Open-access and free articles in Journal of Applied Crystallography
https://journals.iucr.org/j/journalhomepage.html
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 software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.en-gbCopyright (c) 2021 International Union of CrystallographyInternational Union of CrystallographyInternational Union of CrystallographyJournal 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 software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.texttext/htmlOpen-access and free articles in Journal of Applied Crystallographyurn:issn:0021-8898https://journals.iucr.org6yearly2002-02-01T00:00+00:00med@iucr.orgurn:issn:0021-8898Journal of Applied CrystallographyCopyright (c) 2021 International Union of CrystallographyOpen-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
https://journals.iucr.org/j/journalhomepage.html
Still imageGrowing a thriving international community for small-angle scattering through collaboration. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?jl9024
Errors in the article by Jill Trewhella [J. Appl. Cryst. (2021), 54, 1029–1033] are corrected.Errors in the article by Jill Trewhella [J. Appl. Cryst. (2021), 54, 1029–1033] are corrected.texthttps://creativecommons.org/licenses/by/4.0/text/htmlGrowing a thriving international community for small-angle scattering through collaboration. Corrigendumdoi:10.1107/S160057672101164XInternational Union of Crystallography2021-11-16Trewhella, J.Errors in the article by Jill Trewhella [J. Appl. Cryst. (2021), 54, 1029–1033] are corrected.urn:issn:1600-5767SMALL-ANGLE SCATTERING; SAS; TRIENNIAL SAS CONFERENCES; INTERNATIONAL UNION OF CRYSTALLOGRAPHY; IUCR; GUINIER PRIZE; STANDARDSenhttps://creativecommons.org/licenses/by/4.0/2021-11-16Journal of Applied Crystallography1600-5767med@iucr.org1902addenda and errata6December 202119021600-576754Artifact removal in the contour areas of SAXS-CT images by Tikhonov-L1 minimization
http://scripts.iucr.org/cgi-bin/paper?ge5111
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlArtifact removal in the contour areas of SAXS-CT images by Tikhonov-L1 minimizationdoi:10.1107/S1600576721011523International Union of Crystallography2021-11-30Ogawa, H.Ono, S.Watanabe, Y.Nishikawa, Y.Nishitsuji, S.Kabe, T.Takenaka, M.Small-angle X-ray scattering (SAXS) coupled with computed tomography (CT), denoted SAXS-CT, enables the spatial distribution of the characteristic parameters 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 contour regions of the sample.urn:issn:1600-5767SMALL ANGLE X-RAY SCATTERING; COMPUTED TOMOGRAPHY; SAXS-CT; DIFFUSE SCATTERING; SOFT-MATTER; IMAGE PROCESSINGen1600-5767541784December 20211792research papers6med@iucr.org1600-57672021-11-30Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Automated prediction of lattice parameters from X-ray powder diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?vb5020
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlAutomated prediction of lattice parameters from X-ray powder diffraction patternsdoi:10.1107/S1600576721010840International Union of Crystallography2021-11-30Chitturi, S.R.Ratner, D.Walroth, R.C.Thampy, V.Reed, E.J.Dunne, M.Tassone, C.J.Stone, K.H.A method is introduced to determine lattice parameters using machine learning. Analysis is presented of the impact of experimental conditions on machine learning prediction, and possibilities for automated unit-cell solution are explored.urn:issn:1600-5767ANALYSIS AUTOMATION; MACHINE LEARNING; POWDER DIFFRACTION; INDEXINGenresearch papers61810December 20211799541600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2021-11-301600-5767med@iucr.orgEvaluation of extremely steep residual stress gradients based on a combined approach using laboratory-scale equipment
http://scripts.iucr.org/cgi-bin/paper?jo5067
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlEvaluation of extremely steep residual stress gradients based on a combined approach using laboratory-scale equipmentdoi:10.1107/S1600576721010335International Union of Crystallography2021-11-30Fischer, A.Degener, S.Liehr, A.Niendorf, T.This paper reports on high-resolution analysis of residual stress gradients for a laser-hardened surface layer using a combined angle-dispersive X-ray diffraction approach that applies the universal plot method and sin2Ψ evaluation.urn:issn:1600-5767RESIDUAL STRESS ANALYSIS; ENERGY-DISPERSIVE DIFFRACTION; ANGLE-DISPERSIVE DIFFRACTION; LASER SURFACE HARDENINGen1793541600-57671798research papers6December 2021Journal of Applied Crystallography2021-11-301600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Small-angle scattering for beginners
http://scripts.iucr.org/cgi-bin/paper?gj5274
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlSmall-angle scattering for beginnersdoi:10.1107/S1600576721010293International Union of Crystallography2021-11-25Gommes, C.J.Jaksch, S.Frielinghaus, H.A non-technical yet rigorous introduction to small-angle scattering is proposed, through the systematic use of Fresnel–Feynman analysis of interference phenomena.urn:issn:1600-5767SMALL-ANGLE SCATTERING; SAXS; SANS; FORM FACTORS; STRUCTURE FACTORSen1600-57675418321843teaching and education6December 20211600-5767med@iucr.org2021-11-25Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/rmc-discord: reverse Monte Carlo refinement of diffuse scattering and correlated disorder from single crystals
http://scripts.iucr.org/cgi-bin/paper?tu5012
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlrmc-discord: reverse Monte Carlo refinement of diffuse scattering and correlated disorder from single crystalsdoi:10.1107/S1600576721010141International Union of Crystallography2021-11-23Morgan, Z.J.Zhou, H.D.Chakoumakos, B.C.Ye, F.A user-friendly Python-based 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.urn:issn:1600-5767DIFFUSE SCATTERING; CORRELATED DISORDER; SINGLE CRYSTALS; RMC-DISCORD; MONTE CARLO REFINEMENT; SUPERCELLSen2021-11-23Journal of Applied Crystallography1600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/18671600-5767541885computer programs6December 2021Signature of antiphase boundaries in iron oxide nanoparticles
http://scripts.iucr.org/cgi-bin/paper?kc5133
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlSignature of antiphase boundaries in iron oxide nanoparticlesdoi:10.1107/S1600576721010128International Union of Crystallography2021-11-16Köhler, T.Feoktystov, A.Petracic, O.Nandakumaran, N.Cervellino, A.Brückel, T.Antiphase boundaries (APBs) in iron oxide nanoparticles are studied by means of simulations. A strong influence on the spin structure is determined with Monte Carlo simulations, while hkl-dependent peak broadening useful for identifying APBs in real samples is found from Debye scattering equation simulations.urn:issn:1600-5767NANOPARTICLES; X-RAY POWDER DIFFRACTION; MONTE CARLO SIMULATIONS; DEBYE SCATTERING EQUATION; ANTIPHASE BOUNDARIESenDecember 20211729research papers61719541600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2021-11-16med@iucr.org1600-5767Optimizing the geometry of aerodynamic lens injectors for single-particle coherent diffractive imaging of gold nanoparticles
http://scripts.iucr.org/cgi-bin/paper?te5083
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlOptimizing the geometry of aerodynamic lens injectors for single-particle coherent diffractive imaging of gold nanoparticlesdoi:10.1107/S1600576721009973International Union of Crystallography2021-11-16Worbs, L.Roth, N.Lübke, J.Estillore, A.D.Xavier, P.L.Samanta, A.K.Küpper, J.An optimization procedure of an aerodynamic lens injector with variable geometry is presented. The simulation results are validated by performing experiments on gold and sucrose nanoparticles. This work is envisioned to be an important step towards high-resolution single-particle imaging.urn:issn:1600-5767INJECTORS; SINGLE PARTICLES; SAMPLE DELIVERY; X-RAY FREE-ELECTRON LASERS; XFELS; NANOPARTICLES; COHERENT DIFFRACTIVE IMAGING; NUMERICAL SIMULATIONS; HIGH-DENSITY BEAMSen541600-576717306research papers1737December 20211600-5767med@iucr.orgJournal of Applied Crystallography2021-11-16https://creativecommons.org/licenses/by/4.0/Hidden and apparent twins in uranyl-oxide minerals agrinierite and rameauite: a demonstration of metric and reticular merohedry
http://scripts.iucr.org/cgi-bin/paper?vb5019
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlHidden and apparent twins in uranyl-oxide minerals agrinierite and rameauite: a demonstration of metric and reticular merohedrydoi:10.1107/S1600576721009663International Union of Crystallography2021-11-02Plášil, J.Petříček, V.Škoda, R.Meisser, N.Kasatkin, A.V.Two examples of twinning, by metric and reticular merohedry, in uranyl-oxide minerals demonstrate the care that must be taken during structural studies, and not only of such complex materials. This contribution also demonstrates the possibilities of the Jana2020 program in revealing twinning and in subsequent refinement.urn:issn:1600-5767AGRINIERITE; RAMEAUITE; TWINNING; MEROHEDRY; JANA2020enhttps://creativecommons.org/licenses/by/4.0/1600-5767med@iucr.org2021-11-02Journal of Applied Crystallography1663research papers6December 20211600-5767541656Recovering local structure information from high-pressure total scattering experiments
http://scripts.iucr.org/cgi-bin/paper?kc5131
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlRecovering local structure information from high-pressure total scattering experimentsdoi:10.1107/S1600576721009420International Union of Crystallography2021-11-23Herlihy, A.Geddes, H.S.Sosso, G.C.Bull, C.L.Ridley, C.J.Goodwin, A.L.Senn, M.S.Funnell, N.P.A method for subtracting the pairwise correlations of a pressure-transmitting medium from neutron pair distribution functions obtained under hydrostatic compression is presented and applied to Ni, MgO and α-quartz.urn:issn:1600-5767TOTAL SCATTERING; HIGH PRESSURE; NEUTRON DIFFRACTION; PAIR DISTRIBUTION FUNCTIONenmed@iucr.org1600-5767Journal of Applied Crystallography2021-11-23https://creativecommons.org/licenses/by/4.0/541600-57671546December 2021research papers15546The ISOTILT software for discovering cooperative rigid-unit rotations in networks of interconnected rigid units
http://scripts.iucr.org/cgi-bin/paper?iu5016
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlThe ISOTILT software for discovering cooperative rigid-unit rotations in networks of interconnected rigid unitsdoi:10.1107/S1600576721009353International Union of Crystallography2021-11-02Campbell, B.J.Stokes, H.T.Averett, T.B.Machlus, S.Yost, C.J.ISOTILT is a user-friendly web-based software package for discovering the cooperative rigid-unit modes in materials whose structures contain interconnected networks of rigid units.urn:issn:1600-5767RIGID-UNIT MODES; SYMMETRY MODES; GROUP REPRESENTATION THEORY; SINGULAR VALUE DECOMPOSITION; ISOTILTenJournal of Applied Crystallography2021-11-02med@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/1847541600-5767December 2021computer programs61856anaklasis: a compact software package for model-based analysis of specular neutron and X-ray reflectometry data sets
http://scripts.iucr.org/cgi-bin/paper?in5053
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlanaklasis: a compact software package for model-based analysis of specular neutron and X-ray reflectometry data setsdoi:10.1107/S1600576721009262International Union of Crystallography2021-10-20Koutsioubas, A.A new software package (anaklasis) for model-based analysis of specular neutron and X-ray reflectivity is introduced. Key features include a user-friendly compact interfacial model definition scheme and a complete set of methods for co-refining data and estimating parameter uncertainty.urn:issn:1600-5767X-RAY REFLECTOMETRY; NEUTRON REFLECTOMETRY; FITTING SOFTWAREen18571600-5767546computer programs1866December 20212021-10-20Journal of Applied Crystallography1600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/X-ray powder diffraction in education. Part I. Bragg peak profiles
http://scripts.iucr.org/cgi-bin/paper?gj5272
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlX-ray powder diffraction in education. Part I. Bragg peak profilesdoi:10.1107/S1600576721009183International Union of Crystallography2021-10-27Dinnebier, R.Scardi, P.Peak profile functions in powder diffraction are presented with the support of Mathematica scripts, easily usable by interested readers, to explore the effect of different instrumental and microstructural parameters. Subsequent articles will illustrate the most common aberrations to the measured patterns and then total scattering methods.urn:issn:1600-5767POWDER DIFFRACTION; LINE PROFILE ANALYSIS; PEAK SHAPE FUNCTION; MICROSTRUCTURE; MATHEMATICAenteaching and education61831December 20211600-5767541811https://creativecommons.org/licenses/by/4.0/1600-5767med@iucr.org2021-10-27Journal of Applied CrystallographyA self-consistent approach to describe unit-cell-parameter and volume variations with pressure and temperature
http://scripts.iucr.org/cgi-bin/paper?oc5012
