Showing papers in "Journal of Applied Crystallography in 2009"

OLEX2: a complete structure solution, refinement and analysis program

Abstract: New software, OLEX2, has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering

Abstract: DAMMIF, a revised implementation of the ab-initio shape-determination program DAMMIN for small-angle scattering data, is presented. The program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. Symmetry and anisometry constraints can be imposed on the particle shape, similar to DAMMIN. In equivalent conditions, DAMMIF is 25–40 times faster than DAMMIN on a single CPU. The possibility to utilize multiple CPUs is added to DAMMIF. The application is available in binary form for major platforms.

Irena: tool suite for modeling and analysis of small-angle scattering

Abstract: Irena, a tool suite for analysis of both X-ray and neutron small-angle scattering (SAS) data within the commercial Igor Pro application, brings together a comprehensive suite of tools useful for investigations in materials science, physics, chemistry, polymer science and other fields. In addition to Guinier and Porod fits, the suite combines a variety of advanced SAS data evaluation tools for the modeling of size distribution in the dilute limit using maximum entropy and other methods, dilute limit small-angle scattering from multiple non-interacting populations of scatterers, the pair-distance distribution function, a unified fit, the Debye–Bueche model, the reflectivity (X-ray and neutron) using Parratt's formalism, and small-angle diffraction. There are also a number of support tools, such as a data import/export tool supporting a broad sampling of common data formats, a data modification tool, a presentation-quality graphics tool optimized for small-angle scattering data, and a neutron and X-ray scattering contrast calculator. These tools are brought together into one suite with consistent interfaces and functionality. The suite allows robust automated note recording and saving of parameters during export.

Crystallography Open Database - an open-access collection of crystal structures

Abstract: The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

Scherrer grain-size analysis adapted to grazing-incidence scattering with area detectors.

Abstract: A poor divergence value in the paper by Smilgies [J. Appl. Cryst. (2009), 42, 1030–1034] is corrected.

AMPLIMODES: symmetry‐mode analysis on the Bilbao Crystallographic Server

Abstract: 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 uses a mode parameterization that is as close as possible to the crystallographic conventions, expressing all quantities for the asymmetric unit of the low-symmetry structure. Distorted structures are often related to their higher-symmetry counterparts by temperature- and/or pressure-driven phase transitions, ferroic phase transitions being a particular example. The automatic symmetry-mode analysis performed by AMPLIMODES can be very useful for establishing the driving mechanisms of such structural phase transitions or the fundamental instabilities at the origin of the distorted phases.

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 beamline

Abstract: 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-Yvette, France). In the sample changer mode, a few microlitres of sample can be injected between two air bubbles and circulated at a controlled speed of typically 40 µl min−1. A maximum of 14 samples per hour could be measured in this mode by remote controlling the sample injections. In the HPLC mode, an initially polydisperse sample can be separated into each of its components before immediate data acquisition. The sample cell is thermostated, and offers a visualization control and online UV–Vis absorption monitoring.

EXPO2009: structure solution by powder data in direct and reciprocal space

Abstract: 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 compounds, when traditional approaches like direct methods may fail. The EXPO2009 graphical interface has been optimized and made very user friendly.

Ultra‐small‐angle X‐ray scattering at the Advanced Photon Source

Abstract: The design and operation of a versatile ultra-small-angle X-ray scattering (USAXS) instrument at the Advanced Photon Source (APS) at Argonne National Laboratory are presented. The instrument is optimized for the high brilliance and low emittance of an APS undulator source. It has angular and energy resolutions of the order of 10−4, accurate and repeatable X-ray energy tunability over its operational energy range from 8 to 18 keV, and a dynamic intensity range of 108 to 109, depending on the configuration. It further offers quantitative primary calibration of X-ray scattering cross sections, a scattering vector range from 0.0001 to 1 A−1, and stability and reliability over extended running periods. Its operational configurations include one-dimensional collimated (slit-smeared) USAXS, two-dimensional collimated USAXS and USAXS imaging. A robust data reduction and data analysis package, which was developed in parallel with the instrument, is available and supported at the APS.

