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EXPO2009: structure solution by powder data in direct and reciprocal spaceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The program EXPO2009 is the evolution of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025–1028]. EXPO2009 performs all the steps of ab initio structure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced in EXPO2009 for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compo...
Source: Journal of Applied Crystallography - November 17, 2009 Category: Physics Authors: Altomare, A.Camalli, M.Cuocci, C.Giacovazzo, C.Moliterni, A.Rizzi, R. Tags: crystal structure solution EXPO2009 powder diffraction data computer programs Source Type: journals

Neutron powder diffraction in materials with incoherent scattering: an illustration of Rietveld refinement quality from nondeuterated gypsumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The power of the state-of-the-art neutron powder diffractometer suite at the Institut Laue–Langevin for investigating the structure of nondeuterated materials is presented using gypsum, CaSO4·2H2O, as a reference material. It is shown that flexible modern neutron powder diffraction instruments at reactor-based sources can yield data with sufficient counting statistics above the incoherent scattering contribution to perform unconstrained refinements in relatively short time periods (from minutes to a few hours, depending on the sample size and the instrument choice), without the requirement for significant changes to the...
Source: Journal of Applied Crystallography - November 17, 2009 Category: Physics Authors: Henry, P.F.Weller, M.T.Wilson, C.C. Tags: neutron powder diffraction structure hydrogenous materials Rietveld analysis gypsum research papers Source Type: journals

Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The principle of operation and the basic performance of the X-ray CMOS detector (Hamamatsu Photonics KK C10158DK) have been shown to be appropriate to the shutterless continuous rotation method. The data quality of the continuous rotation method is comparable to that of the conventional oscillation method using a CCD detector and, furthermore, the combination with fine ϕ slicing improves the data accuracy without increasin...
Source: Journal of Applied Crystallography - November 17, 2009 Category: Physics Authors: Hasegawa, K.Hirata, K.Shimizu, T.Shimizu, N.Hikima, T.Baba, S.Kumasaka, T.Yamamoto, M. Tags: protein crystallography shutterless continuous rotation method X-ray CMOS detectors X-ray wavelength capabilities research papers Source Type: journals

Depth-dependent local structures in thin films unraveled by grazing-incidence X-ray absorption spectroscopyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A method of using X-ray absorption spectroscopy together with resolved grazing-incidence geometry for depth profiling of atomic, electronic or chemical local structures in thin films is presented. The quantitative deconvolution of thickness-dependent spectral features is performed by fully considering both scattering and absorption formalisms. Surface oxidation and local structural depth profiles in nanometric FePt films are determined, exemplifying the application of the method. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - November 17, 2009 Category: Physics Authors: Souza-Neto, N.M.Ramos, A.Y.Tolentino, H.C.N.Martins, A.Santos, A.D. Tags: X-ray absorption spectroscopy (XAS) synchrotron radiation X-ray absorption near-edge structure (XANES) grazing incidence thin films oxidation depth profiling research papers Source Type: journals

Comparison of X-ray and electron backscatter diffraction textures for back-annealed Al–Mg alloysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The potential of electron backscatter diffraction (EBSD) to determine integral macrotexture data is explored by comparing EBSD-derived textures with standard X-ray texture results. The comparison is performed for an Al–Mg alloy AA 5005 in the cold-rolled and various back-annealed states in order to analyse the impact of the microstructural state on the quality of EBSD-based macrotextures. The number of EBSD single orientation measurements necessary to represent a texture adequately is determined by way of exploring the convergence of the statistical parameter ρ, which represents the relative mean square deviation betwee...
Source: Journal of Applied Crystallography - November 7, 2009 Category: Physics Authors: Engler, O. Tags: macrotexture orientation maps orientation distribution function (ODF) research papers Source Type: journals

Basal plane bending of 6H-SiC single crystals observed by synchrotron radiation X-ray topographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Basal plane bending is a structural defect in SiC single crystals caused mainly by the thermal mismatch between seed and holder, which deteriorates the quality of the wafers and blocks their applications. In this paper, basal plane bending was detected by high-resolution X-ray diffractometry (HRXRD) and transmission synchrotron white-beam X-ray topography (SWBXT). HRXRD reveals that the (0001) Si face is a concave sphere and SWBXT shows that the shapes of the Laue spots are different from that of the cross section of the synchrotron radiation beam. On the basis of a spherical curvature model for a (0001) 6H-SiC single crys...
Source: Journal of Applied Crystallography - November 7, 2009 Category: Physics Authors: Ning, L.Hu, X.Wang, Y.Xu, X.Gao, Y.Peng, Y.Chen, X.Huang, W.Yuan, Q. Tags: basal plane bending SiC single crystals synchrotron white-beam X-ray topography high-resolution X-ray diffractometry research papers Source Type: journals