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlA self-consistent approach to describe unit-cell-parameter and volume variations with pressure and temperaturedoi:10.1107/S1600576721009092International Union of Crystallography2021-10-27Angel, R.Mazzucchelli, M.Gonzalez-Platas, J.Alvaro, M.A method is presented for the self-consistent description of the variations of unit-cell parameters of crystals with pressure and temperature.urn:issn:1600-5767EQUATIONS OF STATE; UNIT-CELL PARAMETERS; EOSFIT; PRESSUREenhttps://creativecommons.org/licenses/by/4.0/1600-5767med@iucr.org2021-10-27Journal of Applied Crystallography1630research papers6December 20211600-5767541621Multiple scattering and resolution effects in small-angle neutron scattering experiments calculated and corrected by the software package MuScatt
http://scripts.iucr.org/cgi-bin/paper?ge5100
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.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.texthttps://creativecommons.org/licenses/by/4.0/text/htmlMultiple scattering and resolution effects in small-angle neutron scattering experiments calculated and corrected by the software package MuScattdoi:10.1107/S1600576721009067International Union of Crystallography2021-10-20Jaksch, S.Pipich, V.Frielinghaus, H.Calculations and desmearing of different multiple scattering effects for the small-angle scattering technique using the software package MuScatt are presented.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; SANS; CORRECTIONS; MULTIPLE SCATTERING; RESOLUTIONen15801600-576754December 20211593research papers62021-10-20Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/Open and strong-scaling tools for atom-probe crystallography: high-throughput methods for indexing crystal structure and orientation
http://scripts.iucr.org/cgi-bin/paper?yr5067
Volumetric crystal structure indexing and orientation mapping are key data processing steps for virtually any quantitative study of spatial correlations between the local chemical composition features and the microstructure of a material. For electron and X-ray diffraction methods it is possible to develop indexing tools which compare measured and analytically computed patterns to decode the structure and relative orientation within local regions of interest. Consequently, a number of numerically efficient and automated software tools exist to solve the above characterization tasks. For atom-probe tomography (APT) experiments, however, the strategy of making comparisons between measured and analytically computed patterns is less robust because many APT data sets contain substantial noise. Given that sufficiently general predictive models for such noise remain elusive, crystallography tools for APT face several limitations: their robustness to noise is limited, and therefore so too is their capability to identify and distinguish different crystal structures and orientations. In addition, the tools are sequential and demand substantial manual interaction. In combination, this makes robust uncertainty quantification with automated high-throughput studies of the latent crystallographic information a difficult task with APT data. To improve the situation, the existing methods are reviewed and how they link to the methods currently used by the electron and X-ray diffraction communities is discussed. As a result of this, some of the APT methods are modified to yield more robust descriptors of the atomic arrangement. Also reported is how this enables the development of an open-source software tool for strong scaling and automated identification of a crystal structure, and the mapping of crystal orientation in nanocrystalline APT data sets with multiple phases.Volumetric crystal structure indexing and orientation mapping are key data processing steps for virtually any quantitative study of spatial correlations between the local chemical composition features and the microstructure of a material. For electron and X-ray diffraction methods it is possible to develop indexing tools which compare measured and analytically computed patterns to decode the structure and relative orientation within local regions of interest. Consequently, a number of numerically efficient and automated software tools exist to solve the above characterization tasks. For atom-probe tomography (APT) experiments, however, the strategy of making comparisons between measured and analytically computed patterns is less robust because many APT data sets contain substantial noise. Given that sufficiently general predictive models for such noise remain elusive, crystallography tools for APT face several limitations: their robustness to noise is limited, and therefore so too is their capability to identify and distinguish different crystal structures and orientations. In addition, the tools are sequential and demand substantial manual interaction. In combination, this makes robust uncertainty quantification with automated high-throughput studies of the latent crystallographic information a difficult task with APT data. To improve the situation, the existing methods are reviewed and how they link to the methods currently used by the electron and X-ray diffraction communities is discussed. As a result of this, some of the APT methods are modified to yield more robust descriptors of the atomic arrangement. Also reported is how this enables the development of an open-source software tool for strong scaling and automated identification of a crystal structure, and the mapping of crystal orientation in nanocrystalline APT data sets with multiple phases.texthttps://creativecommons.org/licenses/by/4.0/text/htmlOpen and strong-scaling tools for atom-probe crystallography: high-throughput methods for indexing crystal structure and orientationdoi:10.1107/S1600576721008578International Union of Crystallography2021-10-01Kühbach, M.Kasemer, M.Gault, B.Breen, A.It is now recognized that, beyond composition mapping in three dimensions, atom-probe tomography can provide partial crystallographic information for the material volume under investigation. Detailed here is an original solution for identifying the crystal structure and crystal orientations within atom-probe tomographic reconstructions. The reported tools are open-source software and scale strongly on at least 3200 computing cores or 160 graphics cards.urn:issn:1600-5767CRYSTAL STRUCTURE IDENTIFICATION; ATOM-PROBE TOMOGRAPHY; ORIENTATION MAPPING; POINT CLOUD DATA; PARALLELIZATIONen1490541600-5767October 202151508research papersJournal of Applied Crystallography2021-10-01med@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/Non-ambient X-ray and neutron diffraction of novel relaxor ferroelectric xBi2(Zn2/3,Nb1/3)O3–(1 – x)BaTiO3
http://scripts.iucr.org/cgi-bin/paper?kc5129
The first determination of the phase diagram of the novel ferroelectric relaxor xBi(Zn2/3Nb1/3)O3–(1 − x)BaTiO3 (BZN-BT) has been achieved with a combination of high-resolution X-ray and neutron diffraction up to the miscibility limit near x(BZN) = 20.0% over a temperature range 20 < T < 400 K. The combined X-ray and neutron data show that the instability within the xBZN-(1−x)BT system reaches a maximum at x = 3.9% and is driven by B-site displacement and distortion of the oxygen octahedra in the polar phases. Composition-dependent effects include a narrow Amm2-dominated region focused at x = 3.9%, significant convergence of the lattice parameters in both P4mm and Amm2 phases, and sharp maxima in piezoelectric coefficient d33 and maximum polarization Pmax. Lattice parameter dilation at x ≥ 4.0% was observed for both P4mm and Amm2 unit cells, alongside the first appearance of Pm3m at 295 K and the onset of significant dielectric relaxation. Low-temperature neutron diffraction indicated a weak or non-existent temperature dependence on the transition from ferroelectric at x = 3.9% to ferroelectric relaxor at x = 4.0%. Temperature-dependent phase transitions were eliminated near x = 3.0%, with the ferroelectric limit observed at x = 5.0% and a transition to a low-loss relaxor dielectric near x = 8.0%.The first determination of the phase diagram of the novel ferroelectric relaxor xBi(Zn2/3Nb1/3)O3–(1 − x)BaTiO3 (BZN-BT) has been achieved with a combination of high-resolution X-ray and neutron diffraction up to the miscibility limit near x(BZN) = 20.0% over a temperature range 20 < T < 400 K. The combined X-ray and neutron data show that the instability within the xBZN-(1−x)BT system reaches a maximum at x = 3.9% and is driven by B-site displacement and distortion of the oxygen octahedra in the polar phases. Composition-dependent effects include a narrow Amm2-dominated region focused at x = 3.9%, significant convergence of the lattice parameters in both P4mm and Amm2 phases, and sharp maxima in piezoelectric coefficient d33 and maximum polarization Pmax. Lattice parameter dilation at x ≥ 4.0% was observed for both P4mm and Amm2 unit cells, alongside the first appearance of Pm3m at 295 K and the onset of significant dielectric relaxation. Low-temperature neutron diffraction indicated a weak or non-existent temperature dependence on the transition from ferroelectric at x = 3.9% to ferroelectric relaxor at x = 4.0%. Temperature-dependent phase transitions were eliminated near x = 3.0%, with the ferroelectric limit observed at x = 5.0% and a transition to a low-loss relaxor dielectric near x = 8.0%.texthttps://creativecommons.org/licenses/by/4.0/text/htmlNon-ambient X-ray and neutron diffraction of novel relaxor ferroelectric xBi2(Zn2/3,Nb1/3)O3–(1 – x)BaTiO3doi:10.1107/S160057672100858XInternational Union of Crystallography2021-09-29Marshall, J.Walker, D.Thomas, P.Combined non-ambient X-ray and neutron diffraction have been used to observe lattice parameter convergence in polar phases of the xBi(Zn2/3 Nb1/3)O3–(1 − x)BaTiO3 system below the ferroelectric composition limit at x < 5.0%. The lattice parameter convergence is correlated with peaks in the dielectric and piezoelectric coefficients.urn:issn:1600-5767POWDER NEUTRON DIFFRACTION; LEAD-FREE RELAXORS; NON-AMBIENT X-RAY DIFFRACTION; PIEZOELECTRICITY; LATTICE PARAMETERSen541600-5767143751454research papersOctober 20211600-5767med@iucr.orgJournal of Applied Crystallography2021-09-29https://creativecommons.org/licenses/by/4.0/Laboratory exploration of mineral precipitates from Europa's subsurface ocean
http://scripts.iucr.org/cgi-bin/paper?gj5269
The precipitation of hydrated phases from a chondrite-like Na–Mg–Ca–SO4–Cl solution is studied using in situ synchrotron X-ray powder diffraction, under rapid- (360 K h−1, T = 250–80 K, t = 3 h) and ultra-slow-freezing (0.3 K day−1, T = 273–245 K, t = 242 days) conditions. The precipitation sequence under slow cooling initially follows the predictions of equilibrium thermodynamics models. However, after ∼50 days at 245 K, the formation of the highly hydrated sulfate phase Na2Mg(SO4)2·16H2O, a relatively recent discovery in the Na2Mg(SO4)2–H2O system, was observed. Rapid freezing, on the other hand, produced an assemblage of multiple phases which formed within a very short timescale (≤4 min, ΔT = 2 K) and, although remaining present throughout, varied in their relative proportions with decreasing temperature. Mirabilite and meridianiite were the major phases, with pentahydrite, epsomite, hydrohalite, gypsum, blödite, konyaite and loweite also observed. Na2Mg(SO4)2·16H2O was again found to be present and increased in proportion relative to other phases as the temperature decreased. The results are discussed in relation to possible implications for life on Europa and application to other icy ocean worlds.The precipitation of hydrated phases from a chondrite-like Na–Mg–Ca–SO4–Cl solution is studied using in situ synchrotron X-ray powder diffraction, under rapid- (360 K h−1, T = 250–80 K, t = 3 h) and ultra-slow-freezing (0.3 K day−1, T = 273–245 K, t = 242 days) conditions. The precipitation sequence under slow cooling initially follows the predictions of equilibrium thermodynamics models. However, after ∼50 days at 245 K, the formation of the highly hydrated sulfate phase Na2Mg(SO4)2·16H2O, a relatively recent discovery in the Na2Mg(SO4)2–H2O system, was observed. Rapid freezing, on the other hand, produced an assemblage of multiple phases which formed within a very short timescale (≤4 min, ΔT = 2 K) and, although remaining present throughout, varied in their relative proportions with decreasing temperature. Mirabilite and meridianiite were the major phases, with pentahydrite, epsomite, hydrohalite, gypsum, blödite, konyaite and loweite also observed. Na2Mg(SO4)2·16H2O was again found to be present and increased in proportion relative to other phases as the temperature decreased. The results are discussed in relation to possible implications for life on Europa and application to other icy ocean worlds.texthttps://creativecommons.org/licenses/by/4.0/text/htmlLaboratory exploration of mineral precipitates from Europa's subsurface oceandoi:10.1107/S1600576721008554International Union of Crystallography2021-09-29Thompson, S.P.Kennedy, H.Butler, B.M.Day, S.J.Safi, E.Evans, A.Precipitation experiments from a model Europan ocean solution subjected to fast and slow freezing suggest that the highly hydrated Na–Mg sulfate phase Na2Mg(SO4)2·16H2O is one of the lowest-temperature mineral phases likely to be stable on Europa's surface and may therefore be astrobiologically significant.urn:issn:1600-5767EUROPA; ICY MOONS; LOW-TEMPERATURE MINERAL PRECIPITATION; OCEAN WORLDS; LONG-DURATION STUDIESen1600-576754145551479research papersOctober 20211600-5767med@iucr.org2021-09-29Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Pixel calculations using Orca or GAUSSIAN for electron density automated within the Oscail package
