Showing papers in "Journal of Applied Crystallography in 1999"

WinGX suite for small-molecule single-crystal crystallography

Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.

SIR97: a new tool for crystal structure determination and refinement

Abstract: SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures. Several new features have been introduced in SIR97 with respect to the previous version, SIR92: greater automatization, increased efficiency of the direct methods section, and a powerful graphics interface. The program also provides publication tables and CIF files.

Rietveld refinement guidelines

Abstract: A set of general guidelines for structure refinement using the Rietveld (whole-profile) method has been formulated by the International Union of Crystallography Commission on Powder Diffraction. The practical rather than the theoretical aspects of each step in a typical Rietveld refinement are discussed with a view to guiding newcomers in the field. The focus is on X-ray powder diffraction data collected on a laboratory instrument, but features specific to data from neutron (both constant-wavelength and time-of-flight) and synchrotron radiation sources are also addressed. The topics covered include (i) data collection, (ii) background contribution, (iii) peak-shape function, (iv) refinement of profile parameters, (v) Fourier analysis with powder diffraction data, (vi) refinement of structural parameters, (vii) use of geometric restraints, (viii) calculation of e.s.d.'s, (ix) interpretation of R values and (x) some common problems and possible solutions.

Phenomenological model of anisotropic peak broadening in powder diffraction

Abstract: Anisotropic line-shape broadening (peak width which is not a smooth function of d-spacing) is frequently observed in powder diffraction patterns, and can be a source of considerable difficulty for whole-pattern fitting or Rietveld analysis. A model of the multi-dimensional distribution of lattice metrics within a powder sample is developed, leading naturally to a few parameters which can be varied to achieve optimal line-shape fits. Conditions on these parameters are derived for all crystal systems, and the method is illustrated with two examples: sodium p-hydroxybenzoate and rubidium fulleride.

The contrast factors of dislocations in cubic crystals: the dislocation model of strain anisotropy in practice

Abstract: It has been shown recently that in many cases strain anisotropy in powder diffraction can be well accounted for by the dislocation model of the mean square strain. The practical application assumes knowledge of the individual contrast factors C of dislocations related to particular Burgers, line and diffraction vectors or to the average contrast factors C¯. A simple procedure for the experimental determination of C¯ has been worked out, enabling the determination of the character of the dislocations in terms of a simple parameter q. The values of the individual C factors were determined numerically for a wide range of elastic constants for cubic crystals. The C¯ factors and q parameters were parametrized by simple analytical functions, which can be used in a straightforward manner in numerical analyses, as e.g. in Rietveld structure refinement procedures.

POwderX: Windows-95-based program for powder X-ray diffraction data processing

Abstract: The crystallographic problem: A Windows-95-based program (PowderX) has been written for powder X-ray data processing and analysis. It can be used for plotting X-ray patterns, data smoothing, background subtraction, 2 elimination, peak search, indexing and zero-angle error correction. PowderX can also be used for data format conversions to prepare the input data for Rietveld re®nement and structure determination programs such as DBWS, FULLPROF, GSAS, SIMPRO and EXPO.

EXPO: a program for full powder pattern decomposition and crystal structure solution

Abstract: EXPO is the integration of two programs, EXTRA and SIRPOW.92, the first devoted to full powder pattern decomposition and the second to the solution and refinement of crystal structures. The program is able to exploit the prior information obtained during the crystal structure solution process for improving the classical decomposition. EXPO also allows preliminary cycles of Rietveld refinement.

PDFFIT, a program for full profile structural refinement of the atomic pair distribution function

Abstract: The program PDFFIT is designed for the full profile structural refinement of the atomic pair distribution function (PDF). In contrast to conventional structure refinement based on Bragg intensities, the PDF probes the local structure of the studied material. The program presented here allows the refinement of atomic positions, anisotropic thermal parameters and site occupancies as well as lattice parameters and experimental factors. By selecting individual atom types one can calculate partial and differential PDFs in addition to the total PDF. Furthermore one can refine multiple data sets and/or multiple structural phases. The program is controlled by a command language which includes a Fortran style interpreter supporting loops and conditional statements. This command language is also used to define the relation between refinement parameters and structural or experimental information, allowing virtually any constraint to be implemented in the model. PDFFIT is written in Fortran-77, and the source code and documentation are available via the World Wide Web.

