RMSD) from the solution, the progress of refining these models is quite slow. It is therefore urgently needed to develop effective methods to bring low-quality models to higher-accuracy ranges (e.g., less than 2 A RMSD). In this thesis, I present several novel computational methods to address the high-accuracy refinement problem. First, an enhanced sampling method, named parallel continuous simulated tempering (PCST), is developed to accelerate the molecular dynamics (MD) simulation. Second, two energy biasing methods, Structure-Based Model (SBM) and Ensemble-Based Model (EBM), are introduced to perform targeted sampling around important conformations. Third, a three-step method is developed to blindly select high-quality models along the MD simulation. These methods work together to make significant refinement of low-quality models without any knowledge of the solution. The effectiveness of these methods is examined in different applications. Using the PCST-SBM method, models with higher global distance test scores (GDT_TS) are generated and selected in the MD simulation of 18 targets from the refinement category of the 10th Critical Assessment of Structure Prediction (CASP10). In addition, in the refinement test of two CASP10 targets using the PCST-EBM method, it is indicated that EBM may bring the initial model to even higher-quality levels. Furthermore, a multi-round refinement protocol of PCST-SBM improves the model quality of a protein to the level that is sufficient high for the molecular replacement in X-ray crystallography. Our results justify the crucial position of enhanced sampling in the protein structure prediction and demonstrate that a considerable improvement of low-accuracy structures is still achievable with current force fields.

Modeling Contamination Migration on the Chandra X-ray Observatory II

NASA Technical Reports Server (NTRS)

O'Dell, Steve; Swartz, Doug; Tice, Neil; Plucinsky, Paul; Grant, Catherine; Marshall, Herman; Vikhlinin, Alexey

2013-01-01

During its first 14 years of operation, the cold (about -60degC) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X-ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low-energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition may have changed, perhaps partially related to changes in the operating temperature of the ACIS housing. This evolution of the accumulation of the molecular contamination has motivated further analysis of contamination migration on the Chandra X-ray Observatory, particularly within and near the ACIS cavity. To this end, the current study employs a higher-fidelity geometric model of the ACIS cavity, detailed thermal modeling based upon monitored temperature data, and an accordingly refined model of the molecular transport.

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PubMed Central

Shevchuk, Roman; Hub, Jochen S.

2017-01-01

Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state. PMID:29045407

X-Ray study of hetero ring flexibility in norbornane, norbornene-fused 1,3-oxazin-2-thiones Structure of 5,8-methano- r-4-phenyl-c-4a, c-5,6,7, c-8, c- 8a-hexahydro-4H- 1 ,3-benzoxazin-2 (3H)-thione

NASA Astrophysics Data System (ADS)

Kálmán, A.; Argay, Gy.; Stájer, G.; Bernáth, G.

1991-08-01

The structure of S,8-methano- r-4-phenyl c4a, c5,6,7 c8 c8ahexahydro4 H 1,3 -benzoxazin- 2 (3 H)-thione (C 15H 17N0S, M r=259.37) has been established by X-ray crystallography from diffractometer data: it crystallizes in the monoclinic space group P2 1/n with a=6.150(2) Å, b=9.655(1) Å, c=22.093(4) Å,β=96.75(2)† V=1302.7(8) Å 3,4,D c=1.32gcm -3and p( Cu K) =20.4cm -. The structure has been solved by direct methods, refined to R=0.050 for 2193 observed reflections. The X-ray analysis substantiated the structure: the NMR spectra in- dicated that the 4-phenyl group assumes an exo-equatorial position. The puckering parameters of D. Cremer, J.A. Pople, J. Am. Chem. Soc., 97 (1975), 1354 (ref.1), of the distorted hetero ring (a transitional form between E 4-envelope, ( 5S 4-screw-boat) show that, depending on the positions of the hetero atoms, both the norbornane, norbornene skeletons markedly alter the characteristic transitional ( 5E/ 5H 6) shape of the 1,3-oxazine ring observed in other saturated, partly saturated l,3-benzoxazin-2-ones, analogous thiones.

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

Modeling Contamination Migration on the Chandra X-ray Observatory - II

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Swartz, Douglas A.; Tice, Neil W.; Plucinsky, Paul P.; Grant, Catherine E.; Marshall, Herman L.; Vikhlinin, Alexey A.; Tennant, Allyn F.

2013-01-01

During its first 14 years of operation, the cold (about -60C) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X-ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low-energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition have changed. This evolution has motivated further analysis of contamination migration within and near the ACIS cavity. To this end, the current study employs a higher-fidelity geometric model of the ACIS cavity, detailed thermal modeling based upon temperature data, and a refined model of the molecular transport.

Acanthite–argentite transformation in nanocrystalline silver sulfide and the Ag{sub 2}S/Ag nanoheterostructure

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

Gusev, A. I., E-mail: gusev@ihim.uran.ru; Sadovnikov, S. I.

Nanocrystalline acanthite-structured silver sulfide of the monoclinic structure and a Ag{sub 2}S/Ag nanoheterostructure are produced. The high-temperature X-ray diffraction technique is applied to the in situ study of the (acanthite α-Ag{sub 2}S)–(argentite β-Ag{sub 2}S) phase transformation in nanocrystalline silver sulfide. The crystal structure of argentite is refined, and it is found that the content of vacant sites in the metal sublattice of argentite exceeds 92%. A model of a resistive switch, whose operation is based on the reversible acanthite–argentite transformation in a Ag{sub 2}S/Ag heterostructure, is considered.

The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

DOE PAGES

Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; ...

2015-10-14

Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C 4H 4N 6O 5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication ofmore » a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.« less

La 3+ doping of the Sr 2CoWO 6 double perovskite: A structural and magnetic study

NASA Astrophysics Data System (ADS)

López, C. A.; Viola, M. C.; Pedregosa, J. C.; Carbonio, R. E.; Sánchez, R. D.; Fernández-Díaz, M. T.

2008-11-01

La-doped Sr 2CoWO 6 double perovskites have been prepared in air in polycrystalline form by solid-state reaction. These materials have been studied by X-ray powder diffraction (XRPD), neutron powder diffraction (NPD) and magnetic susceptibility. The structural refinement was performed from combined XRPD and NPD data (D2B instrument, λ=1.594 Å). At room temperature, the replacement of Sr 2+ by La 3+ induces a change of the tetragonal structure, space group I4/ m of the undoped Sr 2CoWO 6 into the distorted monoclinic crystal structure, space group P2 1/ n, Z=2. The structure of La-doped phases contains alternating CoO 6 and (Co/W)O 6 octahedra, almost fully ordered. On the other hand, the replacement of Sr 2+ by La 3+ induces a partial replacement of W 6+ by Co 2+ into the B sites, i.e. Sr 2-xLa xCoW 1-yCo yO 6 ( y= x/4) with segregation of SrWO 4. Magnetic and neutron diffraction measurements indicate an antiferromagnetic ordering below TN=24 K independently of the La-substitution.

Some Structural Properties of the Mixed Lead-Magnesium Hydroxyapatites

NASA Astrophysics Data System (ADS)

Kaaroud, K.; Ben Moussa, S.; Brigui, N.; Badraoui, B.

2018-02-01

Lead-magnesium hydroxyapatite solid solutions Pb(10- x)Mg x (PO4)6(OH)2 have been prepared via a hydrothermal process. They were characterized by X-ray powder diffraction, Transmission Electron Microscopy (TEM), chemical and IR spectroscopic analyses. The results of the structural refinement indicated that the limits of lead-magnesium solid solutions ( x ≤ 1.5), a regular decrease of the lattice constant a and a preferential magnesium distribution in site S(I). Through the progressive replacement of Pb2+ ( r = 0.133 nm) by the smaller cation Mg2+ ( r = 0.072 nm), all interatomic distances decrease in accordance with the decrease of the cell parameters. According to what could be expected from the coordinance of the metallic sites S(I) (hexacoordination) and S(II) (heptacoordination), the small magnesium cation preferentially occupies the four sites S(I). The results of the TEM analysis confirm the presence of magnesium in the starting solution and reveals the decrease in the average size of crystals. The IR spectra show the presence of the absorption bands characteristic for the apatite structure.

Optical and magnetic properties of Co-doped CuO flower/plates/particles-like nanostructures.

PubMed

Basith, N Mohamed; Vijaya, J Judith; Kennedy, L John; Bououdina, M; Hussain, Shamima

2014-03-01

In this study, pure and Co-doped CuO nanostructures (0.5, 1.0, 1.5, and 2.0 at wt% of Co) were synthesized by microwave combustion method. The prepared samples were characterized by X-ray diffraction (XRD), high resolution scanning electron microscopy (HR-SEM), energy dispersive X-ray analysis (EDX), diffuse reflectance spectroscopy (DRS), photoluminescence (PL) spectroscopy and vibrating sample magnetometry (VSM). Powder X-ray diffraction patterns refined by the Rietveld method indicated the formation of single-phase monoclinic structure. The surface morphology and elemental analysis of Co-doped CuO nanostructures were studied by using HR-SEM and EDX. Interestingly, the morphology was found to change considerably from nanoflowers to nanoplates then to nanoparticles with the variation of Co concentration. The optical band gap calculated using DRS was found to be 2.1 eV for pure CuO and increases up to 3.4 eV with increasing cobalt content. Photoluminescence measurements also confirm these results. The magnetic measurements indicated that the obtained nanostructures were ferromagnetic at room temperature with an optimum value of saturation magnetization at 1.0 wt.% of Co-doped CuO, i.e., 970 micro emu/g.

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™.

Anomalous structural disorder and distortion in metal-to-insulator-transition Ti{sub 2}O{sub 3}

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

Hwang, In-Hui; Jin, Zhenlan; Park, Chang-In

2016-01-07

Mott proposed that impurity bands in corundum-symmetry Ti{sub 2}O{sub 3} at high temperatures caused a collapse in the bandgap. However, the origin of the impurity bands has not yet been clarified. We examine the local structural properties of metal-to-insulator-transition Ti{sub 2}O{sub 3} using in-situ x-ray absorption fine structure (XAFS) measurements at the Ti K edge in the temperature range from 288 to 739 K. The Ti{sub 2}O{sub 3} powder is synthesized by using a chemical reaction method. X-ray diffraction (XRD) measurements from Ti{sub 2}O{sub 3} with a Rietveld refinement demonstrate a single-phased R-3c symmetry without additional distortion. Extended-XAFS combined with XRDmore » reveals a zigzag patterned Ti position and an anomalous structural disorder in Ti-Ti pairs, accompanied by a bond length expansion of the Ti-Ti pairs along the c-axis for T > 450 K. The local structural distortion and disorder of the Ti atoms would induce impurity levels in the band gap between the Ti 3d a{sub 1g} and e{sub g}{sup π} bands, resulting in a collapse of the band gap for T > 450 K.« less

Unraveling the Hydrogenation of TiO 2 and Graphene Oxide/TiO 2 Composites in Real Time by in Situ Synchrotron X-ray Powder Diffraction and Pair Distribution Function Analysis

DOE PAGES

Nguyen-Phan, Thuy-Duong; Liu, Zongyuan; Luo, Si; ...

2016-02-18

The functionalization of graphene oxide (GO) and graphene by TiO 2 and other metal oxides has attracted considerable attention due to numerous promising applications in catalysis, energy conversion, and storage. We propose hydrogenation of this class of materials as a promising way to tune catalytic properties by altering the structural and chemical transformations that occur upon H incorporation. We also investigate the structural changes that occur during the hydrogenation process using in situ powder X-ray diffraction and pair distribution function analysis of GO–TiO 2 and TiO 2 under H 2 reduction. Sequential Rietveld refinement was employed to gain insight intomore » the evolution of crystal growth of TiO 2 nanoparticles in the presence of two-dimensional (2D) GO nanosheets. GO sheets not only significantly retarded the nucleation and growth of rutile impurities, stabilizing the anatase structure, but was also partially reduced to hydrogenated graphene by the introduction of atomic hydrogen into the honeycomb lattice. We discuss the hydrogenation processes and the resulting composite structure that occurs during the incorporation of atomic H and the dynamic structural transformations that leads to a highly active photocatalyst.« less

X-ray and gamma-ray line production by nonthermal ions

NASA Technical Reports Server (NTRS)

Bussard, R. W.; Omidvar, K.; Ramaty, R.

1977-01-01

X-ray production was calculated at approximately 6.8 keV by the 2p to 1s transition in fast hydrogen- and helium-like iron ions, following both electron capture to excited levels and collisional excitation. A refinement of the OBK approximation was used to obtain an improved charge exchange cross section. This, and the corresponding ionization cross section were used to determine equilibrium charge fractions for iron ions as functions of their energy. The effective X-ray line production cross section was found to be sharply peaked in energy at about 8 to 12 MeV/amu. Because fast ions of similar energies can also excite nuclear levels, the ratio of selected strong gamma ray line emissivities to the X-ray line emissivity was also calculated. Limits set by this method on the intensity of gamma ray line emission from the galactic center and the radio galaxy Centaurus A are generally lower than those reported in the literature.

Structural and optical properties of NiFe2O4 synthesized via green technology

NASA Astrophysics Data System (ADS)

Patel, S.; Saleem, M.; Varshney, Dinesh

2018-05-01

The nanoparticles of NiFe2O4 were successfully synthesized via green technology using banana peel extract as the catalyst as well as the medium for reaction technique is reported. Analysis of X-ray diffraction spectrum revealed the cubic structure for the prepared spinel ferrite samples crystallized into cubic spinel structure with the space group Fd3m. The Retvield refinement was carried out which obeyed the results obtained from the XRD spectrum analysis of the sample. Raman spectrum provided confirmation for the spinel structure formation and five active Raman modes were observed. Since the optical band-gap value shows inverse response to the crystallite size, The UV-Vis spectrum study confirmed dual but reduced band-gap value.

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.

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.

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.

X-ray structural studies of the fungal laccase from Cerrena maxima.

PubMed

Lyashenko, Andrey V; Bento, Isabel; Zaitsev, Viatcheslav N; Zhukhlistova, Nadezhda E; Zhukova, Yuliya N; Gabdoulkhakov, Azat G; Morgunova, Ekaterina Y; Voelter, Wolfgang; Kachalova, Galina S; Stepanova, Elena V; Koroleva, Ol'ga V; Lamzin, Victor S; Tishkov, Vladimir I; Betzel, Christian; Lindley, Peter F; Mikhailov, Al'bert M

2006-11-01

Laccases are members of the blue multi-copper oxidase family. These enzymes oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and following the transfer of four electrons is reduced to two molecules of water. The X-ray structure of a laccase from Cerrena maxima has been elucidated at 1.9 A resolution using synchrotron data and the molecular replacement technique. The final refinement coefficients are Rcryst = 16.8% and Rfree = 23.0%, with root mean square deviations on bond lengths and bond angles of 0.015 A and 1.51 degrees , respectively. The type 1 copper centre has an isoleucine residue at the axial position and the "resting" state of the trinuclear centre comprises a single oxygen (OH) moiety asymmetrically disposed between the two type 3 copper ions and a water molecule attached to the type 2 ion. Several carbohydrate binding sites have been identified and the glycan chains appear to promote the formation of well-ordered crystals. Two tyrosine residues near the protein surface have been found in a nitrated state.

Structure and colossal dielectric permittivity of Ca2TiCrO6 ceramics

NASA Astrophysics Data System (ADS)

Yan-Qing, Tan; Meng, Yan; Yong-Mei, Hao

2013-01-01

A colossal permittivity ceramic material, Ca2TiCrO6, was successfully synthesized by the conventional solid-state reaction, and was characterized by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), x-ray photoemission spectroscopy (XPS) and x-ray diffraction (XRD). Rietveld refinement of XRD data indicated that the material crystallized in orthorhombic structure with space group pbnm. SEM displayed Ca2TiCrO6 ceramic grains packed uniformly with the size range 5-20 µm. XPS analyses indicated that elemental chromium and titanium of the material were in mixed valence. The corresponding dielectric property was tested in the frequency range 1 kHz-1 MHz and the temperature range 213-453 K, and the ceramics exhibited a relaxation-like dielectric behaviour. Importantly, the permittivity of Ca2TiCrO6 could reach 80 000 at 298 K (100 Hz) and was maintained at 40 000 up to 398 K at 1 MHz, which could be attributed to the ion disorder and mixed valence of Cr3+/Cr6+ and Ti3+/Ti4+.

Extracting the pair distribution function of liquids and liquid-vapor surfaces by grazing incidence x-ray diffraction mode.

