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CRYSTALLOGRAPHY (23 journals)

Showing 1 - 22 of 22 Journals sorted alphabetically
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 10)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 7)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 6)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 8)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 5)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 12)
Crystal Growth & Design     Hybrid Journal   (Followers: 19)
Crystal Research and Technology     Hybrid Journal   (Followers: 7)
Crystallography Reports     Hybrid Journal   (Followers: 3)
Crystallography Reviews     Hybrid Journal   (Followers: 5)
Crystals     Open Access   (Followers: 5)
IUCrJ     Open Access  
Journal of Applied Crystallography     Hybrid Journal   (Followers: 7)
Journal of Chemical Crystallography     Hybrid Journal   (Followers: 3)
Journal of Crystal Growth     Hybrid Journal   (Followers: 9)
Journal of Crystallization Process and Technology     Open Access   (Followers: 8)
Liquid Crystals     Hybrid Journal   (Followers: 3)
Liquid Crystals Today     Hybrid Journal   (Followers: 3)
Materials and Devices     Open Access   (Followers: 1)
Molecular Crystals and Liquid Crystals     Hybrid Journal   (Followers: 3)
Polymer crystallization     Hybrid Journal   (Followers: 1)
Progress in Crystal Growth and Characterization of Materials     Full-text available via subscription   (Followers: 8)
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Journal of Applied Crystallography
Journal Prestige (SJR): 1.635
Citation Impact (citeScore): 3
Number of Followers: 7  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0021-8898 - ISSN (Online) 1600-5767
Published by IUCr Homepage  [10 journals]
  • Artifact removal in the contour areas of SAXS-CT images by Tikhonov-L1
           minimization

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      Authors: Ogawa; H., Ono, S., Watanabe, Y., Nishikawa, Y., Nishitsuji, S., Kabe, T., Takenaka, M.
      Abstract: Small-angle X-ray scattering (SAXS) coupled with computed tomography (CT), denoted SAXS-CT, has enabled the spatial distribution of the characteristic parameters (e.g. size, shape, surface, length) of nanoscale structures inside samples to be visualized. In this work, a new scheme with Tikhonov regularization was developed to remove the effects of artifacts caused by streak scattering originating from the reflection of the incident beam in the contour regions of the sample. The noise due to streak scattering was successfully removed from the sinogram image and hence the CT image could be reconstructed free from artifacts in the contour regions.
      Keywords: small angle X-ray scattering; computed tomography; SAXS-CT; diffuse scattering; soft-matter; image processing
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-30
      DOI: 10.1107/S1600576721011523
      Issue No: Vol. 54, No. 6 (2021)
       
  • Evaluation of extremely steep residual stress gradients based on a
           combined approach using laboratory-scale equipment

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      Authors: Fischer; A., Degener, S., Liehr, A., Niendorf, T.
      Abstract: Surface treatments characterized by rapid heating and cooling (e.g. laser hardening) can induce very steep residual stress gradients in the direct vicinity of the area being treated. These gradients cannot be characterized with sufficient accuracy by means of the classical sin2Ψ approach applying angle-dispersive X-ray diffraction. This can be mainly attributed to limitations of the material removal method. In order to resolve residual stress gradients in these regions without affecting the residual stress equilibrium, another angle-dispersive approach, i.e. the universal plot method, can be used. A novel combination of the two approaches (sin2Ψ and universal plot) is introduced in the present work. Prevailing limits with respect to profiles as a function of depth can be overcome and, thus, high-resolution surface layer characterization is enabled. The data obtained are discussed comprehensively in comparison with results elaborated by energy-dispersive X-ray diffraction measurements.
      Keywords: residual stress analysis; energy-dispersive diffraction; angle-dispersive diffraction; laser surface hardening
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-30
      DOI: 10.1107/S1600576721010335
      Issue No: Vol. 54, No. 6 (2021)
       
  • Automated prediction of lattice parameters from X-ray powder diffraction
           patterns

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      Authors: Chitturi; S.R., Ratner, D., Walroth, R.C., Thampy, V., Reed, E.J., Dunne, M., Tassone, C.J., Stone, K.H.
      Abstract: A key step in the analysis of powder X-ray diffraction (PXRD) data is the accurate determination of unit-cell lattice parameters. This step often requires significant human intervention and is a bottleneck that hinders efforts towards automated analysis. This work develops a series of one-dimensional convolutional neural networks (1D-CNNs) trained to provide lattice parameter estimates for each crystal system. A mean absolute percentage error of approximately 10% is achieved for each crystal system, which corresponds to a 100- to 1000-fold reduction in lattice parameter search space volume. The models learn from nearly one million crystal structures contained within the Inorganic Crystal Structure Database and the Cambridge Structural Database and, due to the nature of these two complimentary databases, the models generalize well across chemistries. A key component of this work is a systematic analysis of the effect of different realistic experimental non-idealities on model performance. It is found that the addition of impurity phases, baseline noise and peak broadening present the greatest challenges to learning, while zero-offset error and random intensity modulations have little effect. However, appropriate data modification schemes can be used to bolster model performance and yield reasonable predictions, even for data which simulate realistic experimental non-idealities. In order to obtain accurate results, a new approach is introduced which uses the initial machine learning estimates with existing iterative whole-pattern refinement schemes to tackle automated unit-cell solution.
      Keywords: analysis automation; machine learning; powder diffraction; indexing
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-30
      DOI: 10.1107/S1600576721010840
      Issue No: Vol. 54, No. 6 (2021)
       
  • propSym: a tool to establish relationships between property constants for
           material property tensors of any order

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      Authors: Roy; A., Branch, D.W., Jensen, D.S., Kube, C.M.
      Abstract: The properties of crystalline materials can be described mathematically by tensors whose components are generally known as property constants. Tabulations of these constants in terms of the independent components are well known for common material properties (e.g. elasticity, piezoelectricity etc.) aptly described by tensors of lower rank (e.g. ranks 2–4). General relationships between constants of higher rank are often unknown and sometimes reported incorrectly. A computer program is developed here to calculate the property constant relationships of a property of any order, represented by a tensor of any rank and point group. Tensors up to rank 12, e.g. the tensor of sixth-order elastic constants c6ijklmnpqrs, can be calculated on a standard computer, while ranks higher than 12 are best handled on a supercomputer. Output is provided in either full index form or a reduced index form, e.g. the Voigt index notation common to elasticity. As higher-order tensors are often associated with nonlinear material responses, the program provides an accessible means to investigate the important constants involved in nonlinear material modeling. The routine has been used to discover several incorrect relationships reported in the literature.
      Keywords: crystal symmetry; material symmetry; tensors; nonlinear properties; material properties
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-30
      DOI: 10.1107/S160057672101058X
      Issue No: Vol. 54, No. 6 (2021)
       