http://scripts.iucr.org/cgi-bin/paper?oc5011
Many discussions of the intermolecular interactions in crystal structures concentrate almost exclusively on an analysis of hydrogen bonding. A simple analysis of atom–atom distances is all that is required to detect and analyse hydrogen bonding. However, for typical small-molecule organic crystal structures, hydrogen-bonding interactions are often responsible for less than 50% of the crystal lattice energy. It is more difficult to analyse intermolecular interactions based on van der Waals interactions. The Pixel program can calculate and partition intermolecular energies into Coulombic, polarization, dispersion and repulsion energies, and help put crystal structure discussions onto a rational basis. This Windows PC implementation of Pixel within the Oscail package requires minimal setup and can automatically use GAUSSIAN or Orca for the calculation of electron density.Many discussions of the intermolecular interactions in crystal structures concentrate almost exclusively on an analysis of hydrogen bonding. A simple analysis of atom–atom distances is all that is required to detect and analyse hydrogen bonding. However, for typical small-molecule organic crystal structures, hydrogen-bonding interactions are often responsible for less than 50% of the crystal lattice energy. It is more difficult to analyse intermolecular interactions based on van der Waals interactions. The Pixel program can calculate and partition intermolecular energies into Coulombic, polarization, dispersion and repulsion energies, and help put crystal structure discussions onto a rational basis. This Windows PC implementation of Pixel within the Oscail package requires minimal setup and can automatically use GAUSSIAN or Orca for the calculation of electron density.texthttps://creativecommons.org/licenses/by/4.0/text/htmlPixel calculations using Orca or GAUSSIAN for electron density automated within the Oscail packagedoi:10.1107/S1600576721008529International Union of Crystallography2021-09-29McArdle, P.The Pixel program can be run automatically by the Oscail package using either GAUSSIAN or Orca to calculate electron density.urn:issn:1600-5767PIXEL; LATTICE ENERGY; ORCA; GAUSSIANenJournal of Applied Crystallography2021-09-29med@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/1535541600-5767October 2021computer programs15415Symmetry-adapted pair distribution function analysis (SAPA): a novel approach to evaluating lattice dynamics and local distortions from total scattering data
http://scripts.iucr.org/cgi-bin/paper?kc5134
A novel symmetry-adapted pair distribution function analysis (SAPA) method for extracting information on local distortions from pair distribution function data is introduced. The implementation of SAPA is demonstrated in the TOPAS-Academic software using the freely available online software ISODISTORT, and scripts for converting the output from ISODISTORT to a SAPA input file for TOPAS are provided. Finally, two examples are provided to show how SAPA can evaluate the nature of both dynamic distortions in ScF3 and the distortions which act as an order parameter for the phase transitions in BaTiO3.A novel symmetry-adapted pair distribution function analysis (SAPA) method for extracting information on local distortions from pair distribution function data is introduced. The implementation of SAPA is demonstrated in the TOPAS-Academic software using the freely available online software ISODISTORT, and scripts for converting the output from ISODISTORT to a SAPA input file for TOPAS are provided. Finally, two examples are provided to show how SAPA can evaluate the nature of both dynamic distortions in ScF3 and the distortions which act as an order parameter for the phase transitions in BaTiO3.texthttps://creativecommons.org/licenses/by/4.0/text/htmlSymmetry-adapted pair distribution function analysis (SAPA): a novel approach to evaluating lattice dynamics and local distortions from total scattering datadoi:10.1107/S1600576721008499International Union of Crystallography2021-09-13Bird, T.A.Herlihy, A.Senn, M.S.A novel symmetry-adapted approach to analysing X-ray and neutron pair distribution function data is presented. Local deviations from the average structure are determined using representation analysis.urn:issn:1600-5767PDF; PAIR DISTRIBUTION FUNCTIONS; SYMMETRY-ADAPTED APPROACHES; SOFT MODESenhttps://creativecommons.org/licenses/by/4.0/1600-5767med@iucr.orgJournal of Applied Crystallography2021-09-13short communications51520October 2021541600-57671514Small-angle neutron scattering from CuCrZr coupons and components
http://scripts.iucr.org/cgi-bin/paper?vg5143
Small-angle neutron scattering (SANS) is performed to analyse the microstructural state of a reference CuCrZr material with carefully controlled heat treatments, small-scale manufacturing mock-ups of assemblies and high-heat-flux-exposed mock-ups for fusion reactor components. The information derived from the SANS data corresponds well to existing literature data based on microscopic-scale techniques, but is obtained at millimetre scale with minimal surface preparation. The manufacturing method and high-heat-flux testing conditions are confirmed to have little impact on the microstructural properties, demonstrating the validity of these treatments for scaled-up reactor components.Small-angle neutron scattering (SANS) is performed to analyse the microstructural state of a reference CuCrZr material with carefully controlled heat treatments, small-scale manufacturing mock-ups of assemblies and high-heat-flux-exposed mock-ups for fusion reactor components. The information derived from the SANS data corresponds well to existing literature data based on microscopic-scale techniques, but is obtained at millimetre scale with minimal surface preparation. The manufacturing method and high-heat-flux testing conditions are confirmed to have little impact on the microstructural properties, demonstrating the validity of these treatments for scaled-up reactor components.texthttps://creativecommons.org/licenses/by/4.0/text/htmlSmall-angle neutron scattering from CuCrZr coupons and componentsdoi:10.1107/S1600576721008311International Union of Crystallography2021-09-13Schoofs, F.King, S.Cackett, A.J.Leyland, M.Hardie, C.Small-angle neutron scattering (SANS) is performed to analyse the microstructural state of a reference CuCrZr material with carefully controlled heat treatments, small-scale manufacturing mock-ups of assemblies and high-heat-flux-exposed mock-ups. The work demonstrates that SANS can be used for millimetre-scale analysis of small engineering components with minimal surface preparation.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; SANS; ALLOYS; CUCRZRen1394541600-5767October 20211402research papers5Journal of Applied Crystallography2021-09-13med@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/Defocused travelling fringes in a scanning triple-Laue X-ray interferometry setup
http://scripts.iucr.org/cgi-bin/paper?vh5143
The measurement of the silicon lattice parameter by a separate-crystal triple-Laue X-ray interferometer is a key step for the realization of the kilogram by counting atoms. Since the measurement accuracy is approaching nine significant digits, a reliable model of the interferometer operation is required to quantify or exclude systematic errors. This paper investigates both analytically and experimentally the effect of the defocus (the difference between the splitter-to-mirror and analyser-to-mirror distances) on the phase of the interference fringes and the measurement of the lattice parameter.The measurement of the silicon lattice parameter by a separate-crystal triple-Laue X-ray interferometer is a key step for the realization of the kilogram by counting atoms. Since the measurement accuracy is approaching nine significant digits, a reliable model of the interferometer operation is required to quantify or exclude systematic errors. This paper investigates both analytically and experimentally the effect of the defocus (the difference between the splitter-to-mirror and analyser-to-mirror distances) on the phase of the interference fringes and the measurement of the lattice parameter.texthttps://creativecommons.org/licenses/by/4.0/text/htmlDefocused travelling fringes in a scanning triple-Laue X-ray interferometry setupdoi:10.1107/S1600576721007962International Union of Crystallography2021-09-13Sasso, C.P.Mana, G.Massa, E.This paper investigates both analytically and experimentally the effect of the defocus (the difference between the splitter-to-mirror and analyser-to-mirror distances) on the phase of the travelling fringes in a separate-crystal triple-Laue X-ray interferometer.urn:issn:1600-5767X-RAY INTERFEROMETRY; DYNAMICAL THEORY OF X-RAY DIFFRACTION; X-RAY CRYSTAL DENSITY; SI LATTICE PARAMETERenhttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2021-09-13med@iucr.org1600-5767October 202114085research papers1403541600-5767Illustrated formalisms for total scattering data: a guide for new practitioners. Corrigendum and addendum
http://scripts.iucr.org/cgi-bin/paper?gj5273
Errors and ambiguities in the article by Peterson, Olds, McDonnell & Page [J. Appl. Cryst. (2021), 54, 317–332] are corrected and clarified, respectively.Errors and ambiguities in the article by Peterson, Olds, McDonnell & Page [J. Appl. Cryst. (2021), 54, 317–332] are corrected and clarified, respectively.texthttps://creativecommons.org/licenses/by/4.0/text/htmlIllustrated formalisms for total scattering data: a guide for new practitioners. Corrigendum and addendumdoi:10.1107/S1600576721007664International Union of Crystallography2021-09-13Peterson, P.F.Keen, D.A.Errors and ambiguities in the article by Peterson, Olds, McDonnell & Page [J. Appl. Cryst. (2021), 54, 317–332] are corrected and clarified, respectively.urn:issn:1600-5767TOTAL SCATTERING; PAIR DISTRIBUTION FUNCTIONenOctober 20215addenda and errata1545541600-57671542https://creativecommons.org/licenses/by/4.0/med@iucr.org1600-5767Journal of Applied Crystallography2021-09-13Growing a thriving international community for small-angle scattering through collaboration
http://scripts.iucr.org/cgi-bin/paper?jl5024
Small-angle scattering emerged as a tool for studying noncrystalline structures from early observations around 1930 that there was a relationship between the extent of the scattering and the size of the scattering object. André Guinier, a leading figure in the development of the field, noted in his summary findings from the first Conference on Small Angle Scattering in 1958 that the technique would be of value to study `submicroscopical inhomogeneities' and further provided a means of `observation [that had] in the past restricted the field of application of the X-ray method.' In 1965 the first of what became a highly successful series of Small-Angle Scattering (SAS) meetings held approximately every three years took place in Syracuse, NY, USA, and many of these ongoing meetings published their proceedings and highlights in the International Union of Crystallography (IUCr) Journal of Applied Crystallography. Since the early 2000s, the relationship between the international SAS community represented at the triennial SAS meetings and the IUCr has been strengthened and deepened through formal cooperation and collaboration in a number of mutually beneficial activities that have supported the growth and health of the field and the IUCr.Small-angle scattering emerged as a tool for studying noncrystalline structures from early observations around 1930 that there was a relationship between the extent of the scattering and the size of the scattering object. André Guinier, a leading figure in the development of the field, noted in his summary findings from the first Conference on Small Angle Scattering in 1958 that the technique would be of value to study `submicroscopical inhomogeneities' and further provided a means of `observation [that had] in the past restricted the field of application of the X-ray method.' In 1965 the first of what became a highly successful series of Small-Angle Scattering (SAS) meetings held approximately every three years took place in Syracuse, NY, USA, and many of these ongoing meetings published their proceedings and highlights in the International Union of Crystallography (IUCr) Journal of Applied Crystallography. Since the early 2000s, the relationship between the international SAS community represented at the triennial SAS meetings and the IUCr has been strengthened and deepened through formal cooperation and collaboration in a number of mutually beneficial activities that have supported the growth and health of the field and the IUCr.texthttps://creativecommons.org/licenses/by/4.0/text/htmlGrowing a thriving international community for small-angle scattering through collaborationdoi:10.1107/S1600576721007561International Union of Crystallography2021-07-29Trewhella, J.This commentary describes the growth of small-angle scattering as a technique for structural characterization in noncrystalline systems across chemistry, biology and materials and how the international community continues to grow and prosper through highly successful international meetings and a strategic collaborative relationship with the International Union of Crystallography.urn:issn:1600-5767SMALL-ANGLE SCATTERING; SAS; TRIENNIAL SAS CONFERENCES; INTERNATIONAL UNION OF CRYSTALLOGRAPHY; IUCR; GUINIER PRIZE; STANDARDSen1600-576754102941033feature articlesAugust 20211600-5767med@iucr.org2021-07-29Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/An electric field cell for performing in situ single-crystal synchrotron X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?oc5009