The MORPHEUS protein crystallization screenEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A 96-condition initial screen for protein crystallization, called MORPHEUS, has been developed at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). The concept integrates several innovative approaches, such as chemically compatible mixes of potential ligands, new buffer systems and precipitant mixes that also act as cryoprotectants. Instead of gathering a set of crystallization conditions that have already been successful, a selection of molecules frequently observed in the Protein Data Bank (PDB) to co-crystallize with proteins has been made. These have been put together in mixes of similar chemical b...
Source: Journal of Applied Crystallography - November 7, 2009 Category: Physics Authors: Gorrec, F. Tags: macromolecular crystallography macromolecular crystallization crystallization screening crystallization additives research papers Source Type: journals

Efficient calculation of a normal matrix–vector product for anisotropic full-matrix least-squares refinement of macromolecular structuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A novel algorithm is described for multiplying a normal equation matrix by an arbitrary real vector using the fast Fourier transform technique during anisotropic crystallographic refinement. The matrix–vector algorithm allows one to solve normal matrix equations using the conjugate-gradients or conjugate-directions technique without explicit calculation of a normal matrix. The anisotropic version of the algorithm has been implemented in a new version of the computer program FMLSQ. The updated program has been tested on several protein structures at high resolution. In addition, rapid methods for preconditioner and normal...
Source: Journal of Applied Crystallography - November 7, 2009 Category: Physics Authors: Strokopytov, B.V. Tags: full-matrix least-squares refinement fast Fourier transform – vector product research papers Source Type: journals

Energy-dispersive Laue diffraction by means of a frame-store pnCCDEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A frame-store pnCCD detector was applied to the energy-dispersive X-ray Laue diffraction study of a γ-LiAlO2 crystal with white synchrotron radiation. Exploiting the simultaneous spatial and energy resolution of the detector the crystallographic unit cell of γ-LiAlO2 could be determined without any a priori information about the sample. The potential for application in X-ray structure analysis is tested by comparing experimental structure factors taken under a single exposure with those calculated from the known crystal structure. After correcting the measured spot intensities by angular and energy-dependent parameters, ...
Source: Journal of Applied Crystallography - October 30, 2009 Category: Physics Authors: Send, S.von Kozierowski, M.Panzner, T.Gorfman, S.Nurdan, K.Walenta, A.H.Pietsch, U.Leitenberger, W.Hartmann, R.Strüder, L. Tags: energy-dispersive X-ray Laue diffraction pnCCD detectors synchrotron radiation research papers Source Type: journals

Grating-based holographic X-ray diffraction: theory and application to confined fluidsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A grating-based holographic X-ray diffraction technique has been developed for reconstructing density profiles of nano-scale fluids confined in channel arrays. Within this approach, the reference wave is due to diffraction from the fabricated channel array, whereas the object wave is generated by the confinement-induced ordering of the fluid. The ensemble-averaged density profile of the fluid across the confining channel, which constitutes a weak phase object, is then determined in a model-independent manner from the interference between the reference and object waves by direct Fourier inversion. The validity of the linear...
Source: Journal of Applied Crystallography - October 30, 2009 Category: Physics Authors: Nygård, K.Satapathy, D.K.Bunk, O.Perret, E.Buitenhuis, J.David, C.van der Veen, J.F. Tags: holographic X-ray diffraction confined fluids nanofluids channel arrays research papers Source Type: journals

Small-angle neutron scattering analysis of a water-based magnetic fluid with charge stabilization: contrast variation and scattering of polarized neutronsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Structure analysis of a magnetic fluid (nanoparticles of maghemite dispersed in water with charge stabilization and without surfactant) by means of small-angle neutron scattering is presented. A combination of the contrast variation technique and scattering of polarized neutrons was applied. In the first case, the scattering curves obtained for the unmagnetized fluid with variation of the heavy water content in the carrier are treated in terms of the basic functions approach. The almost homogeneous character of the nanoparticles with respect to the nuclear scattering length density makes it possible to separate information...
Source: Journal of Applied Crystallography - October 30, 2009 Category: Physics Authors: Avdeev, M.V.Dubois, E.Mériguet, G.Wandersman, E.Garamus, V.M.Feoktystov, A.V.Perzynski, R. Tags: small-angle neutron scattering contrast variation polarized neutrons magnetic fluids ferrofluids magnetic nanoparticles maghemite research papers Source Type: journals

Design challenges and performance of nested neutron mirrors for microfocusing on SNAPEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Kirkpatrick–Baez (KB) neutron supermirrors can efficiently focus polychromatic neutron beams to micrometre dimensions. The ultimate size is determined mainly by the perfection of the mirrors and by the size of the beam needed to have sufficient experimental signal. Nested or Montel KB mirrors can collect ∼2.6 times more beam than standard sequential KB optics, but require good figure perfection at the edge of one mirror. This paper describes the characterization of the figure errors over the important reflective portions of the two mirrors needed for a Montel focusing pair. The measurements are placed in context with t...
Source: Journal of Applied Crystallography - October 30, 2009 Category: Physics Authors: Ice, G.E.Pang, J.W.L.Tulk, C.Molaison, J.Choi, J.-Y.Vaughn, C.Lytle, L.Takacs, P.Z.Andersen, K.H.Bigault, T.Khounsary, A. Tags: neutron supermirrors nested mirrors spallation neutrons focusing performance research papers Source Type: journals