  • Ce-exchange capacity of zeolite L in different cationic forms: a
           structural investigation

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      Authors: Confalonieri; G., Vezzalini, G., Quattrini, F., Quartieri, S., Dejoie, C., Arletti, R.
      Abstract: Cerium exchange by microporous materials, such as zeolites, has important applications in different fields, for example, rare earth element recovery from waste or catalytic processes. This work investigated the Ce-exchange capacity of zeolite L in three different cationic forms (the as-synthesized K form and Na- and NH4-exchanged ones) from a highly concentrated solution. Chemical analyses and structural investigations allowed determination of the mechanisms involved in the exchanges and give new insights into the interactions occurring between the cations and the zeolite framework. Different cation sites are involved: (i) K present in the original LTL in the cancrinite cage (site KB) cannot be exchanged; (ii) the cations in KD (in the 12-membered ring channel) are always exchanged; while (iii) site KC (in the eight-membered ring channel) is involved only when K+ is substituted by NH4+, thus promoting a higher exchange rate for NH4+ → K+ than for Na+ → K+. In the Ce-exchanged samples, a new site occupied by Ce appears in the centre of the main channel, accompanied by an increase in the number of and a rearrangement of H2O molecules. In terms of Ce exchange, the three cationic forms behave similarly, from both the chemical and structural point of view (exchanged Ce ranges from 38 to 42% of the pristine cation amount). Beyond the intrinsic structural properties of the zeolite L framework, the Ce exchange seems thus also governed by the water coordination sphere of the cation. Complete Ce recovery from zeolite pores was achieved.
      Keywords: Ce-exchanged zeolite; structural analysis; synchrotron high-resolution X-ray powder diffraction
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-25
      DOI: 10.1107/S1600576721010827
      Issue No: Vol. 54, No. 6 (2021)
       
  • Insights into the mechanism of high lipid–detergent crystallization
           of membrane proteins

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      Authors: Trampari; S., Neumann, C., Hjorth-Jensen, S.J., Shahsavar, A., Quistgaard, E.M., Nissen, P.
      Abstract: Obtaining well diffracting crystals of membrane proteins is often challenging, but chances can be improved by crystallizing them in lipidic conditions that mimic their natural membrane environments. One approach is the high lipid–detergent (HiLiDe) method, which works by mixing the target protein with high concentrations of lipid and detergent prior to crystallization. Although this approach is convenient and flexible, understanding the effects of systematically varying lipid/detergent ratios and a characterization of the lipid phases that form during crystallization would be useful. Here, a HiLiDe phase diagram is reported for the model membrane protein MhsT, which tracks the precipitation and crystallization zones as a function of lipid and detergent concentrations, and is augmented with data on crystal sizes and diffraction properties. Additionally, the crystallization of SERCA1a solubilized directly with native lipids is characterized as a function of detergent concentration. Finally, HiLiDe crystallization drops are analysed with transmission electron microscopy, which among other features reveals liposomes, stacked lamellae that may represent crystal precursors, and mature crystals with clearly discernible packing arrangements. The results emphasize the significance of optimizing lipid/detergent ratios over broad ranges and provide insights into the mechanism of HiLiDe crystallization.
      Keywords: X-ray crystallography; membrane proteins; lipid phases; high lipid–detergent (HiLiDe) method; crystallization phase diagrams; electron microscopy
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-25
      DOI: 10.1107/S1600576721010669
      Issue No: Vol. 54, No. 6 (2021)
       
  • Small-angle scattering for beginners

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      Authors: Gommes; C.J., Jaksch, S., Frielinghaus, H.
      Abstract: Many experimental methods are available for the characterization of nanostructures, but most of them are limited by stringent experimental conditions. When it comes to analysing nanostructures in the bulk or in their natural environment – even as ordinary as water at room temperature – small-angle scattering (SAS) of X-rays or neutrons is often the only option. The rapid worldwide development of synchrotron and neutron facilities over recent decades has opened unprecedented possibilities for using SAS in situ and in a time-resolved way. But, in spite of its huge potential in the field of nanomaterials in general, SAS is covered far less than other characterization methods in non-specialized curricula. Presented here is a rigorous discussion of small-angle scattering, at a technical level comparable to the classical undergraduate coverage of X-ray diffraction by crystals and which contains diffraction as a particular case.
      Keywords: small-angle scattering; SAXS; SANS; form factors; structure factors
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-25
      DOI: 10.1107/S1600576721010293
      Issue No: Vol. 54, No. 6 (2021)
       
  • pyRS: a user-friendly package for the reduction and analysis of neutron
           diffraction data measured at the High Intensity Diffractometer for
           Residual Stress Analysis

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      Authors: Fancher; C.M., Bunn, J.R., Bilheux, J., Zhou, W., Whitfield, R.E., Borreguero, J., Peterson, P.F.
      Abstract: The pyRS (Python residual stress) analysis software was designed to address the data reduction and analysis needs of the High Intensity Diffractometer for Residual Stress Analysis (HIDRA) user community. pyRS implements frameworks for the calibration and reduction of measured 2D data into intensity versus scattering vector magnitude and subsequent single-peak-fitting analysis to facilitate texture and residual strain/stress analysis. pyRS components are accessible as standalone user interfaces for peak-fitting and stress/strain analysis or as Python scripts. The scripting interface facilitates automated data reduction and peak-fitting analysis using an autoreduction protocol. Details of the implemented functionality are discussed.
      Keywords: residual stress; neutron diffraction; software
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-25
      DOI: 10.1107/S1600576721010554
      Issue No: Vol. 54, No. 6 (2021)
       
