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Preview: Journal of Applied Crystallography

Journal of Applied Crystallography



Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer



Published: 2017-01-19

 



Approximating the near-edge mass absorption coefficients for Ni using an ultra-thin bimetal foil

2017-02-01

In an effort to improve the characteristics of a fluorescing metal-foil-based beam position monitor, a new bimetal ultra-thin (0.98/0.67 µm) Ti–Ni foil was introduced to replace an existing single-element ultra-thin 0.5 µm thick Cr foil. During characterization it was determined that absorption measurements on the bimetal foil could be used to fit the Ni mass absorption coefficients accurately in the vicinity of the Ni K edge. Comparison with experimental results from the literature demonstrated that the fitting procedure produced coefficients with uncertainties of the order of ±1%. Once determined, these fit coefficients allowed the thickness of an independently mounted 8 µm thick Ni foil to be computed from absorption measurements instead of relying on a tool-based measurement of the foil thickness. Using the 8 µm thick foil, a continuous map of Ni mass absorption coefficients was produced at 1 eV resolution throughout the near-edge region. This high-resolution map marks a significant improvement over the existing NIST XCOM or FFAST database mass absorption coefficients, which have estimated errors of 10–20% for the near-edge region.



Quantitative X-ray pair distribution function analysis of nanocrystalline calcium silicate hydrates: a contribution to the understanding of cement chemistry

2017-02-01

The structural evolution of nanocrystalline calcium silicate hydrate (C–S–H) as a function of its calcium to silicon (Ca/Si) ratio has been probed using qualitative and quantitative X-ray atomic pair distribution function analysis of synchrotron X-ray scattering data. Whatever the Ca/Si ratio, the C–S–H structure is similar to that of tobermorite. When the Ca/Si ratio increases from ∼0.6 to ∼1.2, Si wollastonite-like chains progressively depolymerize through preferential omission of Si bridging tetrahedra. When the Ca/Si ratio approaches ∼1.5, nanosheets of portlandite are detected in samples aged for 1 d, while microcrystalline portlandite is detected in samples aged for 1 year. High-resolution transmission electron microscopy imaging shows that the tobermorite-like structure is maintained to Ca/Si > 3.



Phase equilibria in the ternary reciprocal system Li, Ba // BO2, F and growth of bulk β-BaB2O4 crystals

2017-02-01

In order to find the optimum solvent for the growth of nonlinear optical β-BaB2O4 crystals, the phase relationships in the ternary reciprocal system Li, Ba // BO2, F have been studied using solid state synthesis, differential thermal analysis and X-ray powder diffraction. Isothermal and polythermal sections of the system Li, Ba // BO2, F are reported. In the studied system, the following compounds are formed: LiBa2B5O10 (melts by peritectic reaction at 930°C, i.e. 1203 K) and LiBaF3 (melts incongruently at 850°C, i.e. 1123 K). Visual polythermal analysis of seeding and growth of β-BaB2O4 crystals in this system was carried out. The primary crystallization field of β-BaB2O4 was defined. Using the top-seeded pulling technique, a β-BaB2O4 crystal of 93 mm in diameter, 34 mm in height and 520 g in weight has been grown.



Faceted growth of ({\bf {\overline 1}103})-oriented GaN domains on an SiO2-patterned m-plane sapphire substrate using polarity inversion

2017-02-01

Heteroepitaxial growth of ({\overline 1}103)-oriented GaN domains on m-plane sapphire is energetically unfavourable in comparison with that of (1{\overline 1}0{\overline 3})-oriented GaN domains, but the faceted domains with ({\overline 1}103)-oriented GaN reveal a more m-facet-dominant configuration than (1{\overline 1}0{\overline 3})-oriented GaN in such a way that the quantum-confined Stark effect can be more effectively suppressed. It is reported here, for the first time, that semipolar ({\overline 1}103)-oriented and faceted GaN domains can be grown on an SiO2-patterned m-plane sapphire substrate by employing polarity inversion of initially nucleated (1{\overline 1}0{\overline 3})-oriented GaN domains. This polarity inversion of semipolar GaN was found to occur when the domains were grown with a 20–37.5 times higher V/III ratio and 70 K lower growth temperature than corresponding parameters for polarity-not-inverted domains. This work opens up a new possibility of effective suppression of the quantum-confined Stark effect by polarity-controlled semipolar GaN in an inexpensive manner in comparison with homoepitaxial growth of ({\overline 1}103)-oriented GaN on a GaN substrate.