PubMed

Vaknin, David; Bu, Wei; Travesset, Alex

2008-07-28

We show that the structure factor S(q) of water can be obtained from x-ray synchrotron experiments at grazing angle of incidence (in reflection mode) by using a liquid surface diffractometer. The corrections used to obtain S(q) self-consistently are described. Applying these corrections to scans at different incident beam angles (above the critical angle) collapses the measured intensities into a single master curve, without fitting parameters, which within a scale factor yields S(q). Performing the measurements below the critical angle for total reflectivity yields the structure factor of the top most layers of the water/vapor interface. Our results indicate water restructuring at the vapor/water interface. We also introduce a new approach to extract g(r), the pair distribution function (PDF), by expressing the PDF as a linear sum of error functions whose parameters are refined by applying a nonlinear least square fit method. This approach enables a straightforward determination of the inherent uncertainties in the PDF. Implications of our results to previously measured and theoretical predictions of the PDF are also discussed.

Equations of state of anhydrous AlF 3 and AlI 3 : Modeling of extreme condition halide chemistry

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

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF 3) and separately, aluminum triiodide (AlI 3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF 3 and AlI 3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. In conclusion, results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Equations of state of anhydrous AlF{sub 3} and AlI{sub 3}: Modeling of extreme condition halide chemistry

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

Stavrou, Elissaios, E-mail: stavrou1@llnl.gov; Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, P.O. Box 808 L-350, Livermore, California 94550; Zaug, Joseph M., E-mail: zaug1@llnl.gov

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF{sub 3}) and separately, aluminum triiodide (AlI{sub 3}) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF{sub 3} and AlI{sub 3} were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Equations of state of anhydrous AlF 3 and AlI 3 : Modeling of extreme condition halide chemistry

DOE PAGES

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; ...

2015-06-04

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF 3) and separately, aluminum triiodide (AlI 3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF 3 and AlI 3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. In conclusion, results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Characterization of tetraethylene glycol passivated iron nanoparticles

NASA Astrophysics Data System (ADS)

Nunes, Eloiza da Silva; Viali, Wesley Renato; da Silva, Sebastião William; Coaquira, José Antonio Huamaní; Garg, Vijayendra Kumar; de Oliveira, Aderbal Carlos; Morais, Paulo César; Jafelicci Júnior, Miguel

2014-10-01

The present study describes the synthesis and characterization of iron@iron oxide nanoparticles produced by passivation of metallic iron in tetraethylene glycol media. Structural and chemical characterizations were performed using transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Mössbauer spectroscopy. Pomegranate-like core@shell nanoparticulate material in the size range of 90-120 nm was obtained. According to quantitative phase analysis using Rietveld structure refinement the synthesized iron oxide was identified as magnetite (Fe3O4) whereas the iron to magnetite mass fractions was found to be 47:53. These findings are in good agreement with the data obtained from Mössbauer and thermal gravimetric analysis (TGA). The XPS data revealed the presence of a surface organic layer with higher hydrocarbon content, possibly due to the tetraethylene glycol thermal degradation correlated with iron oxidation. The room-temperature (300 K) saturation magnetization measured for the as-synthesized iron and for the iron-iron oxide were 145 emu g-1 and 131 emu g-1, respectively. The measured saturation magnetizations are in good agreement with data obtained from TEM, XRD and Mössbauer spectroscopy.

Anchoring the Distance Scale via X-Ray/Infrared Data for Cepheid Clusters: SU Cas

NASA Astrophysics Data System (ADS)

Majaess, D.; Turner, D. G.; Gallo, L.; Gieren, W.; Bonatto, C.; Lane, D. J.; Balam, D.; Berdnikov, L.

2012-07-01

New X-ray (XMM-Newton) and JHKs (Observatoire du Mont-Mégantic) observations for members of the star cluster Alessi 95, which Turner et al. discovered hosts the classical Cepheid SU Cas, were used in tandem with UCAC3 (proper motion) and Two Micron All Sky Survey observations to determine precise cluster parameters: E(J - H) = 0.08 ± 0.02 and d = 405 ± 15 pc. The ensuing consensus among cluster, pulsation, and trigonometric distances (d=414+/- 5(\\sigma _{\\bar{x}}) +/- 10 (\\sigma) pc) places SU Cas in a select group of nearby fundamental Cepheid calibrators (δ Cep, ζ Gem). High-resolution X-ray observations may be employed to expand that sample as the data proved pertinent for identifying numerous stars associated with SU Cas. Acquiring X-ray observations of additional fields may foster efforts to refine Cepheid calibrations used to constrain H 0.

Simultaneous broadband observations and high-resolution X-ray spectroscopy of the transitional millisecond pulsar PSR J1023+0038

NASA Astrophysics Data System (ADS)

Coti Zelati, F.; Campana, S.; Braito, V.; Baglio, M. C.; D'Avanzo, P.; Rea, N.; Torres, D. F.

2018-03-01

We report on the first simultaneous XMM-Newton, NuSTAR, and Swift observations of the transitional millisecond pulsar PSR J1023+0038 in the X-ray active state. Our multi-wavelength campaign allowed us to investigate with unprecedented detail possible spectral variability over a broad energy range in the X-rays, as well as correlations and lags among emissions in different bands. The soft and hard X-ray emissions are significantly correlated, with no lags between the two bands. On the other hand, the X-ray emission does not correlate with the UV emission. We refine our model for the observed mode switching in terms of rapid transitions between a weak propeller regime and a rotation-powered radio pulsar state, and report on a detailed high-resolution X-ray spectroscopy using all XMM-Newton Reflection Grating Spectrometer data acquired since 2013. We discuss our results in the context of the recent discoveries on the system and of the state of the art simulations on transitional millisecond pulsars, and show how the properties of the narrow emission lines in the soft X-ray spectrum are consistent with an origin within the accretion disc.

Ternary germanides RERhGe2 (RE = Y, Gd-Ho) - New representatives of the YIrGe2 type

NASA Astrophysics Data System (ADS)

Voßwinkel, Daniel; Heletta, Lukas; Hoffmann, Rolf-Dieter; Pöttgen, Rainer

2016-11-01

The YIrGe2 type ternary germanides RERhGe2 (RE = Y, Gd-Ho) were synthesized from the elements by arc-melting and characterized by powder X-ray diffraction. The structure of DyRhGe2 was refined from single crystal X-ray diffractometer data: Immm, a = 426.49(9), b = 885.0(2), c = 1577.4(3) pm, wR2 = 0.0533, 637 F2 values, 30 variables (300 K data). The structure contains two crystallographically independent dysprosium atoms in pentagonal prismatic and hexagonal prismatic coordination. The three-dimensional [RhGe2] polyanion is stabilized through covalent Rh-Ge (243-261 pm) and Ge-Ge (245-251 pm) bonding. The close structural relationship with the slightly rhodium-poorer germanides RE5Rh4Ge10 (≡ RERh0.8Ge2) is discussed. Temperature-dependent magnetic susceptibility measurements reveal Pauli paramagnetism for YRhGe2 and Curie-Weiss paramagnetism for RERhGe2 with RE = Gd, Tb, Dy and Ho. These germanides order antiferromagnetically at TN = 7.2(5), 10.6(5), 8.1(5), and 6.4(5) K, respectively.

A structural diagnostics diagram for metallofullerenes encapsulating metal carbides and nitrides.

PubMed

Maki, Sachiko; Nishibori, Eiji; Terauchi, Ikuya; Ishihara, Masayuki; Aoyagi, Shinobu; Sakata, Makoto; Takata, Masaki; Umemoto, Hisashi; Inoue, Takashi; Shinohara, Hisanori

2013-01-16

Systematic structural studies of 24 different kinds of endohedral metallofullerenes, M(x)C(2n) (M = La, Y, Sc, Lu, Ti, Eu, Er, Hf, Sc(3)N; 34 ≤ n ≤ 43), as 1:1 cocrystals with solvent toluene molecules have been carried out using synchrotron radiation powder diffraction. Thirteen of the 24 molecular structures, including five metal carbides, one metal nitride endohedral fullerene, and one hollow fullerene, have been determined by a combination of the maximum entropy method and Rietveld refinement of the X-ray diffraction data obtained. We have found that the volume for one fullerene and one toluene molecule depends linearly on the number of carbon atoms in the fullerene cage. Fifteen different kinds of metal carbide endohedral fullerenes have been identified, which can be structurally characterized from the obtained lattice constants using only this linear dependence. The linear dependence found in the present study provides a metallofullerene diagnostics diagram that may have universal importance for structural characterization of the so-called cluster endohedral fullerenes.

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.

On the Tetragonal Forms of KMo 4O 6

NASA Astrophysics Data System (ADS)

McCarroll, W. H.; Ramanujachary, K. V.; Greenblatt, M.; Marsh, Richard E.

1995-06-01

A reexamination of the X-ray diffraction data for the tetragonal form of KMo4O6 prepared by fused salt electrolysis leads to the conclusion that the crystal structure is better described by using space group P 4/mbm and not P4¯ as previously reported. However, refinement in the new space group does not result in any significant changes in the atomic arrangement. Possible reasons for the significant difference between the c lattice parameter of this form of KMo4O6 and that prepared at high pressures are also discussed.

Synthesis of MAX Phases in the Hf-Al-C System.

PubMed

Lapauw, Thomas; Tunca, Bensu; Cabioc'h, Thierry; Lu, Jun; Persson, Per O Å; Lambrinou, Konstantina; Vleugels, Jozef

2016-11-07

For the first time, MAX phases in the Hf-Al-C system were experimentally synthesized using reactive hot pressing. HfC was observed as the main competing phase. The lattice parameters of Hf 2 AlC and Hf 3 AlC 2 were determined by Rietveld refinement based on the X-ray diffraction data. The atomic stacking sequence was revealed by high-resolution scanning transmission electron microscopy. Mixtures of 211 and 312 stacking were observed within the same grain, including 523 layers. This transition in atomic structure is discussed.

The 15-K neutron structure of saccharide-free concanavalin A.

PubMed

Blakeley, M P; Kalb, A J; Helliwell, J R; Myles, D A A

2004-11-23

The positions of the ordered hydrogen isotopes of a protein and its bound solvent can be determined by using neutron crystallography. Furthermore, by collecting neutron data at cryo temperatures, the dynamic disorder within a protein crystal is reduced, which may lead to improved definition of the nuclear density. It has proved possible to cryo-cool very large Con A protein crystals (>1.5 mm3) suitable for high-resolution neutron and x-ray structure analysis. We can thereby report the neutron crystal structure of the saccharide-free form of Con A and its bound water, including 167 intact D2O molecules and 60 oxygen atoms at 15 K to 2.5-A resolution, along with the 1.65-A x-ray structure of an identical crystal at 100 K. Comparison with the 293-K neutron structure shows that the bound water molecules are better ordered and have lower average B factors than those at room temperature. Overall, twice as many bound waters (as D2O) are identified at 15 K than at 293 K. We note that alteration of bound water orientations occurs between 293 and 15 K; such changes, as illustrated here with this example, could be important more generally in protein crystal structure analysis and ligand design. Methodologically, this successful neutron cryo protein structure refinement opens up categories of neutron protein crystallography, including freeze-trapped structures and cryo to room temperature comparisons.

Amorphous boron gasket in diamond anvil cell research

NASA Astrophysics Data System (ADS)

Lin, Jung-Fu; Shu, Jinfu; Mao, Ho-kwang; Hemley, Russell J.; Shen, Guoyin

2003-11-01

Recent advances in high-pressure diamond anvil cell experiments include high-energy synchrotron x-ray techniques as well as new cell designs and gasketing procedures. The success of high-pressure experiments usually depends on a well-prepared sample, in which the gasket plays an important role. Various gasket materials such as diamond, beryllium, rhenium, and stainless steel have been used. Here we introduce amorphous boron as another gasket material in high-pressure diamond anvil cell experiments. We have applied the boron gasket for laser-heating x-ray diffraction, radial x-ray diffraction, nuclear resonant inelastic x-ray scattering, and inelastic x-ray scattering. The high shear strength of the amorphous boron maximizes the thickness of the sample chamber and increases the pressure homogeneity, improving the quality of high-pressure data. Use of amorphous boron avoids unwanted x-ray diffraction peaks and reduces the absorption of incident and x rays exiting the gasket material. The high quality of the diffraction patterns makes it possible to refine the cell parameters with powder x-ray diffraction data under high pressure and high temperature. The reactivity of boron prevents its use at high temperatures, however. When heated, boron may also react with the specimen to produce unwanted phases. The relatively porous boron starting material at ambient conditions also poses some challenges for sample preparation.

Studies of high temperature ternary phases in mixed-metal-rich early transition metal sulfide and phosphide systems

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

Marking, Gregory Allen

1994-01-04

Investigations of ternary mixed early transition metal-rich sulfide and phosphide systems resulted in the discovery of new structures and new phases. A new series of Zr and Hf - group V transition metal - sulfur K-phases was synthesized and crystallographically characterized. When the group V transition metal was Nb or Ta, the unit cell volume was larger than any previously reported K-phase. The presence of adventitious oxygen was determined in two K-phases through a combination of neutron scattering and X-ray diffraction experiments. A compound Hf 10Ta 3S 3 was found to crystallize in a new-structure type similar to the knownmore » gamma brasses. This structure is unique in that it is the only reported "stuffed" gamma-brass type structure. The metal components, Hf and Ta, are larger in size and more electropositive than the metals found in normal gamma brasses (e.g. Cu and Zn) and because of the larger metallic radii, sulfur can be incorporated into the structure where it plays an integral role in stabilizing this phase relative to others. X-ray single-crystal, X-ray powder and neutron powder refinements were performed on this structure. A new structure was found in the ternary Nb-Zr-P system which has characteristics in common with many known early transition metal-rich sulfides, selenides, and phosphides. This structure has the simplest known interconnection of the basic building blocks known for this structural class. Anomalous scattering was a powerful tool for differentiating between Zr and Nb when using Mo Kα X-radiation. The compounds ZrNbP and HfNbP formed in the space group Prima with the simple Co 2Si structure which is among the most common structures found for crystalline solid materials. Solid solution compounds in the Ta-Nb-P, Ta-Zr-P, Nb-Zr-P, Hf-Nb-P, and Hf-Zr-S systems were crystallographically characterized. The structural information corroborated ideas about bonding in metal-rich compounds.« less

Rhombohedrally Distorted γ-Au 5–x Zn 8+y Phases in the Au–Zn System

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

Thimmaiah, Srinivasa; Miller, Gordon J.

2013-02-04

The region of the Au–Zn phase diagram encompassing γ-brass-type phases has been studied experimentally from 45 to 85 atom % Zn. The γ phases were obtained directly from the pure elements by heating to 680 °C in evacuated silica tubes, followed by annealing at 300 °C. Powder X-ray and single-crystal diffraction studies show that γ-“Au5Zn8” phases adopt a rhombohedrally distorted Cr5Al8 structure type rather than the cubic Cu5Zn8 type. The refined compositions from two single crystals extracted from the Zn- and Au-rich loadings are Au4.27(3)Zn8.26(3)γ0.47 (I) and Au4.58(3)Zn8.12(3)γ0.3 (II), respectively (γ = vacancy). These (I and II) refinements indicated bothmore » nonstatistical mixing of Au and Zn atoms as well as partially ordered vacancy distributions. The structures of these γ phases were solved in the acentric space group R3m (No. 160, Z = 6), and the observed lattice parameters from powder patterns were found to be a = 13.1029(6) and 13.1345(8) Å and c = 8.0410(4) and 8.1103(6) Å for crystals I and II, respectively. According to single-crystal refinements, the vacancies were found on the outer tetrahedron (OT) and octahedron (OH) of the 26-atom cluster. Single-crystal structural refinement clearly showed that the vacancy content per unit cell increases with increasing Zn, or valence-electron concentration. Electronic structure calculations, using the tight-binding linear muffin-tin orbital method with the atomic-sphere approximation (TB-LMTO-ASA) method, indicated the presence of a well-pronounced pseudogap at the Fermi level for “Au5Zn8” as the representative composition, an outcome that is consistent with the Hume–Rothery interpretation of γ brass.« less

Single-crystal growth, structure refinement and the properties of Bis(glycine) Strontium Chloride

NASA Astrophysics Data System (ADS)

Balaji, S. R.; Balu, T.; Rajasekaran, T. R.