  • Recovering local structure information from high-pressure total scattering
           experiments

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      Authors: Herlihy; A., Geddes, H.S., Sosso, G.C., Bull, C.L., Ridley, C.J., Goodwin, A.L., Senn, M.S., Funnell, N.P.
      Abstract: High pressure is a powerful thermodynamic tool for exploring the structure and the phase behaviour of the crystalline state, and is now widely used in conventional crystallographic measurements. High-pressure local structure measurements using neutron diffraction have, thus far, been limited by the presence of a strongly scattering, perdeuterated, pressure-transmitting medium (PTM), the signal from which contaminates the resulting pair distribution functions (PDFs). Here, a method is reported for subtracting the pairwise correlations of the commonly used 4:1 methanol:ethanol PTM from neutron PDFs obtained under hydrostatic compression. The method applies a molecular-dynamics-informed empirical correction and a non-negative matrix factorization algorithm to recover the PDF of the pure sample. Proof of principle is demonstrated, producing corrected high-pressure PDFs of simple crystalline materials, Ni and MgO, and benchmarking these against simulated data from the average structure. Finally, the first local structure determination of α-quartz under hydrostatic pressure is presented, extracting compression behaviour of the real-space structure.
      Keywords: total scattering; high pressure; neutron diffraction; pair distribution function
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-23
      DOI: 10.1107/S1600576721009420
      Issue No: Vol. 54, No. 6 (2021)
       
  • Intrinsic roughness and interfaces of Cr/Be multilayers

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      Authors: Pleshkov; R., Chkhalo, N., Polkovnikov, V., Svechnikov, M., Zorina, M.
      Abstract: The structures of Cr/Be multilayer mirror interfaces are investigated using X-ray reflectometry, diffuse X-ray scattering and atomic force microscopy. The combination of these methods makes it possible to separate the contributions of roughness and interlayer diffusion/intermixing for each sample. In the range of period thicknesses of 2.26–0.8 nm, it is found that the growth roughness of the Cr/Be multilayer mirrors does not depend on the period thickness and is ∼0.2 nm. The separation of roughness and diffuseness allows estimation of layer material intermixing and the resulting drop in the optical contrast, which is from 0.85 to 0.17 in comparison with an ideally sharp structure.
      Keywords: multilayers; roughness; interdiffusion; inverse problem
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-23
      DOI: 10.1107/S160057672101027X
      Issue No: Vol. 54, No. 6 (2021)
       
  • Evolution of laser-induced strain in a Ge crystal for the [111] and [100]
           directions probed by time-resolved X-ray diffraction

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      Authors: Rathore; R., Singhal, H., Ansari, A., Chakera, J.A.
      Abstract: Ultra-short laser-pulse-induced strain propagation in a Ge crystal is studied in the [111] and [100] directions using time-resolved X-ray diffraction (TXRD). The strain propagation velocity is derived by analysis of the TXRD signal from the strained crystal planes. Numerical integration of the Takagi–Taupin equations is performed using open source code, which provides a very simple approach to estimate the strain propagation velocity. The present method will be particularly useful for relatively broad spectral bandwidths and weak X-ray sources, where temporal oscillations in the diffracted X-ray intensity at the relevant phonon frequencies would not be visible. The two Bragg reflections of the Ge sample, viz. 111 and 400, give information on the propagation of strain for two different depths, as the X-ray extinction depths are different for these two reflections. The strain induced by femtosecond laser excitation has a propagation velocity comparable to the longitudinal acoustic velocity. The strain propagation velocity increases with increasing laser excitation fluence. This fluence dependence of the strain propagation velocity can be attributed to crystal heating by ambipolar carrier diffusion. Ge is a promising candidate for silicon-based optoelectronics, and this study will enhance the understanding of heat transport by carrier diffusion in Ge induced by ultra-fast laser pulses, which will assist in the design of optoelectronic devices.
      Keywords: time-resolved X-ray diffraction; semiconductors; laser-induced strain; strain propagation velocity; ambipolar carrier diffusion
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-23
      DOI: 10.1107/S1600576721010281
      Issue No: Vol. 54, No. 6 (2021)
       
  • rmc-discord: reverse Monte Carlo refinement of diffuse scattering and
           correlated disorder from single crystals

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      Authors: Morgan; Z.J., Zhou, H.D., Chakoumakos, B.C., Ye, F.
      Abstract: A user-friendly program has been developed to analyze diffuse scattering from single crystals with the reverse Monte Carlo method. The approach allows for refinement of correlated disorder from atomistic supercells with magnetic or structural (occupational and/or displacive) disorder. The program is written in Python and optimized for performance and efficiency. Refinements of two user cases obtained with legacy neutron-scattering data demonstrate the effectiveness of the approach and the developed program. It is shown with bixbyite, a naturally occurring magnetic mineral, that the calculated three-dimensional spin-pair correlations are resolved with finer real-space resolution compared with the pair distribution function calculated directly from the reciprocal-space pattern. With the triangular lattice Ba3Co2O6(CO3)0.7, refinements of occupational and displacive disorder are combined to extract the one-dimensional intra-chain correlations of carbonate molecules that move toward neighboring vacant sites to accommodate strain induced by electrostatic interactions. The program is packaged with a graphical user interface and extensible to serve the needs of single-crystal diffractometer instruments that collect diffuse-scattering data.
      Keywords: diffuse scattering; correlated disorder; single crystals; rmc-discord; Monte Carlo refinement; supercells
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-23
      DOI: 10.1107/S1600576721010141
      Issue No: Vol. 54, No. 6 (2021)
       
  • Fisher information for optimal planning of X-ray diffraction experiments

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      Authors: Mikhalychev; A., Zhevno, K., Vlasenko, S., Benediktovitch, A., Ulyanenkova, T., Ulyanenkov, A.
      Abstract: Fisher information is a powerful mathematical tool suitable for quantification of data `informativity' and optimization of the experimental setup and measurement conditions. Here, it is applied to X-ray diffraction and an informational approach to choosing the optimal measurement configuration is proposed. The core idea is maximization of the information which can be extracted from the measured data set by the selected analysis technique, over the sets of accessible reflections and measurement geometries. The developed approach is applied to high-resolution X-ray diffraction measurements and microstructure analysis of multilayer samples, and its efficiency and consistency are demonstrated with the results of more straightforward Monte Carlo simulations.
      Keywords: X-ray diffraction; X-ray reflectivity; Fisher information; artificial intelligence
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S1600576721009869
      Issue No: Vol. 54, No. 6 (2021)
       