The MORPHEUS protein crystallization screen

Abstract: 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 behaviour and structure, and combined with buffers and precipitant mixes that were also derived from PDB searches, to build the screen de novo. Observations made at the MRC-LMB and many practical aspects were also taken into account when formulating the screen. The resulting screen is easy to use, comprehensive yet small, and has already yielded a list of crystallization hits using both known and novel samples. As an indicator of success, the screen has now become one of the standard screens used routinely at the MRC-LMB when searching initial crystallization conditions for biological macromolecules.

BioXTAS RAW, a software program for high‐throughput automated small‐angle X‐ray scattering data reduction and preliminary analysis

Abstract: 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 averaging, error bar calculation, artifact removal, normalization and q calibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easy via the graphical user interface. BioXTAS RAW also provides preliminary analysis of one-dimensional data in terms of the indirect Fourier transform using the objective Bayesian approach to obtain the pair-distance distribution function, PDDF, and is thereby a free and open-source alternative to existing PDDF estimation software. Apart from the TIFF input format, the program also accepts ASCII-format input files and is currently compatible with one-dimensional data files from SAXS beamlines at a number of synchrotron facilities. BioXTAS RAW is written in Python with C++ extensions.

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

Abstract: 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.

A comparison of a microfocus X‐ray source and a conventional sealed tube for crystal structure determination

Abstract: 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 broader beam with an approximate intensity plateau. Both sources were mounted on the same Bruker D8 goniometer with a SMART APEX II CCD detector and Bruker Kryoflex low-temperature device. Switching between sources simply required changing the software zero setting of the 2θ circle and could be performed in a few minutes, so it was possible to use the same crystal for both sources without changing its temperature or orientation. A representative cross section of compounds (organic, organometallic and salt) with and without heavy atoms was investigated. For each compound, two data sets, one from a small and one from a large crystal, were collected using each source. In another experiment, the data quality was compared for crystals of the same compound that had been chosen so that they had dimensions similar to the width of the beam. The data were processed and the structures refined using standard Bruker and SHELX software. The experiments show that the IµS gives superior data for small crystals whereas the diffracted intensities were comparable for the large crystals. Appropriate scaling is particularly important for the IµS data.

Disordered materials studied using neutron polarization analysis on the multi-detector spectrometer, D7

Abstract: The technique of longitudinal neutron polarization analysis on a multi-detector neutron spectrometer (so-called 'xyz'-polarization analysis) is presented. This technique allows the simultaneous and unambiguous determination of the nuclear, magnetic and nuclear spin-incoherent scattering cross sections as a function of both momentum transfer and energy transfer. The implementation of xyz-polarization analysis on the recently upgraded D7 spectrometer at the Institut Laue-Langevin in Grenoble is described. Several examples of neutron polarization analysis studies of disordered systems on D7 are given, illustrating the valuable information which can be retrieved from the analysis of neutron diffraction patterns between the Bragg peaks.

Determination of the degree of preferred orientation within the March–Dollase approach

Abstract: An analytic expression has been derived connecting the degree of preferred orientation in a polycrystalline material to the March parameter. The latter defines the spread of angular distribution of crystallite inclinations in the March–Dollase approach [March (1932). Z. Kristallogr. 81, 285–297; Dollase (1986). J. Appl. Cryst. 19, 267–272]. In turn, the March parameter can be extracted from experimental data using either the Rietveld refinement of the entire diffraction pattern or the measurement of two diffraction intensities originating in the selected crystallographic planes. Working examples taken with two different types of samples are presented.

Advances in powder diffraction pattern indexing: N-TREOR09

Abstract: 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 diffe ...

Examination of whewellite kidney stones by scanning electron microscopy and powder neutron diffraction techniques

Abstract: # 2009 International Union of Crystallography Printed in Singapore – all rights reserved Kidney stones made of whewellite, i.e. calcium oxalate monohydrate, exhibit various morphological aspects. The crystalline structure of whewellite at the atomic scale was revisited through a single-crystal neutron study at room temperature using a four-circle automated diffractometer. The possible relationships between the various morphological types of whewellite stones and their structural characteristics were examined at the mesoscopic scale by the use of scanning electron microscopy and at the nanometric scale by powder neutron diffraction. All types of whewellite stones displayed a similar structure at the nanometric scale. However, significant differences were found at the mesoscopic scale. In particular, the crystallites in kidney stones resulting from a genetic hyperoxaluria exhibited a peculiar structure. There was a close relationship between stone morphology and crystallite organization at the mesoscopic level and the effectiveness of extracorporeal shockwave lithotripsy.