Detection of the standing X-ray wavefield intensity inside a thin crystal using back-diffraction topography and imagingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The standing X-ray wavefield into a single-crystal bulk is characterized by a combination of the diffracted–reflected h-beams and the diffracted–transmitted o-beam. For different angular positions on the total reflection region, the standing X-ray wavefield has its maximum from the region between the atomic planes (low photoelectric absorption) to the region on the atomic planes (high photoelectric absorption). Historically, the evidence for such a characteristic has come from experiments such as anomalous transmission (Borrmann effect, originally detected in Laue geometry) and fluorescent measurements with a single cr...
Source: Journal of Applied Crystallography - October 30, 2009 Category: Physics Authors: Honnicke, M.G.Cusatis, C. Tags: standing X-ray wavefield intensity X-ray back-diffraction X-ray topography research papers Source Type: journals

Study of structural defects in ZnGeP2 crystals by X-ray topography based on the Borrmann effectEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The first study of structural defects in a ZnGeP2 semiconducting nonlinear optical crystal has been carried out by X-ray topography, based on the Borrmann effect, and the effect of anomalous transmission of X-rays on ZnGeP2 crystals has been examined. It is shown that the rosette technique of defect study under conditions of the Borrmann effect, developed earlier for elementary semiconductors, can be applied to the study and identification of defects in ZnGeP2. Features of contrast from individual edge and screw dislocations, microdefects, and coherent and semi-coherent microinclusions were considered. Defect identificatio...
Source: Journal of Applied Crystallography - October 30, 2009 Category: Physics Authors: Okunev, A.O.Verozubova, G.A.Trukhanov, E.M.Dzjuba, I.V.Galtier, P.R.J.Said Hassani, S.A. Tags: X-ray transmission topography Borrmann effect semiconducting nonlinear optical materials ZnGeP2 research papers Source Type: journals

A robotic arm as a simple sample changer for a diffractometer with very low component costsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Inexpensive model robots are a viable option for automation of simple, repetitive tasks and can be solutions when space restriction and funding are issues, both factors that may eliminate more advanced robots from consideration. A simple-to-program, inexpensive robotic arm has been integrated in a sample changer for room-temperature experiments on a neutron powder diffractometer. In spite of the limited precision inherent in a model, servo-controlled robot, a very reproducible overall system can be made. Simple `tricks' such as incorporating self-centering mechanisms, e.g. mechanically self-centering designs and magnets, c...
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Lian, D.Swainson, I.P.Cranswick, L.M.D.Donaberger, R. Tags: robotics sample changer automation powder diffractometer laboratory notes Source Type: journals

VIBRATE! A program to compute irreducible representations for atomic vibrations in crystalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
VIBRATE! is a computer program that uses group theory to carry out factor group analysis of a crystal structure. The symmetry species of the normal modes of vibration are derived, together with information relating to the symmetry-adapted vectors. The program is simple to use, relying on input mainly from a crystallographic information file. The output is presented in a form that should be familiar not only to crystallographers but also to others such as chemical spectroscopists. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Glazer, A.M. Tags: factor group analysis normal modes symmetry-adapted vectors spectroscopy computer programs Source Type: journals

Measurement of stress factors and residual stress of a film by in situ X-ray diffraction during four-point bendingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A method is proposed for the simultaneous measurement of the stress factors and residual stress state of a film by in-situ X-ray diffraction during four-point bending. The externally applied load acts as an additional degree of freedom in the stress–strain relation, which allows the problem to be solved for both residual stress and elastic moduli without assuming any grain interaction model. The procedure was tested on a galvanic nickel deposit and the predictions of existing grain interaction models were compared with the experimental results. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Ortolani, M.Azanza Ricardo, C.L.Scardi, P. Tags: residual stress X-ray diffraction thin films coatings electrodeposition research papers Source Type: journals

In situ diffraction strain analysis of elastically deformed polycrystalline thin films, and micromechanical interpretationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In situ tensile tests have been carried out under synchrotron radiation on supported gold (Au) thin films exhibiting a pronounced crystallographic texture. The 2θ shift of X-ray diffraction lines has been recorded for different specimen orientations and several loading levels in the elastic domain. The data obtained demonstrate the large strain heterogeneities generated within the specimen because of the intergranular interactions associated with the large elastic anisotropy of Au grains. To interpret these results, the use of a multi-scale micromechanical approach is unavoidable. The theoretical background of such method...
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Faurie, D.Castelnau, O.Brenner, R.Renault, P.-O.Le Bourhis, E.Goudeau, Ph. Tags: gold thin films strain analysis synchrotron radiation micromechanical models research papers Source Type: journals