2018-02-01

Single crystals of Bis (glycine) Strontium Chloride (BGSC) were grown by means of slow evaporation process by using analar grade Glycine and Strontium Chloride Hexahydrate as a parent compound from its aqueous solution at room temperature. The final chemical composition, [{{Sr}}{({{{C}}}2{{{H}}}5{{{NO}}}2)}2{{{Cl}}}2].{{{H}}}4{{{O}}}3+{{{H}}}8{{{O}}}3, formed were metallic light colorless block, about the size of 28 mm × 9 mm × 8 mm. A single-crystal x-ray diffraction study revealed an ordered superstructure with orthorhombic symmetry that could be assigned to the space group Pbcn. The structure in BGSC, revealed in the electron density distribution was analyzed by the direct methods (SHELXS-2014) and refined by least squares full matrix method (SHELXL-2014). The crystal structure, including anisotropic atomic displacement parameters for each atom and isotropic atomic displacement parameters for hydrogen atom, was refined to R1 = 0.0395, wR2 = 0.0776 using 1097 independent reflections. The FTIR spectrum of BGSC confirms the protonation of amino groups and the different molecular groups present in BGSC vibrate in different modes. Reverse Indentation Size Effect (RISE) was revealed in BGSC in the micro-hardness analysis using Vicker’s micro-hardness analysis. DTA and DSC results ruled out the possibility of structural change independent of mass change. The AFM studies shows fine nano size fiber like structure of the grown crystals.

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

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Next Generation X-Ray Optics: High-Resolution, Light-Weight, and Low-Cost

NASA Technical Reports Server (NTRS)

Zhang, William W.

2012-01-01

X-ray telescopes are essential to the future of x-ray astronomy. In this talk I will describe a comprehensive program to advance the technology for x-ray telescopes well beyond the state of the art represented by the three currently operating missions: Chandra, XMM-Newton, and Suzaku. This program will address the three key issues in making an x-ray telescope: (1) angular resolution, (2) effective area per unit mass, and (3) cost per unit effective area. The objectives of this technology program are (1) in the near term, to enable Explorer-class x-ray missions and an IXO-type mission, and (2) in the long term, to enable a flagship x-ray mission with sub-arcsecond angular resolution and multi-square-meter effective area, at an affordable cost. We pursue two approaches concurrently, emphasizing the first approach in the near term (2-5 years) and the second in the long term (4-10 years). The first approach is precision slumping of borosilicate glass sheets. By design and choice at the outset, this technique makes lightweight and low-cost mirrors. The development program will continue to improve angular resolution, to enable the production of 5-arcsecond x-ray telescopes, to support Explorer-class missions and one or more missions to supersede the original IXO mission. The second approach is precision polishing and light-weighting of single-crystal silicon mirrors. This approach benefits from two recent commercial developments: (1) the inexpensive and abundant availability of large blocks of monocrystalline silicon, and (2) revolutionary advances in deterministic, precision polishing of mirrors. By design and choice at the outset, this technique is capable of producing lightweight mirrors with sub-arcsecond angular resolution. The development program will increase the efficiency and reduce the cost of the polishing and the light-weighting processes, to enable the production of lightweight sub-arcsecond x-ray telescopes. Concurrent with the fabrication of lightweight mirror segments is the continued development and perfection of alignment and integration techniques, for incorporating individual mirror segments into a precision mirror assembly. Recently, we have been developing a technique called edge-bonding, which has achieved an accuracy to enable 10-arcsecond x-ray telescopes. Currently, we are investigating and improving the long-term alignment stability of so-bonded mirrors. Next, we shall refine this process to enable 5-arsecond x-ray telescopes. This technology development program includes all elements to demonstrate progress toward TRL-6: metrology; x-ray performance tests; coupled structural, thermal, and optical performance analysis, and environmental testing.

Next Generation X-Ray Optics: High-Resolution, Light-Weight, and Low-Cost

NASA Technical Reports Server (NTRS)

Zhang, William W.

2011-01-01

X-ray telescopes are essential to the future of x-ray astronomy. This paper describes a comprehensive program to advance the technology for x-ray telescopes well beyond the state of the art represented by the three currently operating missions: Chandra, XMM-Newton , and Suzaku . This program will address the three key issues in making an x-ray telescope: (I) angular resolution, (2) effective area per unit mass, and (3) cost per unit effective area. The objectives of this technology program are (1) in the near term, to enable Explorer-class x-ray missions and an IXO type mission, and (2) in the long term, to enable a flagship x-ray mission with sub-arcsecond angular resolution and multi-square-meter effective area, at an affordable cost. We pursue two approaches concurrently, emphasizing the first approach in the near term (2-5 years) and the second in the long term (4-10 years). The first approach is precision slumping of borosilicate glass sheets. By design and choice at the outset, this technique makes lightweight and low-cost mirrors. The development program will continue to improve angular resolution, to enable the production of 5-arcsecond x-ray telescopes, to support Explorer-class missions and one or more missions to supersede the original IXO mission. The second approach is precision polishing and light-weighting of single-crystal silicon mirrors. This approach benefits from two recent commercial developments: (1) the inexpensive and abundant availability of large blocks of mono crystalline silicon, and (2) revolutionary advances in deterministic, precision polishing of mirrors. By design and choice at the outset, this technique is capable of producing lightweight mirrors with sub-arcsecond angular resolution. The development program will increase the efficiency and reduce the cost of the polishing and the lightweighting processes, to enable the production of lightweight sub-arcsecond x-ray telescopes. Concurrent with the fabrication of lightweight mirror segments is the continued development and perfection of alignment and integration techniques, for incorporating individual mirror segments into a precision mirror assembly. Recently, we have been developing a technique called edge-bonding, which has achieved an accuracy to enable 10- arcsecond x-ray telescopes. Currently, we are investigating and improving the long-term alignment stability of so-bonded mirrors. Next, we shall refine this process to enable 5-arsecond x-ray telescopes. This technology development program includes all elements to demonstrate progress toward TRL-6: metrology; x-ray performance tests; coupled structural, thermal, and optical performance analysis, and environmental testing.

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.

Transferability of electronic structure of four energetic materials by using single crystal and high resolution X-ray diffraction experiments

NASA Astrophysics Data System (ADS)

Chen, Yu-Sheng

The electronic structures of four energetic materials, trinitrodiazapentalene (C6H3N5O6, TNDAP), beta-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (C4H8N8O8, beta-HMX), 1,3,3-trinitroazetidine (C3H4N4O6, TNAZ), and hexahydro-1,3,5-trinitro-1,3,5-s-triazine (C3H6N6O6, RDX), have been analyzed using Hansen-Coppens multipole refinements, using high resolution X-ray diffraction data collected at low temperature, as well as from theoretical calculated structure factors from the solid state phase using density functional theory (DFT), plus B3LYP level theory, and the 6-31G* basis set. However, when comparing both the deformation density and the electrostatic potentials from the theoretical results in TNDAP and TNAZ, they disagree with the experimental results. Therefore, those results have been deposited in appendices A4 and A6, for future reference. In HMX and RDX the theoretical results are in good agreement with experimental results. The physical properties derived from the electronic structure in these four energetic materials, such as multipole populations, the values of the electron density and its Laplacian of the electron density at the bond critical points, have also been calculated using "Atoms in Molecules" (AIM) theory both from the solid state phase calculation, and the experiment, as well as directly calculated from the free molecule in the gas phase. The electron density and the magnitude of its Laplacian from the gas phase are always larger than for the solid state phase calculation and the experiment. This may be due to the packing effect. The transferability of the experimental electronic structure of the NO 2 groups from HMX to TNDAP, TNAZ and RDX are also presented here. Even though the major populated multipoles are robust (small e.s.d.'s), these are few in number, compared with other lower populated multipoles for which the populations span a larger range. Since the deformation electron density distributions are reconstructed using linear combinations of the multipoles, it is necessary to give more degrees of freedom in the refinements. Therefore, those electron density distributions which have a wider range of the multipole populations should not be fixed in the refinements. Utilizing the same coordinate system setup in the multipole refinements of the functional groups, this system can be used as a starting point for solving the charge distribution of a larger system.

Two-dimensional time-resolved X-ray diffraction study of liquid/solid fraction and solid particle size in Fe-C binary system with an electrostatic levitator furnace

NASA Astrophysics Data System (ADS)

Yonemura, M.; Okada, J.; Watanabe, Y.; Ishikawa, T.; Nanao, S.; Shobu, T.; Toyokawa, H.

2013-03-01

Liquid state provides functions such as matter transport or a reaction field and plays an important role in manufacturing processes such as refining, forging or welding. However, experimental procedures are significantly difficult for an observation of solidification process of iron and iron-based alloys in order to identify rapid transformations subjected to fast temperature evolution. Therefore, in order to study the solidification in iron and iron-based alloys, we considered a combination of high energy X-ray diffraction measurements and an electrostatic levitation method (ESL). In order to analyze the liquid/solid fraction, the solidification of melted spherical specimens was measured at a time resolution of 0.1 seconds during rapid cooling using the two-dimensional time-resolved X-ray diffraction. Furthermore, the observation of particle sizes and phase identification was performed on a trial basis using X-ray small angle scattering with X-ray diffraction.

Non Destructive 3D X-Ray Imaging of Nano Structures & Composites at Sub-30 NM Resolution, With a Novel Lab Based X-Ray Microscope

DTIC Science & Technology

2006-11-01

NON DESTRUCTIVE 3D X-RAY IMAGING OF NANO STRUCTURES & COMPOSITES AT SUB-30 NM RESOLUTION, WITH A NOVEL LAB BASED X- RAY MICROSCOPE S H Lau...article we describe a 3D x-ray microscope based on a laboratory x-ray source operating at 2.7, 5.4 or 8.0 keV hard x-ray energies. X-ray computed...tomography (XCT) is used to obtain detailed 3D structural information inside optically opaque materials with sub-30 nm resolution. Applications include

X-ray and optical observations of four polars

NASA Astrophysics Data System (ADS)

Worpel, H.; Schwope, A. D.; Granzer, T.; Reinsch, K.; Schwarz, R.; Traulsen, I.

2016-08-01

Aims: We investigate the temporal and spectral behaviour of four polar cataclysmic variables from the infrared to X-ray regimes, refine our knowledge of the physical parameters of these systems at different accretion rates, and search for a possible excess of soft X-ray photons. Methods: We obtained and analysed four XMM-Newton X-ray observations of three of the sources, two of them discovered with the SDSS and one in the RASS. The X-ray data were complemented by optical photometric and spectroscopic observations and, for two sources, archival Swift observations. Results: SDSSJ032855.00+052254.2 was X-ray bright in two XMM-Newton and two Swift observations, and shows transitions from high and low accretion states on a timescale of a few months. The source shows no significant soft excess. We measured the magnetic field strength at the main accreting pole to be 39 MG and the inclination to be 45° ≤ I ≤ 77°, and we refined the long-term ephemeris. SDSSJ133309.20+143706.9 was X-ray faint. We measured a faint phase X-ray flux and plasma temperature for this source, which seems to spend almost all of its time accreting at a low level. Its inclination is less than about 76°. 1RXSJ173006.4+033813 was X-ray bright in the XMM-Newton observation. Its spectrum contained a modest soft blackbody component, not luminous enough to be considered a significant soft excess. We inferred a magnetic field strength at the main accreting pole of 20 to 25 MG, and that the inclination is less than 77° and probably less than 63°. V808 Aur, also known as CSS081231:J071126+440405, was X-ray faint in the Swift observation, but there is nonetheless strong evidence for bright and faint phases in X-rays and perhaps in UV. Residual X-ray flux from the faint phase is difficult to explain by thermal emission from the white dwarf surface, or by accretion onto the second pole. We present a revised distance estimate of 250 pc. Conclusions: The three systems we were able to study in detail appear to be normal polars with luminosities and magnetic field strengths typical for this class of accreting binary. None of the four systems studied shows the strong soft excess thought commonplace in polars prior to the XMM-Newton era. Based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member States and NASA.Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).

Structural investigation of Y1-xNixBa2Cu3O7-δ superconductor

NASA Astrophysics Data System (ADS)

Hadi-Sichani, Behnaz; Shakeripour, Hamideh; Salamati, Hadi

2018-07-01

Y1-xNixBa2Cu3O7-δ superconducting samples with 0 ≤ x ≤ 0.02 were synthesized by standard solid-state reaction and characterized by the X-ray powder diffraction technique. The Rietveld fitted XRD refinements show that all samples are crystallized in single phase, having orthorhombic structure with Pmmm space group. We investigated the effect of adding a magnetic element on the structure of this superconductor. The c cell parameter increases by doping of Ni until to an optimal value of Ni content, x ∼ 0.004, and then starts to decrease by higher value of Ni substitution. Moreover, it is seen that Cu(2)sbnd O(2) bond length decreases with increasing Ni up to the optimal concentration of Ni, too. The CuO2 planes become more distorted and hence charge carriers may have better chances of transportation to the CuO2 planes. By further increasing of Ni content than the optimal value, the Cu(2)sbnd O(2) bond lengths start to increase, and cause CuO2 planes to be flatten. We suggest, besides affecting the magnetic characteristic of Ni impurity, the Ni substitution leads to interesting crystallographic changes.

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.

Synchrotron hard X-ray imaging of shock-compressed metal powders

NASA Astrophysics Data System (ADS)

Rutherford, Michael E.; Chapman, David J.; Collinson, Mark A.; Jones, David R.; Music, Jasmina; Stafford, Samuel J. P.; Tear, Gareth R.; White, Thomas G.; Winters, John B. R.; Drakopoulos, Michael; Eakins, Daniel E.

2015-06-01

This poster will present the application of a new, high-energy (50 to 250 keV) synchrotron X-ray radiography technique to the study of shock-compressed granular materials. Following plate-impact loading, transmission radiography was used to quantitatively observe the compaction and release processes in a range of high-Z metal powders (e.g. Fe, Ni, Cu). By comparing the predictions of 3D numerical models initialized from X-ray tomograms-captured prior to loading-with experimental results, this research represents a new approach to refining mesoscopic compaction models. The authors gratefully acknowledge the ongoing support of Imperial College London, EPSRC, STFC and the Diamond Light Source, and AWE Plc.

Applied Crystallography - Proceedings of the XVth Conference

NASA Astrophysics Data System (ADS)

Morawiec, H.; Ströż, D.

1993-06-01

The Table of Contents for the full book PDF is as follows: * Foreword * The International Centre for Diffraction Data and Its Future Developments * The Rietveld Method - A Historical Perspective * Real Structure in Quantitative Powder Diffraction Phase Analysis * Neutron Focusing Optics in Applied Crystallography * The Crystal Structures of Oxygen Deficient Rare Earth Oxides * Short-Range Order in Layer-Structured Ba1-xSrxBi2Nb2O9 Ferroelectrics * Radial Distribution Function as a Tool of Structural Studies on Noncrystalline Materials * Determination of Radial Distribution Function (RDF) of Electrodeposited Cu-Cd Alloys After Annealing * Spheres Packing as a Factor Describing the Local Environment and Structure Stability * X-Ray Stress Measurement of Samples Combined with Diffraction Line Analysis * Phase Stability and Martensitic Transformation in Cu-Zn and Cu-Zn-Al Single Crystals * Order, Defects, Precipitates and the Martensitic Transformation in β Cu-Zn-Al * Effect of γ Precipitates on the Martensitic Transformation in Cu-Zn-Al Alloys * Phase Transitions and Shape Memory Effect in a Thermomechanically Treated NiTi Alloy * Structure of Martensite and Bainite in CuAlMn Alloys * Glass-Ceramics * Mechanism of Texture Formation at the Rolling of Low Stacking Fault Energy Metals and Alloys * Shear Texture of Zinc and the Conditions of Its Occuring * The Development of Texture of ZnAlMg Sheets Depending on Deformation Geometry * Texture Stability of the D.S. NiAlMoCrTi Alloy After Heat Treatment * X-Ray Diffraction Method for Controlling of Texture Evolution in Layers * Texture and Lattice Imperfections Study of Some Low Alloyed Copper Alloys * Selected Examples of the Calculation of the Orientation Distribution Function for Low Crystal and Sample Symmetries * Automatical X-Ray Quantitative Phase Analysis * Application of a PC Computer for Crystallographic Calculations * Electron Diffraction Analysis using a Personal Computer * CA.R.INE Crystallography Version 2.1-1992 * PC-MINREF: The Computer Program Package for Neutron Refinement of Incommensurate Multiphase Crystal and Magnetic Structures on IBM PC Computers * Possibilities of Deflections from Stoichiometry Investigation for Phases of b1-b37 Structure by X-Ray Method * A Computer Program: “Measurement of Elastic Constants of Phases in Nontextured Polycrystalline Materials by X-Ray Method” * Crystallite Sizes and Lattice Strains of Hydrogenatid Tungsten Carbid Powder * The Bragg-Case Images of Dislocations at Different Absorption * Extended X-Ray Bremsstrahlung Isochromat of Molybdenum * Size Distribution Determination of Heterogeneity Regions in Electrodeposited Metals by Saxs Method * The Possibility of the Application of the CH2I2 - Paraffin Oil Mixture as a Masking Liquid for Metal/Carrier Systems in Saxs Investigations * Investigation on Mechanical Alloying and Amorphisation Processes by the Rietveld Method * Growth of β' Phase Single Crystals of Sn-Sb Alloy * Effect of Oxygen Agglomeration on Structure of Annealed Cz-Si Single Crystal * X-Ray Investigation of Non-Uniform Stress Fields * Problem of Polytype Structures Series for Martensitic Phases of Metals and Alloys * Structure of Strain-Induced Martensite in β-CuZnAl Alloy * The Effect of Heat Treatment on the Phase Transitions in NiTiCo Shape Memory Alloy * 9R → 18R Phase Transformation in Cu-13Zn-8Al Alloy * Effect of Austenite Thermal Instability on Characteristics of Martensitic Transformation in Fe-Ni Alloys * Vacuum Annealing Study of Thin Ti Layers on High Carbon Steel Substrates * Vacuum Annealing Study of Thin Ta Layers on High Carbon Steel Substrates * Investigation of Speed of Ionic Sputtering of NiTi Alloys in Sea 02 Auger Spectrometer * Effect of Precipitation Hardening on Thermal Stability of Austenite in Fe-Ni Alloys * Structure of 18Cr-25Ni-Nb L Steel After Two Years Operation in Catalytic Tubes * Influence of Magnetic Field on Mechanical Barkhausen Effect Stress Dependence in Steel * Precipitation Structure in High Strength Aluminium Alloys * Morphology of Laser Treated Al-Zn and Al-Fe Alloys * Structure of Rapidly Solidified AlFe and AlFeNi Ribbons After Continuous Heating * X-Ray Diffractometric Investigations of Anatase—Rutile Titanium Dioxide Forms Transformation in the Presence of Some Additives * Investigations on Phase Transformation of Coprecipitated Iron-Magnesium Hydroxides * Determination of the Crystallinity of Polymer Blends by X-Ray Diffraction Method * XPD Study of the Selected Magnesium Compounds with the Expected Pharmacological Activity * Supermolecular Structure of the Nylon 6.10 Crystallized from the Melt and Its Changes During Heating * The Analysis of Substructural Parameters of PZT-Type Ferroelectric Ceramics

Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.