Modelling of glass-like carbon structure and its experimental verification by neutron and X-ray diffraction

2017-02-01

Glass-like carbon is a well known carbon form that still poses many challenges for structural characterization owing to a very complex internal atomic organization. Recent research suggests that glassy carbon has a fullerene-related structure that evolves with the synthesis temperature. This article reports on direct evidence of curved planes in glassy carbons using neutron and X-ray diffraction measurements and their analysis in real space using the atomic pair distribution function formalism. Changes in the structure including the degree of curvature of the non-graphitizing glassy carbons as a function of the pyrolysis temperature in the range 800–2500°C (1073–2773 K) are studied using optimized models of the atomic structure. Averaged models of single coherent scattering domains as well as larger structural fragments consisting of thousands of atoms were relaxed using classical molecular dynamics. For such models the diffraction intensities and the pair distribution functions were computed. The compatibility of the computer-generated models was verified by comparison of the simulations with the experimental diffraction data in both reciprocal and real spaces. On the basis of features of the developed structural models for glass-like carbons, the origin of the properties such as high strength and hardness and low gas permeability can be better understood.



Neutron diffraction of Cu–Zn–Sn ternary alloys: non-invasive assessment of the compositions of historical bronze/brass copper ternary alloys

2017-02-01

Neutron diffraction can be used as a tool for the characterization of metal materials in a totally non-invasive mode. In binary alloys with two elements in solid solution, crystallographic structure analysis provides information on the overall element compositions of the metal, based on the linear relationship between elemental fractions and lattice parameters known as Vegard's rule. However, for ternary solid-solution alloys the derivation of the overall metal composition is not straightforward because the problem is mathematically underdetermined. A number of artificially produced samples in the ternary system Cu–Zn–Sn, widely used in antiquity for gunmetal, were investigated by time-of-flight neutron diffraction, inductively coupled plasma mass spectroscopy, scanning electron microscopy with energy-dispersive X-ray spectroscopy and electron microprobe analysis. The multi-analysis approach allows definition of the limits and capabilities of neutron diffraction for obtaining the overall composition of a small sample set of ternary alloys, and thus moves the methodical approach a step forward even though it is applicable to the present sample set only. A relation showing an increasing Cu and Sn fraction counterbalanced by decreasing Zn content is presented, which allows the determination of the δ-phase composition from a lattice parameter measurement. Furthermore, the observed Zn loss up to 1.8 wt% for each melting step is of significance for the reconstruction of ancient technologies.



Evolution of the pore structure during the early stages of the alkali-activation reaction: an in situ small-angle neutron scattering investigation

2017-02-01

The long-term durability of cement-based materials is influenced by the pore structure and associated permeability at the sub-micrometre length scale. With the emergence of new types of sustainable cements in recent decades, there is a pressing need to be able to predict the durability of these new materials, and therefore nondestructive experimental techniques capable of characterizing the evolution of the pore structure are increasingly crucial for investigating cement durability. Here, small-angle neutron scattering is used to analyze the evolution of the pore structure in alkali-activated materials over the initial 24 h of reaction in order to assess the characteristic pore sizes that emerge during these short time scales. By using a unified fitting approach for data modeling, information on the pore size and surface roughness is obtained for a variety of precursor chemistries and morphologies (metakaolin- and slag-based pastes). Furthermore, the impact of activator chemistry is elucidated via the analysis of pastes synthesized using hydroxide- and silicate-based activators. It is found that the main aspect influencing the size of pores that are accessible using small-angle neutron scattering analysis (approximately 10–500 Å in diameter) is the availability of free silica in the activating solution, which leads to a more refined pore structure with smaller average pore size. Moreover, as the reaction progresses the gel pores visible using this scattering technique are seen to increase in size.