With the recent increase in research into ferroelectric, anti-ferroelectric and piezoelectric materials, studying the solid-state properties in situ under applied electric fields is vital in understanding the underlying processes. Where this behaviour is the result of atomic displacements, crystallographic insight has an important role. This work presents a sample environment designed to apply an electric field to single-crystal samples in situ on the small-molecule single-crystal diffraction beamline I19, Diamond Light Source (UK). The configuration and operation of the cell is described as well as its application to studies of a proton-transfer colour-change material.With the recent increase in research into ferroelectric, anti-ferroelectric and piezoelectric materials, studying the solid-state properties in situ under applied electric fields is vital in understanding the underlying processes. Where this behaviour is the result of atomic displacements, crystallographic insight has an important role. This work presents a sample environment designed to apply an electric field to single-crystal samples in situ on the small-molecule single-crystal diffraction beamline I19, Diamond Light Source (UK). The configuration and operation of the cell is described as well as its application to studies of a proton-transfer colour-change material.texthttps://creativecommons.org/licenses/by/4.0/text/htmlAn electric field cell for performing in situ single-crystal synchrotron X-ray diffractiondoi:10.1107/S1600576721007469International Union of Crystallography2021-09-04Saunders, L.K.Yeung, H.H.-M.Warren, M.R.Smith, P.Gurney, S.Dodsworth, S.F.Vitorica-Yrezabal, I.J.Wilcox, A.Hathaway, P.V.Preece, G.Roberts, P.Barnett, S.A.Allan, D.R.This paper describes the design and implementation of an electric field sample cell, used to perform in situ single-crystal synchrotron X-ray diffraction under an applied electric field and suitable for single-crystal samples that are greater than 100 µm in size.urn:issn:1600-5767ELECTRIC FIELD CRYSTALLOGRAPHY; SYNCHROTRON INSTRUMENTATION; PROTON TRANSFERenhttps://creativecommons.org/licenses/by/4.0/med@iucr.org1600-57672021-09-04Journal of Applied CrystallographyOctober 202113595research papers1600-5767541349Data reduction for serial crystallography using a robust peak finder
http://scripts.iucr.org/cgi-bin/paper?te5078
A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.texthttps://creativecommons.org/licenses/by/4.0/text/htmlData reduction for serial crystallography using a robust peak finderdoi:10.1107/S1600576721007317International Union of Crystallography2021-09-13Hadian-Jazi, M.Sadri, A.Barty, A.Yefanov, O.Galchenkova, M.Oberthuer, D.Komadina, D.Brehm, W.Kirkwood, H.Mills, G.Wijn, R. deLetrun, R.Kloos, M.Vakili, M.Gelisio, L.Darmanin, C.Mancuso, A.P.Chapman, H.N.Abbey, B.This article focuses on the challenges of hit finding and data reduction in serial crystallography (SX). An effective and reliable Bragg-peak-finding method, called robust peak finder (RPF), has been developed. RPF is based on the principle of robust statistics and can be used for SX data analysis.urn:issn:1600-5767DATA REDUCTION; SERIAL CRYSTALLOGRAPHY; ROBUST STATISTICS; BRAGG PEAK FINDINGenOctober 2021research papers5137813601600-576754https://creativecommons.org/licenses/by/4.0/2021-09-13Journal of Applied Crystallographymed@iucr.org1600-5767Grazing-incidence X-ray diffraction tomography for characterizing organic thin films
http://scripts.iucr.org/cgi-bin/paper?vh5142
Characterization of thin films is of paramount importance for evaluating material processing outcomes/efficiency as well as establishing structure–property/performance relationships. This article introduces grazing-incidence diffraction tomography (GID tomography), a technique that combines grazing-incidence X-ray scattering and computed tomography to quantitatively determine the dimension and orientation of crystalline domains in thin films without restrictions on the beam coherence, substrate type or film thickness. This computational method extends the capability of synchrotron beamlines by utilizing standard X-ray scattering experiment setups.Characterization of thin films is of paramount importance for evaluating material processing outcomes/efficiency as well as establishing structure–property/performance relationships. This article introduces grazing-incidence diffraction tomography (GID tomography), a technique that combines grazing-incidence X-ray scattering and computed tomography to quantitatively determine the dimension and orientation of crystalline domains in thin films without restrictions on the beam coherence, substrate type or film thickness. This computational method extends the capability of synchrotron beamlines by utilizing standard X-ray scattering experiment setups.texthttps://creativecommons.org/licenses/by/4.0/text/htmlGrazing-incidence X-ray diffraction tomography for characterizing organic thin filmsdoi:10.1107/S1600576721007184International Union of Crystallography2021-09-04Tsai, E.H.R.Xia, Y.Fukuto, M.Loo, Y.-L.Li, R.A computational method that directly translates the scattering peak information to crystalline domain shapes and orientations is presented. The method is demonstrated at a synchrotron beamline with a standard X-ray scattering setup.urn:issn:1600-5767GRAZING-INCIDENCE WIDE-ANGLE X-RAY SCATTERING; GIWAXS; TOMOGRAPHY; THIN FILMS; ORGANIC TRANSISTORSen1600-5767med@iucr.org2021-09-04Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-576754132713395research papersOctober 2021Real-space modeling for complex structures based on small-angle X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?vg5130
A three-dimensional real-space model has been created for hierarchical materials by matching observed and simulated small-angle X-ray scattering patterns. The simulation is performed by arranging the positions of small primary particles and constructing an aggregate structure in a finite-sized cell. In order to avoid the effect of the finite size of the cell, the cell size is extended to infinity by introducing an asymptotic form of the long-range correlations among the primary particles. As a result, simulations for small-angle X-ray scattering patterns can be performed correctly in the low-wavenumber regime (<0.1 nm−1), allowing the model to handle hundred-nanometre-scale structures composed of primary particles of a few nanometres in size. An aerogel structure was determined using this model, resulting in an excellent match with the experimental scattering pattern. The resultant three-dimensional model can generate cross-sectional images similar to those obtained by transmission electron microscopy, and the calculated pore-size distribution is in accord with that derived from the gas adsorption method.A three-dimensional real-space model has been created for hierarchical materials by matching observed and simulated small-angle X-ray scattering patterns. The simulation is performed by arranging the positions of small primary particles and constructing an aggregate structure in a finite-sized cell. In order to avoid the effect of the finite size of the cell, the cell size is extended to infinity by introducing an asymptotic form of the long-range correlations among the primary particles. As a result, simulations for small-angle X-ray scattering patterns can be performed correctly in the low-wavenumber regime (<0.1 nm−1), allowing the model to handle hundred-nanometre-scale structures composed of primary particles of a few nanometres in size. An aerogel structure was determined using this model, resulting in an excellent match with the experimental scattering pattern. The resultant three-dimensional model can generate cross-sectional images similar to those obtained by transmission electron microscopy, and the calculated pore-size distribution is in accord with that derived from the gas adsorption method.texthttps://creativecommons.org/licenses/by/4.0/text/htmlReal-space modeling for complex structures based on small-angle X-ray scatteringdoi:10.1107/S1600576721006701International Union of Crystallography2021-08-18Omote, K.Iwata, T.A three-dimensional real-space model has been created for complex hierarchical materials by matching observed and simulated small-angle X-ray scattering patterns. The simulation is performed by arranging the positions of small primary particles and constructing an aggregate structure in a finite-sized cell.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; SAXS; HIERARCHICAL STRUCTURES; REVERSE MONTE CARLO; AEROGELS; COMPUTER SIMULATIONSenhttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2021-08-181600-5767med@iucr.org5research papers1297October 20211290541600-5767Separation of the inelastic and elastic scattering in time-of-flight mode on the pinhole small-angle neutron scattering diffractometer KWS-2
http://scripts.iucr.org/cgi-bin/paper?jl5020
To study and control the incoherent inelastic background in small-angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS-2 small-angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz-Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single-disc chopper that is placed in front of the sample stage. This makes it possible to record in time-of-flight mode the scattered neutrons in the high-Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS-2 are presented. When only the elastic region of the spectrum is used in the data-reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.To study and control the incoherent inelastic background in small-angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS-2 small-angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz-Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single-disc chopper that is placed in front of the sample stage. This makes it possible to record in time-of-flight mode the scattered neutrons in the high-Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS-2 are presented. When only the elastic region of the spectrum is used in the data-reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.texthttps://creativecommons.org/licenses/by/4.0/text/htmlSeparation of the inelastic and elastic scattering in time-of-flight mode on the pinhole small-angle neutron scattering diffractometer KWS-2doi:10.1107/S1600576721006610International Union of Crystallography2021-07-30Balacescu, L.Brandl, G.Radulescu, A.A new chopper has been installed at the sample position in front of the sample stage at the KWS-2 small-angle neutron-scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time-of-flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.urn:issn:1600-5767TOF-SANS; INCOHERENT NEUTRON SCATTERING; INELASTIC NEUTRON SCATTERING; HYDROCARBON SYSTEMSen541600-57671217August 2021research papers12244med@iucr.org1600-5767Journal of Applied Crystallography2021-07-30https://creativecommons.org/licenses/by/4.0/GIDInd: an automated indexing software for grazing-incidence X-ray diffraction data
http://scripts.iucr.org/cgi-bin/paper?vh5146