PubMed Central

Hummer, G; García, A E; Soumpasis, D M

1995-01-01

A computationally efficient method to describe the organization of water around solvated biomolecules is presented. It is based on a statistical mechanical expression for the water-density distribution in terms of particle correlation functions. The method is applied to analyze the hydration of small nucleic acid molecules in the crystal environment, for which high-resolution x-ray crystal structures have been reported. Results for RNA [r(ApU).r(ApU)] and DNA [d(CpG).d(CpG) in Z form and with parallel strand orientation] and for DNA-drug complexes [d(CpG).d(CpG) with the drug proflavine intercalated] are described. A detailed comparison of theoretical and experimental data shows positional agreement for the experimentally observed water sites. The presented method can be used for refinement of the water structure in x-ray crystallography, hydration analysis of nuclear magnetic resonance structures, and theoretical modeling of biological macromolecules such as molecular docking studies. The speed of the computations allows hydration analyses of molecules of almost arbitrary size (tRNA, protein-nucleic acid complexes, etc.) in the crystal environment and in aqueous solution. Images FIGURE 1 FIGURE 2 FIGURE 5 FIGURE 6 FIGURE 9 FIGURE 12 FIGURE 13 PMID:7542034

Electronic and Crystalline Structure, Magnetic Response, and Optical Characterization of Rare-Earth Ruthenate Sr2HoRuO6

NASA Astrophysics Data System (ADS)

Velásquez Moya, X. A.; Cardona, R.; Villa Hernández, J. I.; Landínez Téllez, D. A.; Roa-Rojas, J.

2018-03-01

Sr2HoRuO6 ceramic has been synthesized and its structural, morphological, magnetic, optical, and electronic properties studied. Rietveld refinement of x-ray diffraction patterns revealed that this oxide material crystallizes in monoclinic perovskite structure in space group P2 1 /n (no. 14). Scanning electron microscopy revealed polycrystalline surface morphology. x-Ray dispersive spectroscopy suggested that Sr2HoRuO6 was obtained with expected stoichiometry. Magnetic susceptibility curves as a function of temperature revealed ferrimagnetic feature of this material below the Néel temperature T N of 14 K. Evidence of magnetic disorder was provided by the irreversibility observed in the zero-field-cooled and field-cooled responses of the susceptibility below T irr = 169 K. Analysis of the diffuse reflectance spectrum suggested that this material behaves as a semiconductor with energy gap E g of 1.38 eV. Results of band structure and density-of-states calculations are in agreement with the interpretation of Sr2HoRuO6 as a semiconductor. The ferrimagnetic behavior is interpreted as due to exchange mechanisms of d-f (Ru-O-Ho) electrons. The effective magnetic moment calculated from density functional theory was 93.5% of the experimental value obtained from Curie-Weiss fitting of the susceptibility curve.

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.

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.

Crystallization and preliminary X-ray diffraction analysis of mouse galectin-4 N-terminal carbohydrate recognition domain in complex with lactose

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

Krejčiříková, Veronika; Fábry, Milan; Marková, Vladimíra

2008-07-01

Mouse galectin-4 carbohydrate binding domain was overexpressed in E. coli and crystallized in the presence of lactose. The crystals belong to tetragonal space group P42{sub 1}2 and diffraction data were collected to 2.1 Å resolution. Galectin-4 is thought to play a role in the process of tumour conversion of cells of the alimentary tract and the breast tissue; however, its exact function remains unknown. With the aim of elucidating the structural basis of mouse galectin-4 (mGal-4) binding specificity, we have undertaken X-ray analysis of the N-terminal domain, CRD1, of mGal-4 in complex with lactose (the basic building block of knownmore » galectin-4 carbohydrate ligands). Crystals of CRD1 in complex with lactose were obtained using vapour-diffusion techniques. The crystals belong to tetragonal space group P42{sub 1}2 with unit-cell parameters a = 91.1, b = 91.16, c = 57.10 Å and preliminary X-ray diffraction data were collected to 3.2 Å resolution. An optimized crystallization procedure and cryocooling protocol allowed us to extend resolution to 2.1 Å. Structure refinement is currently under way; the initial electron-density maps clearly show non-protein electron density in the vicinity of the carbohydrate binding site, indicating the presence of one lactose molecule. The structure will help to improve understanding of the binding specificity and function of the potential colon cancer marker galectin-4.« less

Structural and Microstructural Correlations of Physical Properties in Natural Almandine-Pyrope Solid Solution: Al70Py29

NASA Astrophysics Data System (ADS)

Sibi, N.; Subodh, G.

2017-12-01

Garnets are naturally occurring minerals with the general formula X3Y2Z3O12 having various applications. In the present study, the structural and physical properties of a garnet mineral obtained from Indian Rare Earth Ltd., Manavalakurichi, Tamil Nadu, India were comprehensively investigated. The compositional analysis using electron probe micro analysis (EPMA) revealed that the mineral belongs to almandine-pyrope solid solution (Al70Py29) with the chemical formula (Fe1.72Mg0.8Mn0.01Ca0.02) (Fe0.04Al2.36) Si2.93O12. Rietveld refinement of the x-ray diffraction pattern confirms that the space group is Ia{ - }\\overline{3} d with refined cubic lattice parameter a = 11.550(4) Å. The refined occupancy values of multiple cations in the dodecahedral and octahedral sites are in agreement with the EPMA data. Fourier transform infrared and FT Raman spectra show bands corresponding to almandine-pyrope solid solution. Peak splitting of IR and Raman bands confirms presence of multiple cations in the dodecahedral site. Thermogravimetric/differential thermal analysis shows that the mineral is stable up to 600°C in spite of the presence of Fe2+ ions. Low temperature magnetic susceptibility data is in agreement with the amount of Fe2+ ions present in the mineral. The dielectric constant of the mineral varied from 6 to 16.5 when sintered at temperatures ranging from 600°C to 1250°C.

Finite element analyses of thin film active grazing incidence x-ray optics

NASA Astrophysics Data System (ADS)

Davis, William N.; Reid, Paul B.; Schwartz, Daniel A.

2010-09-01

The Chandra X-ray Observatory, with its sub-arc second resolution, has revolutionized X-ray astronomy by revealing an extremely complex X-ray sky and demonstrating the power of the X-ray window in exploring fundamental astrophysical problems. Larger area telescopes of still higher angular resolution promise further advances. We are engaged in the development of a mission concept, Generation-X, a 0.1 arc second resolution x-ray telescope with tens of square meters of collecting area, 500 times that of Chandra. To achieve these two requirements of imaging and area, we are developing a grazing incidence telescope comprised of many mirror segments. Each segment is an adjustable mirror that is a section of a paraboloid or hyperboloid, aligned and figure corrected in situ on-orbit. To that end, finite element analyses of thin glass mirrors are performed to determine influence functions for each actuator on the mirrors, in order to develop algorithms for correction of mirror deformations. The effects of several mirror mounting schemes are also studied. The finite element analysis results, combined with measurements made on prototype mirrors, will be used to further refine the correction algorithms.

From the X-rays to a reliable “low cost” computational structure of caffeic acid: DFT, MP2, HF and integrated molecular dynamics-X-ray diffraction approach to condensed phases

NASA Astrophysics Data System (ADS)

Lombardo, Giuseppe M.; Portalone, Gustavo; Colapietro, Marcello; Rescifina, Antonio; Punzo, Francesco

2011-05-01

The ability of caffeic acid to act as antioxidant against hyperoxo-radicals as well as its recently found therapeutic properties in the treatment of hepatocarcinoma, still make this compound, more than 20 years later the refinement of its crystal structure, object of study. It belongs to the vast family of humic substances, which play a key role in the biodegradation processes and easily form complexes with ions widely diffused in the environment. This class of compounds is therefore interesting for potential environmental chemistry applications concerning the possible complexation of heavy metals. Our study focused on the characterization of caffeic acid as a starting necessary step, which will be followed in the future by the application of our findings on the study of the properties of caffeate anion interaction with heavy metal ions. To reach this goal, we applied a low cost approach - in terms of computational time and resources - aimed at the achievement of a high resolution, robust and trustable structure using the X-ray single crystal data, recollected with a higher resolution, as touchstone for a detailed check. A comparison between the calculations carried out with density functional theory (DFT), Hartree-Fock (HF) method and post SCF second order Møller-Plesset perturbation method (MP2), at the 6-31G ** level of the theory, molecular mechanics (MM) and molecular dynamics (MD) was performed. As a consequence we explained on one hand the possible reasons for the pitfalls of the DFT approach and on the other the benefits of using a good and robust force field developed for condensed phases, as AMBER, with MM and MD. The reliability of the latter, highlighted by the overall agreement extended up to the anisotropic displacement parameters calculated by means of MD and the ones gathered by X-ray measurements, makes it very promising for the above-mentioned goals.

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR

PubMed Central

Macpherson, Alex; Smith-Penzel, Susanne; Basse, Nicolas; Lecomte, Fabien; Deboves, Hervé; Taylor, Richard D.; Norman, Tim; Porter, John; Waters, Lorna C.; Westwood, Marta; Cossins, Ben; Cain, Katharine; White, James; Griffin, Robert; Prosser, Christine; Kelm, Sebastian; Sullivan, Amy H.; Fox, David; Carr, Mark D.; Henry, Alistair; Taylor, Richard; Meier, Beat H.; Oschkinat, Hartmut; Lawson, Alastair D.

2018-01-01

Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)–Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and β2-microglobulin (β2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to β2m, both of which participate in the FcRnECD–IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns. PMID:29782488

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR.

PubMed

Stöppler, Daniel; Macpherson, Alex; Smith-Penzel, Susanne; Basse, Nicolas; Lecomte, Fabien; Deboves, Hervé; Taylor, Richard D; Norman, Tim; Porter, John; Waters, Lorna C; Westwood, Marta; Cossins, Ben; Cain, Katharine; White, James; Griffin, Robert; Prosser, Christine; Kelm, Sebastian; Sullivan, Amy H; Fox, David; Carr, Mark D; Henry, Alistair; Taylor, Richard; Meier, Beat H; Oschkinat, Hartmut; Lawson, Alastair D

2018-05-01

Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and β2-microglobulin (β2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to β2m, both of which participate in the FcRnECD-IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns.

Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument

DOEpatents

Shu, Deming; Shvydko, Yuri; Stoupin, Stanislav A.; Khachatryan, Ruben; Goetze, Kurt A.; Roberts, Timothy

2015-04-14

A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Cunsolo, A; Rossky, Peter J

2014-01-21

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm(-1). At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm(-1) para-hydrogen provides a test case for improved approximations to quantum dynamics.

Automated MAD and MIR structure solution

PubMed Central

Terwilliger, Thomas C.; Berendzen, Joel

1999-01-01

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations. PMID:10089316

X-Ray Structure determination of the Glycine Cleavage System Protein H of Mycobacterium tuberculosis Using An Inverse Compton Synchrotron X-Ray Source

PubMed Central

Abendroth, Jan; McCormick, Michael S.; Edwards, Thomas E.; Staker, Bart; Loewen, Roderick; Gifford, Martin; Rifkin, Jeff; Mayer, Chad; Guo, Wenjin; Zhang, Yang; Myler, Peter; Kelley, Angela; Analau, Erwin; Hewitt, Stephen Nakazawa; Napuli, Alberto J.; Kuhn, Peter; Ruth, Ronald D.; Stewart, Lance J.

2010-01-01

Structural genomics discovery projects require ready access to both X-ray and NMR instrumentation which support the collection of experimental data needed to solve large numbers of novel protein structures. The most productive X-ray crystal structure determination laboratories make extensive frequent use of tunable synchrotron X-ray light to solve novel structures by anomalous diffraction methods. This requires that frozen cryo-protected crystals be shipped to large government-run synchrotron facilities for data collection. In an effort to eliminate the need to ship crystals for data collection, we have developed the first laboratory-scale synchrotron light source capable of performing many of the state-of-the-art synchrotron applications in X-ray science. This Compact Light Source is a first-in-class device that uses inverse Compton scattering to generate X-rays of sufficient flux, tunable wavelength and beam size to allow high-resolution X-ray diffraction data collection from protein crystals. We report on benchmarking tests of X-ray diffraction data collection with hen egg white lysozyme, and the successful high-resolution X-ray structure determination of the Glycine cleavage system protein H from Mycobacterium tuberculosis using diffraction data collected with the Compact Light Source X-ray beam. PMID:20364333

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

Synthesis, crystal structure and spectroscopy properties of Na 3AZr(PO 4) 3 ( A=Mg, Ni) and Li 2.6Na 0.4NiZr(PO 4) 3 phosphates

NASA Astrophysics Data System (ADS)

Chakir, M.; El Jazouli, A.; de Waal, D.

2006-06-01

Na 3AZr(PO 4) 3 ( A=Mg, Ni) phosphates were prepared at 750 °C by coprecipitation route. Their crystal structures have been refined at room temperature from X-ray powder diffraction data using Rietveld method. Li 2.6Na 0.4NiZr(PO 4) 3 was synthesized through ion exchange from the sodium analog. These materials belong to the Nasicon-type structure. Raman spectra of Na 3AZr(PO 4) 3 ( A=Mg, Ni) phosphates present broad peaks in favor of the statistical distribution in the sites around PO 4 tetrahedra. Diffuse reflectance spectra indicate the presence of octahedrally coordinated Ni 2+ ions.

Structure elucidation of 3-[1-(6-methoxy-2-naphtyl)ethyl]-6-(2,4-dichlorophenyl)-7H-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazine, C 23H 18Cl 2N 4OS from synchrotron X-ray powder diffraction

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

Gündoğdu, Gülsüm; Aytaç, Sevim Peri; Müller, Melanie

The 3-[1-(6-methoxy-2-naphtyl)ethyl]-6-(2,4-dichlorophenyl)-7H-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazine, C 23H 18Cl 2N 4OS compound was synthesized, as a member of the family of novel potential anticancer agents. The structure of the title compound was characterized by IR, 1H-NMR, mass spectroscopy, and elemental analysis, previously. In this study, the crystal structure of this compound has been determined from synchrotron X-ray powder diffraction data. The crystal structure was solved by simulated annealing and the final structure was achieved by Rietveld refinement method using soft restrains on all interatomic bond lengths and angles. This compound crystallizes in space groupP21,Z= 2, with the unit-cell parametersa= 15.55645(11) Å,b= 8.61693(6) Å,c= 8.56702(6)more » Å,β= 104.3270(4)°, andV= 1112.68(1) Å 3. In the crystal structure, strong C-H∙∙∙πand weak intermolecular hydrogen-bonding interactions link the molecules into a three-dimensional network. The molecules are in a head-to-head arrangement in the unit cell.« less

Spin canting and magnetic transition in NixZn1-xFe2O4 (x=0.0, 0.5 and 1.0) nanoparticles

NASA Astrophysics Data System (ADS)

Rani, Stuti; Raghav, Dharmendra Singh; Yadav, Prashant; Varma, G. D.