Radiation attenuation by single-crystal diamond windows

2017-02-01

As artificial diamond becomes more cost effective it is likely to see increasing use as a window for sample environment equipment used in diffraction experiments. Such windows are particularly useful as they exhibit exceptional mechanical properties in addition to being highly transparent to both X-ray and neutron radiation. A key application is in high-pressure studies, where diamond anvil cells (DACs) are used to access extreme sample conditions. However, despite their utility, an important consideration when using single-crystal diamond windows is their interaction with the incident beam. In particular, the Bragg condition will be satisfied for specific angles and wavelengths, leading to the appearance of diamond Bragg spots on the diffraction detectors but also, unavoidably, to loss of transmitted intensity of the beam that interacts with the sample. This effect can be particularly significant for energy-dispersive measurements, for example, in time-of-flight neutron diffraction work using DACs. This article presents a semi-empirical approach that can be used to correct for this effect, which is a prerequisite for the accurate determination of diffraction intensities.



Neutron total scattering of crystalline materials in the gigapascal regime

2017-02-01

Neutron total scattering of disordered crystalline materials provides direct experimental access to the local (short-range) structure. The ways in which this local structure agrees (or disagrees) with the long-range crystal structure can provide important insight into structure–property relationships. High-pressure neutron diffraction using a Paris–Edinburgh (P–E) pressure cell allows experimenters to explore the ways in which materials are affected by pressure, can reveal new synthetic routes to novel functional materials and has important applications in many areas, including geology, engineering and planetary science. However, the combination of these two experimental techniques poses unique challenges for both data collection and analysis. In this paper it is shown that, with only minor modifications to the standard P–E press setup, high-quality total scattering data can be obtained from crystalline materials in the gigapascal pressure regime on the PEARL diffractometer at ISIS. The quality of the data is assessed through the calculation of coordination numbers and the use of reverse Monte Carlo refinements. The time required to collect data of sufficient quality for detailed analysis is assessed and is found to be of the order of 8 h for a quartz sample. Finally, data from the perovskite LaCo0.35Mn0.65O3 are presented and reveal that PEARL total scattering data offer the potential of extracting local structural information from complex materials at high pressure.



How many water molecules are detected in X-ray protein crystal structures?

2017-02-01

The positions of several water molecules can be determined in protein crystallography, either buried in internal cavities or at the protein surface. It is important to be able to estimate the expected number of these water molecules to facilitate crystal structure determination. Here, a multiple Poisson regression model implemented on nearly 10 000 protein crystal structures shows that the number of detectable water molecules depends on eight variables: crystallographic resolution, R factor, percentage of solvent in the crystal, average B factor of the protein atoms, percentage of amino acid residues in loops, average solvent-accessible surface area of the amino acid residues, grand average of hydropathy of the protein(s) in the asymmetric unit and normalized number of heteroatoms that are not water molecules. Furthermore, a secondary analysis tested the effect of different software packages. Given the values of these eight variables, it is possible to compute the expected number of water molecules detectable in electron-density maps with reasonable accuracy (as suggested by an external validation of the model).



Crystallometric and projective properties of Kikuchi diffraction patterns

2017-02-01

Kikuchi diffraction patterns can provide fundamental information about the lattice metric of a crystalline phase. In order to improve the possible precision and accuracy of lattice parameter determination from the features observed in Kikuchi patterns, some useful fundamental relationships of geometric crystallography are reviewed, which hold true independently of the actual crystal symmetry. The Kikuchi band positions and intersections and the Kikuchi band widths are highly interrelated, which is illustrated by the fact that all lattice plane trace positions of the crystal are predetermined by the definition of only four traces. If, additionally, the projection centre of the gnomonic projection is known, the lattice parameter ratios and the angles between the basis vectors are fixed. A further definition of one specific Kikuchi band width is sufficient to set the absolute sizes of all lattice parameters and to predict the widths of all Kikuchi bands. The mathematical properties of the gnomonic projection turn out to be central to an improved interpretation of Kikuchi pattern data, emphasizing the importance of the exact knowledge of the projection centre.



