Showing papers in "Journal of Applied Crystallography in 2008"

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

Abstract: The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.

VESTA: a three-dimensional visualization system for electronic and structural analysis

Abstract: A cross-platform program, VESTA, has been developed to visualize both structural and volumetric data in multiple windows with tabs. VESTA represents crystal structures by ball-and-stick, space-filling, polyhedral, wireframe, stick, dot-surface and thermal-ellipsoid models. A variety of crystal-chemical information is extractable from fractional coordinates, occupancies and oxidation states of sites. Volumetric data such as electron and nuclear densities, Patterson functions, and wavefunctions are displayed as isosurfaces, bird's-eye views and two-dimensional maps. Isosurfaces can be colored according to other physical quantities. Translucent isosurfaces and/or slices can be overlapped with a structural model. Collaboration with external programs enables the user to locate bonds and bond angles in the `graphics area', simulate powder diffraction patterns, and calculate site potentials and Madelung energies. Electron densities determined experimentally are convertible into their Laplacians and electronic energy densities.

A novel pole figure inversion method: specification of the MTEX algorithm

Abstract: A novel algorithm for ODF (orientation density function) estimation from diffraction pole figures is presented which is especially well suited for sharp textures and high-resolution pole figures measured with respect to arbitrarily scattered specimen directions, e.g. by area detectors. The estimated ODF is computed as the solution of a minimization problem which is based on a model of the diffraction counts as a Poisson process. The algorithm applies discretization by radially symmetric functions and fast Fourier techniques to guarantee smooth approximation and high performance. An implementation of the algorithm is freely available as part of the texture analysis software MTEX.

Determination of absolute structure using Bayesian statistics on Bijvoet differences.

Abstract: A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The outcome of this type of analysis can also be cast in the form of a new value, along with associated standard uncertainty, that resembles the value of the well known Flack x parameter. The standard uncertainty we obtain is often about half of the standard uncertainty in the value of the Flack x parameter. The proposed formalism is suited in particular to absolute configuration determination from diffraction data of biologically active (pharmaceutical) compounds where the strongest resonant scattering signal often comes from oxygen. It is shown that a reliable absolute configuration assignment in such cases can be made on the basis of Cu Kα data, and in some cases even with carefully measured Mo Kα data.

CHAINSAW: a program for mutating pdb files used as templates in molecular replacement

Abstract: CHAINSAW is a model editing program for use in molecular replacement. Given a sequence alignment between template and target, it modifies the template structure on a residue-by-residue basis by pruning nonconserved residues while leaving conserved residues unchanged. Three degrees of pruning are possible. An internal alignment algorithm is used to cope with any residues that may be missing from the X-ray structure. CHAINSAW has been successfully used as a tool to assist in solving a number of protein structures.

Symmetry determination following structure solution in P1

Abstract: A new method for space-group determination is described. It is based on a symmetry analysis of the structure-factor phases resulting from a structure solution in space group P1. The output of the symmetry analysis is a list of all symmetry operations compatible with the lattice. Each symmetry operation is assigned a symmetry agreement factor that is used to select the symmetry operations that are the elements of the space group of the structure. On the basis of the list of the selected operations the complete space group of the structure is constructed. The method is independent of the number of dimensions, and can also be used in solution of aperiodic structures. A number of cases are described where this method is particularly advantageous compared with the traditional symmetry analysis.

X-ray diffraction contrast tomography: a novel technique for three-dimensional grain mapping of polycrystals. I. Direct beam case

Abstract: The principles of a novel technique for nondestructive and simultaneous mapping of the three-dimensional grain and the absorption microstructure of a material are explained. The technique is termed X-ray diffraction contrast tomography, underlining its similarity to conventional X-ray absorption contrast tomography with which it shares a common experimental setup. The grains are imaged using the occasionally occurring diffraction contribution to the X-ray attenuation coefficient each time a grain fulfils the diffraction condition. The three-dimensional grain shapes are reconstructed from a limited number of projections using an algebraic reconstruction technique. An algorithm based on scanning orientation space and aiming at determining the corresponding crystallographic grain orientations is proposed. The potential and limitations of a first approach, based on the acquisition of the direct beam projection images only, are discussed in this first part of the paper. An extension is presented in the second part of the paper [Johnson, King, Honnicke, Marrow & Ludwig (2008). J. Appl. Cryst. 41, 310–318], addressing the case of combined direct and diffracted beam acquisition.