  • BioSAXS on the SWING beamline at Synchrotron SOLEIL

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      Authors: Thureau; A., Roblin, P., Pérez, J.
      Abstract: Small-angle X-ray scattering (SAXS) of proteins in solution has become a key tool for biochemists and structural biologists, thanks especially to the availability of beamlines with high-throughput capabilities at synchrotron sources. Despite the large spectrum of scientific disciplines tackled on the SWING beamline since its opening in 2008, there has always been a strong commitment to offering state-of-the-art biological SAXS (BioSAXS) instrumentation and data reduction methods to the scientific community. The extremely reliable in-vacuum EigerX-4M detector allows collection of an unlimited number of frames without noise. A small beamstop including a diamond diode-based monitor enables measurements of the transmitted intensity with 0.1% precision as well as a qmax/qmin ratio as large as 140 at a single distance. The parasitic scattering has been strongly reduced by the installation of new hybrid blades. A new thermally controlled in-vacuum capillary holder including fibre-optics-based spectroscopic functionalities allows the simultaneous use of three spectroscopic techniques in addition to SAXS measurements. The addition of a second high-performance liquid chromatography (HPLC) circuit has virtually eliminated the waiting time associated with column equilibration. The easy in-line connection of a multi-angle light scattering spectrometer and a refractometer allows for an independent determination of the molecular mass and of the concentration of low-UV-absorption samples such as detergents and sugars, respectively. These instrumental improvements are combined with important software developments. The HPLC injection Agilent software is controlled by the SAXS beamline acquisition software, allowing a virtually unlimited series of automated SAXS measurements to be synchronized with the sample injections. All data-containing files and reports are automatically stored in the same folders, with names related to both the user and sample. In addition, all raw SAXS images are processed automatically on the fly, and the analysed data are stored in the ISPyB database and made accessible via a web page.
      Keywords: biological small-angle X-ray scattering; BioSAXS; size-exclusion chromatography small-angle X-ray scattering; SEC-SAXS; structural biology; SWING
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S1600576721008736
      Issue No: Vol. 54, No. 6 (2021)
       
  • In situ small-angle X-ray scattering investigation of X-ray-induced gold
           nanoparticle synthesis without stabilizer

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      Authors: Li; F., Xu, Q., Xia, W., Zhang, X., Zhao, W., Zhou, L., Zhong, H., Peng, W., Liu, Z., Sun, T.
      Abstract: The X-ray irradiation of gold salt aqueous solutions in the synthesis of gold nanoparticles (AuNPs) in the absence of any reducing agent or stabilizer is presented. The size, dispersion, number of particles, yield and morphology evolution during the radiolytic formation of AuNPs were followed simultaneously using in situ small-angle X-ray scattering. This study provides an insight into the overall kinetics and formation mechanisms at the initial stage of AuNP synthesis without reductants and stabilizers. The pH-dependent speciation of aqueous HAuCl4 and its influence on the synthesis, structure and properties of AuNPs were observed. The result sheds light on the key parameters required to obtain stable monomodal particles and the influence of the surface charge and reactivity of the chemical solution on the final particle size and shape.
      Keywords: gold nanoparticles; X-ray radiolysis; nanoparticle synthesis; in situ analysis; small-angle X-ray scattering
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S1600576721010207
      Issue No: Vol. 54, No. 6 (2021)
       
  • Signature of antiphase boundaries in iron oxide nanoparticles

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      Authors: Köhler; T., Feoktystov, A., Petracic, O., Nandakumaran, N., Cervellino, A., Brückel, T.
      Abstract: Iron oxide nanoparticles find a wide variety of applications, including targeted drug delivery and hyperthermia in advanced cancer treatment methods. An important property of these particles is their maximum net magnetization, which has been repeatedly reported to be drastically lower than the bulk reference value. Previous studies have shown that planar lattice defects known as antiphase boundaries (APBs) have an important influence on the particle magnetization. The influence of APBs on the atomic spin structure of nanoparticles with the γ-Fe2O3 composition is examined via Monte Carlo simulations, explicitly considering dipole–dipole interactions between the magnetic moments that have previously only been approximated. For a single APB passing through the particle centre, a reduction in the magnetization of 3.9% (for 9 nm particles) to 7.9% (for 5 nm particles) is found in saturation fields of 1.5 T compared with a particle without this defect. Additionally, on the basis of Debye scattering equation simulations, the influence of APBs on X-ray powder diffraction patterns is shown. The Fourier transform of the APB peak profile is developed to be used in a whole powder pattern modelling approach to determine the presence of APBs and quantify them by fits to powder diffraction patterns. This is demonstrated on experimental data, where it could be shown that the number of APBs is related to the observed reduction in magnetization.
      Keywords: nanoparticles; X-ray powder diffraction; Monte Carlo simulations; Debye scattering equation; antiphase boundaries
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S1600576721010128
      Issue No: Vol. 54, No. 6 (2021)
       
  • Optimizing the geometry of aerodynamic lens injectors for single-particle
           coherent diffractive imaging of gold nanoparticles

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      Authors: Worbs; L., Roth, N., Lübke, J., Estillore, A.D., Xavier, P.L., Samanta, A.K., Küpper, J.
      Abstract: Single-particle X-ray diffractive imaging (SPI) of small (bio-)nanoparticles (NPs) requires optimized injectors to collect sufficient diffraction patterns to allow for the reconstruction of the NP structure with high resolution. Typically, aerodynamic lens-stack injectors are used for NP injection. However, current injectors were developed for larger NPs (>100 nm), and their ability to generate high-density NP beams suffers with decreasing NP size. Here, an aerodynamic lens-stack injector with variable geometry and a geometry-optimization procedure are presented. The optimization for 50 nm gold-NP (AuNP) injection using a numerical-simulation infrastructure capable of calculating the carrier-gas flow and the particle trajectories through the injector is also introduced. The simulations were experimentally validated using spherical AuNPs and sucrose NPs. In addition, the optimized injector was compared with the standard-installation `Uppsala injector' for AuNPs. Results for these heavy particles showed a shift in the particle-beam focus position rather than a change in beam size, which results in a lower gas background for the optimized injector. Optimized aerodynamic lens-stack injectors will allow one to increase NP beam density, reduce the gas background, discover the limits of current injectors and contribute to structure determination of small NPs using SPI.
      Keywords: injectors; single particles; sample delivery; X-ray free-electron lasers; XFELs; nanoparticles; coherent diffractive imaging; numerical simulations; high-density beams
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S1600576721009973
      Issue No: Vol. 54, No. 6 (2021)
       