Reliability of multigrain indexing for orthorhombic polycrystals above 1 Mbar: application to MgSiO3 post-perovskite

2017-02-01

This paper describes a methodology for characterizing the orientation and position of grains of an orthorhombic polycrystalline material at high pressure in a diamond anvil cell. The applicability and resolution of the method are validated by simulations and tested on an experimental data set collected on MgSiO3 post-perovskite at 135 GPa. In the simulations, ∼95% of the grains can be indexed successfully with ∼80% of the peaks assigned. The best theoretical average resolutions in grain orientation and position are 0.02° and 1.4 µm, respectively. The indexing of experimental data leads to 159 grains of post-perovskite with 30% of the diffraction peaks assigned with a 0.2–0.4° resolution in grain orientation. The resolution in grain location is not sufficient for in situ analysis of spatial relationships at high pressure. The grain orientations are well resolved and sufficient for following processes such as plastic deformation or phase transformation. The paper also explores the effect of the indexing parameters and of experimental constraints such as rotation range and step on the validity of the results, setting a basis for optimized experiments.



Precision and accuracy of stress measurement with a portable X-ray machine using an area detector

2017-02-01

The use of portable X-ray stress analyzers, which utilize an area detector along with the newly adopted `cosα' or full-ring fitting method, has recently attracted increasing interest. In laboratory conditions, these measurements are fast, convenient and precise because they employ a single-exposure technique that does not require sample rotation. In addition, the effects of grain size and orientation can be evaluated from the Debye ring recorded on the area detector prior to data analysis. The accuracy of the measured stress, however, has been questioned because in most cases just a single reflection is analyzed and the sample-to-detector distances are relatively short. This article presents a comprehensive analysis of the uncertainty associated with a state-of-the-art commercial portable X-ray device. Annealed ferrite reference powders were used to quantify the instrument precision, and the accuracy of the stress measurement was tested by in situ tensile loading on 1018 carbon steel and 6061 aluminium alloy bar samples. The results show that the precision and accuracy are sensitive to the instrument (or sample) tilt angle (ψ0) as well as to the selected hkl reflection of the sample. The instrument, sample and data analysis methods all affect the overall uncertainty, and each contribution is described for this specific portable X-ray system. Finally, on the basis of the conclusions reached, desirable measurement/analysis protocols for accurate stress assessments are also presented.



Homogeneous self-standing curved monocrystals, obtained using sandblasting, to be used as manipulators of hard X-rays and charged particle beams

2017-02-01

A technique to obtain self-standing curved crystals has been developed. The method is based on a sandblasting process capable of producing an amorphized layer on the substrate. It is demonstrated that the amorphized layer behaves as a thin compressive film, causing the curvature of the substrate. This procedure permits the fabrication of homogeneously curved crystals in a fast and economical way. It is shown that a sandblasted crystal can be used as an X-ray optical element for astrophysical or medical applications. A sandblasted bent crystal can also be used as an optical element for steering charged particles in accelerator beamlines. Several samples were manufactured and bent using the sandblasting method at the Sensor and Semiconductor Laboratory of Ferrara, Italy. Their curvature was verified using interferometric profilometry, showing a deformation in agreement with the Stoney formalism. The curvature of the machined samples was also tested using γ-ray diffraction at the Institut Laue–Langevin (ILL), Grenoble, France. A good agreement with the dynamical theory of diffraction was observed. In particular, the experiment showed that the crystalline quality of the bulk was preserved. Moreover, the method allowed curved samples to be obtained free of any additional material. Finally, a crystalline undulator was produced using sandblasting and tested using γ-ray diffraction at the ILL. The crystal showed a precise undulating pattern, so it will be suitable for hard X-ray production.