Grazing-incidence X-ray diffraction (GIXD) is a widely used technique for the crystallographic characterization of thin films. The identification of a specific phase or the discovery of an unknown polymorph always requires indexing of the associated diffraction pattern. However, despite the importance of this procedure, only a few approaches have been developed so far. Recently, an advanced mathematical framework for indexing of these specific diffraction patterns has been developed. Here, the successful implementation of this framework in the form of an automated indexing software, named GIDInd, is introduced. GIDInd is based on the assumption of a triclinic unit cell with six lattice constants and a distinct contact plane parallel to the substrate surface. Two approaches are chosen: (i) using only diffraction peaks of the GIXD pattern and (ii) combining the GIXD pattern with a specular diffraction peak. In the first approach the six unknown lattice parameters have to be determined by a single fitting procedure, while in the second approach two successive fitting procedures are used with three unknown parameters each. The output unit cells are reduced cells according to approved crystallographic conventions. Unit-cell solutions are additionally numerically optimized. The computational toolkit is compiled in the form of a MATLAB executable and presented within a user-friendly graphical user interface. The program is demonstrated by application on two independent examples of thin organic films.Grazing-incidence X-ray diffraction (GIXD) is a widely used technique for the crystallographic characterization of thin films. The identification of a specific phase or the discovery of an unknown polymorph always requires indexing of the associated diffraction pattern. However, despite the importance of this procedure, only a few approaches have been developed so far. Recently, an advanced mathematical framework for indexing of these specific diffraction patterns has been developed. Here, the successful implementation of this framework in the form of an automated indexing software, named GIDInd, is introduced. GIDInd is based on the assumption of a triclinic unit cell with six lattice constants and a distinct contact plane parallel to the substrate surface. Two approaches are chosen: (i) using only diffraction peaks of the GIXD pattern and (ii) combining the GIXD pattern with a specular diffraction peak. In the first approach the six unknown lattice parameters have to be determined by a single fitting procedure, while in the second approach two successive fitting procedures are used with three unknown parameters each. The output unit cells are reduced cells according to approved crystallographic conventions. Unit-cell solutions are additionally numerically optimized. The computational toolkit is compiled in the form of a MATLAB executable and presented within a user-friendly graphical user interface. The program is demonstrated by application on two independent examples of thin organic films.texthttps://creativecommons.org/licenses/by/4.0/text/htmlGIDInd: an automated indexing software for grazing-incidence X-ray diffraction datadoi:10.1107/S1600576721006609International Union of Crystallography2021-07-30Kainz, M.P.Legenstein, L.Holzer, V.Hofer, S.Kaltenegger, M.Resel, R.Simbrunner, J.The GIDInd software package is a MATLAB-based application for automated indexing of grazing-incidence X-ray diffraction data.urn:issn:1600-5767GRAZING-INCIDENCE X-RAY DIFFRACTION; INDEXING; CRYSTALLOGRAPHIC UNIT CELLS; SOFTWAREenhttps://creativecommons.org/licenses/by/4.0/med@iucr.org1600-57672021-07-30Journal of Applied CrystallographyAugust 202112674computer programs1600-5767541256Quantitative powder diffraction using a (2 + 3) surface diffractometer and an area detector
http://scripts.iucr.org/cgi-bin/paper?kc5126
X-ray diffractometers primarily designed for surface X-ray diffraction are often used to measure the diffraction from powders, textured materials and fiber-texture samples in 2θ scans. Unlike in high-energy powder diffraction, only a fraction of the powder rings is typically measured, and the data consist of many detector images across the 2θ range. Such diffractometers typically scan in directions not possible on a conventional laboratory diffractometer, which gives enhanced control of the scattering vector relative to the sample orientation. There are, however, very few examples where the measured intensity is directly used, such as for profile/Rietveld refinement, as is common with other powder diffraction data. Although the underlying physics is known, converting the data is time consuming and the appropriate corrections are dispersed across several publications, often not with powder diffraction in mind. This paper presents the angle calculations and correction factors required to calculate meaningful intensities for 2θ scans with a (2 + 3)-type diffractometer and an area detector. Some of the limitations with respect to texture, refraction and instrumental resolution are also discussed, as is the kind of information that one can hope to obtain.X-ray diffractometers primarily designed for surface X-ray diffraction are often used to measure the diffraction from powders, textured materials and fiber-texture samples in 2θ scans. Unlike in high-energy powder diffraction, only a fraction of the powder rings is typically measured, and the data consist of many detector images across the 2θ range. Such diffractometers typically scan in directions not possible on a conventional laboratory diffractometer, which gives enhanced control of the scattering vector relative to the sample orientation. There are, however, very few examples where the measured intensity is directly used, such as for profile/Rietveld refinement, as is common with other powder diffraction data. Although the underlying physics is known, converting the data is time consuming and the appropriate corrections are dispersed across several publications, often not with powder diffraction in mind. This paper presents the angle calculations and correction factors required to calculate meaningful intensities for 2θ scans with a (2 + 3)-type diffractometer and an area detector. Some of the limitations with respect to texture, refraction and instrumental resolution are also discussed, as is the kind of information that one can hope to obtain.texthttps://creativecommons.org/licenses/by/4.0/text/htmlQuantitative powder diffraction using a (2 + 3) surface diffractometer and an area detectordoi:10.1107/S1600576721006245International Union of Crystallography2021-07-16Abbondanza, G.Larsson, A.Carlá, F.Lundgren, E.Harlow, G.S.Conversion of 2D detector images measured on a (2 + 3) surface diffractometer to meaningful intensities that can be used for quantitative analysis of powdered and textured materials is discussed.urn:issn:1600-5767POWDER DIFFRACTION; RIETVELD REFINEMENT; ANGLE CALCULATIONS; GRAZING INCIDENCE; AREA DETECTORSen11401600-576754research papers41152August 20212021-07-16Journal of Applied Crystallography1600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/PyQCstrc.ico: a computing package for structural modelling of icosahedral quasicrystals
http://scripts.iucr.org/cgi-bin/paper?tu5010
The atomic structure of quasicrystals (QCs) is described as a section of a higher-dimensional structure that consists of a periodic arrangement of occupation domains (ODs). Determination of the shape of ODs and their partitioning is crucial in the structural analysis of QCs. However, owing to the complicated shape of ODs, building the initial structure model requires a great deal of time and effort. Thus, a computer program for building structure models of QCs is needed. Presented here is a Python3 package for structure modelling of icosahedral QCs.The atomic structure of quasicrystals (QCs) is described as a section of a higher-dimensional structure that consists of a periodic arrangement of occupation domains (ODs). Determination of the shape of ODs and their partitioning is crucial in the structural analysis of QCs. However, owing to the complicated shape of ODs, building the initial structure model requires a great deal of time and effort. Thus, a computer program for building structure models of QCs is needed. Presented here is a Python3 package for structure modelling of icosahedral QCs.texthttps://creativecommons.org/licenses/by/4.0/text/htmlPyQCstrc.ico: a computing package for structural modelling of icosahedral quasicrystalsdoi:10.1107/S1600576721005951International Union of Crystallography2021-07-16Yamada, T.PyQCstrc.ico is a computer package for building a 6D structure model of icosahedral quasicrystals with the Python3 programming language.urn:issn:1600-5767QUASICRYSTALS; HIGHER-DIMENSIONAL CRYSTALLOGRAPHYen541600-57671252August 202112554computer programsmed@iucr.org1600-5767Journal of Applied Crystallography2021-07-16https://creativecommons.org/licenses/by/4.0/GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?cw5031
The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It is an iterative algorithm that reconstructs the electron density of the sample by matching the computed fluctuation X-ray scattering data to the external observations, and by simultaneously enforcing constraints in real and Fourier space. This paper presents the first ever MTIP algorithm acceleration efforts on contemporary graphics processing units (GPUs). The Compute Unified Device Architecture (CUDA) programming model is used to accelerate the MTIP algorithm on NVIDIA GPUs. The computational performance of the CUDA-based MTIP algorithm implementation outperforms the CPU-based version by an order of magnitude. Furthermore, the Heterogeneous-Compute Interface for Portability (HIP) runtime APIs are used to demonstrate portability by accelerating the MTIP algorithm across NVIDIA and AMD GPUs.The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It is an iterative algorithm that reconstructs the electron density of the sample by matching the computed fluctuation X-ray scattering data to the external observations, and by simultaneously enforcing constraints in real and Fourier space. This paper presents the first ever MTIP algorithm acceleration efforts on contemporary graphics processing units (GPUs). The Compute Unified Device Architecture (CUDA) programming model is used to accelerate the MTIP algorithm on NVIDIA GPUs. The computational performance of the CUDA-based MTIP algorithm implementation outperforms the CPU-based version by an order of magnitude. Furthermore, the Heterogeneous-Compute Interface for Portability (HIP) runtime APIs are used to demonstrate portability by accelerating the MTIP algorithm across NVIDIA and AMD GPUs.texthttps://creativecommons.org/licenses/by/4.0/text/htmlGPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scatteringdoi:10.1107/S1600576721005744International Union of Crystallography2021-07-30Kommera, P.R.Ramakrishnaiah, V.Sweeney, C.Donatelli, J.Zwart, P.H.The paper presents efforts to accelerate the multitiered iterative phasing (MTIP) algorithm on contemporary graphics processing units (GPUs). Application portability is demonstrated by accelerating the MTIP algorithm on NVIDIA and AMD GPUs using a single codebase.urn:issn:1600-5767FLUCTUATION X-RAY SCATTERING; MULTITIERED ITERATIVE PHASING; POLAR FOURIER TRANSFORM; SPHERICAL HARMONIC TRANSFORM; GPU ACCELERATION; CUDA PROGRAMMING; HIP PROGRAMMING; NVIDIA GPUS; AMD GPUSen1600-5767541179research papers11884August 20211600-5767med@iucr.org2021-07-30Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Determining the maximum information gain and optimizing experimental design in neutron reflectometry using the Fisher information
http://scripts.iucr.org/cgi-bin/paper?ge5096
An approach based on the Fisher information (FI) is developed to quantify the maximum information gain and optimal experimental design in neutron reflectometry experiments. In these experiments, the FI can be calculated analytically and used to provide sub-second predictions of parameter uncertainties. This approach can be used to influence real-time decisions about measurement angle, measurement time, contrast choice and other experimental conditions based on parameters of interest. The FI provides a lower bound on parameter estimation uncertainties, and these are shown to decrease with the square root of the measurement time, providing useful information for the planning and scheduling of experimental work. As the FI is computationally inexpensive to calculate, it can be computed repeatedly during the course of an experiment, saving costly beam time by signalling that sufficient data have been obtained or saving experimental data sets by signalling that an experiment needs to continue. The approach's predictions are validated through the introduction of an experiment simulation framework that incorporates instrument-specific incident flux profiles, and through the investigation of measuring the structural properties of a phospholipid bilayer.An approach based on the Fisher information (FI) is developed to quantify the maximum information gain and optimal experimental design in neutron reflectometry experiments. In these experiments, the FI can be calculated analytically and used to provide sub-second predictions of parameter uncertainties. This approach can be used to influence real-time decisions about measurement angle, measurement time, contrast choice and other experimental conditions based on parameters of interest. The FI provides a lower bound on parameter estimation uncertainties, and these are shown to decrease with the square root of the measurement time, providing useful information for the planning and scheduling of experimental work. As the FI is computationally inexpensive to calculate, it can be computed repeatedly during the course of an experiment, saving costly beam time by signalling that sufficient data have been obtained or saving experimental data sets by signalling that an experiment needs to continue. The approach's predictions are validated through the introduction of an experiment simulation framework that incorporates instrument-specific incident flux profiles, and through the investigation of measuring the structural properties of a phospholipid bilayer.texthttps://creativecommons.org/licenses/by/4.0/text/htmlDetermining the maximum information gain and optimizing experimental design in neutron reflectometry using the Fisher informationdoi:10.1107/S160057672100563XInternational Union of Crystallography2021-07-07Durant, J.H.Wilkins, L.Butler, K.Cooper, J.F.K.A framework is developed using the Fisher information for information quantification in neutron reflectometry. The framework's utility is demonstrated in the rapid estimation of model parameter uncertainties, as well as in experimental design to maximize information gain about given systems.urn:issn:1600-5767NEUTRON REFLECTIVITY; NEUTRON REFLECTOMETRY; FISHER INFORMATION; INFORMATION THEORY; ANALYSIS; EXPERIMENTAL DESIGNen541600-57671100August 20211110research papers4med@iucr.org1600-5767Journal of Applied Crystallography2021-07-07https://creativecommons.org/licenses/by/4.0/Combining a multi-analyzer stage with a two-dimensional detector for high-resolution powder X-ray diffraction: correcting the angular scale