The design and implementation of SnB version 2.0

Abstract: SnB is a direct-methods program based on the Shake-and-Bake methodology. It has been used to solve difficult or large structures that could not be solved by traditional reciprocal-space routines based on the tangent formula. Recently, it has also been used to determine the Se sites in large selenomethionyl-substituted proteins. SnB version 1.5 has been available for several years and is being used regularly in many laboratories. In this paper, we introduce SnB version 2.0, which incorporates a graphical user interface written in Java, a dynamic histogram display, and an interactive Java/VRML-based visualization facility. In addition, it provides the user with several utility routines and a variety of new algorithmic options.

Modeling hydroxyl and water H atoms

Abstract: The coordinates of hydroxyl (alcohol, phenol, etc.) and water H atoms can be easily calculated, within acceptable approximation, by combined geometric and force-field calculations on the basis of hydrogen-bonding interactions. To perform this kind of calculation the computer program HYDROGEN has been developed.

PowderSolve – a complete package for crystal structure solution from powder diffraction patterns

Abstract: Powder diffraction techniques are becoming increasingly popular as tools for the determination of crystal structures. The authors of this paper have developed a software package, named PowderSolve, to solve crystal structures from experimental powder diffraction patterns and have applied this package to solve the crystal structures of organic compounds with up to 18 variable degrees of freedom (defined in terms of the positions, orientations, and internal torsions of the molecular fragments in the asymmetric unit). The package employs a combination of simulated annealing and rigid-body Rietveld refinement techniques to maximize the agreement between calculated and experimental powder diffraction patterns. The agreement is measured by a full-profile comparison (using the R factor Rwp). As an additional check at the end of the structure solution process, accurate force-field energies may be used to confirm the stability of the proposed structure solutions. To generate the calculated powder diffraction pattern, lattice parameters, peak shape parameters and background parameters must be determined accurately before proceeding with the structure solution calculations. For this purpose, a novel variant of the Pawley algorithm is proposed, which avoids the instabilities of the original Pawley method. The successful application and performance of PowderSolve for crystal structure solution of 14 organic compounds of differing complexity are discussed.

Small-angle scattering of interacting particles. II. Generalized indirect Fourier transformation under consideration of the effective structure factor for polydisperse systems

Abstract: The indirect Fourier transformation (IFT) is the method of choice for the model-free evaluation of small-angle scattering data Unfortunately, this technique is only useful for dilute solutions because, for higher concentrations, particle interactions can no longer be neglected Thus an advanced technique was developed as a generalized version, the so-called generalized indirect Fourier transformation (GIFT) It is based on the simultaneous determination of the form factor, representing the intraparticle contributions, and the structure factor, describing the interparticle contributions The former can be determined absolutely free from model assumptions, whereas the latter has to be calculated according to an adequate model In this paper, various models for the structure factor are compared, eg the effective structure factor for polydisperse hard spheres, the averaged structure factor, the local monodisperse approximation and the decoupling approximation Furthermore, the structure factor for polydisperse rod-like particles is presented As the model-free evaluation of small-angle scattering data is an essential point of the GIFT technique, the use of a structure factor without any influence of the form amplitude is advisable, at least during the first evaluation procedure Therefore, a series of simulations are performed to check the possibility of the representation of various structure factors (such as the effective structure factor for hard spheres or the structure factor for rod-like particles) by the less exact but much simpler averaged structure factor In all the observed cases, it was possible to recover the exact form factor with a free determined parameter set for the structure factor The resulting parameters of the averaged structure factor have to be understood as apparent model parameters and therefore have only limited physical relevance Thus the GIFT represents a technique for the model independent evaluation of scattering data with a minimum of a priori information

Combined method for ab initio structure solution from powder diffraction data

Abstract: A new direct-space method for ab initio solution of crystal structures from powder diffraction diagrams is presented. The approach consists of a combined global optimization (`Pareto optimization') of the difference between the calculated and the measured diffraction pattern and of the potential energy of the system. This concept has been tested successfully on a large variety of ionic and intermetallic compounds.