Odd electron diffraction patterns in silicon nanowires and silicon thin films explained by microtwins and nanotwins.

Abstract: Odd electron diffraction patterns (EDPs) have been obtained by transmission electron microscopy (TEM) on silicon nanowires grown via the vapour–liquid–solid method and on silicon thin films deposited by electron beam evaporation. Many explanations have been given in the past, without consensus among the scientific community: size artifacts, twinning artifacts or, more widely accepted, the existence of new hexagonal Si phases. In order to resolve this issue, the microstructures of Si nanowires and Si thin films have been characterized by TEM, high-resolution transmission electron microscopy (HRTEM) and high-resolution scanning transmission electron microscopy. Despite the differences in the geometries and elaboration processes, the EDPs of the materials show great similarities. The different hypotheses reported in the literature have been investigated. It was found that the positions of the diffraction spots in the EDPs could be reproduced by simulating a hexagonal structure with c/a = 12(2/3)1/2, but the intensities in many EDPs remained unexplained. Finally, it was established that all the experimental data, i.e. EDPs and HRTEM images, agree with a classical cubic silicon structure containing two microstructural defects: (i) overlapping Σ3 microtwins which induce extra spots by double diffraction, and (ii) nanotwins which induce extra spots as a result of streaking effects. It is concluded that there is no hexagonal phase in the Si nanowires and the Si thin films presented in this work.

Twinning on pyramidal planes in hexagonal close packed crystals determined along with other defects by X-ray line profile analysis

Abstract: A systematic procedure is developed to evaluate the frequency of {10.1}〈10.\overline 2〉 and {11.2}〈11.\overline 3〉 compressive twins and {10.2}〈10.\overline 1〉 and {11.1}〈\overline 1\overline 1.6〉 tensile twins together with dislocation densities, active slip systems and crystallite size in hexagonal close packed (hcp) metals. The effect of pyramidal twinning on X-ray line broadening in hcp metals is fundamentally different from the effect of twinning on close packed planes in face centred cubic (fcc) crystals. Therefore, the usual theoretical descriptions developed previously for fcc crystals cannot be used for pyramidal twinning in hcp crystals. The profile functions of sub-reflections for this type of twinning are derived to be the sum of a symmetrical and an antisymmetrical Lorentzian function. Sub-profile properties are parameterized and the parameter files are incorporated into the convolutional multiple whole profile (CMWP) procedure. The extended procedure, eCMWP, is applied to determine pyramidal twin frequencies together with dislocation densities, active slip systems and crystallite size in Mg deformed at different temperatures, in commercial purity Ti deformed at high temperature and in high-purity Ti deformed at room temperature.

Predicting the quaternary structure attribute of a protein by hybridizing functional domain composition and pseudo amino acid composition

Abstract: In vivo, some proteins exist as monomers (single polypeptide chains) and others as oligomers. The latter are composed of two or more chains (subunits) that are associated with each other through noncovalent interactions and, occasionally, disulfide bonds. Oligomers can be further classified into homo-oligomers (formed by identical subunits) and hetero-oligomers (formed by different subunits), and they form the structural basis of various biological functions such as cooperative effects, the allosteric mechanism and ion-channel gating. Therefore, it would be of less interest or of low priority for crystallographic scientists to crystallize a single protein chain and determine its three-dimensional structure if it is already known as part of an oligomer. However, it is both time-consuming and laborious to acquire such information on the quaternary structure attribute purely by experiment. In particular, with the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop an automated method by which crystallographic scientists can rapidly and effectively identify which quaternary attribute a particular protein chain has according to its sequence information. In view of this, a computational method has been developed by hybridizing the approaches of functional domain composition and pseudo amino acid composition. For the convenience of crystallographic scientists, a user-friendly web server, PQSA-Pred, has been established at http://218.65.61.89:8080/bioinfo/pqsa-pred, by which the desired information can be easily obtained.