Characterization of order domains in γ-TiAl by orientation microscopy based on electron backscatter diffractionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new approach to resolve the slight tetragonality of L10-ordered γ-TiAl by electron backscatter diffraction (EBSD) is presented. The phase has a c/a ratio of only about 2% larger than unity. The corresponding EBSD patterns therefore exhibit cubic pseudosymmetry. As a consequence, different order variants cannot be easily distinguished on the basis of their EBSD patterns. Automated orientation mapping results in frequent misindexing. In the past, either this problem was overcome by identifying order domains by relatively laborious transmission electron microscopy, or the order domain structure was ignored altogether by us...
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Zambaldi, C.Zaefferer, S.Wright, S.I. Tags: γ -TiAl electron backscatter diffraction (EBSD) backscattered Kikuchi diffraction patterns order domain microstructure pseudosymmetry high-resolution Hough transform AuCu prototypes research papers Source Type: journals

Structural studies on carbon nanotube fibres by synchrotron radiation microdiffraction and microfluorescenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study reports on the characterization of a carbon nanotube fibre using synchrotron radiation microbeam small- and wide-angle X-ray scattering in combination with microfluorescence. The fibre, spun directly from a chemical vapour deposition reaction zone, is imaged in terms of microstructural heterogeneities. The results reveal a fibre consisting of highly oriented nanotube bundles and unoriented carbonaceous material. Within the oriented component there is a variable orientation distribution and evidence of differences in nanotube packing. Single catalyst crystallites can be located within the fibre from their wide-an...
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Davies, R.J.Riekel, C.Koziol, K.K.Vilatela, J.J.Windle, A.H. Tags: wide-angle X-ray scattering (WAXS) X-ray fluorescence (XRF) nanotubes research papers Source Type: journals

Simulation of the powder diffraction pattern of randomly restacked Ca2Nb3O10 nanosheetsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
From X-ray powder diffraction pattern features, layered KCa2Nb3O10·nH2O synthesized through flocculation of delaminated Ca2Nb3O10 nanosheets with K ions appeared to be composed of randomly stacked nanosheets. Powder pattern simulation was conducted based on the matrix method using a random stacking model. When seven sheets were used as the coherent thickness, agreement in pattern fitting between the experimental and calculated intensities was satisfactory, and information about textures and atomic positions was obtained. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Onoda, M.Ebina, Y.Sasaki, T. Tags: stacking faults nanosheets X-ray powder diffraction diffuse scattering research papers Source Type: journals

Scherrer grain-size analysis adapted to grazing-incidence scattering with area detectorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ever since its formulation, the Scherrer formula has been the workhorse for quantifying finite size effects in X-ray scattering. Various aspects of Scherrer-type grain-size analysis are discussed with regard to the characterization of thin films with grazing-incidence scattering methods utilizing area detectors. After a brief review of the basic features of Scherrer analysis, a description of resolution-limiting factors in grazing-incidence scattering geometry is provided. As an application, the CHESS D1 beamline is characterized for typical scattering modes covering length scales from the molecular scale to the nanoscale....
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Smilgies, D.-M. Tags: Scherrer formula grazing-incidence small-angle scattering (GISAXS) grazing-incidence wide-angle scattering (GIWAXS) thin films soft materials research papers Source Type: journals

Management of metadata and automation for mail-in measurements with the APS 11-BM high-throughput, high-resolution synchrotron powder diffractometerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A high-resolution and high-throughput synchrotron powder diffractometer has been automated for use with samples that are mailed in by Advanced Photon Source users. Implementation of a relational database with web interfaces for both outside users and beamline staff, which is integrated into the facility-wide proposal and safety system, allows all aspects of beamline management to be integrated. This system permits users to request kits for mounting samples, to provide sample safety information, to obtain their collected data and to provide usage information upon project completion in a quick and simple manner. Beamline sta...
Source: Journal of Applied Crystallography - October 14, 2009 Category: Physics Authors: Toby, B.H.Huang, Y.Dohan, D.Carroll, D.Jiao, X.Ribaud, L.Doebbler, J.A.Suchomel, M.R.Wang, J.Preissner, C.Kline, D.Mooney, T.M. Tags: Advanced Photon Source automation synchrotron powder diffraction research papers Source Type: journals

Dependence of small-angle neutron scattering contrast on the difference in thermal expansions of phases in two-phase alloysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Theoretical expressions describing small-angle neutron scattering (SANS) contrast dependence on temperature in the region where no phase-composition changes occur were derived for two-phase Ni superalloys. The theory is based on the difference in thermal expansion of the two primary phases, γ and γ′. The simulations show that the scattering contrast temperature evolution is significant enough to be considered in in situ SANS experiments with superalloys at elevated temperatures. The simulations performed show that the magnitude of the scattering contrast at room temperature is firmly connected with the particular shape...
Source: Journal of Applied Crystallography - October 3, 2009 Category: Physics Authors: Strunz, P.Gilles, R.Mukherji, D.Hofmann, M.del Genovese, D.Roesler, J.Hoelzel, M.Davydov, V. Tags: superalloys misfit in situ neutron scattering small-angle neutron diffraction scattering contrast high-resolution neutron diffraction research papers Source Type: journals

Test tube for obtaining crystalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A design for an air-cooled test tube with a series of sockets and plugs (`crystallization socket-outlet adaptor') installed in a laboratory furnace is presented. The setup allows easy regulation and simultaneous crystallization tests of a series of different crystallization parameters and substances, enabling fast studies of single-crystal growth. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Cabric, B.Danilovic, N. Tags: apparatus for crystal growth obtaining crystals from melt laboratory notes Source Type: journals