Determination of symmetries and idealized cell parameters for simulated structures

Abstract: A robust algorithm is presented that determines the symmetries present in an atomic configuration and idealizes the cell parameters according to the crystal system suggested by the symmetries detected. No information besides the coordinates of the atoms within some arbitrary unit cell of the crystal is required.

Imaging of the helical arrangement of cellulose fibrils in wood by synchrotron X-ray microdiffraction

Abstract: A complete image of the helical arrangement of cellulose fibrils in the S2 layer of adjacent wood cells of Picea abies (Norwegian spruce) was obtained by applying position-resolved synchrotron X-ray microdiffraction on cells in cross section. In contrast to conventional fiber diffraction studies, the incident beam was parallel to the longitudinal cell axis, resulting in a glancing angle μ far from 90° with respect to the cellulose fibrils. This special choice of diffraction geometry allowed us to take advantage of an asymmetry effect in the two-dimensional diffraction patterns arising from the curvature of the Ewald sphere to obtain information on the local orientation of the cellulose fibrils. The small size of the beam, smaller than the thickness of a single cell wall, allowed mesh scans over intact transverse sections of adjacent wood cells with a microscopic position resolution. The scan yielded a map of diffraction patterns that could readily serve as a microscopic image. Each of the diffraction patterns was then used to evaluate the local orientation of the cellulose fibrils at the actual beam position. The combination of these results gave an image of cellulose fibrils forming (Z) helices in several adjacent wood cells.

Fourier modelling of the anisotropic line broadening of X-ray diffraction profiles due to line and plane lattice defects

Abstract: A new model of line-profile broadening due to the effect of linear and planar lattice defects has been incorporated into the conventional Rietveld algorithm for the structural refinement and whole-pattern fitting of powder data. The proposed procedure, applied to face-centred cubic (f.c.c.) structure materials, permits better modelling, even in the case of anisotropic line broadening and other hkl-dependent effects that can be related to the presence of dislocations and planar defects (stacking faults and twinning). Besides better quality of the profile fitting, detailed information on the defect structure can be produced: dislocation density and cut-off radius, stacking- and twin-fault probabilities can be refined together with the structural parameters. For each phase (in different samples or in multi-phase samples) the appropriate size–strain model can be selected. The Fourier formalism, which is the basis of the line-profile modelling, also permits an easy adaptation to different lattice-defect models. New approaches can be easily introduced and tested against or together with the existing ones. Finally, the devised program can also be used for the simulation of powder patterns for materials with different types and amounts of line and plane lattice defects.

LSCALE - the new normalization, scaling and absorption correction program in the Daresbury Laue software suite

Abstract: A new program in the Daresbury Laue software suite has been developed for the scaling and normalization of Laue intensity data, to yield fully corrected structure amplitudes. Previously available routines have been improved, and additional options for refinement, control and statistical diagnostic output provided. A new feature, namely a wavelength- and position-dependent absorption correction that models a two-dimensional surface derived from the Laue data alone, is discussed in detail; it is tested on simulated and real data, and the improvement in data quality is demonstrated. The wavelength normalization function is now able, when sufficiently redundant experimental data are available, to model fine details such as the features arising from the modification of the incident intensity spectrum by a platinum mirror in the beamline optics. A full data set for tetragonal lysozyme is processed with the new program, and extensive statistical output is given.