  • Development and performance evaluation of a multi-layer boron-lined
           detector for the CPHS-SANS instrument

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      Authors: Jiang; Z., Gong, H., Li, J., Wang, X., Wang, Y.
      Abstract: A position-sensitive thermal neutron detector module based on multi-layer boron-lined tubes has been developed. It is designed for the CPHS (compact pulsed hadron source) SANS (small-angle neutron scattering) instrument [Loong et al. (2012). Phys. Procedia, 26, 8–18]. The detector module consists of 64 boron-lined tubes, arranged into an eight row by eight column structure. Several key aspects of the development of the detector prototype are briefly covered, including the detector module structure design, the readout electronic system and the digital filter of neutron waveforms. Preliminary characterization reveals that the detector module could achieve an average axial spatial resolution of 5.62 mm and a good position linearity. The detection efficiency measurement shows that more than 30% efficiency can be achieved for thermal neutrons on the CPHS. A virtual experiment was conducted to evaluate the performance of the multi-layer boron-lined tubes in SANS measurement; the effect of inside detector scattering of the multi-layer detector was simulated. The result shows that, by implementing proper data reduction, the impact of inside detector scattering on the Q (momentum transfer) value and Q resolution is negligible.
      Keywords: CPHS-SANS; boron-lined tubes; spatial resolution; virtual experiments; inside detector scattering
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S1600576721010025
      Issue No: Vol. 54, No. 6 (2021)
       
  • Growing a thriving international community for small-angle scattering
           through collaboration. Corrigendum

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      Authors: Trewhella; J.
      Abstract: Errors in the article by Jill Trewhella [J. Appl. Cryst. (2021), 54, 1029–1033] are corrected.
      Keywords: small-angle scattering; SAS; triennial SAS conferences; International Union of Crystallography; IUCr; Guinier Prize; standards
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-16
      DOI: 10.1107/S160057672101164X
      Issue No: Vol. 54, No. 6 (2021)
       
  • The structural and magnetic properties of single-crystal Gd4Ga2O9

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      Authors: Yin; X., Zhong, Y., Cao, Y., Li, Y., Wang, G., Zhao, J., Xu, K., Li, Z., Hong, G., Qian, D.
      Abstract: The crystalline structures and magnetic and thermodynamic properties of a Gd4Ga2O9 single crystal grown with the optical floating zone technique have been investigated. Gd4Ga2O9 crystallizes in a monoclinic structure with the space group P21/c at room temperature. Temperature-dependent magnetic susceptibility measurements along the three crystallographic axes reveal a paramagnetic (PM) behavior between 2 and 300 K. A Curie–Weiss (CW) law fit was carried out and the CW temperature θCW and magnetic frustration parameter f were calculated; these suggest antiferromagnetic (AFM) interactions between Gd3+ spins and a strong magnetic frustration. The field dependence of the magnetization at 2 K further confirms the magnetic frustration characteristics. A distinct λ-shaped peak at 1.4 K in the heat capacity curves suggests a transition from the PM to AFM phase. The magnetic entropy is contributed solely by Gd3+ ions.
      Keywords: X-ray powder diffraction; Rietveld refinement; single-crystal growth; antiferromagnetic phase transitions; magnetic frustration
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-02
      DOI: 10.1107/S1600576721009845
      Issue No: Vol. 54, No. 6 (2021)
       
  • Neutron diffraction investigation of copper tellurite glasses with high
           real-space resolution

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      Authors: Kaur; N., Khanna, A., Hannon, A.C.
      Abstract: High real-space resolution neutron diffraction measurements up to 34 Å−1 were performed on a series of xCuO–(100 − x)TeO2 (x = 30, 40 and 50 mol%) glasses that were synthesized by the melt-quenching technique. The Fourier transformation of neutron diffraction structure factors was used to generate the pair distribution functions, with the first peak at 1.90 Å due to the overlapping Te–O and Cu–O atomic pairs. Reverse Monte Carlo (RMC) simulations were performed on the structure factors and the six partial atomic pair distributions of Cu–Cu, Cu–Te, Cu–O, Te–Te, Te–O and O–O were calculated. The Te–O and Cu–O distributions are very similar and asymmetrical, which revealed that there is a significant short-range disorder in the tellurite network due to the existence of a wide range of Te—O and Cu—O bond lengths. A high-Q (magnitude of momentum transfer function) neutron diffraction study revealed that the average Te–O coordination number decreases steadily from 3.45 to 3.18 with an increase in CuO concentration from 30 to 50 mol% in the glass network. Similar coordination number modifications were earlier found by the RMC analysis of neutron diffraction data sets of copper tellurite glasses that were performed up to lower Q maximum values of 9.5 Å−1. The comparison of high-Q and low-Q neutron diffraction studies reveals that RMC is a powerful and possibly the only technique that is available to elucidate the glass short-range and medium-range structural properties when diffraction data are available up to low Q values of, say, 9.5 Å−1, and when cation–oxygen bond lengths are strongly overlapping and cannot be resolved by Fourier transformation. In situ high-temperature (473 K) neutron diffraction studies of 50CuO–50TeO2 glass revealed that significant distortion of the tellurite network occurs with heating.
      Keywords: high-Q neutron diffraction; tellurite glasses; reverse Monte Carlo simulation; short-range order; medium-range order
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-02
      DOI: 10.1107/S1600576721009365
      Issue No: Vol. 54, No. 6 (2021)
       