A method for the indexation of back-reflection Laue X-ray photographsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article presents a variation of the traditional method for indexing and determining the crystal orientation from Laue back-photographs with a demonstration of its applicability to low-quality diffraction patterns from imperfect metallic single crystals. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Sidokhine, F.A.Sidokhine, E.F.Sidokhine, A.F. Tags: Laue back-photographs indexing imperfect metallic single crystals laboratory notes Source Type: journals

PeckCryst: a program for structure determination from powder diffraction data using a particle swarm optimization algorithmEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PeckCryst has been developed for the solution of molecular crystal structures from powder diffraction data using a particle swarm optimization (PSO) algorithm. In order to speed up the calculation process, a modified Bragg R factor is used as the evaluation function for the PSO algorithm. The effectiveness of the program has been tested by solving four known structures from powder diffraction data. A Python script is also provided for convenient repetitive running of PeckCryst. The distributed PeckCryst program is freely available from the authors upon request, and runs on Linux and Windows (32- and 64-bit) platforms. (Sou...
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Feng, Z.J.Dong, C.Jia, R.R.Deng, X.D.Cao, S.X.Zhang, J.C. Tags: PeckCryst particle swarm optimization computer programs powder diffraction Source Type: journals

Towards extracting the charge density from normal-resolution dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The limiting factor for charge-density studies is crystal quality. Although area detection and low temperatures enable redundant data collection, only compounds that form well diffracting single crystals without disorder are amenable to these studies. If thermal motion and electron density ρ(r) were de-convoluted, multipole parameters could also be refined with lower-resolution data, such as those commonly collected for macromolecules. Using the invariom database for first refining conventional parameters (x, y, z and atomic displacement parameters), de-convolution can be achieved. In a subsequent least-squares refinement...
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Dittrich, B.Hübschle, C.B.Holstein, J.J.Fabbiani, F.P.A. Tags: charge-density studies normal-resolution data macromolecular crystallography invariom modeling research papers Source Type: journals

Structural characterization of manganese-substituted nanocrystalline zinc oxide using small-angle neutron scattering and high-resolution transmission electron microscopyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A series of zinc oxide (ZnO) nanoparticles, substituted with manganese di-oxide, have been synthesized through a modified ceramic route using urea as a fuel. X-ray diffraction and high-resolution transmission electron microscopy studies indicate that the sizes of the ZnO particles are of nanometer dimension. Particles remain as single phase when the doping concentration is below 15 mol%. Small-angle neutron scattering indicates fractal-like agglomerates of these nanoparticles in powder form. The size distributions of the particles have been estimated from scattering experiments as well as microscopy studies. The average ...
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Roy, B.Karmakar, B.Bahadur, J.Mazumder, S.Sen, D.Pal, M. Tags: nanocrystals Mn-substituted ZnO ceramic route small-angle neutron scattering (SANS) high-resolution transmission electron microscopy (HRTEM) research papers Source Type: journals

The crystal structure of perdeuterated methanol monoammoniate (CD3OD·ND3) determined from neutron powder diffraction data at 4.2 and 180 KEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The crystal structure of perdeuterated methanol monoammoniate, CD3OD·ND3, has been solved from neutron powder diffraction data collected at 4.2 and 180 K. The crystal structure is orthorhombic, space group Pbca (Z = 8), with unit-cell dimensions a = 11.02320 (7), b = 7.66074 (6), c = 7.59129 (6) Å, V = 641.053 (5) Å3 [ρcalc = 1162.782 (9) kg m−3] at 4.2 K, and a = 11.21169 (5), b = 7.74663 (4), c = 7.68077 (5) Å, V = 667.097 (4) Å3 [ρcalc = 1117.386 (7) kg m−3] at 180 K. The crystal structure was determined by ab initio methods from the powder data; atomic coordinates an...
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Fortes, A.D.Wood, I.G.Knight, K.S. Tags: ammonia – methanol system perdeuterated methanol monoammoniate neutron powder diffraction research papers Source Type: journals

Aspherical electron scattering factors and their parameterizations for elements from H to XeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The formalism for, and the values of, aspherical electron scattering factors using relativistic wavefunctions are presented. The parameterizations of electron form factors valid for a full range of scattering vectors from 0.0 to 6.0 Å−1 were obtained for atoms with atomic number 1 (H) to 54 (Xe) by fitting a linear combination of Gaussian functions. Eight Gaussians were needed to achieve high-quality fittings. The tabulated aspherical p- and d-orbital parameters are invaluable for probing orbital electrons and calculating high-resolution electron microscopy images and diffractions, especially those involving interface...
Source: Journal of Applied Crystallography - October 2, 2009 Category: Physics Authors: Zheng, J.-C.Wu, L.Zhu, Y. Tags: aspherical electron scattering factors parameterizations anisotropy relativistic wavefunctions research papers Source Type: journals