A versatile sample‐environment cell for non‐ambient X‐ray scattering experiments

Abstract: A compact reaction cell is described for in-situ experiments requiring control of both the temperature of the sample and the atmosphere over the sample. The cell incorporates an optional furnace capable of temperatures of up to ∼1273 K. The compact design and ability of the cell to mount directly on a standard goniometer head allows portability to a large number of diffraction instruments at synchrotron sources.

MULCh: modules for the analysis of small-angle neutron contrast variation data from biomolecular assemblies

Abstract: Small-angle neutron scattering with contrast variation can fill important gaps in our understanding of biomolecular assemblies, providing constraints that can aid in the construction of molecular models and in subsequent model refinements. This paper describes the implementation of simple tools for analysing neutron contrast variation data, accessible via a user-friendly web-based interface (http://www.mmb.usyd.edu.au/NCVWeb/). There are three modules accessible from the website to analyse neutron contrast variation data from bimolecular complexes. The first module, Contrast, computes neutron contrasts of each component of the complex required by the other two modules; the second module, Rg, analyses the contrast dependence of the radii of gyration to yield information relating to the size and disposition of each component in the complex; and the third, Compost, decomposes the contrast variation series into composite scattering functions, which contain information regarding the shape of each component of the complex, and their orientation with respect to each other.

Scatterless hybrid metal–single-crystal slit for small-angle X-ray scattering and high-resolution X-ray diffraction

Abstract: A simple hybrid design has been developed to produce practically scatterless aperture slits for small-angle X-ray scattering and high-resolution X-ray diffraction The hybrid slit consists of a rectangular single-crystal substrate (eg Si or Ge) bonded to a high-density metal base with a large taper angle (> 10°) The beam-defining single-crystal tip is oriented far from any Bragg peak position with respect to the incident beam and hence produces none of the slit scattering commonly associated with conventional metal slits It has been demonstrated that the incorporation of the scatterless slits leads to a much simplified design in small-angle X-ray scattering instruments employing only one or two apertures, with dramatically increased intensity (a threefold increase observed in the test setup) and improved low-angle resolution

Microstrain and grain-size analysis from diffraction peak width and graphical derivation of high-pressure thermomechanics

Abstract: An analytical method is presented for deriving the thermomechanical properties of polycrystalline materials under high-pressure (P) and high-temperature (T) conditions. This method deals with non-uniform stress among heterogeneous crystal grains and surface strain in nanocrystalline materials by examining peak-width variation under different P–T conditions. Because the method deals directly with lattice d spacing and local deformation caused by stress, it can be applied to process any diffraction profile, independent of detection mode. In addition, a correction routine is developed using diffraction elastic ratios to deal with severe surface strain and/or strain anisotropy effects related to nano-scale grain sizes, so that significant data scatter can be reduced in a physically meaningful way. Graphical illustration of the resultant microstrain analysis can identify micro/local yields at the grain-to-grain interactions resulting from high stress concentration, and macro/bulk yield of the plastic deformation over the entire sample. This simple and straightforward approach is capable of revealing the corresponding micro and/or macro yield stresses, grain crushing or growth, work hardening or softening, and thermal relaxation under high-P–T conditions, as well as the intrinsic residual strain and/or surface strain in the polycrystalline bulk. In addition, this approach allows the instrumental contribution to be illustrated and subtracted in a straightforward manner, thus avoiding the potential complexities and errors resulting from instrument correction. Applications of the method are demonstrated by studies of α-SiC (6H, moissanite) and of micro- and nanocrystalline nickel by synchrotron X-ray and time-of-flight neutron diffraction.

Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33

Abstract: There is a rapidly increasing interest in the use of synchrotron small-angle X-ray scattering (SAXS) for large-scale studies of biological macromolecules in solution, and this requires an adequate means of automating the experiment. A prototype has been developed of an automated sample changer for solution SAXS, where the solutions are kept in thermostatically controlled well plates allowing for operation with up to 192 samples. The measuring protocol involves controlled loading of protein solutions and matching buffers, followed by cleaning and drying of the cell between measurements. The system was installed and tested at the X33 beamline of the EMBL, at the storage ring DORIS-III (DESY, Hamburg), where it was used by over 50 external groups during 2007. At X33, a throughput of approximately 12 samples per hour, with a failure rate of sample loading of less than 0.5%, was observed. The feedback from users indicates that the ease of use and reliability of the user operation at the beamline were greatly improved compared with the manual filling mode. The changer is controlled by a client–server-based network protocol, locally and remotely. During the testing phase, the changer was operated in an attended mode to assess its reliability and convenience. Full integration with the beamline control software, allowing for automated data collection of all samples loaded into the machine with remote control from the user, is presently being implemented. The approach reported is not limited to synchrotron-based SAXS but can also be used on laboratory and neutron sources.