  • Hidden and apparent twins in uranyl-oxide minerals agrinierite and
           rameauite: a demonstration of metric and reticular merohedry

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      Authors: Plášil; J., Petříček, V., Škoda, R., Meisser, N., Kasatkin, A.V.
      Abstract: In this work, the structures of chemically related uranyl-oxide minerals agrinierite and rameauite have been revisited and some corrections to the available structure data are provided. Both structures were found to be twinned. The two minerals are chemically similar, and though their structures differ considerably, their unit-cell metrics are similar. Agrinierite was found to be twinned by metric merohedry (diffraction type I), whereas the structure of rameauite is twinned by reticular merohedry (diffraction type II). The twinning of the monoclinic unit cells (true cells) leads to pseudo-orthorhombic or pseudo-tetragonal supercells in the single-crystal diffraction patterns of both minerals. According to the new data and refinement, agrinierite is monoclinic (space group Cm), with a = 14.069 (3), b = 14.220 (3), c = 13.967 (3) Å, β = 120.24 (12)° and V = 2414.2 (12) Å3 (Z = 2). The twinning can be expressed as a mirror in (101) (apart from the inversion twin), which leads to a supercell with a = 14.121, b = 14.276, c = 24.221 Å and V = 2 × 2441 Å3, which is F centered. The new structure refinement converged to R = 3.54% for 6545 unique observed reflections with I > 3σ(I) and GOF = 1.07. Rameauite is also monoclinic (space group Cc), with a = 13.947 (3), b = 14.300 (3), c = 13.888 (3) Å, β = 118.50 (3)° and V = 2434.3 (11) Å3 (Z = 2). The twinning can be expressed as a mirror in (101) (apart from the inversion twin), which leads to a supercell with a = 14.223, b = 14.300, c = 23.921 Å and V = 2 × 2434 Å3, which is C centered. The new structure refinement of rameauite converged to R = 4.23% for 2344 unique observed reflections with I > 3σ(I) and GOF = 1.48. The current investigation documented how peculiar twinning can be, not only for this group of minerals, and how care must be taken in handling the data biased by twinning.
      Keywords: agrinierite; rameauite; twinning; merohedry; Jana2020
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-02
      DOI: 10.1107/S1600576721009663
      Issue No: Vol. 54, No. 6 (2021)
       
  • Theoretical and computational improvements to the algebraic method for
           discovering cooperative rigid-unit modes

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      Authors: Campbell; B.J., Stokes, H.T., Averett, T.B., Machlus, S., Yost, C.J.
      Abstract: A linear-algebraic algorithm for identifying rigid-unit modes in networks of interconnected rigid units has recently been demonstrated. This article presents a series of enhancements to the original algorithm, which greatly improve its conceptual simplicity, numerical robustness, computational efficiency and interpretability. The improvements include the efficient isolation of constraints, the observation of variable-block separability, the use of singular value decomposition and a quantitative measure of solution inexactness.
      Keywords: rigid-unit modes; symmetry modes; group representation theory; singular value decomposition; Gaussian elimination
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-02
      DOI: 10.1107/S1600576721009341
      Issue No: Vol. 54, No. 6 (2021)
       
  • The ISOTILT software for discovering cooperative rigid-unit rotations in
           networks of interconnected rigid units

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      Authors: Campbell; B.J., Stokes, H.T., Averett, T.B., Machlus, S., Yost, C.J.
      Abstract: A user-friendly web-based software tool called `ISOTILT' is introduced for detecting cooperative rigid-unit modes (RUMs) in networks of interconnected rigid units (e.g. molecules, clusters or polyhedral units). This tool implements a recently described algorithm in which symmetry-mode patterns of pivot-atom rotation and displacement vectors are used to construct a linear system of equations whose null space consists entirely of RUMs. The symmetry modes are first separated into independent symmetry-mode blocks and the set of equations for each block is solved separately by singular value decomposition. ISOTILT is the newest member of the ISOTROPY Software Suite. Here, it is shown how to prepare structural and symmetry-mode information for use in ISOTILT, how to use each of ISOTILT's input fields and options, and how to use and interpret ISOTILT output.
      Keywords: rigid-unit modes; symmetry modes; group representation theory; singular value decomposition; ISOTILT
      Citation: urn:issn:1600-5767
      PubDate: 2021-11-02
      DOI: 10.1107/S1600576721009353
      Issue No: Vol. 54, No. 6 (2021)
       
  • Iterative diffraction pattern retrieval from a single focal construct
           geometry image

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      Authors: Chen; X.-H., Xue, T., Tan, B.-Z., Li, X.-Y., Li, J.
      Abstract: Understanding the crystal structure of materials under extreme conditions of pressure and temperature has been revolutionized by major advances in laser-driven dynamic compression and in situ X-ray diffraction (XRD) technology. Instead of the well known Debye–Scherrer configuration, the focal construct geometry (FCG) was introduced to produce high-intensity diffraction data from laser-based in situ XRD experiments without increasing the amount of laser energy, but the resulting reflections suffered from profoundly asymmetrical broadening, leading to inaccuracy in determination of the crystal structure. Inspired by fast-neutron energy spectrum measurements, proposed here is an iterative retrieval method for recovering diffraction data from a single FCG image. This iterative algorithm restores both the peak shape and relative intensity with rapid convergence and requires no prior knowledge about the expected diffraction pattern, allowing the FCG to increase the in situ XRD intensity while simultaneously preserving the angular resolution. The feasibility and validity of the method are shown by successful recovery of the diffraction pattern from both a single simulated FCG image and a single laser-based nanosecond XRD measurement.
      Keywords: focal construct geometry; iterative algorithms; in situ X-ray diffraction; phase transitions
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-27
      DOI: 10.1107/S1600576721009626
      Issue No: Vol. 54, No. 6 (2021)
       