Characterization of the hierarchical structures of a dry nanopowder in a polymer matrix by X-ray scattering techniquesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a commercially available dry titania nanopowder with a mean primary particle diameter of approximately 30 nm was mixed into an epoxy resin/hardener system to produce nanocomposite samples. Processing techniques such as ultrasonication and particle surface modification were used to produce nanocomposites with varying degrees of particle mixture homogeneity. The extent of nanoparticle dispersion was characterized by a combination of small-angle X-ray scattering and ultra-small-angle X-ray scattering. The measurement length scale ranged between 1 nm and several micrometres. Both measurement techniques provi...
Source: Journal of Applied Crystallography - September 15, 2009 Category: Physics Authors: Kane, M.C.Londono, J.D.Beyer, F.L.Brennan, A.B. Tags: nanoparticles agglomerates aggregates dispersion small-angle X-ray scattering (SAXS) ultra-small-angle X-ray scattering (USAXS) composites research papers Source Type: journals

A simple technique to convert sitting-drop vapor diffusion into hanging-drop vapor diffusion by solidifying the reservoir solution with agaroseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A simple protocol to convert sitting-drop vapor-diffusion plating into a hanging-drop vapor-diffusion experiment in protein crystallization is reported. After making a sitting-drop plate, agarose solution was added to solidify the reservoir solution, and the plates were incubated upside down. Crystallization experiments with hen egg white lysozyme, thaumatin and glucose isomerase showed that the `upside-down sitting-drop' method could produce single crystals with all the benefits of the hanging-drop crystallization method. (Source: Journal of Applied Crystallography)
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Whon, T.W.Lee, Y.-H.An, D.-S.Song, H.K.Kim, S.-G. Tags: protein crystallography upside-down sitting-drop vapor diffusion solidified reservoirs lysozyme thaumatin glucose isomerase crystallization agarose gel laboratory notes Source Type: journals

SMEPOC – a computer program for the automatic generation of trial structural models for inorganic compounds with symmetry restrictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new structure modelling algorithm that can automatically generate trial structure models based on a prior knowledge of the unit-cell content and space-group information is proposed. It can enumerate all possible equivalent position combination (EPC) models and eliminate unreasonable ones with symmetry restriction. Unlike other methods, it does not require the internal molecular connectivity or coordination polyhedron information and is mostly suitable for modelling inorganic crystals with independent atoms. Therefore, these EPC models can be used as input to global optimization procedures for inorganic crystal structure ...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Deng, X.Dong, C. Tags: inorganic structures model generation equivalent position combination computer programs Source Type: journals

Nonstoichiometry, amorphicity and microstructural evolution during phase transformations of photocatalytic titania powdersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The performance of photocatalytic titania powders is regulated, in part, by nonstoichiometry and the proportions of the crystalline and amorphous components. These variables can be quantitatively established by Rietveld analysis of diffraction data when internal standards are used to fix absolutely the crystallochemical parameters during quantitative phase analysis and to correct for mass absorption. Here, fixed-wavelength neutron and multiple-wavelength X-ray powder diffraction are used to assess phase development in alkoxide-derived titania gel as a function of temperature. In this manner, it is shown that the amorphous ...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Lim, S.H.Ritter, C.Ping, Y.Schreyer, M.White, T.J. Tags: titania neutron powder diffraction X-ray microabsorption X-ray powder diffraction – multiple wavelength phase transformation anatase rutile amorphous research papers Source Type: journals

A fast X-ray chopper for single-bunch extraction at synchrotron sourcesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new X-ray chopper system based on air-bearing technology was developed in a joint project between the Paul Scherrer Institut and DESY. The X-ray chopper wheel of 150 mm diameter has a slit width of 50 µm, which corresponds to an opening time of 230 ns at 30 000 r min−1. The wheel is equipped with either one or two slits at slightly different radii, resulting in repetition frequencies of 500 and 1000 Hz. To reduce air friction the wheel is operated in a reduced-pressure environment. The chopper is controlled by a specially developed phase lock loop controller, which is synchronized to the master bunch clo...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Meents, A.Reime, B.Kaiser, M.Wang, X.-Y.Abela, R.Weckert, E.Schulze-Briese, C. Tags: time-resolved experiments pump and probe synchrotron sources research papers Source Type: journals

Round robin on Rietveld quantitative phase analysis of Portland cementsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Interlaboratory studies on the precision and accuracy of Rietveld quantitative phase analysis (R-QPA) of mixtures of crystalline phases have already been carried out. However, cement-related materials are samples of variable complexity, ranging from three phases in white Portland clinkers to more than eight phases in grey cements, that need to be specifically investigated. Here, the results are reported from a round robin on the R-QPA of cement-related materials from laboratories with experience in this type of analysis. The aim of the work was to evaluate the levels of precision and accuracy associated with Portland clink...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: León-Reina, L.De la Torre, A.G.Porras-Vázquez, J.M.Cruz, M.Ordonez, L.M.Alcobé, X.Gispert-Guirado, F.Larrañaga-Varga, A.Paul, M.Fuellmann, T.Schmidt, R.Aranda, M.A.G. Tags: Portland clinker Portland cement Rietveld analysis QPA precision and accuracy research papers Source Type: journals

Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamlineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Small-angle X-ray scattering for macromolecules in solution is now widely used in structural biology to complement high-resolution structure determination obtained by X-ray crystallography or NMR. In the context of third-generation synchrotron sources, this increasing interest leads to developments in sample environments and automation. The presence of an online purification system is justified by the need for sample monodispersity. A combined system including an auto-sampler robot and online high-performance liquid chromatography (HPLC) has been developed and optimized at the SWING beamline of Synchrotron SOLEIL (Gif-sur-...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: David, G.Pérez, J. Tags: monodisperse protein solutions low-resolution structures liquid chromatography circulation cell solution sample changer small-angle X-ray scattering (SAXS) macromolecular crystallography research papers Source Type: journals

A comparison of a microfocus X-ray source and a conventional sealed tube for crystal structure determinationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Experiments are described in which a direct comparison was made between a conventional 2 kW water-cooled sealed-tube X-ray source and a 30 W air-cooled microfocus source with focusing multilayer optics, using the same goniometer, detector, radiation (Mo Kα), crystals and software. The beam characteristics of the two sources were analyzed and the quality of the resulting data sets compared. The Incoatec Microfocus Source (IµS) gave a narrow approximately Gaussian-shaped primary beam profile, whereas the Bruker AXS sealed-tube source, equipped with a graphite monochromator and a monocapillary collimator, had a broade...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Schulz, T.Meindl, K.Leusser, D.Stern, D.Graf, J.Michaelsen, C.Ruf, M.Sheldrick, G.M.Stalke, D. Tags: microfocus X-ray sources crystal structure determination research papers Source Type: journals

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomoleculesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute–solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Bardhan, J.Park, S.Makowski, L. Tags: small-angle X-ray scattering (SAXS) wide-angle X-ray scattering (WAXS) proteins SoftWAXS computer programs research papers Source Type: journals

Conoscopic method for determination of main refractive indices and thickness of a uniaxial crystal cut out parallel to its optical axisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper presents a simplified data acquisition and analysis technique for use in determining the main refractive indices and thickness of a uniaxial anisotropic layer cut out parallel to the optical axis, by processing the conoscopic interference figures obtained using a polarizing microscope equipped with a CCD camera. For negative uniaxial crystals, the equations used permit the calculation of the optical sign of the studied material so it is not necessary to insert a quartz wedge into the conoscopic beam. The technique can also be applied to the study of liquid crystal layers in a planar orientation. (Source: Journal...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Dumitrascu, L.Dumitrascu, I.Dorohoi, D.O. Tags: birefringence microscopy polarization research papers Source Type: journals

Phase behaviour and thermoelastic properties of perdeuterated ammonia hydrate and ice polymorphs from 0 to 2 GPaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The results are described of a series of neutron powder diffraction experiments over the pressure and temperature ranges 0 < P < 2 GPa, 150 < T < 240 K, which were carried out with the objective of determining the phase behaviour and thermoelastic properties of perdeuterated ammonia dihydrate (ND3·2D2O). In addition to the low-pressure cubic crystalline phase, ADH I, two closely related monoclinic polymorphs of ammonia dihydrate have been identified, which commonly occur as a composite in the range 450–550 MPa at 175 K; these are labelled ADH IIa and IIb, and each has unit-cell volume V ≃ 310 Å3 and number ...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Fortes, A.D.Wood, I.G.Vočadlo, L.Knight, K.S.Marshall, W.G.Tucker, M.G.Fernandez-Alonso, F. Tags: ammonia dihydrate ammonia monohydrate ice neutron diffraction polymorphism crystal growth kinetics research papers Source Type: journals

AMPLIMODES: symmetry-mode analysis on the Bilbao Crystallographic ServerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
AMPLIMODES is a computer program available on the Bilbao Crystallographic Server that can perform a symmetry-mode analysis of any distorted structure of displacive type. The analysis consists in decomposing the symmetry-breaking distortion present in the distorted structure into contributions from different symmetry-adapted modes. Given the high- and the low-symmetry structures, AMPLIMODES determines the atomic displacements that relate them, defines a basis of symmetry-adapted modes, and calculates the amplitudes and polarization vectors of the distortion modes of different symmetry frozen in the structure. The program us...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Orobengoa, D.Capillas, C.Aroyo, M.I.Perez-Mato, J.M. Tags: AMPLIMODES computer programs Bilbao Crystallographic Server distorted structures symmetry-mode analysis research papers Source Type: journals

Re-evaluation of formulae for X-ray stress analysis in polycrystalline specimens with fibre texture: experimental confirmationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Line splitting or line broadening of an X-ray Bragg reflection owing to a three-dimensional or biaxial load on a cubic polycrystalline specimen with 〈111〉 fibre texture has been predicted by Yokoyama & Harada [J. Appl. Cryst. (2009), 42, 185–191] if the specimen is in the symmetry of the Laue class m{\overline 3}m. By using a TiN film specimen and a high-precision four-circle diffractometer with a laboratory X-ray source, it is shown that the profile of the 420 reflection is substantially different with and without biaxial load and also depends on the measurement direction, while the profile of the 222 reflection doe...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Yokoyama, R.Harada, J.Akiniwa, Y. Tags: line broadening residual stress fibre texture Laue classes research papers Source Type: journals

