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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: 2016-10-21


Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)


The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration ( is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.

A multi-slice simulation algorithm for grazing-incidence small-angle X-ray scattering


Grazing-incidence small-angle X-ray scattering (GISAXS) is an important technique in the characterization of samples at the nanometre scale. A key aspect of GISAXS data analysis is the accurate simulation of samples to match the measurement. The distorted-wave Born approximation (DWBA) is a widely used model for the simulation of GISAXS patterns. For certain classes of sample such as nanostructures embedded in thin films, where the electric field intensity variation is significant relative to the size of the structures, a multi-slice DWBA theory is more accurate than the conventional DWBA method. However, simulating complex structures in the multi-slice setting is challenging and the algorithms typically used are designed on a case-by-case basis depending on the structure to be simulated. In this paper, an accurate algorithm for GISAXS simulations based on the multi-slice DWBA theory is presented. In particular, fundamental properties of the Fourier transform have been utilized to develop an algorithm that accurately computes the average refractive index profile as a function of depth and the Fourier transform of the portion of the sample within a given slice, which are key quantities required for the multi-slice DWBA simulation. The results from this method are compared with the traditionally used approximations, demonstrating that the proposed algorithm can produce more accurate results. Furthermore, this algorithm is general with respect to the sample structure, and does not require any sample-specific approximations to perform the simulations.

Towards high-flux X-ray beam compressing channel-cut monochromators


The issue of a high-flux X-ray beam compressing channel-cut monochromator for applications in X-ray metrology is addressed. A Ge(111) compressor with compression ratio 20.3 was designed on the principle of a combination of symmetric and highly asymmetric diffractions. A pilot application of the single-point diamond technology (SPDT) to finish active surfaces of X-ray optics was tested, providing 50% flux enhancement as compared to a Ge(220) counterpart prepared by traditional surface treatment. This is much more than the theoretical 22% forecast and shows the potential of SPDT for preparation of high-flux X-ray compressors with a high compression ratio, where highly asymmetric diffraction with a very low exit angle is inevitable. The implications for efficient collection of X-rays from microfocus X-ray sources are discussed. A comparison of Ge compressors with Ge parallel channel-cut monochromators combined with a 50 µm slit shows the several times higher flux of the former, making them applicable in X-ray diffraction experiments at medium resolution. Furthermore, the Ge(111) compressor was tested as a collimator in high-resolution grazing-incidence small-angle X-ray scattering (GISAXS) measurements of surface gratings, providing experimental resolution close to 400 nm. This is ∼100 nm smaller than that achieved with the Ge(220) compressor but still approximately twice that of commercial SAXS/GISAXS laboratory setups.

First-principles study of structural and surface properties of (001) and (010) surfaces of hydroxylapatite and carbonated hydroxylapatite


Since it was first discovered that the main component of the mineral phase of bone, dentine and enamel is made from non-stoichiometric hydroxylapatite [Ca10(PO4)6(OH)2; OHAp], many successful efforts have been made to characterize its structure physico-chemically and to use it as a biomaterial for tissue repair and reconstruction. For the latter, it has been suggested that the biomimetic features of OHAp can be improved by vacancies and ionic substitutions, as typically found in natural bone tissues. In the present work, this line of thought has been followed, and the structural and electrostatic potential features of the (001) and (010) surfaces of OHAp and defective type A, type B and type AB carbonated hydroxylapatite (COHAp) have been studied using ab initio quantum mechanics at the DFT/B3LYP level. The results are in good agreement with previous experimental and preliminary theoretical work. They provide a deep analysis of the modulation of OHAp features caused by carbonate substitutions, and extend the current knowledge of the structural and surface properties of apatites.

A synchrotron X-ray diffraction deconvolution method for the measurement of residual stress in thermal barrier coatings as a function of depth


The average residual stress distribution as a function of depth in an air plasma-sprayed yttria stabilized zirconia top coat used in thermal barrier coating (TBC) systems was measured using synchrotron radiation X-ray diffraction in reflection geometry on station I15 at Diamond Light Source, UK, employing a series of incidence angles. The stress values were calculated from data deconvoluted from diffraction patterns collected at increasing depths. The stress was found to be compressive through the thickness of the TBC and a fluctuation in the trend of the stress profile was indicated in some samples. Typically this fluctuation was observed to increase from the surface to the middle of the coating, decrease a little and then increase again towards the interface. The stress at the interface region was observed to be around 300 MPa, which agrees well with the reported values. The trend of the observed residual stress was found to be related to the crack distribution in the samples, in particular a large crack propagating from the middle of the coating. The method shows promise for the development of a nondestructive test for as-manufactured samples.

Robust background modelling in DIALS


A method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution. It is shown that traditional methods can result in the systematic underestimation of background values. This then results in the reflection intensities being overestimated and gives rise to a change in the overall distribution of reflection intensities in a dataset such that too few weak reflections appear to be recorded. Statistical tests performed during data reduction may mistakenly attribute this to merohedral twinning in the crystal. Application of the robust generalized linear model algorithm is shown to correct for this bias.