2018-04-01

Nanoparticles of NixZn1-xFe2O4(x=0.0, 0.5 and 1.0) have been synthesized via co-precipitation method and studied thestructural and magnetic properties. Rietveld refinement of X ray diffraction data of as synthesized samples revealthat the samples have mixed spinel structure with space group Fd-3m. The lattice parameter of the samples decreases as doping concentration of Ni ions increases. Magnetic measurements show paramagnetic to ferrimagnetic transition at room temperature on Ni doping in ZnFe2O4 nanoparticles. The magnetic measurements also show spin canting in samples possibly due to their nanocrystalline nature. The spin canting angles have been calculated with the help of Yafet-Kittel (Y-K) model. Furthermore, the Law of approach (LA) fitting of M-H curves indicates that the samples are highly anisotropicin nature. The Arrot plots of as synthesized samples also indicate the paramagnetic to ferrimagnetic transition. The correlation between the structural and observed magnetic properties of NixZn1-xFe2O4(x=0.0, 0.5 and 1.0) nanocrystals will be described and discussed in this paper.

Crystal-structure analysis of four mineral samples of anhydrite, CaSO[subscript 4], using synchrotron high-resolution powder X-ray diffraction data

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

Antao, Sytle M.

2014-05-28

The crystal structures of four samples of anhydrite, CaSO{sub 4}, were obtained by Rietveld refinements using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and space group Amma. As an example, for one sample of anhydrite from Hants County, Nova Scotia, the unit-cell parameters are a = 7.00032(2), b = 6.99234(1), c = 6.24097(1) {angstrom}, and V = 305.487(1) {angstrom}{sup 3} with a > b. The eight-coordinated Ca atom has an average distance of 2.4667(4) {angstrom}. The tetrahedral SO{sub 4} group has two independent S-O distances of 1.484(1) to O1 and 1.478(1) {angstrom} to O2 and an average distancemore » of 1.4810(5) {angstrom}. The three independent O-S-O angles [108.99(8) x 1, 110.38(3) x 4, 106.34(9){sup o} x 1; average [6] = 109.47(2){sup o}] and S-O distances indicate that the geometry of the SO{sub 4} group is quite distorted in anhydrite. The four anhydrite samples have structural trends where the a, b, and c unit-cell parameters increase linearly with increasing unit-cell volume, V, and their average and distances are nearly constant. The grand mean = 2.4660(2) {angstrom}, and grand mean = 1.4848(3) {angstrom}, the latter is longer than 1.480(1) {angstrom} in celestite, SrSO{sub 4}, as expected.« less

Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm.

PubMed

Powell, Harold R; Battye, T Geoff G; Kontogiannis, Luke; Johnson, Owen; Leslie, Andrew G W

2017-07-01

X-ray crystallography is the predominant source of structural information for biological macromolecules, providing fundamental insights into biological function. The availability of robust and user-friendly software to process the collected X-ray diffraction images makes the technique accessible to a wider range of scientists. iMosflm/MOSFLM (http://www.mrc-lmb.cam.ac.uk/harry/imosflm) is a software package designed to achieve this goal. The graphical user interface (GUI) version of MOSFLM (called iMosflm) is designed to guide inexperienced users through the steps of data integration, while retaining powerful features for more experienced users. Images from almost all commercially available X-ray detectors can be handled using this software. Although the program uses only 2D profile fitting, it can readily integrate data collected in the 'fine phi-slicing' mode (in which the rotation angle per image is less than the crystal mosaic spread by a factor of at least 2), which is commonly used with modern very fast readout detectors. The GUI provides real-time feedback on the success of the indexing step and the progress of data processing. This feedback includes the ability to monitor detector and crystal parameter refinement and to display the average spot shape in different regions of the detector. Data scaling and merging tasks can be initiated directly from the interface. Using this protocol, a data set of 360 images with ∼2,000 reflections per image can be processed in ∼4 min.

Integrating macromolecular X-ray diffraction data with the graphical user interface iMOSFLM

PubMed Central

Powell, Harold R; Battye, T Geoff G; Kontogiannis, Luke; Johnson, Owen; Leslie, Andrew GW

2017-01-01

X-ray crystallography is the overwhelmingly dominant source of structural information for biological macromolecules, providing fundamental insights into biological function. Collection of X-ray diffraction data underlies the technique, and robust and user-friendly software to process the diffraction images makes the technique accessible to a wider range of scientists. iMosflm/MOSFLM (www.mrc-lmb.cam.ac.uk/harry/imosflm) is a software package designed to achieve this goal. The graphical user interface (GUI) version of MOSFLM (called iMosflm) is designed to guide inexperienced users through the steps of data integration, while retaining powerful features for more experienced users. Images from almost all commercially available X-ray detectors can be handled. Although the program only utilizes two-dimensional profile fitting, it can readily integrate data collected in “fine phi-slicing” mode (where the rotation angle per image is less than the crystal mosaic spread by a factor of at least 2) that is commonly employed with modern very fast readout detectors. The graphical user interface provides real-time feedback on the success of the indexing step and the progress of data processing. This feedback includes the ability to monitor detector and crystal parameter refinement and to display the average spot shape in different regions of the detector. Data scaling and merging tasks can be initiated directly from the interface. Using this protocol, a dataset of 360 images with ~2000 reflections per image can be processed in approximately four minutes. PMID:28569763

Luminescence concentration quenching and site-occupancy of Eu2+ ions in Na2Ca2Si3O9 phosphors derived from 45S5 glass-ceramics

NASA Astrophysics Data System (ADS)

Zhu, Yangguang; Tong, Chao; Xu, Chuanyan; Li, Yadong; Seo, Hyo Jin

2016-04-01

The phosphors of Na2Ca2-2xEu2xSi3O9 (x = 0, 0.03, 0.05, 0.07, 0.09) were first synthesized by sol-gel method. The crystal phase formations of the phosphors were detected by X-ray powder diffraction (XRD) measurements and the structure refinement. The photoluminescence spectra, the concentration quenching, the luminescence decay curves and the luminescence color chromaticity were measured, respectively. The excitation spectra indicate that the phosphors can be effectively excited by near UV-LED chips. Two kinds of Eu2+ sites centered at 545 nm and 505 nm were discussed by analyzing the spectra, concentration-dependent luminescence intensity and lifetimes. This is a potential tool for monitoring the bioactivity of 45S5 glass-ceramics in situ.

Plasma properties of hot coronal loops utilizing coordinated SMM and solar research rocket observations

NASA Technical Reports Server (NTRS)

Moses, J. Daniel

1989-01-01

Three improvements in photographic x-ray imaging techniques for solar astronomy are presented. The testing and calibration of a new film processor was conducted; the resulting product will allow photometric development of sounding rocket flight film immediately upon recovery at the missile range. Two fine grained photographic films were calibrated and flight tested to provide alternative detector choices when the need for high resolution is greater than the need for high sensitivity. An analysis technique used to obtain the characteristic curve directly from photographs of UV solar spectra were applied to the analysis of soft x-ray photographic images. The resulting procedure provides a more complete and straightforward determination of the parameters describing the x-ray characteristic curve than previous techniques. These improvements fall into the category of refinements instead of revolutions, indicating the fundamental suitability of the photographic process for x-ray imaging in solar astronomy.

The Mapping X-Ray Fluorescence Spectrometer (MAPX)

NASA Technical Reports Server (NTRS)

Blake, David; Sarrazin, Philippe; Bristow, Thomas; Downs, Robert; Gailhanou, Marc; Marchis, Franck; Ming, Douglas; Morris, Richard; Sole, Vincente Armando; Thompson, Kathleen;

Structure analysis on synthetic emerald crystals

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

Refinement of atomic and magnetic structures using neutron diffraction for synthesized bulk and nano-nickel zinc gallate ferrite

NASA Astrophysics Data System (ADS)

Ata-Allah, S. S.; Balagurov, A. M.; Hashhash, A.; Bobrikov, I. A.; Hamdy, Sh.

2016-01-01

The parent NiFe2O4 and Zn/Ga substituted spinel ferrite powders have been prepared by solid state reaction technique. As a typical example, the Ni0.7Zn0.3Fe1.5Ga0.5O4 sample has been prepared by sol-gel auto combustion method with the nano-scale crystallites size. X-ray and Mössbauer studies were carried out for the prepared samples. Structure and microstructure properties were investigated using the time-of-flight HRFD instrument at the IBR-2 pulsed reactor, at a temperatures range 15-473 K. The Rietveld refinement of the neutron diffraction data revealed that all samples possess cubic symmetry corresponding to the space group Fd3m. Cations distribution show that Ni2+ is a complete inverse spinel ion, while Ga3+ equally distributed between the two A and B-sublattices. The level of microstrains in bulk samples was estimated as very small while the size of coherently scattered domains is quite large. For nano-structured sample the domain size is around 120 Å.

Improvement of thermoelectric properties and their correlations with electron effective mass in Cu1.98SxSe1-x.

PubMed

Zhao, Lanling; Fei, Frank Yun; Wang, Jun; Wang, Funing; Wang, Chunlei; Li, Jichao; Wang, Jiyang; Cheng, Zhenxiang; Dou, Shixue; Wang, Xiaolin

2017-01-16

Sulphur doping effects on the crystal structures, thermoelectric properties, density-of-states, and effective mass in Cu 1.98 S x Se 1-x were studied based on the electrical and thermal transport property measurements, and first-principles calculations. The X-ray diffraction patterns and Rietveld refinements indicate that room temperature Cu 1.98 S x Se 1-x (x = 0, 0.02, 0.08, 0.16) and Cu 1.98 S x Se 1-x (x = 0.8, 0.9, 1.0) have the same crystal structure as monoclinic-Cu 2 Se and orthorhombic-Cu 2 S, respectively. Sulphur doping can greatly enhance zT values when x is in the range of 0.8≤ × ≤1.0. Furthermore, all doped samples show stable thermoelectric compatibility factors over a broad temperature range from 700 to 1000 K, which could greatly benefit their practical applications. First-principles calculations indicate that both the electron density-of-sates and the effective mass for all the compounds exhibit non-monotonic sulphur doping dependence. It is concluded that the overall thermoelectric performance of the Cu 1.98 S x Se 1-x system is mainly correlated with the electron effective mass and the density-of-states.

Cation distribution of Ni-Zn-Mn ferrite nanoparticles

NASA Astrophysics Data System (ADS)

Parvatheeswara Rao, B.; Dhanalakshmi, B.; Ramesh, S.; Subba Rao, P. S. V.

2018-06-01

Mn substituted Ni-Zn ferrite nanoparticles, Ni0.4Zn0.6-xMnxFe2O4 (x = 0.00-0.25 in steps of 0.05), using metal nitrates were prepared by sol-gel autocombustion in citric acid matrix. The samples were examined by X-ray diffraction and vibrating sample magnetometer techniques. Rietveld structural refinements using the XRD data were performed on the samples to consolidate various structural parameters like phase (spinel), crystallite size (24.86-37.43 nm), lattice constant (8.3764-8.4089 Å) etc and also to determine cation distributions based on profile matching and integrated intensity ratios. Saturation magnetization values (37.18-68.40 emu/g) were extracted from the measured M-H loops of these nanoparticles to estimate their magnetic moments. Experimental and calculated magnetic moments and lattice constants were used to confirm the derived cation distributions from Rietveld analysis. The results of these ferrite nanoparticles are discussed in terms of the compositional modifications, particle sizes and the corresponding cation distributions as a result of Mn substitutions.

Quantum crystallographic charge density of urea

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

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

DOE PAGES

Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan; ...

2016-11-04

Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less

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.

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.

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.; Stanford University, Stanford, CA 94305; Stanford University, Stanford, CA 94305

A microfluidic platform has been developed for the capture and X-ray analysis of protein microcrystals, affording a means to improve the efficiency of XFEL and synchrotron experiments. 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, addressablemore » 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 for 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

Electronic and atomic structures of Ti{sub 1-x}Al{sub x}N thin films related to their damage behavior

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

Tuilier, M.-H.; Pac, M.-J.; Girleanu, M.

2008-04-15

Ti and Al K-edge x-ray absorption spectroscopy is used to investigate the electronic structure of Ti{sub 1-x}Al{sub x}N thin films deposited by reactive magnetron sputtering. The experimental near edge spectra of TiN and AlN are interpreted in the light of unoccupied density of state band structure calculations. The comparison of the structural parameters derived from x-ray absorption fine structure and x-ray diffraction reveals segregation between Al-rich and Ti-rich domains within the Ti{sub 1-x}Al{sub x}N films. Whereas x-ray diffraction probes only the crystallized domains, the structural information derived from extended x-ray absorption fine structure analysis turns on both crystalline and grainmore » boundaries. The results are discussed by considering the damage behavior of the films depending on the composition.« less

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

A series of PDB related databases for everyday needs.

PubMed

Joosten, Robbie P; te Beek, Tim A H; Krieger, Elmar; Hekkelman, Maarten L; Hooft, Rob W W; Schneider, Reinhard; Sander, Chris; Vriend, Gert

2011-01-01

The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.

Nano sized La2Co2O6 double perovskite synthesized by sol gel method

NASA Astrophysics Data System (ADS)

Solanki, Neha; Lodhi, Pavitra Devi; Choudhary, K. K.; Kaurav, Netram

2018-05-01

We report here the synthesis of double perovskite La2Co2O6 (LCO) compound by a sol gel route method. The double perovskite structure of LCO system was confirmed via X-ray diffraction (XRD) analysis. Further, the lattice parameter, unit cell volume and bond length were refined by means of rietveld analysis using the full proof software. Debye Scherer formula was used to determine the particle size. The compound crystallized in triclinic structure with space group P-1 in ambient condition. We also obtained Raman modes from XRD spectra of poly-crystalline LCO sample. These results were interpreted for the observation of phonon excitations in this compound.

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.

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.

Electronic structure and optical properties of CdSxSe1-x solid solution nanostructures from X-ray absorption near edge structure, X-ray excited optical luminescence, and density functional theory investigations

NASA Astrophysics Data System (ADS)

Murphy, M. W.; Yiu, Y. M.; Ward, M. J.; Liu, L.; Hu, Y.; Zapien, J. A.; Liu, Yingkai; Sham, T. K.

2014-11-01

The electronic structure and optical properties of a series of iso-electronic and iso-structural CdSxSe1-x solid solution nanostructures have been investigated using X-ray absorption near edge structure, extended X-ray absorption fine structure, and X-ray excited optical luminescence at various absorption edges of Cd, S, and Se. It is found that the system exhibits compositions, with variable local structure in-between that of CdS and CdSe accompanied by tunable optical band gap between that of CdS and CdSe. Theoretical calculation using density functional theory has been carried out to elucidate the observations. It is also found that luminescence induced by X-ray excitation shows new optical channels not observed previously with laser excitation. The implications of these observations are discussed.

Crystal structures of (Mg1-x,Fex)SiO3postperovskite at high pressures

PubMed Central

Yamanaka, Takamitsu; Hirose, Kei; Mao, Wendy L.; Meng, Yue; Ganesh, P.; Shulenburger, Luke; Shen, Guoyin; Hemley, Russell J.