Round robin on Rietveld quantitative phase analysis of Portland cements

Abstract: 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 clinkers and cements. Two sets of samples have been investigated, artificial mixtures and commercial samples. Artificial mixtures were prepared by mixing (weighing) synthesized single-crystalline phases in the appropriate proportions: (i) white clinker (Ca3SiO5, Ca2SiO4 and Ca3Al2O6) and (ii) grey cement (Ca3SiO5, Ca2SiO4, Ca3Al2O6, Ca4Al2Fe2O10, CaCO3 and CaSO4·2H2O). These two samples were used to assess the accuracy and uncertainty of the procedure, as an expected mineralogical phase fraction, the `true mineral­ogical percentage', is available under the assumption of negligible non-diffracting contents. In order to assess the validity and limitations of the Rietveld-based approach for cement materials, three commercial samples were measured: (i) white Portland clinker, (ii) grey Portland clinker and (iii) a type-I grey Portland cement. The samples studied have been chosen in order to cover most of the different typologies of binders. Reproducibilities and general uncertainty values, with a level of confidence of 95%, are reported and discussed.

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules

Abstract: 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 high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

ReX: a computer program for structural analysis using powder diffraction data

Abstract: Multi-platform software has been developed for the analysis of powder diffraction data, with particular focus on structure solution. The program provides a Rietveld optimization engine, with the possibility of refining parameters describing both the sample and the instrument model. Geometric constraints such as rigid fragments and torsion angles can be defined for the atomic structure, to reduce the number of degrees of freedom of the model. An innovative hierarchical description of the asymmetric unit has been adopted, which allows, in principle, the definition of arbitrarily complex geometric relationships. Additionally, global optimization algorithms may be used in place of the standard nonlinear least squares, when particularly challenging problems are being faced.

Towards extracting the charge density from normal-resolution data

Abstract: 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 of multipole parameters only, information on the charge density becomes accessible also for data not fulfilling charge-density requirements. A critical aspect of this procedure is the missing information on the correlation between refined and non-refined parameters. This correlation is investigated in detail by comparing a full multipole refinement on high-resolution and a blocked refinement on `normal-resolution' data sets of ciprofloxacin hexahydrate. Topological properties and dipole moments are shown to be in excellent agreement for the two refinements. A `normal-resolution' data set of ciprofloxacin hydrochloride 1.4-hydrate is also evaluated in this manner.

In situ X-ray diffraction of the transformation of gibbsite to α-alumina through calcination: effect of particle size and heating rate

Abstract: A study was conducted on the gibbsite to α-alumina (α-Al2O3) transformation dynamics with particular reference to the influence of particle size and heating rate. Coarse- and fine-grained gibbsites were used to examine the transformation paths for the two materials, with particular reference to the upper and lower branch sequences described by Wefers & Misra [Oxides and Hydroxides of Aluminium, (1987), Alcoa Technical Paper No. 19 Revised, Aluminium Company of America]. The main techniques used to assess gibbsite calcination were thermogravimetric differential scanning calorimetry and in situ X-ray diffraction, which provided complementary information on transformation behaviour. Whilst the quantitative phase analysis results indicated that the coarse- and fine-grained gibbsites followed both the upper and the lower branch sequences, detailed analysis of the results highlighted specific differences in the transformation behaviour for the two materials. With the loss of three molecules of water as gibbsite transformed to transition aluminas and finally α-Al2O3, there was a high degree of disorder in the crystal structure, resulting in broad and diffuse reflections in the diffraction patterns.

Automatic multiple-zone rigid-body refinement with a large convergence radius

Abstract: Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.

Structural and thermal properties of the monoclinic Lu2SiO5 single crystal: evaluation as a new laser matrix