Simulating X-ray diffraction of textured films

Abstract: Computationally efficient simulations of grazing-incidence X-ray diffraction (GIXD) are discussed, with particular attention given to textured thin polycrystalline films on supporting substrates. A computer program has been developed for simulating scattering from thin films exhibiting varying degrees of preferred orientation. One emphasized common case is that of a `fibre' symmetry axis perpendicular to the sample plane, resulting from crystallites having one well defined crystal facet towards the substrate, but no preferred in-plane orientation. Peak splitting caused by additional scattering from the totally substrate-reflected beam (two-beam approximation) and refraction effects are also included in the program, together with the geometrical intensity corrections associated with GIXD measurements. To achieve `user friendliness' for scientists less familiar with diffraction, the mathematically simplest possible descriptions are sought whenever feasible. The practical use of the program is demonstrated for a selected thin-film example, perylene, which is of relevance for organic electronics.

Incorporation of a new design of backing seat and anvil in a Merrill–Bassett diamond anvil cell

Abstract: A modification to the Merrill–Bassett miniature diamond anvil cell is reported here, with the inclusion of tungsten carbide backing seats with Boehler–Almax-cut diamonds to replace the previously used beryllium seats and (typically) modified brilliant-cut anvils. This has led to the removal of troublesome beryllium powder lines from diffraction images, while maintaining the pressure range and opening angle of the original design.

Analysis of spin-echo small-angle neutron scattering measurements

Abstract: Spin-echo small-angle neutron scattering (SESANS) is, in contrast to conventional small-angle neutron scattering (SANS), a real-space technique. SESANS measures the projection of the density–density correlation function of a sample, rather than, as in SANS, its Fourier transform. This paper introduces a toolkit for interpretion and analysis of a SESANS measurement. Models that are used in SANS are discussed and translated into a SESANS formalism. These models can be used to analyse and fit the data obtained by SESANS. Dilute, concentrated, random, fractal and anisotropic density distributions are considered. Numerical methods used to calculate the projection from numerical data are presented, either by using Fourier transformation or via the real-space pair correlation function.

MESPEUS: a database of the geometry of metal sites in proteins

Abstract: A database with details of the geometry of metal sites in proteins has been set up The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura & Markley (2006) Nucleic Acids Res 35, D301–D303] and have been determined at 25 A resolution or better The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn The stored information includes PDB code, crystal data, resolution of structure determination, refinement program and R factor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies, B values, coordination numbers, information on coordination shapes, and metal–metal distances This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole Nδ of histidine] or which delivers details of all the metal sites in a specified protein The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://edulissbchedacuk/MESPEUS/ Some applications are briefly described, including a study of the characteristics of Mg sites that bind adenosine triphosphate, the derivation of an average Mg—Ophosphate distance and some problems that arise when average bond distances with high precision are required

Structural characterization of the clay mineral illite-1M

Abstract: This work reports the structural characterization of illite-1M from northern Hungary, with the first attempt to refine the structure model and locate the interlayer water molecule. Structural characterization was accomplished using state-of-the-art analytical methods available for clays. The results illustrate the status of techniques for clay structure determination, as well as providing a structural model for illite. The chemical formula for the illite-1M under investigation can be written as K0.78Ca0.02Na0.02(Mg0.34Al1.69FeIII0.02)[Si3.35Al0.65]O10(OH)2·nH2O. Structure simulations with WILDFIRE yielded a model with 30% of cis-vacant layers and an expandability percentage of 10%. The value of the percentage of expandability was confirmed with NEWMOD, with which the best simulation was obtained with 90% of di-octahedral mica with K (80% site population) in the interlayer region and 10% of expandable layers. The best structure simulation obtained with DIFFaX was also obtained with a population of K atoms of 80%, six cells along c (in agreement with the results of a transmission electron microscopy study) and an average dimension of the particles in the ab plane of 300 nm. Besides the determination of the basic structure unit (the results are consistent with those obtained with the local information provided by a fit of the pair distribution function data) and the model of disorder, refinement with DIFFaX+ allowed the calculation of a possible position for the interlayer water molecule. Although physically sound, both the observed tetrahedral layer corrugation and the location of the water molecule need further experimental evidence, because the final fit of the observed pattern is still imperfect. The reasons for this misfit are discussed.

Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography

Abstract: New software tools are introduced to facilitate diffraction experiments involving large numbers of crystals While existing programs have long provided a framework for lattice indexing, Bragg spot integration, and symmetry determination, these initial data processing steps often require significant manual effort This limits the timely availability of data analysis needed for high-throughput procedures, including the selection of the best crystals from a large sample pool, and the calculation of optimal data collection parameters to assure complete spot coverage with minimal radiation damage To make these protocols more efficient, a network of software applications and application servers has been developed, collectively known as Web-Ice When the package is installed at a crystallography beamline, a programming interface allows the beamline control software (eg Blu-Ice, DCSS) to trigger data analysis automatically Results are organized based on a list of samples that the user provides, and are examined within a Web page, accessible both locally at the beamline and remotely Optional programming interfaces permit the user to control data acquisition through the Web browser The system as a whole is implemented to support multiple users and multiple processors, and can be expanded to provide additional scientific functionality Web-Ice has a distributed architecture consisting of several stand-alone software components working together via a well defined interface Other synchrotrons or institutions may integrate selected components or the whole of Web-Ice with their own data acquisition software Updated information about current developments may be obtained at http://smbslacstanfordedu/research/developments/webice

Optimization and evaluation of data quality for charge density studies

Abstract: Criteria for the evaluation of hardware and software for the collection of charge density diffraction data are presented with examples. Evaluation of charge density studies using area detectors (based on 61 data sets) indicates that, although it is possible to obtain excellent data using such detectors, there are significant shortcomings which need to be addressed.

Stochastic fitting of specular X-ray reflectivity data using StochFit

Abstract: Specular X-ray reflectivity data provide detailed information on the electron density distribution at an interface. Typical modeling methods involve choosing a generic electron density distribution based on an initial speculation of the electron density profile from the physical parameters of the experimental system. This can lead to a biased set of solutions. StochFit provides stochastic model-independent and model-dependent methods for analyzing X-ray reflectivities of thin films at an interface. StochFit divides an electron density profile into many small boxes and stochastically varies the electron density of these boxes to locate the best fit to a measured reflectivity. Additionally, it provides the ability to perform model-dependent fitting with a stochastic search of the parameter space in order to locate the best possible fit. While model-independent profile search algorithms have been described previously, they are difficult to implement because of the heavy computational requirements, and there is a dearth of software available to the general scientific public utilizing these techniques. Several cases that illustrate the usefulness of these techniques are presented, with a demonstration of how they can be used in tandem.

Structure refinement: some background theory and practical strategies

Abstract: Most modern small-molecule refinement programs are based on similar algorithms. Details of these methods are scattered through the literature, sometimes in books that are no longer in print and usually in mathematical detail that makes them unattractive to nonprogrammers. This paper aims to discuss these well established algorithms in nonmathematical language, with the intention of enabling crystallographers to use their favourite programs effectively.

Finite size effects on the real-space pair distribution function of nanoparticles

Abstract: The pair distribution function (PDF) method is a powerful approach for the analysis of the structure of nanoparticles. An important approximation used in nanoparticle PDF simulations is the incorporation of a form factor describing nanoparticle size and shape. The precise effect of the form factor on the PDF is determined by both particle shape and structure if these characteristics are both anisotropic and correlated. The correct incorporation of finite size effects is important for distinguishing and quantifying the structural consequences of small particle size in nanomaterials.

Size-broadening anisotropy in whole powder pattern fitting. Application to zinc oxide and interpretation of the apparent crystallites in terms of physical models

Abstract: A new anisotropic size-broadening model based on a spherical-harmonics representation allowing determination of both volume- and area-averaged apparent crystallites and convenient for implementation into Rietveld programs is described. The model effectiveness is demonstrated on a ZnO powder pattern exhibiting strongly anisotropic size broadening and pronounced super-Lorentzian peak shapes. Moreover, it is shown how the apparent crystallites can be interpreted in terms of physical models by using ellipsoidal and cylindrical crystallites with lognormal size distributions. This interpretation is critically assessed and it is argued that both simplified physical models and a priori complementary information (obtained by transmission electron microscopy, for instance) are often needed to avoid unstable and non-unique solutions.

A novel electrochemical cell for in situ neutron diffraction studies of electrode materials for lithium-ion batteries

Abstract: Lithium-ion batteries are based on the principle of intercalation of lithium ions in host materials, both at the anode and at the cathode. These materials are in general crystalline and, during the operation of the battery, they undergo numerous phase transitions and structural rearrangements, often amplified by the presence of an applied potential difference. While in situ X-ray diffraction is an established technique in this field, in situ neutron diffraction is still in its pioneering stages and only a few attempts have been made to design an electrochemical cell suitable for these experiments. The technical development of such a device, along with a discussion of its serviceability to combine electrochemical measurements with neutron diffraction experiments, is hereby presented.