2012-01-01

X-ray diffraction experiments on postperovskite (ppv) with compositions (Mg0.9Fe0.1)SiO3 and (Mg0.6Fe0.4)SiO3 at Earth core-mantle boundary pressures reveal different crystal structures. The former adopts the CaIrO3-type structure with space group Cmcm, whereas the latter crystallizes in a structure with the Pmcm (Pmma) space group. The latter has a significantly higher density (ρ = 6.119(1) g/cm3) than the former (ρ = 5.694(8) g/cm3) due to both the larger amount of iron and the smaller ionic radius of Fe2+ as a result of an electronic spin transition observed by X-ray emission spectroscopy (XES). The smaller ionic radius for low-spin compared to high-spin Fe2+ also leads to an ordered cation distribution in the M1 and M2 crystallographic sites of the higher density ppv structure. Rietveld structure refinement indicates that approximately 70% of the total Fe2+ in that phase occupies the M2 site. XES results indicate a loss of 70% of the unpaired electronic spins consistent with a low spin M2 site and high spin M1 site. First-principles calculations of the magnetic ordering confirm that Pmcm with a two-site model is energetically more favorable at high pressure, and predict that the ordered structure is anisotropic in its electrical and elastic properties. These results suggest that interpretations of seismic structure in the deep mantle need to treat a broader range of mineral structures than previously considered. PMID:22223656

Structural, magnetic, and electrical properties of (1-x)Bi0.85La0.15FeO3-(x)CoFe2O4 multiferroic composites

NASA Astrophysics Data System (ADS)

Pandey, Rabichandra; Pradhan, Lagen Kumar; Kar, Manoranjan

2018-04-01

In this study, the tartaric acid modified sol-gel method was used to synthesize (1-x)Bi0.85La0.15FeO3-(x)CoFe2O4 (BLFO-CFO) composites where x = 0.00, 0.10, 0.20, 0.30, 0.40, and 0.50. The X-ray diffraction (XRD) patterns indicated the formation of composites with both BLFO and CFO crystal symmetry, i.e., perovskite and spinel structures, respectively. Rietveld refinement of the XRD patterns was performed for all of the samples in order to analyze the crystal phases and obtain the structural parameters. There were decreases in the lattice parameters of the perovskite phase as the CFO spinel phase increased in the composites, which may be explained by the strain at the interface of the BLFO and CFO phases. Electrical polarization and dielectric constant enhancements were observed in the BLFO-CFO composites compared with BLFO. The saturation magnetization increased as the CFO phase increased in the composites. The theoretical saturation magnetization (calculated using Vegard's law) was less than the experimentally observed value, possibly due to the spin interaction at the interface of BLFO and CFO.

Experimental and Theoretical Investigations on Intermediate Band in Doped Nano-SnS2

NASA Astrophysics Data System (ADS)

Heiba, Zein K.; Mohamed, Mohamed Bakr; Abdel Kader, M. H.

2018-03-01

Nano-SnS2 and Sn0.75 X 0.25S2 (X = Cr, Fe, Y) have been prepared by thermolysis method. Phase analysis of x-ray diffraction data confirmed the single-phase nature of all prepared samples, with some residual carbon contributing to the background. Rietveld refinement revealed high anisotropy in crystallite size, signifying a cylindrical structure for the particle shape, as confirmed by transmission electron microscopy. The refined occupancies obtained for the doped cations were found to be smaller than the nominal target doping ratio (25%). Fourier-transform infrared spectra showed presence of Sn-S bond in all samples. The energy was found to be 3.42 eV, 3.33 eV, 2.1 eV and 3.14 eV, and 3.62 eV for undoped SnS2 and when doped with Cr, Fe, and Y, respectively. Density functional theory calculations illustrated that Fe-doped SnS2 has two bandgaps [normal and intermediate (IB) bands]. Meanwhile, Sn0.75Fe0.25S2 sample showed anti-Stokes and an extra photoluminescence peak related to the newly created intermediate band (IB) inside the energy gap. On the other hand, pure SnS2 and Sn0.75 X 0.25S2 (X = Cr, Y) samples emitted four photoluminescence subspectra in ultraviolet, violet, and blue regions.

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

Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan

Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less

The Mapping X-ray Fluorescence Spectrometer (MapX)

NASA Astrophysics Data System (ADS)

Sarrazin, P.; Blake, D. F.; Marchis, F.; Bristow, T.; Thompson, K.

2017-12-01

Many planetary surface processes leave traces of their actions as features in the size range 10s to 100s of microns. The Mapping X-ray Fluorescence Spectrometer (MapX) will provide elemental imaging at 100 micron spatial resolution, yielding elemental chemistry at a scale where many relict physical, chemical, or biological features can be imaged and interpreted in ancient rocks on planetary bodies and planetesimals. MapX is an arm-based instrument positioned on a rock or regolith with touch sensors. During an analysis, an X-ray source (tube or radioisotope) bombards the sample with X-rays or alpha-particles / gamma-rays, resulting in sample X-ray Fluorescence (XRF). X-rays emitted in the direction of an X-ray sensitive CCD imager pass through a 1:1 focusing lens (X-ray micro-pore Optic (MPO)) that projects a spatially resolved image of the X-rays onto the CCD. The CCD is operated in single photon counting mode so that the energies and positions of individual X-ray photons are recorded. In a single analysis, several thousand frames are both stored and processed in real-time. Higher level data products include single-element maps with a lateral spatial resolution of 100 microns and quantitative XRF spectra from ground- or instrument- selected Regions of Interest (ROI). XRF spectra from ROI are compared with known rock and mineral compositions to extrapolate the data to rock types and putative mineralogies. When applied to airless bodies and implemented with an appropriate radioisotope source for alpha-particle excitation, MapX will be able to analyze biogenic elements C, N, O, P, S, in addition to the cations of the rock-forming elements >Na, accessible with either X-ray or gamma-ray excitation. The MapX concept has been demonstrated with a series of lab-based prototypes and is currently under refinement and TRL maturation.

Effect of Nano CeO2 Addition on the Microstructure and Properties of a Cu-Al-Ni Shape Memory Alloy

NASA Astrophysics Data System (ADS)

Pandey, Abhishek; Jain, Ashish Kumar; Hussain, Shahadat; Sampath, V.; Dasgupta, Rupa

2016-08-01

This article deals with the effect of adding nano CeO2 to act as a grain pinner/refiner to a known Cu-Al-Ni shape memory alloy. Elements were taken in a predefined ratio to prepare 300 g alloy per batch and melted in an induction furnace. Casting was followed by homogenization at 1173 K (900 °C) and rolling to make sheets of 0.5-mm thickness. Further, samples were characterized for microstructure using optical and electron microscope, hardness, and different phase studies by X-ray and transformation temperatures by differential scanning calorimetry. X-ray peak broadenings and changes were investigated to estimate the crystallite size, lattice strain, and phase changes due to different processing steps. A nearly uniform distribution of CeO2 and better martensitic structure were observed with increasing CeO2. The addition of CeO2 also shows a visible effect on the transformation temperature and phase formation.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

PubMed Central

Rodríguez Guilbe, María M.; Alfaro Malavé, Elisa C.; Akerboom, Jasper; Marvin, Jonathan S.; Looger, Loren L.; Schreiter, Eric R.

2008-01-01

Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, this protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way. PMID:18607093

Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

PubMed

Potrzebowski, Wojciech; André, Ingemar

2015-07-01

For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

PyXRD v0.6.7: a free and open-source program to quantify disordered phyllosilicates using multi-specimen X-ray diffraction profile fitting

NASA Astrophysics Data System (ADS)

Dumon, M.; Van Ranst, E.

2016-01-01

This paper presents a free and open-source program called PyXRD (short for Python X-ray diffraction) to improve the quantification of complex, poly-phasic mixed-layer phyllosilicate assemblages. The validity of the program was checked by comparing its output with Sybilla v2.2.2, which shares the same mathematical formalism. The novelty of this program is the ab initio incorporation of the multi-specimen method, making it possible to share phases and (a selection of) their parameters across multiple specimens. PyXRD thus allows for modelling multiple specimens side by side, and this approach speeds up the manual refinement process significantly. To check the hypothesis that this multi-specimen set-up - as it effectively reduces the number of parameters and increases the number of observations - can also improve automatic parameter refinements, we calculated X-ray diffraction patterns for four theoretical mineral assemblages. These patterns were then used as input for one refinement employing the multi-specimen set-up and one employing the single-pattern set-ups. For all of the assemblages, PyXRD was able to reproduce or approximate the input parameters with the multi-specimen approach. Diverging solutions only occurred in single-pattern set-ups, which do not contain enough information to discern all minerals present (e.g. patterns of heated samples). Assuming a correct qualitative interpretation was made and a single pattern exists in which all phases are sufficiently discernible, the obtained results indicate a good quantification can often be obtained with just that pattern. However, these results from theoretical experiments cannot automatically be extrapolated to all real-life experiments. In any case, PyXRD has proven to be useful when X-ray diffraction patterns are modelled for complex mineral assemblages containing mixed-layer phyllosilicates with a multi-specimen approach.

Crystal Chemistry and Magnetism of Ternary Actinoid Boron Carbides UB 1- xC 1+ x and U 1- xMxB 2C with M = Sc, Lu, and Th

NASA Astrophysics Data System (ADS)

Rogl, P.; Rupp, B.; Felner, I.; Fischer, P.

1993-06-01

Within the homogeneous range of uranium monocarbide UB 1- xC 1+ x, the crystal structures of stoichiometric UBC and of the carbon-rich solid solution UB 0.78C 1.22, have been refined from single-crystal X-ray counter data. From X-ray analysis crystal symmetry in both cases is consistent with the centro-symmetric space group Cmcm and there are no indications of superstructure formation. In contrast to the fully ordered atom arrangement revealed for stoichiometric UBC ( a = 0.35899(4), b = 1.19781(12), c = 0.33474(3) nm), random occupation by boron and carbon atoms is observed for the boron site in UB 0.78C 1.22 ( a = 0.35752(4), b = 1.18584(3), c = 0.33881(4) nm). For 279(278) reflections (|F 0| > 3σ) the obtained reliability factors R x = ∑|ΔF|/∑| F0| were R x = 0.069 for UBC and R x = 0.050 for UB 0.78C 1.22. Neutron powder diffraction experiments at 9 and 295 K unambiguously revealed full occupancy by the nonmetal atoms in UB 0.78C 1.22 and prove the statistical occupation of B and C atoms in the B-sites. For the orthorhombic symmetry Cmcm, refinement was not better than R1 = 0.044. A model calculation in monoclinic symmetry C12/ m1, however, resulted in a significant reduction of the residual value to R1 = 0.030, releasing spatial constraints on the boron atoms. Thus the boron-boron chain in Cmcm (B-B = 0.1874 nm) is dissolved into boron pairs (B-B = 0.1706 nm) which are loosely bound at a distance of 0.2043 nm. The formation of C-B-B-C groups corresponds to the structure types of ThBC and Th 3B 2C 3. The magnetic behavior has been investigated in the temperature range from 4.2 K to 1000 K for UB 1- xC 1+ x (UBC-type) and U 1- xMxB 2C (ThB 2C-type for the high temperature modification and 1-UB 2C-type for the low temperature modification) with U partially substituted by Th or Sc, Lu. From magnetic susceptibilities, the alloys UB 1- xC 1+ x reveal temperature independent paramagnetism with typical intermediate valence fluctuation behavior ( TSF ˜ 350 K). ThB 2C and 1-UB 2C both are temperature independent paramagnets, whereas h-UB 2C is a ferromagnet with the rather high Curie temperature TM = 80(2) K. TM and the saturation magnetiziation per U atom both successively decrease on substitution of U by Th, Sc, or Lu in UB 2C, whereas the U-moments remain practically unchanged at μ eff(U) ˜ 1.9 μ B. Uranium L 3-XANES (X-ray Absorption Near Edge Structure) spectroscopy revealed increased d-band localization, comparable to uranium-transition metal alloys, in nonmagnetic UB 1- xC 1+ x ( x = 0, 0.22). No superconductivity was observed down to 1.5 K; no hydrogen uptake was observed for UB 2C and ThB 2C even under hydrogen pressures as high as 7 × 10 7 Pa at 670 K.

Computational Insights into the O2-evolving complex of photosystem II

PubMed Central

Sproviero, Eduardo M.; McEvoy, James P.; Gascón, José A.; Brudvig, Gary W.; Batista, Victor S.

2009-01-01

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based but comprises important modifications due to structural refinement, hydration and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies. PMID:18483777

Revision of the Li13Si4 structure.

PubMed

Zeilinger, Michael; Fässler, Thomas F

2013-11-06

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

Oxidation kinetics for conversion of U 3O 8 to ε-UO 3 with NO 2

DOE PAGES

Johnson, J. A.; Rawn, C. J.; Spencer, B. B.; ...

2017-04-04

The oxidation kinetics of U 3O 8 powder to ε-UO 3 in an NO 2 environment was measured by in situ x-ray diffraction (XRD). Experiments were performed at temperatures of 195, 210, 235, and 250°C using a custom designed and fabricated sample isolation stage. Data were refined to quantify phase fractions using a newly proposed structure for the ε-UO 3 polymorph. The kinetics data were modeled using a shrinking core approach. A proposed two-step reaction process is presented based on the developed models.

Solution Structure of the 128 kDa Enzyme I Dimer from Escherichia coli and Its 146 kDa Complex with HPr Using Residual Dipolar Couplings and Small- and Wide-Angle X-ray Scattering

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

Schwieters, Charles D.; Suh, Jeong-Yong; Grishaev, Alexander

2010-09-17

The solution structures of free Enzyme I (EI, {approx}128 kDa, 575 x 2 residues), the first enzyme in the bacterial phosphotransferase system, and its complex with HPr ({approx}146 kDa) have been solved using novel methodology that makes use of prior structural knowledge (namely, the structures of the dimeric EIC domain and the isolated EIN domain both free and complexed to HPr), combined with residual dipolar coupling (RDC), small- (SAXS) and wide- (WAXS) angle X-ray scattering and small-angle neutron scattering (SANS) data. The calculational strategy employs conjoined rigid body/torsion/Cartesian simulated annealing, and incorporates improvements in calculating and refining against SAXS/WAXS datamore » that take into account complex molecular shapes in the description of the solvent layer resulting in a better representation of the SAXS/WAXS data. The RDC data orient the symmetrically related EIN domains relative to the C{sub 2} symmetry axis of the EIC dimer, while translational, shape, and size information is provided by SAXS/WAXS. The resulting structures are independently validated by SANS. Comparison of the structures of the free EI and the EI-HPr complex with that of the crystal structure of a trapped phosphorylated EI intermediate reveals large ({approx}70-90{sup o}) hinge body rotations of the two subdomains comprising the EIN domain, as well as of the EIN domain relative to the dimeric EIC domain. These large-scale interdomain motions shed light on the structural transitions that accompany the catalytic cycle of EI.« less

Resolution of structural heterogeneity in dynamic crystallography

PubMed Central

Ren, Zhong; Chan, Peter W. Y.; Moffat, Keith; Pai, Emil F.; Royer, William E.; Šrajer, Vukica; Yang, Xiaojing

2013-01-01

Dynamic behavior of proteins is critical to their function. X-­ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic ‘structural changes’ are often indirectly inferred from ‘structural differences’ by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods. PMID:23695239

Resolution of structural heterogeneity in dynamic crystallography.

PubMed

Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

2013-06-01

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

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.

Anomalous magnetic and spin glass behavior in Nb-substituted LaCo1 -xNbxO3

NASA Astrophysics Data System (ADS)

Shukla, Rishabh; Dhaka, R. S.

2018-01-01

We report the structural, magnetic, transport, and electronic properties of Nb-substituted LaCo1 -xNbxO3 (x =0 -0.2 ). The Rietveld refinement of x-ray diffraction data demonstrate structural phase transitions from rhombohedral to orthorhombic and further to monoclinic with increasing the Nb concentration up to x ≥0.2 . Interestingly, we observed dramatic changes in the magnetization (M ) with increasing the Nb concentration, as the M sharply increases below 10 K even at 2.5% substitution. Furthermore, ac susceptibility data show the spin glass behavior in x =0.1 sample. We find that the density of states near the Fermi level decreases and the activation energy increases, which results in the decreasing conductivity with higher Nb concentration. A significant shift in the peak position of A2 g phonon mode has been observed using Raman spectroscopy, which indicates the change in the coupling due to the structural distortion with Nb substitution. The core-level photoemission study confirms that the Nb is present in 5 + valence state. Our study reveals that the nonmagnetic Nb5 + (d0) substitution converts Co3 + ions to Co2 + and stabilizes both in the high-spin state. Our results suggest that structural and spin-state transitions as well as the difference in the ionic radii between Nb5 + and Co3 + are playing an important role in tuning the physical properties.