On the forbidden and the optimum crystallographic variant of rutile in garnet


In many inclusion–host systems with similar oxygen packing schemes, the optimum crystallographic orientation relationship (COR) between the inclusion and the host is mostly determined by matching the similar oxygen sublattices of the two structures. In contrast, the prediction of the optimum COR or even just the rationalization of the observed COR(s) between an inclusion and host with incompatible oxygen sublattices, like rutile–garnet, is not straightforward. The related documentation for such cases is therefore limited. Given the abundant crystallographic data for the rutile–garnet system acquired by transmission electron microscopy and electron backscatter diffraction methods recently, this problem can now be examined in detail for the critical structural factors dictating the selection of optimum COR in such a structurally complicated system. On the basis of the unconstrained three-dimensional lattice point match and structural polyhedron match calculated for the observed CORs, it becomes clear that the prerequisite of optimum COR for rutile (rt) in garnet (grt) is to have most of their octahedra similarly oriented/inclined in space by aligning 〈103〉rt and 〈111〉grt for needle extension growth. Further rotation along the 〈103〉rt//〈111〉grt direction then leads to the energetically most favorable COR-2 variant with a good lattice point match defined by the coincidence site lattice (CSL) and a good topotaxial match of the constituent polyhedra at the CSL points, leaving unfavorable COR-1′ in the forbidden zones. This understanding sheds light not only on hierarchical energetics for the selection of inclusion variants in a complicated inclusion–host system, but also on yet-to-be-explored [UVW]-specific CORs and hetero-tilt boundaries for composite materials in general.

MAGNDATA: towards a database of magnetic structures. II. The incommensurate case


A free web page under the name MAGNDATA, which provides detailed quantitative information on more than 400 published magnetic structures, has been made available at the Bilbao Crystallographic Server ( It includes both commensurate and incommensurate structures. In the first article in this series, the information available on commensurate magnetic structures was presented [Gallego, Perez-Mato, Elcoro, Tasci, Hanson, Momma, Aroyo & Madariaga (2016). J. Appl. Cryst. 49, 1750–1776]. In this second article, the subset of the database devoted to incommensurate magnetic structures is discussed. These structures are described using magnetic superspace groups, i.e. a direct extension of the non-magnetic superspace groups, which is the standard approach in the description of aperiodic crystals. The use of magnetic superspace symmetry ensures a robust and unambiguous description of both atomic positions and magnetic moments within a common unique formalism. The point-group symmetry of each structure is derived from its magnetic superspace group, and any macroscopic tensor property of interest governed by this point-group symmetry can be retrieved through direct links to other programs of the Bilbao Crystallographic Server. The fact that incommensurate magnetic structures are often reported with ambiguous or incomplete information has made it impossible to include in this collection a good number of the published structures which were initially considered. However, as a proof of concept, the published data of about 30 structures have been re-interpreted and transformed, and together with ten structures where the superspace formalism was directly employed, they form this section of MAGNDATA. The relevant symmetry of most of the structures could be identified with an epikernel or isotropy subgroup of one irreducible representation of the space group of the parent phase, but in some cases several irreducible representations are active. Any entry of the collection can be visualized using the online tools available on the Bilbao server or can be retrieved as a magCIF file, a file format under development by the International Union of Crystallography. These CIF-like files are supported by visualization programs like Jmol and by analysis programs like JANA and ISODISTORT.

Influence of stress on the properties of Ge nanocrystals in an SiO2 matrix


In this work, self-assembled Ge quantum dot (QD) formation in a dielectric matrix is explored. Of particular interest were their structural and optical properties, in order to understand the stress build-up in such a process and its impact on the material properties during processing. To this end, thin films consisting of (Ge + SiO2)/SiO2 multilayers grown by RF magnetron sputtering were deposited at room temperature. Annealing of such films at 873 K in inert N2 atmosphere produced, at the position of the Ge-rich SiO2 layers, a high lateral density (about 1012 cm−2) of Ge QDs with a good crystallinity. SiO2 spacer layers separated the adjacent Ge-rich layers, where the Ge QDs were formed with a diameter of about the size of the (Ge + SiO2) as-deposited layer thickness, and created a good vertical repeatability, confirmed by the appearance of a Bragg sheet in two-dimensional small-angle X-ray scattering patterns. The structural analysis, by wide-angle X-ray diffraction, grazing-incidence small-angle X-ray scattering and transmission electron microscopy, has shown that the described processing of the films induced large compressive stress on the formed QDs. Optical analysis by time-resolved photoluminescence (PL) revealed that the high density of crystalline Ge QDs embedded in the amorphous SiO2 matrix produced a strong luminescence in the visible part of the spectrum at 2–2.5 eV photon energy. It is shown that the decay dynamics in this energy range are very fast, and therefore the transitions that create such PL are attributed to matrix defects present in the shell surrounding the Ge QD surface (interface region with the matrix). The measured PL peak, though wide at its half-width, when analysed in consecutive short spectral segments showed the same decay dynamics, suggesting the same mechanism of relaxation.

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances


Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.