Nanoscale stability of two- and three-dimensional defects in Cu/Ag–Mo thin films

2017-02-01

A comparative study of the thermal stability of nanocrystalline Cu–Mo and Ag–Mo alloy thin films was performed. Phase decomposition, texture evolution, grain coarsening and segregation of Mo to planar faults of both films, before and after heat treatment, were studied using X-ray diffraction measurements and (high-resolution) transmission electron microscopy with energy-dispersive spectroscopy. The evolution of stress/strain in the thin films was traced by in situ X-ray diffraction measurements. The segregation of Mo solute atoms at twin boundaries in both films already occurs at room temperature. By first segregation and then precipitation of Mo atoms at grain boundaries, the columnar grain microstructure is preserved upon heat treatment. In the case of Ag–Mo thin films, the twin boundaries are also more or less preserved at elevated temperature, but in the case of Cu–Mo thin films the annihilation of twin boundaries takes place concomitantly with the precipitation of Mo in columnar grain interiors.



CADEM: calculate X-ray diffraction of epitaxial multilayers

2017-02-01

Epitaxial multilayers and superlattice (SL) structures are gaining increasing importance as they offer the opportunity to create artificial crystals with new functionalities. These crystals deviate from the parent bulk compounds not only in terms of the lattice constants but also in the symmetry classification, which renders calculation of their X-ray diffraction (XRD) patterns tedious. Nevertheless, XRD is essential to get information on the multilayer/SL structure such as, for example, out-of-plane lattice constants, strain relaxation and period length of the crystalline SL. This article presents a powerful yet simple program, based on the general one-dimensional kinematic X-ray diffraction theory, which calculates the XRD patterns of tailor-made multilayers and thus enables quantitative comparison of measured and calculated XRD data. As the multilayers are constructed layer by layer, the final material stack can be entirely arbitrary. Moreover, CADEM is very flexible and can be straightforwardly adapted to any material system. The source code of CADEM is available as supporting material for this article.



WinPSSP: a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

2017-02-01

The direct-space methods software Powder Structure Solution Program (PSSP) [Pagola & Stephens (2010). J. Appl. Cryst. 43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.



SUePDF: a program to obtain quantitative pair distribution functions from electron diffraction data

2017-02-01

SUePDF is a graphical user interface program written in MATLAB to achieve quantitative pair distribution functions (PDFs) from electron diffraction data. The program facilitates structural studies of amorphous materials and small nanoparticles using electron diffraction data from transmission electron microscopes. It is based on the physics of electron scattering as well as the total scattering methodology. A method of background modeling is introduced to treat the intensity tail of the direct beam, inelastic scattering and incoherent multiple scattering. Kinematical electron scattering intensity is scaled using the electron scattering factors. The PDFs obtained after Fourier transforms are normalized with respect to number density, nanoparticle form factor and the non-negativity of probability density. SUePDF is distributed as free software for academic users.



CBED Tools for semi-automatic measurement of crystal thicknesses

2017-02-01

Convergent-beam electron diffraction (CBED) is one of the most popular techniques to measure crystal thickness. The traditional measurement involves linear fitting of several fringes across the CBED disc, but for a thin crystal with fewer than three fringes the usefulness of this method will be limited. CBED Tools, a free plugin for the DigitalMicrograph software, provides a fast (∼1–2 min) and accurate algorithm to measure the crystal thickness on the basis of the linear fitting method, but it is also capable of determining the crystal thickness when it is very thin and only one fringe or part of the first fringe is recorded. CBED Tools can also be utilized to handle the severely distorted CBED pattern obtained when the zero-order Laue zone Kikuchi lines overlap with the fringes.



Oscail, a program package for small-molecule single-crystal crystallography with crystal morphology prediction and molecular modelling

2017-02-01

Oscail is a program for small-molecule crystallography which includes crystal morphology prediction and an interface to molecular modelling. The Oscail graphical user interface can drive SHELX and Superflip for structure solution and SHELXL for structure refinement. The lattice analysis includes hydrogen bonding, halogen bonding and van der Waals contact stacking. Other facilities include interactive bar charts of space-group frequencies in the Cambridge Structural Database, powder diffraction pattern calculation and reduced cell cluster analysis of structures. The graphics output includes thermal ellipsoid plots and rendered OpenGL and Raster3D photorealism in stills and movies. The molecular modelling includes quantum calculations (MOPAC, extended Hückel and density functional theory) and TINKER molecular mechanics.