Influence of Fe-substitution on structural, magnetic and magnetocaloric properties of Nd2Fe17-xCox solid solutions

NASA Astrophysics Data System (ADS)

Bouchaala, N.; Jemmali, M.; Bartoli, T.; Nouri, K.; Hentech, I.; Walha, S.; Bessais, L.; Salah, A. Ben

2018-02-01

Nd2Fe17-xCox (x = 0 , 1 , 2 , 3 , 4) intermetallic compounds, obtained under arc-melting conditions, have been investigated by means of X-ray diffraction analysis (XRD), Mössbauer spectrometry and magnetic measurements. The Rietveld refinement revealed that the sample is a pure compound with rhombohedral Th2Zn17-type structure (R 3 bar m space group) with the following lattice parameters: a = 8.5792 (2) Å, c = 12.4615 (2) Å. Using Mössbauer spectrometry analysis coupled with structural consideration we have unambiguously determined the cobalt atoms preferred inequivalent crystallographic site. Nd2Fe17 show an increase of 3.5 T in their weighted average hyperfine fields upon cobalt substitution. Whatever the cobalt content, the hyperfine field of these compounds follow this sequence Hhf { 6 c } >Hhf { 9 d } >Hhf { 18 f } >Hhf { 18 h }. The magnetic measurements showed that the Curie temperature increases with the Co content. The magnetic entropy change (ΔSM) was estimated from isothermal magnetization curves and it increases from 3.35 J/Kg K for x = 0 to 5.83 J/Kg K for x = 2 at μ0 H = 1.6 T . The relative cooling power (RCP) is in the range of 11.6 J/kg (x = 0) and 16 J/kg (x = 2).

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.

Insights into channel dysfunction from modelling and molecular dynamics simulations.

PubMed

Musgaard, Maria; Paramo, Teresa; Domicevica, Laura; Andersen, Ole Juul; Biggin, Philip C

2018-04-01

Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.' Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Broad-Band Measurements of Cen X-3 With XTE and CGRO

NASA Technical Reports Server (NTRS)

Vestrand, W. Thomas

1999-01-01

Centaurus X-3 has played a key role in the development of our understanding of galactic x-ray binary sources. Timing analysis of the UHURU x-ray observations for the luminous Cen X-3 source (L approximately 10(exp 38) erg/s) revealed the first evidence for coherent x-ray pulsations from an object in a binary system (Giaconni 1971; Schreier 1972). It was quickly understood that the luminous pulsed x-ray emission could be generated by the accretion of matter from a companion star onto a rotating neutron star and led to the adoption of binary star models as the fundamental model for galactic x-ray sources (e.g. Pringle and Rees 1972; Lamb 1973). Based on modeling and refined observations since the original measurements, we now believe that Cen X-3 is a high mass x-ray binary system that contains a disk-fed pulsar with a period of 4.84 seconds that is in a 2.087 day orbit around an O-star companion. Since the pulsar discovery, its period has been intermittently monitored and those studies show a long term spin-up of the pulsar punctuated by short intervals of spin-down (e.g. Finger 1994). The implied torques are thought to originate from the interaction of an accretion disk with the magnetic field of a neutron star (Ghosh and Lamb 1979).

Low temperature structures of dCpG-proflavine. Conformational and hydration effects.

PubMed Central

Schneider, B; Ginell, S L; Berman, H M

1992-01-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296 A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks. Images FIGURE 2 PMID:1489914

Low temperature structures of dCpG-proflavine.

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

Schneider, B.; Ginell, S. L.; Berman, H. M.

1992-12-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296more » A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks.« less

Structure determination of two structural analogs, named 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-fluorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C23H16F2N4S) and 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-chlorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C23H16ClFN4S) by synchrotron X-ray powder diffraction

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

Gündoğdu, Gülsüm; Aytaç, Sevim Peri; Müller, Melanie

Two novel compounds, 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-fluorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C 23H 16F 2N 4S) (1) and 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-chlorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C 23H 16ClFN 4S) (2), have been designed and synthesized as cytotoxic agents. The compounds were characterized by infrared, proton nuclear magnetic resonance, mass spectral data, elemental analysis and X-ray powder diffraction. The present study comprises spectral data and crystal structures of these novel compounds determined from synchrotron X-ray powder diffraction data. The structure solutions were obtained by simulated annealing. The final structures were achieved by Rietveld refinement using soft restraints for all bond lengths, bond angles, and planar groups. Both compounds crystallize in space groupmore » $$P\\bar 1$$,Z= 2, with the unit-cell parametersa= 6.37433(9),b= 11.3641(2),c= 14.09115(19) Å,α= 80.1740(8)°,β= 85.1164(8)°,γ= 80.9831(10)°,V= 991.55(3) Å 3of compound (1) anda= 6.53736(6),b= 11.55725(15),c= 14.01373(13) Å,α= 80.3323(7)°,β= 84.8939(6)°,γ= 79.3954(8)°,V= 1024.08(2) Å 3of compound (2). Structural analyses reveal that the title compounds are isostructural.« less

Magnetic properties and microstructure of melt-spun Ce17Fe78-xB6Hfx (x = 0-1.0) alloys

NASA Astrophysics Data System (ADS)

Jiang, Qingzheng; Zhong, Minglong; Quan, Qichen; Lei, Weikai; Zeng, Qingwen; Hu, Yongfeng; Xu, Yaping; Hu, Xianjun; Zhang, Lili; Liu, Renhui; Ma, Shengcan; Zhong, Zhenchen

2017-12-01

Ce17Fe78-xB6Hfx (x = 0-1.0) alloys were fabricated by a melt-spinning technique in order to study their magnetic properties and microstructure. Magnetic investigations of Ce17Fe78-xB6Hfx (x = 0-1.0) alloys show that the room-temperature coercivity increases linearly from 352 kA/m at x = 0 to 420 kA/m at x = 1.0. The Curie temperature (Tc) decreases monotonically from 424.5 K to 409.1 K. The Ce L3-edge X-ray absorption near edge structure (XANES) spectrums reveal that there is more Ce4+ in ribbons under total electron yield (TEY) than fluorescence yield (FY). Hf addition has no effect on the weight of Ce3+ and Ce4+ in CeFeB-based alloys. The grain refinement and microstructure uniformity are essential for improving the magnetic properties of Hf-doped alloys. This paper may shed light on the further development of the Ce-based magnets and offer a feasible way for using the rare earth resources effectively.

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

Voßwinkel, Daniel; Heletta, Lukas; Hoffmann, Rolf-Dieter

The YIrGe{sub 2} type ternary germanides RERhGe{sub 2} (RE = Y, Gd-Ho) were synthesized from the elements by arc-melting and characterized by powder X-ray diffraction. The structure of DyRhGe{sub 2} was refined from single crystal X-ray diffractometer data: Immm, a = 426.49(9), b = 885.0(2), c = 1577.4(3) pm, wR2 = 0.0533, 637 F{sup 2} values, 30 variables (300 K data). The structure contains two crystallographically independent dysprosium atoms in pentagonal prismatic and hexagonal prismatic coordination. The three-dimensional [RhGe{sub 2}] polyanion is stabilized through covalent Rh–Ge (243–261 pm) and Ge–Ge (245–251 pm) bonding. The close structural relationship with the slightlymore » rhodium-poorer germanides RE{sub 5}Rh{sub 4}Ge{sub 10} (≡ RERh{sub 0.8}Ge{sub 2}) is discussed. Temperature-dependent magnetic susceptibility measurements reveal Pauli paramagnetism for YRhGe{sub 2} and Curie-Weiss paramagnetism for RERhGe{sub 2} with RE = Gd, Tb, Dy and Ho. These germanides order antiferromagnetically at T{sub N} = 7.2(5), 10.6(5), 8.1(5), and 6.4(5) K, respectively. - Graphical abstract: The germanides RERhGe{sub 2} (RE = Y, Gd-Ho) are new representatives of the YIrGe{sub 2} type.« less

X-ray diffraction investigation of amorphous calcium phosphate and hydroxyapatite under ultra-high hydrostatic pressure

NASA Astrophysics Data System (ADS)

Lam, Elisa; Gu, Qinfen; Swedlund, Peter J.; Marchesseau, Sylvie; Hemar, Yacine

2015-11-01

The changes in the crystal structures of synthetically prepared amorphous calcium phosphate (ACP) and hydroxyapatite (HAP) in water (1:1 mass ratio) were studied by synchrotron X-ray diffraction (XRD) under ultra-high hydrostatic pressures as high as 2.34 GPa for ACP and 4 GPa for HAP. At ambient pressure, the XRD patterns of the ACP and HAP samples in capillary tubes and their environmental scanning electron micrographs indicated amorphous and crystalline characteristics for ACP and HAP, respectively. At pressures greater than 0.25 GPa, an additional broad peak was observed in the XRD pattern of the ACP phase, indicating a partial phase transition from an amorphous phase to a new high-pressure amorphous phase. The peak areas and positions of the ACP phase, as obtained through fitting of the experimental data, indicated that the ACP exhibited increased pseudo-crystalline behavior at pressures greater than 0.96 GPa. Conversely, no structural changes were observed for the HAP phase up to the highest applied pressure of 4 GPa. For HAP, a unit-cell reduction during compression was evidenced by a reduction in both refined lattice parameters a and c. Both ACP and HAP reverted to their original structures when the pressure was fully released to ambient pressure.

Synchrotron X-Ray Diffraction Studies of Olivine from Comet Wild 2

NASA Technical Reports Server (NTRS)

2008-01-01

We have analyzed a collection of the Comet Wild 2 coma grains returned by the NASA Stardust Mission, using micro-area Laue diffraction equipment. The purpose of the diffraction experiment is to permit the structure refinement of olivine including site occupancies. In addition to the intrinsic importance of the olivine structures for revealing the thermal history of Wild 2 materials, we wish to test reports that olivine recovered after hypervelocity capture in silica aerogel has undergone a basic structural change due to capture heating [1]. The diffraction equipment placed at beam line BL- 4B1 of PF, KEK was developed with a micropinhole and an imaging plate (Fuji Co. Ltd.) using the Laue method combined with polychromatic X-ray of synchrotron radiation operated at energy of 2.5 GeV. The incident beam is limited to 1.6 m in diameter by a micropinhole set just upstream of the sample [2, 3]. It is essential to apply a microbeam to obtain diffracted intensities with high signal to noise ratios. This equipment has been successfully applied to various extraterrestrial materials, including meteorites and interplanetary dust particles [4]. The Laue pattern of the sample C2067,1,111,4 (Fig. 1) was successfully taken on an imaging plate after a 120 minute exposure (Fig. 2).

Synthesis, DFT calculations of structure, vibrational and thermal decomposition studies of the metal complex Pb[Mn(C3H2O4)2(H2O)2].

PubMed

Gil, Diego M; Carbonio, Raúl E; Gómez, María Inés

2015-04-15

The metallo-organic complex Pb[Mn(C3H2O4)2(H2O)2] was synthesized and characterized by IR and Raman spectroscopy and powder X-ray diffraction methods. The cell parameters for the complex were determined from powder X-ray diffraction using the autoindexing program TREOR, and refined by the Le Bail method with the Fullprof program. A hexagonal unit cell was determined with a=b=13.8366(7)Å, c=9.1454(1)Å, γ=120°. The DFT calculated geometry of the complex anion [Mn(C3H2O4)2(H2O)2](2-) is very close to the experimental data reported for similar systems. The IR and Raman spectra and the thermal analysis of the complex indicate that only one type of water molecules is present in the structure. The thermal decomposition of Pb[Mn(C3H2O4)2(H2O)2] at 700 °C in air produces PbO and Pb2MnO4 as final products. The crystal structure of the mixed oxide is very similar to that reported for Pb3O4. Copyright © 2015 Elsevier B.V. All rights reserved.

3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study

PubMed Central

Klementieva, Oxana; Werner, Stephan; Guttmann, Peter; Pratsch, Christoph; Cladera, Josep

2017-01-01

Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis. PMID:28376110

Brillouin function characteristics for La-Co substituted barium hexaferrites

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

Wu, Chuanjian, E-mail: wcjuestc2005@gmail.com, E-mail: ksun@uestc.edu.cn; Yu, Zhong; Sun, Ke, E-mail: wcjuestc2005@gmail.com, E-mail: ksun@uestc.edu.cn

2015-09-14

La-Co substituted barium hexaferrites with the chemical formula of Ba{sub 1−x}La{sub x}Fe{sub 12−x}Co{sub x}O{sub 19} (x = 0.0, 0.1, 0.3, and 0.5), prepared by a conventional ceramic method, were systematically investigated by Raman spectra, X-ray photoelectron spectroscopy, Rietveld refinement of X-ray diffraction patterns, and vibrating sample magnetometer. The result manifests that all the compounds are crystallized in magnetoplumbite hexagonal structure. Trivalent cobalt ions prevailingly occupy the 2a, 4f{sub 1}, and 12k sites. According to Néel model of collinear-spin ferrimagnetism, the molecular-field coefficients ω{sub bf2}, ω{sub kf1}, ω{sub af1}, ω{sub kf2}, and ω{sub bk} of La-Co substituted barium hexaferrites have been calculated usingmore » the nonlinear fitting method, and the magnetic moment of five sublattices (2a, 2b, 4f{sub 1}, 4f{sub 2}, and 12k) versus temperature T has been also investigated. The fitting results are coincided well with the experimental data. Moreover, with the increase of La-Co substitution amount x, the molecular-field coefficients ω{sub bf2} and ω{sub af1} decrease constantly, while the molecular-field coefficients ω{sub kf1}, ω{sub kf2}, and ω{sub bk} show a slight change.« less

Refinement of the crystal structure of the high-temperature phase G0 in (NH4)2WO2F4 (powder, x-ray, and neutron scattering)

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

Novak, D. M.; Smirnov, Lev S; Kolesnikov, Alexander I

2013-01-01

The (NH4)2WO2F4 compound undergoes a series of phase transitions: G0 -> 201 K -> G1 -> 160 K -> G2, with a significant change in entropy ( S1 ~ Rln10 at the G0 -> G1 transition), which indicates significant orientational disordering in the G0 phase and the order disorder type of the phase transition. X-ray diffraction is used to identify the crystal structure of the G0 phase as rhombohedral (sp. gr. Cmcm, Z = 4), determine the lattice parameters and the positions of all atoms (except hydrogen), and show that [WO2F4]2 ions can form a superposition of dynamic and staticmore » orientational disorders in the anionic sublattice. A determination of the orientational position of [NH4]+ ions calls for the combined method of elastic and inelastic neutron scattering. Inelastic neutron scattering is used to determine the state of hindered rotation for ammonium ions in the G0 phase. Powder neutron diffraction shows that the orientational disorder of NH4 ions can adequately be described within the free rotation approximation.« less

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

Wang, Zihan; Swantek, Andrew; Scarcelli, Riccardo

This paper focuses on detailed numerical simulations of direct injection diesel and gasoline sprays from production grade, multi-hole injectors. In a dual-fuel engine the direct injection of both the fuels can facilitate appropriate mixture preparation prior to ignition and combustion. Diesel and gasoline sprays were simulated using high-fidelity Large Eddy Simulations (LES) with the dynamic structure sub-grid scale model. Numerical predictions of liquid penetration, fuel density distribution as well as transverse integrated mass (TIM) at different axial locations versus time were compared against x-ray radiography data obtained from Argonne National Laboratory. A necessary, but often overlooked, criterion of grid-convergence ismore » ensured by using Adaptive Mesh Refinement (AMR) for both diesel and gasoline. Nine different realizations were performed and the effects of random seeds on spray behavior were investigated. Additional parametric studies under different ambient and injection conditions were performed to study their influence on global and local flow structures for gasoline sprays. It is concluded that LES can generally well capture all experimental trends and comes close to matching the x-ray data. Discrepancies between experimental and simulation results can be correlated to uncertainties in boundary and initial conditions such as rate of injection and spray and turbulent dispersion sub-model constants.« less

Influence of stacking fault energy on defect structures and microhardness of Cu and Cu alloys.

PubMed

Tao, Jing-Mei; Li, Dai; Li, Cai-Ju; Zhu, Xin-Kun

2011-12-01

Nano-structured Cu, Cu-10 wt%Zn and Cu-2 wt%Al with stacking fault energies (SFE) of 78, 35 and 37 mJ/m2, respectively, were preprared through high energy ball milling. X-ray diffraction and Vickers microharness test were used to investigate the microstructure and microhardness of all the samples after ball milling. X-ray diffraction measurements indicate that lower SFEs lead both to decrease in grain size and increase in microstrain, dislocation and twin densities for Cu-10 wt%Zn and Cu-2 wt%Al after 5 h of ball milling. The microhardnesses of Cu-10 wt%Zn and Cu-2 wt%Al reach to nearly the same values of 2.5 GPa after 5 h of ball milling, which is higher than that of Cu of 2.0 GPa. Two factors are considered to contribute to the finer grian size and higher microhardness of Cu-10 wt%Zn and Cu-2 wt%Al: (1) the effect of solid solution strengthening, which result in the interaction of solute atoms with screw dislocations; (2) the introduction of deformation twins during ball milling process by the decreasing of SFE, which results in the grain refinement.