A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography

Abstract: Protein crystals have been cross-linked by a gentle technique whereby glutaraldehyde is introduced by vapor diffusion into the crystallization droplet containing the crystals. Diffraction analyses of crystals of three different proteins show that cross-linking prevents, in a large part, the lattice disorder normally observed on rapid cooling of these crystals. The diffraction results suggest that this cross-linking procedure, performed as a simple extension of the standard vapor-diffusion crystallization experiment, may generally aid in the cooling of fragile protein crystals for which standard procedures of cryopreservation prove inadequate.

Superscrew dislocation contrast on synchrotron white-beam topographs: an accurate description of the direct dislocation image

Abstract: A kinematic (geometrical) diffraction simulation model has been developed to provide understanding of direct dislocation images on synchrotron white-beam X-ray topographs, and has been successfully applied to illustrate the contrast formation mechanisms involved in images of micropipe-related superscrew dislocations in silicon carbide crystals. The coincidence of the simulations with the contrast features of the superscrew dislocation images, recorded using a series of synchrotron topography techniques, shows that this model is capable of revealing the detailed diffraction behavior of the highly distorted region around the dislocation core and determining the quantitative characteristics of the dislocations. The simulation technique is thus demonstrated to be a simple but efficient method for interpretation of synchrotron topographs, and may be applied to explain the topographic contrast characters of general crystal defects.

Topological analysis of experimental electron densities

Abstract: Practical computing algorithms are described for analysing the topology of experimental electron density distributions represented as either three-dimensional grid densities or multipolar pseudoatom superpositions. The algorithms are implemented in the program NEWPROP, results from which are illustrated with applications to two N-acetyl, C-methylamide blocked amino acid crystal structures.

Angle calculations for a `4S+2D' six-circle diffractometer

Abstract: Angle calculations are derived for the operation of a `4S+2D' six-circle X-ray or neutron diffractometer. The six degrees of freedom [four sample-orienting (`4S') and two detector-orienting (`2D')] of the diffractometer are used to control the scattering vector and a reference vector in the laboratory frame of reference. Several modes of operation unavailable in other types of diffractometer are presented.

Combined Rietveld and stereochemical restraint refinement of a protein crystal structure

Abstract: By combining high-resolution X-ray powder diffraction data and stereochemical restraints, Rietveld refinement of protein crystal structures has been shown to be feasible. A refinement of the 1261-atom protein metmyoglobin was achieved by combining 5338 stereochemical restraints with a 4648-step (dmin = 3.3 A) powder diffraction pattern to give the residuals Rwp = 2.32%, Rp = 1.66%, R(F2) = 3.10%. The resulting tertiary structure of the protein is essentially identical to that obtained from previous single-crystal studies.

Quantitative texture analysis of small domains with synchrotron radiation X-rays

Abstract: Quantitative analysis of crystallographic preferred orientation (texture) of very small volumes in fine-grained polycrystalline materials has been carried out with a monochromatic X-ray microbeam (≤30 µm) at the microfocus beamline of the European Synchrotron Radiation Facility (ESRF). The experimental procedure is described and illustrated with textures of rolled aluminium, aluminium and steel wires, polymer fibers and natural bone material (apatite).

Cryocrystallography with oil – an old idea revived

Abstract: A method is described that permits the cooling of protein crystals without the use of conventional cryoprotective agents. Covering the crystal completely with highly liquid dry paraffin oil (Merck) prevents ice formation. It is suggested that this method, because of its simplicity, be tried as a first choice in cryocrystallography, since it does not require the growth or soaking of crystals in solvents which could disturb the packing by diffusing into the crystal.