http://scripts.iucr.org/cgi-bin/paper?kc5125
In a test experiment, a two-dimensional pixel detector was mounted on the nine-channel multi-analyzer stage of the high-resolution powder diffraction beamline ID22 at the ESRF. This detector replaces a bank of scintillation counters that detect the diffracted intensity passing via the analyzer crystals as the diffractometer arm is scanned. At each diffractometer detector arm angle 2Θ, a 2D image is recorded that displays nine distinct regions of interest corresponding to the diffraction signals transmitted by each of the analyzer crystals. Summing pixels from within each region of interest allows the diffracted intensity to be extracted for each channel. X-rays are diffracted from the sample at various angles, 2θ, into Debye–Scherrer cones. Depending on the azimuthal angle around the cone, diffracted photons satisfy the analyzer-crystal Bragg condition at different diffractometer 2Θ values and arrive on the detector at different horizontal (axial) positions. The more the azimuthal angle deviates from diffraction in the vertical plane, the lower the 2Θ angle at which it is transmitted by an analyzer crystal, and the greater the distance of the detecting pixel from the centerline of the detector. This paper illustrates how the axial resolution afforded by the pixel detector can be used to correct the apparent diffraction angle, 2Θ, given by the diffractometer arm to its true diffraction angle, 2θ. This allows a reduction in peak asymmetry at low angle, and even with a relatively small axial acceptance, the correction leads to narrower peaks than if no correction is applied. By varying axial acceptance with diffraction angle, it is possible to optimize angular resolution at low diffraction angles and counting statistics at high angles. In addition, there is an intrinsic peak broadening with increasing azimuthal angle, dependent on the axial beam and detector pixel sizes. This effect reduces with 2θ, as the curvature of the Debye–Scherrer cones decreases. This broadening can be estimated and used to help choose the axial range to include as a function of diffraction angle.In a test experiment, a two-dimensional pixel detector was mounted on the nine-channel multi-analyzer stage of the high-resolution powder diffraction beamline ID22 at the ESRF. This detector replaces a bank of scintillation counters that detect the diffracted intensity passing via the analyzer crystals as the diffractometer arm is scanned. At each diffractometer detector arm angle 2Θ, a 2D image is recorded that displays nine distinct regions of interest corresponding to the diffraction signals transmitted by each of the analyzer crystals. Summing pixels from within each region of interest allows the diffracted intensity to be extracted for each channel. X-rays are diffracted from the sample at various angles, 2θ, into Debye–Scherrer cones. Depending on the azimuthal angle around the cone, diffracted photons satisfy the analyzer-crystal Bragg condition at different diffractometer 2Θ values and arrive on the detector at different horizontal (axial) positions. The more the azimuthal angle deviates from diffraction in the vertical plane, the lower the 2Θ angle at which it is transmitted by an analyzer crystal, and the greater the distance of the detecting pixel from the centerline of the detector. This paper illustrates how the axial resolution afforded by the pixel detector can be used to correct the apparent diffraction angle, 2Θ, given by the diffractometer arm to its true diffraction angle, 2θ. This allows a reduction in peak asymmetry at low angle, and even with a relatively small axial acceptance, the correction leads to narrower peaks than if no correction is applied. By varying axial acceptance with diffraction angle, it is possible to optimize angular resolution at low diffraction angles and counting statistics at high angles. In addition, there is an intrinsic peak broadening with increasing azimuthal angle, dependent on the axial beam and detector pixel sizes. This effect reduces with 2θ, as the curvature of the Debye–Scherrer cones decreases. This broadening can be estimated and used to help choose the axial range to include as a function of diffraction angle.texthttps://creativecommons.org/licenses/by/4.0/text/htmlCombining a multi-analyzer stage with a two-dimensional detector for high-resolution powder X-ray diffraction: correcting the angular scaledoi:10.1107/S1600576721005288International Union of Crystallography2021-07-07Fitch, A.Dejoie, C.The correction of the angular scale of powder diffraction data resolved axially by a two-dimensional pixel detector after an analyzer crystal or multi-analyzer stage is discussed. Angular correction reduces peak asymmetry at low angles and can be combined with a scheme that varies axial acceptance with angle to optimize angular resolution or statistical quality as required.urn:issn:1600-5767HIGH-RESOLUTION POWDER X-RAY DIFFRACTION; ANALYZER CRYSTALS; TWO-DIMENSIONAL DETECTORS; AXIAL DIVERGENCEen10881600-576754August 20211099research papers42021-07-07Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/Intragranular strain estimation in far-field scanning X-ray diffraction using a Gaussian process
http://scripts.iucr.org/cgi-bin/paper?nb5298
A new method for estimation of intragranular strain fields in polycrystalline materials based on scanning three-dimensional X-ray diffraction (scanning 3DXRD) data is presented and evaluated. Given an a priori known anisotropic compliance, the regression method enforces the balance of linear and angular momentum in the linear elastic strain field reconstruction. By using a Gaussian process (GP), the presented method can yield a spatial estimate of the uncertainty of the reconstructed strain field. Furthermore, constraints on spatial smoothness can be optimized with respect to measurements through hyperparameter estimation. These three features address weaknesses discussed for previously existing scanning 3DXRD reconstruction methods and, thus, offer a more robust strain field estimation. The method is twofold validated: firstly by reconstruction from synthetic diffraction data, and secondly by reconstruction of a previously studied tin (Sn) grain embedded in a polycrystalline specimen. Comparison against reconstructions achieved by a recently proposed algebraic inversion technique is also presented. It is found that the GP regression consistently produces reconstructions with lower root-mean-square errors, mean absolute errors and maximum absolute errors across all six components of strain.A new method for estimation of intragranular strain fields in polycrystalline materials based on scanning three-dimensional X-ray diffraction (scanning 3DXRD) data is presented and evaluated. Given an a priori known anisotropic compliance, the regression method enforces the balance of linear and angular momentum in the linear elastic strain field reconstruction. By using a Gaussian process (GP), the presented method can yield a spatial estimate of the uncertainty of the reconstructed strain field. Furthermore, constraints on spatial smoothness can be optimized with respect to measurements through hyperparameter estimation. These three features address weaknesses discussed for previously existing scanning 3DXRD reconstruction methods and, thus, offer a more robust strain field estimation. The method is twofold validated: firstly by reconstruction from synthetic diffraction data, and secondly by reconstruction of a previously studied tin (Sn) grain embedded in a polycrystalline specimen. Comparison against reconstructions achieved by a recently proposed algebraic inversion technique is also presented. It is found that the GP regression consistently produces reconstructions with lower root-mean-square errors, mean absolute errors and maximum absolute errors across all six components of strain.texthttps://creativecommons.org/licenses/by/4.0/text/htmlIntragranular strain estimation in far-field scanning X-ray diffraction using a Gaussian processdoi:10.1107/S1600576721005112International Union of Crystallography2021-06-14Henningsson, A.Hendriks, J.A novel regression method for estimating intragranular strain in polycrystalline materials from three-dimensional X-ray diffraction data is presented and evaluated. The method incorporates an equilibrium constraint to the reconstructed strain field by using a Gaussian process.urn:issn:1600-5767THREE-DIMENSIONAL X-RAY DIFFRACTION (3DXRD); INTRAGRANULAR STRAIN; GAUSSIAN PROCESSES; SCANNING X-RAY DIFFRACTIONenhttps://creativecommons.org/licenses/by/4.0/med@iucr.org1600-5767Journal of Applied Crystallography2021-06-14August 20211070research papers4541600-57671057Robust surface structure analysis with reliable uncertainty estimation using the exchange Monte Carlo method. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?to9205
An error in the article by Nagai, Anada, Nakanishi-Ohno, Okada & Wakabayashi [J. Appl. Cryst. (2020), 53, 387–392] is corrected.An error in the article by Nagai, Anada, Nakanishi-Ohno, Okada & Wakabayashi [J. Appl. Cryst. (2020), 53, 387–392] is corrected.textCopyright (c) 2021 International Union of Crystallographytext/htmlRobust surface structure analysis with reliable uncertainty estimation using the exchange Monte Carlo method. Corrigendumdoi:10.1107/S1600576721004520International Union of Crystallography2021-05-09Nagai, K.Anada, M.Nakanishi-Ohno, Y.Okada, M.Wakabayashi, Y.An error in the article by Nagai, Anada, Nakanishi-Ohno, Okada & Wakabayashi [J. Appl. Cryst. (2020), 53, 387–392] is corrected.urn:issn:1600-5767SURFACE DIFFRACTION; BAYESIAN INFERENCE; MONTE CARLO; OXIDE FILMS; EPITAXIAL FILMSenJune 2021addenda and errata1023310231600-576754Copyright (c) 2021 International Union of Crystallography2021-05-09Journal of Applied Crystallographymed@iucr.org1600-5767Alignment facility and software for single-crystal time-of-flight neutron spectroscopy
http://scripts.iucr.org/cgi-bin/paper?tu5008
An instrument and software algorithm are described for the purpose of characterization of large single crystals at the Alignment Facility of the ISIS spallation neutron source. A method for both characterizing the quality of the sample and aligning it in a particular scattering plane is introduced. A software package written for this instrument is presented, and its utility is demonstrated by way of an example of the structural characterization of large single crystals of Pb(Mg1/3Nb2/3)O3. Extensions and modifications of characterization instruments for future improved beamlines are suggested. It is hoped that this software will be used by the neutron community for pre-characterizing large single crystals for spectroscopy experiments and that in the future such a facility will be included as part of the spectroscopy suite at other spallation neutron sources.An instrument and software algorithm are described for the purpose of characterization of large single crystals at the Alignment Facility of the ISIS spallation neutron source. A method for both characterizing the quality of the sample and aligning it in a particular scattering plane is introduced. A software package written for this instrument is presented, and its utility is demonstrated by way of an example of the structural characterization of large single crystals of Pb(Mg1/3Nb2/3)O3. Extensions and modifications of characterization instruments for future improved beamlines are suggested. It is hoped that this software will be used by the neutron community for pre-characterizing large single crystals for spectroscopy experiments and that in the future such a facility will be included as part of the spectroscopy suite at other spallation neutron sources.texthttps://creativecommons.org/licenses/by/4.0/text/htmlAlignment facility and software for single-crystal time-of-flight neutron spectroscopydoi:10.1107/S1600576721004234International Union of Crystallography2021-05-31Liu, Z.Lane, H.Frost, C.D.Ewings, R.A.Attfield, J.P.Stock, C.The paper describes an algorithm and formalism for visualizing neutron diffraction data from the Alignment Facility diffractometer at ISIS. Their use is demonstrated by performing test measurements on the piezoelectric PbMg1/3Nb2/3O3.urn:issn:1600-5767POLE FIGURES; NEUTRONS; CHARACTERIZATIONenJune 20213962research papers9571600-576754https://creativecommons.org/licenses/by/4.0/2021-05-31Journal of Applied Crystallographymed@iucr.org1600-5767Crystallographic analysis of the lattice metric (CALM) from single electron backscatter diffraction or transmission Kikuchi diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?nb5295