Optimal local axes and symmetry assignment for charge-density refinement

Abstract: In the perspective of building an expanded electron-density library based on multipolar modelling for common chemical atom types, new consistent local axes systems are proposed. Optimal symmetry constraints can consequently be applied to atoms and a large number of multipole populations can be fixed to a zero value. The introduction of symmetry constraints in the multipolar refinement of small compounds allows a reduction in the number of multipolar parameters stored in the library and required for the description of the atomic electron density. In a refinement where the symmetry constraints are not applied, the use of optimal axes enables the deviations from the local pseudo-symmetry to be highlighted. The application of symmetry constraints or restraints on multipoles is more effective when the axes are in accordance with the local geometry of the atom and can lead to improved crystallographic Rfree residuals. The new local axes systems, based on two or three atom neighbours, can also be usefully applied to the description of transition metal complexes.

Quantitative estimation of incompatibility stresses and elastic energy stored in ferritic steel

Abstract: Plastic incompatibility second-order stresses were determined for different orientations of a polycrystalline grain, using X-ray diffraction data and results of the self-consistent elasto-plastic model. The stresses in cold rolled ferritic steel were determined both in as-received and under tensile loaded conditions. It has been shown that the Reuss model and the self-consistent model applied to near surface volume provide the best approaches to determine diffraction elastic constants. For the first time, the elastic energy in an anisotropic material (arising from plastic incompatibilities between grains having various lattice orientations) has been determined. The second-order incompatibility stresses and stored elastic energy are presented in Euler space.

High hydrostatic pressure small-angle X-ray scattering cell for protein solution studies featuring diamond windows and disposable sample cells

Abstract: A high-pressure cell for synchrotron small-angle X-ray scattering (SAXS) studies of protein solutions is described. The design was optimized for use at up to 400 MPa in liquid pressure and with 8−12 keV X-rays with particular emphasis on the ease of use. The high-pressure cell was fabricated from corrosion-resistant Inconel 725 (Special Metals Corporation, Huntington, WV, USA) and featured Poulter-type windows [Poulter (1932). Phys. Rev. 40, 861–871]. Flat natural diamonds, 500 µm thick, were recycled from diamond anvil cells and were shown to perform well as high-pressure SAXS windows. For a simple and effective method of sample isolation, disposable plastic sample cells with a defined path length and reproducible parasitic scattering were designed. These sample cells enable efficient use of synchrotron time. The cells facilitate rapid and easy sample changes, eliminate the need to clean the cell between sample changes, and reduce the sample volume to as low as 12 µl. The disposable cells can also be used separately from the high-pressure cell for SAXS measurements at ambient pressure and temporary storage of samples. The performance of the apparatus is demonstrated with T4 lysozyme.

QUALX: a computer program for qualitative analysis using powder diffraction data

Abstract: QUALX is a new computer program for phase identification using powder diffraction data. It uses the Powder Diffraction File database, where a search for the phase best matching the experimental powder diffraction pattern is carried out. The program is characterized by a high level of automation: the traditional steps aimed at interpreting the experimental pattern before the search (background estimation, peak search, peak intensity evaluation) are executed automatically. The search may be carried out via constraints on compound name and/or chemical elements. In addition, several graphical options requested interactively enable the user to perform zero point correction evaluation, Kα2 stripping and smoothing. The program, written in Fortran95 and C++, runs on PCs under the Windows XP operating system. It is supported by a very effective graphical interface.

Reproducibility in X-ray reflectometry: results from the first world-wide round-robin experiment

Abstract: X-ray reflectometry (XRR) is a well established technique to evaluate quantitatively electron density, thickness and roughness of thin layers. In this paper, results of the first world-wide XRR round-robin experiment, involving 20 laboratories, are presented and discussed. The round-robin experiment was performed within the framework of the VAMAS Project `X-ray reflectivity measurements for evaluation of thin films and multilayers', the aim of which is to produce a `good practice' manual for XRR. The reproducibility of measurements obtained using different equipment has been investigated. The influence of the fitting of the experimental data was shown to be non-negligible compared with the experimental factors. The dynamic intensity range proves to be an important parameter for obtaining a good quality measurement. A simpler test sample which does not develop a surface oxide layer over time is now the subject of a follow-up study.

A toolkit for publishing enhanced figures.

Abstract: An editing toolkit has been developed to allow authors to create enhanced interactive figures for publication in crystallography journals. The visualization engine is Jmol, a Java program that can be manipulated as an applet in a web browser. The toolkit provides user-friendly widgets to manipulate the graphics state of Jmol, and persistent storage of graphics state, scripts and associated data files.