A self-consistent method for X-ray diffraction analysis of multiaxial residual-stress fields in the near-surface region of polycrystalline materials. I. Theoretical concept

Abstract: The application of the formalism for residual-stress gradient evaluation based on the measuring principle of the scattering-vector method, which has been derived in the first paper of this series [Genzel (1999). J. Appl. Cryst. 32, 770–778], is demonstrated by practical examples. Depending on the statistical scattering of the experimental data, either biaxial or even triaxial residual-stress states may be analysed; the latter case yields self-consistently the depth profiles of the in-plane stresses, σ11(τ) and σ22(τ), the normal stress component, σ33(τ), as well as the strain-free lattice spacing, d0(hkl). The results obtained by this new evaluation procedure are compared with those obtained by X-ray stress-gradient analysis performed on the basis of the sin2ψ method.

Difference structure‐factor normalization for heavy‐atom or anomalous‐scattering substructure determinations

Abstract: Procedures are described for normalizing structure-factor difference magnitudes, |Δ|F||SIR = ||FDer| − |FNat|| ≤ |FHeavy| or |Δ|F||SAS = ||F+h| − |F−h|| ≤ 2|F′′|, to prepare data for probabilistic direct methods phasing to determine heavy-atom or anomalous-scattering substructures in SIR (single-derivative isomorphous replacement) or SAS (single-wavelength anomalous scattering) cases. Applications of the procedures in several recent determinations of multi-selenium substructures in selenomethionyl proteins via SnB direct-methods phasing are briefly summarized.

Measurement of single-crystal elastic constants by neutron diffraction from polycrystals

Abstract: The relationships of diffraction averaged elastic compliances for an ideally random polycrystal to the single-crystal elastic compliances are given, within the Reuss approximation, for crystal systems with orthorhombic and higher symmetry. For anisotropic materials, these diffraction elastic compliances are dependent on the reflection index hkl. Expressions for the conventional elastic constants (Young's modulus, Poisson's ratio) are also given. A connection is made to the `X-ray elastic constants' used for diffraction-based measurements of residual stress. The relationships are used to calculate diffraction averaged constants for comparison with neutron diffraction data recorded from samples under applied uniaxial stress. The Reuss approximation works well for materials with the capacity for plastic deformation, such as metals and transformation toughening ceramics, whereas for other materials the Voigt–Reuss–Hill approximation gives better results. Based on the given relationships and experimental determinations of the diffraction elastic compliances for polycrystalline materials, a method is developed for determining the single-crystal elastic constants. The method for estimating single-crystal compliances is demonstrated here by application to extant data on Ni–Cr–Fe and Ti–6 wt% Al–4 wt% V alloys, and new measurements on cubic zirconia. It has been applied very recently [Kisi & Howard (1998). J. Am. Ceram. Soc. 81, 1682–1684] to determine the previously unknown elastic constants for a tetragonal zirconia.

Zeolite structure determination from powder diffraction data: applications of the FOCUS method

Abstract: The FOCUS approach to zeolite structure determination from powder diffraction data has been applied to data from four different zeolitic materials. The solutions of the structures of two aluminophosphate molecular sieves, YUL-89 (AWO topology) and YUL-90 (ZON topology), are used to demonstrate routine applications of the procedure. The high-silica zeolite ZSM-5 (MFI topology), which has 12 Si atoms (38 framework atoms) in the asymmetric unit, and the gallophosphate cloverite (-CLO topology), the framework of which is not fully fourfold connected, provide examples of extreme cases, which challenge the limits of the FOCUS algorithm. Taken together, the four examples give an overview of the practical aspects of the FOCUS method and illustrate its potential and its limitations.

Automatic orientation determination from Kikuchi patterns

Abstract: Some formal aspects of crystal orientation determination from Kikuchi patterns are discussed, with respect to writing general and fast algorithms for automatic indexing of the patterns and orientation determination. The geometry of the problem is presented in a general form which is also suitable for channeling patterns or X-ray Kossel patterns. Moreover, geometrical ambiguities and other reliability issues are considered. Some strategies designed to handle artifacts of automatic pattern analysis are presented. Finally, the reliability and the accuracy of the described procedures and the sensitivity of the results to the errors of the basic measurement parameters were tested on computer-generated patterns.