  • High-accuracy polarimetric studies on lead germinate single crystals

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      Authors: Shopa; M., Ftomyn, N., Shopa, Y.
      Abstract: A high-accuracy polarimetric technique has been used for the characterization of a lead germanate ferroelectric single crystal. The measurement results of the linear and circular birefringence in the [010] direction at a wavelength of 633 nm under the influence of an electric field are presented. Gyration–electric field hysteresis loops at alternative crystal positions in the polarization system have been used to determine the ellipticity of the eigenwaves. A temperature dependence of the gyration tensor component g11 in the temperature range of 300–450 K was found.
      Keywords: lead germanate; gyration; polarimetry; electro-optic effects; phase transitions
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-27
      DOI: 10.1107/S1600576721009286
      Issue No: Vol. 54, No. 6 (2021)
       
  • A self-consistent approach to describe unit-cell-parameter and volume
           variations with pressure and temperature

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      Authors: Angel; R., Mazzucchelli, M., Gonzalez-Platas, J., Alvaro, M.
      Abstract: A method for the self-consistent description of the large variations of unit-cell parameters of crystals with pressure and temperature is presented. It employs linearized versions of equations of state (EoSs) together with constraints to ensure internal consistency. The use of polynomial functions to describe the variation of the unit-cell angles in monoclinic and triclinic crystals is compared with the method of deriving them from linearized EoSs for d spacings. The methods have been implemented in the CrysFML Fortran subroutine library. The unit-cell parameters and the compressibility and thermal expansion tensors of crystals can be calculated from the linearized EoSs in an internally consistent manner in a new utility in the EosFit7c program, which is available as freeware at http://www.rossangel.net.
      Keywords: equations of state; unit-cell parameters; EosFit; pressure
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-27
      DOI: 10.1107/S1600576721009092
      Issue No: Vol. 54, No. 6 (2021)
       
  • Evaluation of sample cell materials for aqueous solutions used in
           quasi-elastic neutron scattering measurements

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      Authors: Tominaga; T., Sahara, M., Kawakita, Y., Nakagawa, H., Yamada, T.
      Abstract: For quasi-elastic neutron scattering (QENS) studies, sample cells made of pure or alloyed aluminium are frequently employed. Although the Al surface is protected by a passivating film, this film is not robust. Therefore, when the sample is an aqueous solution, chemical interactions between the Al surface and sample, promoted by corrosive entities such as chloride ions and certain conditions of pH, can compromise the integrity of the cell and interfere with the experiment. In this study, the corrosion susceptibilities of Al and its alloys were investigated by subjecting them to various treatments; the results were compared with those of other candidate materials with low chemical reactivity. This work showed that alloys with higher Al content and boehmite-coated surfaces are resistant to corrosion. In particular, for Al, the resistance is due to a reduction in the contact area achieved by reducing the surface roughness. QENS measurements of empty sample cells made of these materials revealed two results: (1) the profile of the cell fabricated with a copper-free Al alloy showed a minor dependence on the scattering vector magnitude Q and (2) reducing the real surface area of Al effectively suppresses its scattering intensity, while boehmite coating strengthens the scattering. Cells fabricated with Mo, Nb and single-crystal sapphire can be used as alternatives to Al because of their low scattering intensity and reduced dependence on Q.
      Keywords: aluminium; corrosion; quasi-elastic neutron scattering; QENS; sample cells; sapphire
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-27
      DOI: 10.1107/S1600576721009687
      Issue No: Vol. 54, No. 6 (2021)
       
  • X-ray powder diffraction in education. Part I. Bragg peak profiles

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      Authors: Dinnebier; R., Scardi, P.
      Abstract: A collection of scholarly scripts dealing with the mathematics and physics of peak profile functions in X-ray powder diffraction has been written using the Wolfram language in Mathematica. Common distribution functions, the concept of convolution in real and Fourier space, instrumental aberrations, and microstructural effects are visualized in an interactive manner and explained in detail. This paper is the first part of a series dealing with the mathematical description of powder diffraction patterns for teaching and education purposes.
      Keywords: powder diffraction; line profile analysis; peak shape function; microstructure; Mathematica
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-27
      DOI: 10.1107/S1600576721009183
      Issue No: Vol. 54, No. 6 (2021)
       
  • A remark on ab initio indexing of electron backscatter diffraction
           patterns

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      Authors: Morawiec; A.
      Abstract: There is a growing interest in ab initio indexing of electron backscatter diffraction (EBSD) patterns. The methods of solving the problem are presented as innovative. The purpose of this note is to point out that ab initio EBSD indexing belongs to the field of indexing single-crystal diffraction data, and it is solved on the same principles as indexing of patterns of other types. It is shown that reasonably accurate EBSD-based data can be indexed by programs designed for X-ray data.
      Keywords: crystal diffraction; indexing; electron backscatter diffraction; EBSD; lattice parameters
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-27
      DOI: 10.1107/S1600576721009304
      Issue No: Vol. 54, No. 6 (2021)
       
  • Geometrical-optics formalism to model contrast in dark-field X-ray
           microscopy

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      Authors: Poulsen; H.F., Dresselhaus-Marais, L.E., Carlsen, M.A., Detlefs, C., Winther, G.
      Abstract: Dark-field X-ray microscopy, DFXM, is a new full-field imaging technique that non-destructively maps the structure and local strain inside deeply embedded crystalline elements in three dimensions. In DFXM an objective lens is placed along the diffracted beam to generate a magnified projection image of the local diffracted volume. In this work, a general formalism based on geometrical optics is provided for the diffraction imaging, valid for any crystallographic space group. This allows the simulation of DFXM images based on micro-mechanical models. Example simulations are presented with the formalism, demonstrating how this may be used to design new experiments or to interpret existing ones. In particular, it is shown how modifications to the experimental design may tailor the reciprocal-space resolution function to map specific components of the deformation-gradient tensor. The formalism supports multi-length-scale experiments, as it enables DFXM to be interfaced with 3D X-ray diffraction. To illustrate the use of the formalism, DFXM images are simulated from different contrast mechanisms on the basis of the strain field around a straight dislocation.
      Keywords: X-ray diffraction microscopy; diffraction-contrast tomography; structural characterization; diffraction imaging; geometrical optics; dark-field microscopy
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-20
      DOI: 10.1107/S1600576721007287
      Issue No: Vol. 54, No. 6 (2021)
       
  • Probabilistic parameter estimation using a Gaussian mixture density
           network: application to X-ray reflectivity data curve fitting