A new software is presented for the determination of crystal lattice parameters from the positions and widths of Kikuchi bands in a diffraction pattern. Starting with a single wide-angle Kikuchi pattern of arbitrary resolution and unknown phase, the traces of all visibly diffracting lattice planes are manually derived from four initial Kikuchi band traces via an intuitive graphical user interface. A single Kikuchi bandwidth is then used as reference to scale all reciprocal lattice point distances. Kikuchi band detection, via a filtered Funk transformation, and simultaneous display of the band intensity profile helps users to select band positions and widths. Bandwidths are calculated using the first derivative of the band profiles as excess-deficiency effects have minimal influence. From the reciprocal lattice, the metrics of possible Bravais lattice types are derived for all crystal systems. The measured lattice parameters achieve a precision of <1%, even for good quality Kikuchi diffraction patterns of 400 × 300 pixels. This band-edge detection approach has been validated on several hundred experimental diffraction patterns from phases of different symmetries and random orientations. It produces a systematic lattice parameter offset of up to ±4%, which appears to scale with the mean atomic number or the backscatter coefficient.A new software is presented for the determination of crystal lattice parameters from the positions and widths of Kikuchi bands in a diffraction pattern. Starting with a single wide-angle Kikuchi pattern of arbitrary resolution and unknown phase, the traces of all visibly diffracting lattice planes are manually derived from four initial Kikuchi band traces via an intuitive graphical user interface. A single Kikuchi bandwidth is then used as reference to scale all reciprocal lattice point distances. Kikuchi band detection, via a filtered Funk transformation, and simultaneous display of the band intensity profile helps users to select band positions and widths. Bandwidths are calculated using the first derivative of the band profiles as excess-deficiency effects have minimal influence. From the reciprocal lattice, the metrics of possible Bravais lattice types are derived for all crystal systems. The measured lattice parameters achieve a precision of <1%, even for good quality Kikuchi diffraction patterns of 400 × 300 pixels. This band-edge detection approach has been validated on several hundred experimental diffraction patterns from phases of different symmetries and random orientations. It produces a systematic lattice parameter offset of up to ±4%, which appears to scale with the mean atomic number or the backscatter coefficient.texthttps://creativecommons.org/licenses/by/4.0/text/htmlCrystallographic analysis of the lattice metric (CALM) from single electron backscatter diffraction or transmission Kikuchi diffraction patternsdoi:10.1107/S1600576721004210International Union of Crystallography2021-05-28Nolze, G.Tokarski, T.Rychłowski, Ł.Cios, G.Winkelmann, A.New software and algorithms for the accurate measurement of crystal lattice parameters from Kikuchi bands in a diffraction pattern are presented.urn:issn:1600-5767ELECTRON BACKSCATTER DIFFRACTION; KIKUCHI PATTERNS; LATTICE PARAMETERS; RADON TRANSFORMen2021-05-28Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/10121600-576754June 20211022computer programs3A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening
http://scripts.iucr.org/cgi-bin/paper?te5077
A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.texthttps://creativecommons.org/licenses/by/4.0/text/htmlA capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screeningdoi:10.1107/S1600576721004155International Union of Crystallography2021-06-14Sui, S.Mulichak, A.Kulathila, R.McGee, J.Filiatreault, D.Saha, S.Cohen, A.Song, J.Hung, H.Selway, J.Kirby, C.Shrestha, O.K.Weihofen, W.Fodor, M.Xu, M.Chopra, R.Perry, S.L.A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported.urn:issn:1600-5767COMPOUND SCREENING; MICROFLUIDICS; STRUCTURAL BIOLOGY; PROTEIN CRYSTALLOGRAPHY; X-RAY DIFFRACTIONen541600-57671034August 2021research papers41046med@iucr.org1600-5767Journal of Applied Crystallography2021-06-14https://creativecommons.org/licenses/by/4.0/Aerosol-based ligand soaking of reservoir-free protein crystals
http://scripts.iucr.org/cgi-bin/paper?gj5259
Soaking of macromolecular crystals allows the formation of complexes via diffusion of molecules into a preformed crystal for structural analysis. Soaking offers various advantages over co-crystallization, e.g. small samples and high-throughput experimentation. However, this method has disadvantages, such as inducing mechanical stress on crystals and reduced success rate caused by low affinity/solubility of the ligand. To bypass these issues, the Picodropper was previously developed in the authors' laboratory. This technique aimed to deliver small volumes of compound solution in response to crystal dehydration supported by the Free Mounting System humidity control or by IR-laser-induced protein crystal transformation. Herein, a new related soaking development, the Aerosol-Generator, is introduced. This device delivers compounds onto the solution-free surface of protein crystals using an ultrasonic technique. The produced aerosol stream enables an easier and more accurate control of solution volumes, reduced crystal handling, and crystal-size-independent soaking. The Aerosol-Generator has been used to produce complexes of DPP8 crystals, where otherwise regular soaking did not achieve complex formation. These results demonstrate the potential of this device in challenging ligand-binding scenarios and contribute to further understanding of DPP8 inhibitor binding.Soaking of macromolecular crystals allows the formation of complexes via diffusion of molecules into a preformed crystal for structural analysis. Soaking offers various advantages over co-crystallization, e.g. small samples and high-throughput experimentation. However, this method has disadvantages, such as inducing mechanical stress on crystals and reduced success rate caused by low affinity/solubility of the ligand. To bypass these issues, the Picodropper was previously developed in the authors' laboratory. This technique aimed to deliver small volumes of compound solution in response to crystal dehydration supported by the Free Mounting System humidity control or by IR-laser-induced protein crystal transformation. Herein, a new related soaking development, the Aerosol-Generator, is introduced. This device delivers compounds onto the solution-free surface of protein crystals using an ultrasonic technique. The produced aerosol stream enables an easier and more accurate control of solution volumes, reduced crystal handling, and crystal-size-independent soaking. The Aerosol-Generator has been used to produce complexes of DPP8 crystals, where otherwise regular soaking did not achieve complex formation. These results demonstrate the potential of this device in challenging ligand-binding scenarios and contribute to further understanding of DPP8 inhibitor binding.texthttps://creativecommons.org/licenses/by/4.0/text/htmlAerosol-based ligand soaking of reservoir-free protein crystalsdoi:10.1107/S1600576721003551International Union of Crystallography2021-05-28Ross, B.Krapp, S.Geiss-Friedlander, R.Littmann, W.Huber, R.Kiefersauer, R.A novel aerosol device for protein crystal complexation using ultrasonic vibrations is described.urn:issn:1600-5767AEROSOLS; SOAKING; ULTRASONIC; DPP8enmed@iucr.org1600-57672021-05-28Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-576754895June 20213research papers902ASAXS measurements on ferritin and apoferritin at the bioSAXS beamline P12 (PETRA III, DESY)
http://scripts.iucr.org/cgi-bin/paper?ge5089
Small-angle X-ray scattering is widely utilized to study biological macromolecules in solution. For samples containing specific (e.g. metal) atoms, additional information can be obtained using anomalous scattering. Here, measuring samples at different energies close to the absorption edges of relevant elements provides specific structural details. However, anomalous small-angle X-ray scattering (ASAXS) applications to dilute macromolecular solutions are challenging owing to the overall low anomalous scattering effect. Here, pilot ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin are reported. These samples were investigated near the resonance X-ray K edges of Fe and Co, respectively, at the EMBL P12 bioSAXS beamline at PETRA III, DESY. Thanks to the high brilliance of the P12 beamline, ASAXS experiments are feasible on dilute protein solutions, allowing one to extract the Fe- or Co-specific anomalous dispersion terms from the ASAXS data. The data were subsequently used to determine the spatial distribution of either iron or cobalt atoms incorporated into the ferritin/apoferritin protein cages.Small-angle X-ray scattering is widely utilized to study biological macromolecules in solution. For samples containing specific (e.g. metal) atoms, additional information can be obtained using anomalous scattering. Here, measuring samples at different energies close to the absorption edges of relevant elements provides specific structural details. However, anomalous small-angle X-ray scattering (ASAXS) applications to dilute macromolecular solutions are challenging owing to the overall low anomalous scattering effect. Here, pilot ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin are reported. These samples were investigated near the resonance X-ray K edges of Fe and Co, respectively, at the EMBL P12 bioSAXS beamline at PETRA III, DESY. Thanks to the high brilliance of the P12 beamline, ASAXS experiments are feasible on dilute protein solutions, allowing one to extract the Fe- or Co-specific anomalous dispersion terms from the ASAXS data. The data were subsequently used to determine the spatial distribution of either iron or cobalt atoms incorporated into the ferritin/apoferritin protein cages.texthttps://creativecommons.org/licenses/by/4.0/text/htmlASAXS measurements on ferritin and apoferritin at the bioSAXS beamline P12 (PETRA III, DESY)doi:10.1107/S1600576721003034International Union of Crystallography2021-05-25Wieland, D.C.F.Schroer, M.A.Gruzinov, A.Y.Blanchet, C.E.Jeffries, C.M.Svergun, D.I.Anomalous small-angle X-ray scattering (ASAXS) allows one to obtain information about the spatial distribution of specific atoms in a sample, but its application to dilute biological samples is challenging because of weak anomalous effects. ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin near the resonance X-ray K edges of Fe and Co, respectively, have been performed at the P12 bioSAXS beamline of the EMBL at PETRA III synchrotron, DESY.urn:issn:1600-5767ANOMALOUS SMALL-ANGLE X-RAY SCATTERING; ASAXS; MACROMOLECULES; ABSORPTION EDGES; IONSenhttps://creativecommons.org/licenses/by/4.0/med@iucr.org1600-5767Journal of Applied Crystallography2021-05-25June 20213838research papers541600-5767830Grazing-incidence X-ray scattering of lamellar thin films. Erratum
http://scripts.iucr.org/cgi-bin/paper?vh5141
Errors in the article by Smilgies [J. Appl. Cryst. (2019), 52, 247–251] are corrected.Errors in the article by Smilgies [J. Appl. Cryst. (2019), 52, 247–251] are corrected.texttext/htmlGrazing-incidence X-ray scattering of lamellar thin films. Erratumdoi:10.1107/S1600576721002971International Union of Crystallography2021-05-25Smilgies, D.-M.Errors in the article by Smilgies [J. Appl. Cryst. (2019), 52, 247–251] are corrected.urn:issn:1600-5767SOFT MATERIALS; LAMELLAE; GRAZING INCIDENCE SCATTERING; AREA DETECTORSen2021-05-25Journal of Applied Crystallographymed@iucr.org1600-5767June 2021addenda and errata1024310241600-576754CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals
http://scripts.iucr.org/cgi-bin/paper?oc5008
CrystalExplorer is a native cross-platform program supported on Windows, MacOS and Linux with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. Over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the Gaussian and NWChem programs to calculate quantum-mechanical properties of molecules. The current version, CrystalExplorer21, incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.CrystalExplorer is a native cross-platform program supported on Windows, MacOS and Linux with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. Over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the Gaussian and NWChem programs to calculate quantum-mechanical properties of molecules. The current version, CrystalExplorer21, incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.texthttps://creativecommons.org/licenses/by/4.0/text/htmlCrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystalsdoi:10.1107/S1600576721002910International Union of Crystallography2021-04-27Spackman, P.R.Turner, M.J.McKinnon, J.J.Wolff, S.K.Grimwood, D.J.Jayatilaka, D.Spackman, M.A.CrystalExplorer is a native cross-platform program for the visualization and investigation of molecular crystal structures.urn:issn:1600-5767INTERMOLECULAR INTERACTIONS; HIRSHFELD SURFACES; FINGERPRINTS; VISUALIZATION; QUANTUM-MECHANICAL PROPERTIES; COMPUTER PROGRAMS; CRYSTALEXPLORERen10061600-576754June 202131011computer programs2021-04-27Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/Characterizing dislocation loops in irradiated polycrystalline Zr alloys by X-ray line profile analysis of powder diffraction patterns with satellites