Temperature dependent x-ray diffraction and dielectric studies of multiferroic GaFeO{sub 3}

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

Kumar, Rajeev; Mall, Ashish Kumar, E-mail: ashishm@iitk.ac.in; Gupta, Rajeev

2016-05-06

Polycrystalline GaFeO{sub 3} (GFO) samples were synthesized by sol-gel method. The structural and dielectric properties of GaFeO{sub 3} ceramic have been investigated by a combination of XRD and permittivity measurement. The X-ray diffraction spectra shows single phase orthorhombically distorted perovskite structure with Pc2{sub 1}n symmetry over a wide range of temperature 300 K to 600 K, with no evidence of any phase transition. Refined lattice parameters (a, b, c and V) increases with increasing temperature. Temperature dependent dielectric properties were investigated in the frequency range from 100Hz–5MHz. Impedance spectroscopy study on the sample showed that the dielectric constant and acmore » conductivity with frequency increases on increasing the temperature. Cole-Cole plots suggest that the response from grain is dominant at low temperature whereas grain boundary response overcomes as temperature increases. The relaxation activation energy (calculated from Cole-Cole plots) value is found to be 0.32 eV for the grain boundary. We believe that the oxygen ion vacancies play an important role in conduction processes at higher temperatures.« less

Sr 2Fe 1.5Mo 0.5O 6- δ as a regenerative anode for solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Liu, Qiang; Bugaris, Daniel E.; Xiao, Guoliang; Chmara, Maxwell; Ma, Shuguo; zur Loye, Hans-Conrad; Amiridis, Michael D.; Chen, Fanglin

Sr 2Fe 1.5Mo 0.5O 6- δ (SFM) was prepared using a microwave-assisted combustion synthesis method. Rietveld refinement of powder X-ray diffraction data reveals that SFM crystallizes in the simple cubic perovskite structure with iron and molybdenum disordered on the B-site. No structure transition was observed by variable temperature powder X-ray diffraction measurements in the temperature range of 25-800 °C. XPS results show that the iron and molybdenum valences change with an increase in temperature, where the mixed oxidation states of both iron and molybdenum are believed to be responsible for the increase in the electrical conductivity with increasing temperature. SFM exhibits excellent redox stability and has been used as both anode and cathode for solid oxide fuel cells. Presence of sulfur species in the fuel or direct utilization of hydrocarbon fuel can result in loss of activity, however, as shown in this paper, the anode performance can be regenerated from sulfur poisoning or coking by treating the anode in an oxidizing atmosphere. Thus, SFM can be used as a regenerating anode for direct oxidation of sulfur-containing hydrocarbon fuels.

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands.

PubMed

Saleh, Noureldin; Ibrahim, Passainte; Saladino, Giorgio; Gervasio, Francesco Luigi; Clark, Timothy

2017-05-22

A generally applicable metadynamics scheme for predicting the free energy profile of ligand binding to G-protein-coupled receptors (GPCRs) is described. A common and effective collective variable (CV) has been defined using the ideally placed and highly conserved Trp6.48 as a reference point for ligand-GPCR distance measurement and the common orientation of GPCRs in the cell membrane. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like boundary allows an efficient exploration of the entire ligand binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites. The protocol can be used with X-ray structures or high-quality homology models (based on a high-quality template and after thorough refinement) for the receptor and is universally applicable to agonists, antagonists, and partial and reverse agonists. The root-mean-square error (RMSE) in predicted binding free energies for 12 diverse ligands in five receptors (a total of 23 data points) is surprisingly small (less than 1 kcal mol -1 ). The RMSEs for simulations that use receptor X-ray structures and homology models are very similar.

X-ray beamsplitter

DOEpatents

Ceglio, N.M.; Stearns, D.G.; Hawryluk, A.M.; Barbee, T.W. Jr.

1987-08-07

An x-ray beamsplitter which splits an x-ray beam into two coherent parts by reflecting and transmitting some fraction of an incident beam has applications for x-ray interferometry, x-ray holography, x-ray beam manipulation, and x-ray laser cavity output couplers. The beamsplitter is formed of a wavelength selective multilayer thin film supported by a very thin x-ray transparent membrane. The beamsplitter resonantly transmits and reflects x-rays through thin film interference effects. A thin film is formed of 5--50 pairs of alternate Mo/Si layers with a period of 20--250 A. The support membrane is 10--200 nm of silicon nitride or boron nitride. The multilayer/support membrane structure is formed across a window in a substrate by first forming the structure on a solid substrate and then forming a window in the substrate to leave a free-standing structure over the window. 6 figs.

X-ray beamsplitter

DOEpatents

Ceglio, Natale M.; Stearns, Daniel S.; Hawryluk, Andrew M.; Barbee, Jr., Troy W.

1989-01-01

An x-ray beamsplitter which splits an x-ray beam into two coherent parts by reflecting and transmitting some fraction of an incident beam has applications for x-ray interferometry, x-ray holography, x-ray beam manipulation, and x-ray laser cavity output couplers. The beamsplitter is formed of a wavelength selective multilayer thin film supported by a very thin x-ray transparent membrane. The beamsplitter resonantly transmits and reflects x-rays through thin film interference effects. A thin film is formed of 5-50 pairs of alternate Mo/Si layers with a period of 20-250 A. The support membrane is 10-200 nm of silicon nitride or boron nitride. The multilayer/support membrane structure is formed across a window in a substrate by first forming the structure on a solid substrate and then forming a window in the substrate to leave a free-standing structure over the window.

On Calibrations Using the Crab Nebula as a Standard Candle

NASA Technical Reports Server (NTRS)

Weisskopf, Martin; Guainazzi, Matteo; Jahoda, Keith; Shaposhnikov, Nikolai; ODell, Stephen; Zavlin, Vyacheslav; Wilson-Hodge, Colleen; Elsner, Ronald

2009-01-01

Inspired by a recent paper (Kirsch et al. 2005) on possible use of the Crab Nebula as a standard candle for calibrating X-ray response func tions, we examine possible consequences of intrinsic departures from a single (absorbed) power law upon such calibrations. We limited our analyses to three more modern X-ray instruments -- the ROSAT/PSPC, th e RXTE/PCA, and the XMM-Newton/EPIC-pn. The results are unexpected an d indicate a need to refine two of the three response functions studi ed. The implications for Chandra will be discussed.

X-Ray Wind Tomography of IGR J17252-3616

NASA Astrophysics Data System (ADS)

Manousakis, Antonios; Walter, Roland

2010-07-01

IGR J17252-3616, a highly absorbed High Mass X-ray Binary (HMXB) with Hydrogen column density NH~(2-4)×1023 cm-2, has been observed with XMM-Newton for about one month. Observations were scheduled in order to cover the orbital-phase space as much as possible. IGR J17252-3616 shows a varying column density NH and Fe Kα line when fit with simple phenomenological models. A refined orbital solution can be derived. Spectral timing analysis allows derivation of the wind properties of the massive star.

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.

Structural and transport properties of NdCrO{sub 3} nanoceramics

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

Saha, Sujoy; Sakhya, Anup Pradhan; Sinha, T. P.

2013-02-05

Reitveld refinement of the room temperature powder X-ray diffraction profile of NdCrO{sub 3} (NCO) nanoceramics synthesized by sol-gel processing shows orthorhombic Pnma (D{sub 2h}{sup 16}) space group symmetry. The refined lattice parameters are a = 5.482(3) A, b = 7.689(4) A and c = 5.416(3) A. Transmission electron microscopy (TEM) of NCO shows that the average particle size is around 70 nm. The electrical transport property of NCO is investigated by both conductivity and electric modulus formalism. The electrical data is taken by a LCR meter in a temperature range from 303 K to 573 K and in a frequencymore » range from 42 Hz to 1.1 MHz. The ac conductivity follows a power law. The Cole-Cole plot of impedance at 303 K shows grain effect.« less

Calcio-olivine γ-Ca2SiO4: I. Rietveld refinement of the crystal structure

NASA Astrophysics Data System (ADS)

Gobechiya, E. R.; Yamnova, N. A.; Zadov, A. E.; Gazeev, V. M.

2008-05-01

The structure of the natural mineral calcio-olivine (γ-Ca2SiO4) found in skarn xenoliths in the region of the Lakargi Mountain (North Caucasus, Kabardino-Balkaria, Russia) is refined by the Rietveld method [ a = 5.07389(7) Å, b = 11.21128(14) Å, c = 6.75340(9) Å, V = 384.170(5) Å3, Z = 4, ρcalcd = 2.98 g/cm3, space group Pbnm]. The X-ray diffraction pattern of a powdered sample is recorded on a STOE STADI MP diffractometer [λCu K α1; Ge(111) primary monochromator; 6.00° < 2θ < 100.88°; step width, 2.5° in 2θ; number of reflections, 224]. All calculations are performed with the WYRIET (version 3.3) software package. The structural model is refined in the anisotropic approximation to R p = 6.44, R wp = 8.52, R exp = 5.85, R B = 4.98, R F = 6.90, and s = 1.46. It is shown that the sample under investigation is a mixture of several mineral phases, among which calcio-olivine (the natural analogue of the γ-Ca2SiO4 compound) (83%), hillebrandite (13%), and wadalite (4%) are dominant. Only the scale factors and the unit cell parameters are refined for hillebrandite Ca2SiO3(OH)2 [ a = 3.63472(16) Å, b = 16.4140(10) Å, c = 11.7914(8) Å, space group Cmc21, Z = 6] and wadalite Ca6Al5Si2O16Cl3 ( a = 12.0088 Å, space group, I bar 4 3 d Z = 4). The results of the structure refinement of the main component of the sample confirm that the mineral calcio-olivine is isostructural to the synthetic compound γ-Ca2SiO4. The structure of this compound is formed by the heteropolyhedral framework composed of Ca octahedra joined together into olivine-like ribbons and isolated Si tetrahedra.

High-pressure behavior of cuprospinel CuFe 2O 4: Influence of the Jahn-Teller effect on the spinel structure

DOE PAGES

Kyono, Atsushi; Gramsch, Stephen A.; Nakamoto, Yuki; ...

2015-08-14

The Jahn-Teller-effect at Cu 2+ in cuprospinel CuFe 2O 4 was investigated using high-pressure, single crystal synchrotron x-ray diffraction (XRD) techniques at beamline BL10A at the Photon Factory, KEK, Japan. Six data sets were collected in the pressure range from ambient to 5.9 GPa at room temperature. Structural refinements based on the data were performed at 0.0, 1.8, 2.7, and 4.6 GPa. The unit cell volume of cuprospinel decreases continuously from 590.8 (6) Å 3 to 579.5 (8) Å 3 up to 3.8 GPa. Leastsquares fitting to a third-order Birch-Murnaghan equation of state yields zero-pressure volume V 0 = 590.7more » (1) Å 3 and bulk modulus K 0 = 188.1 (4.4) GPa with K’ fixed at 4.0. The crystal chemical composition determined by electron-probe analysis and x-ray site-occupancy refinement is represented as [Cu 0.526Fe 0.474] [6][Cu 0.074Fe 1.926]O 4. Most of the Cu 2+ are preferentially distributed onto the tetrahedral (T) site of the spinel structure. At 4.6 GPa, a cubic-tetragonal phase transition is indicated by a splitting of the a axis of the cubic structure into a smaller a axis and a longer c axis, with unit cell parameters a = 5.882 (1) Å and c = 8.337 (1) Å. The tetragonal crystal structure with space group I4 1/amd was refined to R1 = 0.0182 and wR2 = 0.0134 using observed 35 x-ray reflections. At the T site, the tetrahedral O-T-O bond angles along the c-axis direction of the unit cell decreases slightly from 109.47 ° to 108.7 (4) °, which generates a stretched tetrahedral geometry along the c-axis. The cubic-totetragonal transition induced by the Jahn-Teller effect at Cu 2+ is attributable to the angular distortion at the tetrahedral site. At the octahedral (M) site, on the other hand, the two M-O bonds parallel to the caxis are shortened with respect to the four M-O bonds parallel to the ab-plane, which are lengthened as a result of the phase transition, leading to a compressed octahedral geometry along the c-axis. With the competing distortions between the stretched tetrahedron and the compressed octahedron along the c-axis, the a unit cell parameter is shortened with respect to the c unit cell parameter, giving a c/a ratio slightly greater than unity as referred to cubic lattice (c/a = 1.002). The c/a value increases to 1.007 with pressure, suggesting a further evolution of the stretched tetrahedron and the compressed octahedron. The variation of c/a ratio of the cuprospinel is similar to that observed in the tetragonally distorted cuprospinel with Cu 2+ fully occupying the octahedral site of the structure.« less

Structural, electrical and mechanical properties of selenium doped thallium based high-temperature superconductors

NASA Astrophysics Data System (ADS)

Cavdar, S.; Kol, N.; Koralay, H.; Ozturk, O.; Asikuzun, E.; Tasci, A. T.

2016-01-01

In this study, highly-refined chemical powders were synthesized by having them ready in appropriate stoichiometric proportions with conventional solid state reaction method so that they would produce the superconductor TlPb0.3Sr2Ca1-xSexCu2Oy (x = 0; 0.4; 0.6; 1.0). This study aims to understand effect of the selenium doping on the superconducting, structural and mechanical properties of the aforementioned superconducting material. The effect of the doping rates on the structural and electrical properties of the sample has been identified. Electrical characteristics of the TlPb0.3Sr2Ca1-xSexCu2Oy material were measured using standard four point probe method. Structural characteristics were examined with the powder X-ray diffractometer (XRD) and scanning electron microscope (SEM). Mechanical properties were analyzed with Vickers microhardness measurements on the sample surface. According to the results, it was observed that the reflection comes from the (00l) and parallel planes increased with Se doping. Particle size increases with increasing doping ratio. According to results of the mechanical measurements, all samples exhibit indentation size effect (ISE) behavior. Comparing the obtained results with theoretical studies, it was understood that Hays Kendall approach is the best method in determination of mechanical properties and analyzing microhardness of the materials.

Changes in the chemical composition and spectroscopy of loblolly pine medium density fiberboard furnish as a function of age and refining pressure

Treesearch

Stephen S. Kelley; Thomas Elder; Leslie H. Groom

2005-01-01

Loblolly pine wood between the ages of 5-35 was refined into medium density fiberboard furnish at steam pressures from 2 to 18 bar, The effect of age and processing conditions on the properties of the fibers was assessed by wet chemical analyses, Near Infared Spectroscopy (NIR) and powder X-ray diffraction (XRD).In general ,the percentages of extractives and glucose...

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

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

Akparov, V. Kh., E-mail: valery@akparov.ru; Timofeev, V. I., E-mail: tostars@mail.ru; Maghsoudi, N. N., E-mail: maghsudi@yahoo.com

2017-03-15

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and themore » acetate ion is different from that reported by Yoshimoto et al.« less

Crystallite size strain analysis of nanocrystalline La0.7Sr0.3MnO3 perovskite by Williamson-Hall plot method

NASA Astrophysics Data System (ADS)

Kumar, Dinesh; Verma, Narendra Kumar; Singh, Chandra Bhal; Singh, Akhilesh Kumar

2018-04-01

The nanocrystalline Sr-doped LaMnO3 (La0.7Sr0.3MnO3 = LSMO) perovskite manganites having different crystallite size were synthesized using the nitrate-glycine auto-combustion method. The phase purity of the manganites was checked by X-ray diffraction (XRD) measurement. The XRD patterns of the sample reveal that La0.7S0.3MnO3 crystallizes into rhombohedral crystal structure with space group R-3c. The size-dependence of structural lattice parameters have been investigated with the help of Rietveld refinement. The structural parameters increase as a function of crystallite size. The crystallite-size and internal strain as a function of crystallite-size have been calculated using Williamson-Hall plot.

Protein Data Bank depositions from synchrotron sources.

PubMed

Jiang, Jiansheng; Sweet, Robert M

2004-07-01

A survey and analysis of Protein Data Bank (PDB) depositions from international synchrotron radiation facilities, based on the latest released PDB entries, are reported. The results (http://asdp.bnl.gov/asda/Libraries/) show that worldwide, every year since 1999, more than 50% of the deposited X-ray structures have used synchrotron facilities, reaching 75% by 2003. In this web-based database, all PDB entries among individual synchrotron beamlines are archived, synchronized with the weekly PDB release. Statistics regarding the quality of experimental data and the refined model for all structures are presented, and these are analysed to reflect the impact of synchrotron sources. The results confirm the common impression that synchrotron sources extend the size of structures that can be solved with equivalent or better quality than home sources.

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.

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