Advances in powder diffraction pattern indexing: N-TREOR09Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Powder pattern indexing can still be a challenge, despite the great recent advances in theoretical approaches, computer speed and experimental devices. More plausible unit cells, belonging to different crystal systems, are frequently found by the indexing programs, and recognition of the correct one may not be trivial. The task is, however, of extreme importance: in case of failure a lot of effort and computing time may be wasted. The classical figures of merit for estimating the unit-cell reliability {i.e. M20 [de Wolff (1968). J. Appl. Cryst. 1, 108–113] and FN [Smith & Snyder (1979). J. Appl. Cryst. 12, 60–65]} some...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Altomare, A.Campi, G.Cuocci, C.Eriksson, L.Giacovazzo, C.Moliterni, A.Rizzi, R.Werner, P.-E. Tags: powder pattern indexing extinction groups figures of merit N-TREOR09 research papers Source Type: journals

Elastic deformations in a perfect bulk Si crystal studied by high-energy X-raysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this report a quantitative examination of the diffraction characteristics of a perfect silicon bulk crystal with long-range strain fields in a well defined geometry is presented. The experiments were carried out using a high-energy X-ray laboratory source. By simulating the elastic deformation of the crystal by a finite element program the strain fields of the diffracting crystal are accessed. From these, simulated data values for integrated intensities can be derived on the basis of the dynamical diffraction theory for slightly distorted crystals. The theoretical calculations show good agreement with the experimental m...
Source: Journal of Applied Crystallography - September 7, 2009 Category: Physics Authors: Gröschel, A.Grillenberger, H.Magerl, A. Tags: high-energy X-ray diffraction dynamical diffraction strain research papers Source Type: journals

PolySNAP3: a computer program for analysing and visualizing high-throughput data from diffraction and spectroscopic sourcesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PolySNAP3 is a computer program for the classification of powder diffraction, spectroscopic and numerical data either separately or combined. A correlation matrix is generated by matching full data profiles; for numerical data the standard Euclidean distance is calculated. The matrices are combined by the INDSCAL method [Carroll & Chang (1970). Psychometria, 35, 283–319] to give either a single interpretation of the data or combinations of any of the data types. Cluster analysis, multivariate data analysis and extensive data visualization routines are used to automatically classify the patterns into groups, validate the ...
Source: Journal of Applied Crystallography - August 7, 2009 Category: Physics Authors: Barr, G.Dong, W.Gilmore, C.J. Tags: PolySNAP3 computer programs pattern classification data analysis Source Type: journals

BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering (SAXS) data is presented. The program is freely distributed, following the open-source philosophy, and does not rely on any commercial software packages. BioXTAS RAW is a fully automated program that, via an online feature, reads raw two-dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes mask creation, radial averag...
Source: Journal of Applied Crystallography - August 7, 2009 Category: Physics Authors: Nielsen, S.S.Toft, K.N.Snakenborg, D.Jeppesen, M.G.Jacobsen, J.K.Vestergaard, B.Kutter, J.P.Arleth, L. Tags: BioXTAS RAW open-source software computer programs small-angle X-ray scattering (SAXS) Source Type: journals

In situ monitoring by synchrotron radiation of the formation of ZnO nanoparticles by aqueous chemical growthEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Synchrotron radiation experiments were carried out during the in situ growth of ZnO nanoparticles by the aqueous chemical growth technique. The first results of this exploratory in situ grazing-incidence diffraction (GID) experiment are reported, with emphasis on the difficulties encountered. In particular, it is shown that, when in situ GID experiments are carried out in a 25 mm-long cell, scattering by the solvent dominates. This impedes the observation of the formation of ZnO nanoparticles during the early stages of the growth process. Nevertheless, it is clearly shown that the wurzite hexagonal structure is present i...
Source: Journal of Applied Crystallography - August 7, 2009 Category: Physics Authors: Fall, S.Konovalov, O.Maaza, M.Beye, A.C.Gibaud, A. Tags: kinetics ZnO growth grazing-incidence diffraction research papers Source Type: journals

Finding crystal structures of peptides by random search and evolutionary algorithmsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Structures of crystalline peptides can be established using a special computer program, PTRY, which needs only limited diffraction data, the lattice constants, space group and primary structure. Crystal structures can be found by doing a random search in the internal-coordinate space and `combinations' among the plausible solutions found according to the genetic rules (crossover and mutation). PTRY, which also performs structural refinement, is simple and user friendly. Because only limited diffraction data are needed, data from powder diffraction spectra could be used, as well as single-crystal data. (Source: Journal of A...
Source: Journal of Applied Crystallography - August 7, 2009 Category: Physics Authors: Immirzi, A.Erra, L.Tedesco, C. Tags: PTRY computer programs crystalline peptides random search research papers Source Type: journals