Abstract: The crystal structure of monoclinic Lu2SiO5 (LSO) crystals, grown by the Czochralski method, was determined at room temperature by X-ray diffraction. The unit-cell parameters are a = 10.2550 (2), b = 6.6465 (2), c = 12.3626 (4) A, β = 102.422 (1)° in space group I2/a. The linear thermal expansion tensor was determined along the a, b, c and c* directions over the temperature range from 303.15 to 768.15 K, and the principal coefficients of the thermal expansion tensor are found to be αI = −1.0235 × 10−6 K, αII = 4.9119 × 10−6 K and αIII = 10.1105 × 10−6 K. The temperature dependence of the cell volume and monoclinic angle were also evaluated. In addition, the specific heat and the thermal diffusivity were measured over the temperature ranges from 293.15 to 673.15 K and from 303.15 to 572.45 K, respectively. As a result, the anisotropic thermal conductivity could be calculated and is reported for the first time, to the best of the authors' knowledge. The specific heat capacity of LSO is 139.54 J mol−1 K−1, and the principal components of the thermal conductivity are kI = 2.26 W m−1 K−1, kII = 3.14 W m−1 K−1 and kII = 3.67 W m−1 K−1 at 303.15 K. A new structure model was proposed to better understand the relationships between the crystal structure and anisotropic thermal properties. In comparison with other laser matrix crystals, it is found that LSO possesses relatively large anisotropic thermal properties, and owing to its small heat capacity it has a moderate thermal conductivity, which is similar to those of the tungstates but lower than those of the vanadates.

A Combined Fit of Total Scattering and Extended X-ray Absorption Fine Structure Data for Local-Structure Determination in Crystalline Materials

Abstract: Reverse Monte Carlo (RMC) refinements of local structure using a simultaneous fit of X-ray/neutron total scattering and extended X-ray absorption fine structure (EXAFS) data were developed to incorporate an explicit treatment of both single- and multiple-scattering contributions to EXAFS. The refinement algorithm, implemented as an extension to the public domain computer software RMCProfile, enables accurate modeling of EXAFS over distances encompassing several coordination shells around the absorbing species. The approach was first tested on Ni, which exhibits extensive multiple scattering in EXAFS, and then applied to perovskite-like SrAl1/2Nb1/2O3. This compound crystallizes with a cubic double-perovskite structure but presents a challenge for local-structure determination using a total pair-distribution function (PDF) alone because of overlapping peaks of the constituent partial PDFs (e.g. Al—O and Nb—O or Sr—O and O—O). The results obtained here suggest that the combined use of the total scattering and EXAFS data provides sufficient constraints for RMC refinements to recover fine details of local structure in complex perovskites. Among other results, it was found that the probability density distribution for Sr in SrAl1/2Nb1/2O3 adopts Td point-group symmetry for the Sr sites, determined by the ordered arrangement of Al and Nb, as opposed to a spherical distribution commonly assumed in traditional Rietveld refinements.

Bond valence sum: a new soft chemical constraint for RMCProfile

Abstract: The implementation of a new soft chemical constraint for the reverse Monte Carlo (RMC) program RMCProfile, based on bond valence sum (BVS) calculations, is described and its advantages for the analysis of 'total scattering' diffraction data collected from disordered crystalline systems discussed. The inclusion of the BVS formalism proves particularly valuable in the early stages of the RMC fitting procedure, by avoiding the formation of regions containing chemically unreasonable local configurations which can become frozen in. Furthermore, this approach provides the fitting procedure with additional chemical information to differentiate between cation species that share the same crystallographic sites within the averaged unit cell and possess similar neutron scattering lengths. These issues are illustrated using total neutron scattering data collected at room temperature on the oxide-ion conductor Zr2Y2O7 and the nonlinear optical material KTiOPO4.

Determination of crystal phase from an electron backscatter diffraction pattern

Abstract: Electron backscatter diffraction (EBSD) is a scanning electron microscope-based technique principally used for the determination and mapping of crystal orientation. This work describes an adaptation of the EBSD technique into a potential tool for crystal phase determination. The process can be distilled into three steps: (1) extracting a triclinic cell from a single EBSD pattern, (2) identifying the crystal symmetry from an examination of the triclinic cell, and (3) determining the lattice parameters. The triclinic cell is determined by finding the bands passing through two zone axes in the pattern including a band connecting the two. A three-dimensional triclinic unit cell is constructed based on the identified bands. The EBSD pattern is indexed in terms of the triclinic cell thus formed and the crystal orientation calculated. The pattern indexing results in independent multiple orientations due to the symmetry the crystal actually possesses. By examining the relationships between these multiple orientations, the crystal system is established. By comparing simulated Kikuchi bands with the pattern the lattice parameters can be determined. Details of the method are given for a test case of EBSD patterns obtained from the hexagonal phase of titanium.