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      Authors: Kim; K.T., Lee, D.R.
      Abstract: X-ray reflectivity (XRR) is widely used for thin-film structure analysis, and XRR data analysis involves minimizing the difference between experimental data and an XRR curve calculated from model parameters describing the thin-film structure. This analysis takes a certain amount of time because it involves many unavoidable iterations. However, the recently introduced artificial neural network (ANN) method can dramatically reduce the analysis time in the case of repeated analyses of similar samples. Here, the analysis of XRR data using a mixture density network (MDN) is demonstrated, which enables probabilistic prediction while maintaining the advantages of an ANN. First, under the assumption of a unimodal probability distribution of the output parameter, the trained MDN can estimate the best-fit parameter and, at the same time, estimate the confidence interval (CI) corresponding to the error bar of the best-fit parameter. The CI obtained in this manner is similar to that obtained using the Neumann process, a well known statistical method. Next, the MDN method provides several possible solutions for each parameter in the case of a multimodal distribution of the output parameters. An unsupervised machine learning method is used to cluster possible parameter sets in order of probability. Determining the true value by examining the candidates of the parameter sets obtained in this manner can help solve the inherent inverse problem associated with scattering data.
      Keywords: X-ray reflectivity; mixture density networks; artificial neural networks; confidence intervals; machine learning
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-20
      DOI: 10.1107/S1600576721009043
      Issue No: Vol. 54, No. 6 (2021)
       
  • Multiple scattering and resolution effects in small-angle neutron
           scattering experiments calculated and corrected by the software package
           MuScatt

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      Authors: Jaksch; S., Pipich, V., Frielinghaus, H.
      Abstract: This article deals with multiple scattering effects that are important for the method of small-angle neutron scattering (SANS). It considers three channels for the coherent elastic, the incoherent elastic and the incoherent inelastic scattering processes. The first channel contains the desired information on the experiment. Its multiple scattering effects can be desmeared, as shown in the later sections of the article. The other two channels display a nearly constant background as a function of the scattering angle. The incoherent elastic scattering is treated by the theory of Chandrasekhar, allowing for multiple scattering even at large scattering angles. The transfer to a single representative thermalized wavelength by the inelastic scattering – as a simplification – is assumed to happen by a single scattering event. Once the transition to this altered wavelength has happened, further incoherent multiple scattering is considered. The first part of the paper deals with the multiple scattering effects of light water. In the later part of the article, deconvolution algorithms for multiple scattering and instrumental resolution of the elastic coherent signal as implemented in the program MuScatt are described. All of these considerations are interesting for both reactor-based instruments with velocity selectors and time-of-flight SANS instruments and may improve the reliability of the data treatment.
      Keywords: small-angle neutron scattering; SANS; corrections; multiple scattering; resolution
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-20
      DOI: 10.1107/S1600576721009067
      Issue No: Vol. 54, No. 6 (2021)
       
  • Symmetry and chirality in crystals

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      Authors: Nespolo; M., Benahsene, A.H.
      Abstract: A classification scheme relating the chirality of molecules to the type of crystal structures (chiral or achiral) they may form is presented. With respect to similar classifications proposed in the past, some corrections and extensions are introduced. In particular, (1) it is shown that chiral crystal structures from achiral molecules can occur in 28 types of space group having screw axes np, with p ≠ n/2, not in any Sohncke type of space group; (2) it is shown that the restriction on Z′ > 1 for kryptoracemates is contradicted by examples with Z′ = 1; and (3) the case of scalemic enantioenriched solutions, absent from most classifications, is included. Chiral crystal structures from purely inorganic (non-molecular) compounds are addressed too.
      Keywords: chirality; handedness; kryptoracemate; racemic; scalemic
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-20
      DOI: 10.1107/S1600576721009109
      Issue No: Vol. 54, No. 6 (2021)
       
  • Estimating electron density at the bond critical point through atomic
           Hirshfeld surfaces

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      Authors: Pinto; C.B., Rodrigues, B.L., Dos Santos, L.H.R.
      Abstract: Interatomic surfaces often carry information related to the electron distribution in a molecule or crystal, not only being a visual aid but also enabling quantitative analyses. Under certain conditions, atomic Hirshfeld surfaces present a high resemblance to the interatomic surfaces obtained through the quantum theory of atoms in molecules (QTAIM), with the advantage of being easily calculated, even for crystal structures determined at low resolutions (i.e. when a charge-density refinement is not performed). Here an empirical relation between the curvedness property of the Hirshfeld surfaces and the electron density at the bond critical point for certain types of covalent and coordination interactions involving carbon atoms has been obtained. The exponential function was tested to estimate the electron density in different crystalline systems, and the highest deviation from reference values obtained through QTAIM was just 16%. Additionally, fine details of this fit may be salient to the difference in electronegativity of the atoms involved in the bond.
      Keywords: curvedness; interatomic surfaces; Hirshfeld surfaces; bond critical points
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-20
      DOI: 10.1107/S1600576721009213
      Issue No: Vol. 54, No. 6 (2021)
       
  • anaklasis: a compact software package for model-based analysis of specular
           neutron and X-ray reflectometry data sets

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      Authors: Koutsioubas; A.
      Abstract: anaklasis constitutes a set of open-source Python scripts that facilitate a range of specular neutron and X-ray reflectivity calculations, involving the generation of theoretical curves and the comparison/fitting of interfacial model reflectivity against experimental data sets. The primary focus of the software is twofold: on one hand to offer a more natural framework for model definition, requiring minimum coding literacy, and on the other hand to include advanced analysis methods that have been proposed in recent work. Particular attention is given to the ability to co-refine reflectivity data and to the estimation of model-parameter uncertainty and covariance using bootstrap analysis and Markov chain Monte Carlo sampling. The compactness and simplicity of model definition together with the streamlined analysis do not present a steep learning curve for the user, an aspect that may accelerate the generation of reproducible, easily readable and statistically accurate reports in future neutron and X-ray reflectivity related literature.
      Keywords: X-ray reflectometry; neutron reflectometry; fitting software
      Citation: urn:issn:1600-5767
      PubDate: 2021-10-20
      DOI: 10.1107/S1600576721009262
      Issue No: Vol. 54, No. 6 (2021)
       
 
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