http://scripts.iucr.org/cgi-bin/paper?nb5274
This work extends the convolutional multiple whole profile (CMWP) line profile analysis (LPA) procedure to determine the total dislocation density and character of irradiation-induced dislocation loops in commercial polycrystalline Zr specimens. Zr alloys are widely used in the nuclear industry as fuel cladding materials in which irradiation-induced point defects evolve into dislocation loops. LPA has long been established as a powerful tool to determine the density and nature of lattice defects in plastically deformed materials. The CMWP LPA procedure is based on the Krivoglaz–Wilkens theory in which the dislocation structure is characterized by the total dislocation density ρ and the dislocation arrangement parameter M. In commercial Zr alloys irradiation-induced dislocation loops broaden the peak profiles, mainly in the tail regions, and occasionally generate small satellites next to the Bragg peaks. In this work, two challenges in powder diffraction patterns of irradiated Zr alloys are solved: (i) determination of the M values from the long tail regions of peaks has been made unequivocal and (ii) satellites have been fitted separately, using physically well established principles, in order to exclude them from the dislocation determination process. Referring to the theory of heterogeneous dislocation distributions, determination of the total dislocation density from the main peaks free of satellites has been justified. The dislocation loop structure has been characterized by the total dislocation density of loops and the M parameter correlated to the dipole character of dislocation loops. The extended CMWP procedure is applied to determine the total dislocation density, the dipole character of dislocation loops, and the fractions of 〈a〉- and 〈c〉-type loops in proton- or neutron-irradiated polycrystalline Zr alloys used in the nuclear energy industry.This work extends the convolutional multiple whole profile (CMWP) line profile analysis (LPA) procedure to determine the total dislocation density and character of irradiation-induced dislocation loops in commercial polycrystalline Zr specimens. Zr alloys are widely used in the nuclear industry as fuel cladding materials in which irradiation-induced point defects evolve into dislocation loops. LPA has long been established as a powerful tool to determine the density and nature of lattice defects in plastically deformed materials. The CMWP LPA procedure is based on the Krivoglaz–Wilkens theory in which the dislocation structure is characterized by the total dislocation density ρ and the dislocation arrangement parameter M. In commercial Zr alloys irradiation-induced dislocation loops broaden the peak profiles, mainly in the tail regions, and occasionally generate small satellites next to the Bragg peaks. In this work, two challenges in powder diffraction patterns of irradiated Zr alloys are solved: (i) determination of the M values from the long tail regions of peaks has been made unequivocal and (ii) satellites have been fitted separately, using physically well established principles, in order to exclude them from the dislocation determination process. Referring to the theory of heterogeneous dislocation distributions, determination of the total dislocation density from the main peaks free of satellites has been justified. The dislocation loop structure has been characterized by the total dislocation density of loops and the M parameter correlated to the dipole character of dislocation loops. The extended CMWP procedure is applied to determine the total dislocation density, the dipole character of dislocation loops, and the fractions of 〈a〉- and 〈c〉-type loops in proton- or neutron-irradiated polycrystalline Zr alloys used in the nuclear energy industry.texthttps://creativecommons.org/licenses/by/4.0/text/htmlCharacterizing dislocation loops in irradiated polycrystalline Zr alloys by X-ray line profile analysis of powder diffraction patterns with satellitesdoi:10.1107/S1600576721002673International Union of Crystallography2021-05-25Ungár, T.Ribárik, G.Topping, M.Jones, R.M.A.Dan Xu, X.Hulse, R.Harte, A.Tichy, G.Race, C.P.Frankel, P.Preuss, M.Satellites generated by small dislocation loops in polycrystalline proton- or neutron-irradiated Zr alloys are characterized by X-ray line profile analysis. The convolutional multiple whole-profile procedure has been extended to characterize irradiation-induced satellites around fundamental Bragg peaks.urn:issn:1600-5767X-RAY LINE PROFILE ANALYSIS; SMALL DISLOCATION LOOPS; TOTAL DISLOCATION DENSITY OF LOOPS; DIPOLE CHARACTER OF SMALL LOOPS; SATELLITE PEAKS; TYPES OF DISLOCATION LOOP; SCATTERING BY IRRADIATION-INDUCED DISLOCATION LOOPSenmed@iucr.org1600-5767Journal of Applied Crystallography2021-05-25https://creativecommons.org/licenses/by/4.0/541600-5767803June 2021821research papers3Design and use of a sapphire single-crystal gas-pressure cell for in situ neutron powder diffraction
http://scripts.iucr.org/cgi-bin/paper?in5050
A sapphire single-crystal gas-pressure cell without external support allowing unobstructed optical access by neutrons has been developed and optimized for elastic in situ neutron powder diffraction using hydrogen (deuterium) gas at the high-intensity two-axis diffractometer D20 at the Institut Laue-Langevin (Grenoble, France). Given a proper orientation of the single-crystal sample holder with respect to the detector, parasitic reflections from the sample holder can be avoided and the background can be kept low. Hydrogen (deuterium) gas pressures of up to 16.0 MPa at 298 K and 8.0 MPa at 655 K were tested successfully for a wall thickness of 3 mm. Heating was achieved by a two-sided laser heating system. The typical time resolution of in situ investigations of the reaction pathway of hydrogen (deuterium) uptake or release is on the order of 1 min. Detailed descriptions of all parts of the sapphire single-crystal gas-pressure cell are given, including materials information, technical drawings and instructions for use.A sapphire single-crystal gas-pressure cell without external support allowing unobstructed optical access by neutrons has been developed and optimized for elastic in situ neutron powder diffraction using hydrogen (deuterium) gas at the high-intensity two-axis diffractometer D20 at the Institut Laue-Langevin (Grenoble, France). Given a proper orientation of the single-crystal sample holder with respect to the detector, parasitic reflections from the sample holder can be avoided and the background can be kept low. Hydrogen (deuterium) gas pressures of up to 16.0 MPa at 298 K and 8.0 MPa at 655 K were tested successfully for a wall thickness of 3 mm. Heating was achieved by a two-sided laser heating system. The typical time resolution of in situ investigations of the reaction pathway of hydrogen (deuterium) uptake or release is on the order of 1 min. Detailed descriptions of all parts of the sapphire single-crystal gas-pressure cell are given, including materials information, technical drawings and instructions for use.texthttps://creativecommons.org/licenses/by/4.0/text/htmlDesign and use of a sapphire single-crystal gas-pressure cell for in situ neutron powder diffractiondoi:10.1107/S1600576721002685International Union of Crystallography2021-05-25Finger, R.Kurtzemann, N.Hansen, T.C.Kohlmann, H.A gas-pressure cell for in situ neutron powder diffraction based on a sapphire single crystal is described. Materials information, technical drawings and instructions for use are included.urn:issn:1600-5767NEUTRON DIFFRACTION; HYDROGENATION; NEUTRON INSTRUMENTATION; SOLID-GAS; METAL HYDRIDES; SAPPHIRE; POWDER DIFFRACTIONen3research papers846June 2021541600-5767839https://creativecommons.org/licenses/by/4.0/1600-5767med@iucr.orgJournal of Applied Crystallography2021-05-25Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
http://scripts.iucr.org/cgi-bin/paper?vk5045
A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.texthttps://creativecommons.org/licenses/by/4.0/text/htmlStructure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexingdoi:10.1107/S1600576721002569International Union of Crystallography2021-05-09Schlesinger, C.Habermehl, S.Prill, D.A new automated method to solve organic crystal structures from scratch by a fit to the pair distribution function, without prior knowledge of lattice parameters and space group, has been developed.urn:issn:1600-5767PAIR DISTRIBUTION FUNCTION ANALYSIS; STRUCTURE DETERMINATION; TOTAL SCATTERING TECHNIQUE; SIMILARITY MEASURES; PDF-GLOBAL-FITenJune 20213786research papers7761600-576754https://creativecommons.org/licenses/by/4.0/2021-05-09Journal of Applied Crystallographymed@iucr.org1600-5767lamaGOET: an interface for quantum crystallography
http://scripts.iucr.org/cgi-bin/paper?in5046
In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.texthttps://creativecommons.org/licenses/by/4.0/text/htmllamaGOET: an interface for quantum crystallographydoi:10.1107/S1600576721002545International Union of Crystallography2021-04-16Malaspina, L.A.Genoni, A.Grabowsky, S.The program lamaGOET serves as an interface between quantum-mechanical and crystallographic refinement software to enhance the flexibility of the quantum-crystallographic methods Hirshfeld atom refinement and X-ray constrained wavefunction fitting.urn:issn:1600-5767QUANTUM CRYSTALLOGRAPHY; HIRSHFELD ATOM REFINEMENT; X-RAY CONSTRAINED WAVEFUNCTION FITTINGen2021-04-16Journal of Applied Crystallography1600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/9871600-5767543995computer programsJune 2021Unifying the concepts of scattering and structure factor in ordered and disordered samples
http://scripts.iucr.org/cgi-bin/paper?in5043
Scattering methods are widely used in many research areas to analyze and resolve material structures. Given its importance, a large number of textbooks are devoted to this topic. However, technical details in experiments and disconnection between explanations from different perspectives often confuse and frustrate beginner students and researchers. To create an effective learning path, the core concepts of scattering and structure factor are reviewed in this article in a self-contained way. Classical examples of scattering photography and intensity scanning are calculated. Sample CPU and GPU codes are provided to facilitate the understanding and application of these methods.Scattering methods are widely used in many research areas to analyze and resolve material structures. Given its importance, a large number of textbooks are devoted to this topic. However, technical details in experiments and disconnection between explanations from different perspectives often confuse and frustrate beginner students and researchers. To create an effective learning path, the core concepts of scattering and structure factor are reviewed in this article in a self-contained way. Classical examples of scattering photography and intensity scanning are calculated. Sample CPU and GPU codes are provided to facilitate the understanding and application of these methods.textCopyright (c) 2021 International Union of Crystallographytext/htmlUnifying the concepts of scattering and structure factor in ordered and disordered samplesdoi:10.1107/S1600576721001965International Union of Crystallography2021-03-31Li, D.Zhang, K.This article reviews the core concepts of scattering and structure factor that are used to analyze structures of ordered and disordered samples. Simulations of scattering photography and intensity scanning of typical examples are provided, along with CPU and GPU source codes.urn:issn:1600-5767SCATTERING; STRUCTURE FACTORS; COMPUTATION; GPU CODEenCopyright (c) 2021 International Union of Crystallography2021-03-31Journal of Applied Crystallographymed@iucr.org1600-5767April 20216602teaching and education6441600-576754Numerically stable form factor of any polygon and polyhedron
http://scripts.iucr.org/cgi-bin/paper?vg5135
Coordinate-free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small-angle scattering by nanocrystals.Coordinate-free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small-angle scattering by nanocrystals.texthttps://creativecommons.org/licenses/by/4.0/text/htmlNumerically stable form factor of any polygon and polyhedrondoi:10.1107/S1600576721001710International Union of Crystallography2021-03-25Wuttke, J.Coordinate-free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities.urn:issn:1600-5767FORM FACTORS; POLYHEDRA; FOURIER SHAPE TRANSFORMen2021-03-25Journal of Applied Crystallography1600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/5801600-576754587research papers2April 2021Comparison and evaluation of pair distribution functions, using a similarity measure based on cross-correlation functions
http://scripts.iucr.org/cgi-bin/paper?kc5119
An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross-correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross-correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product-moment correlation coefficient, using polymorph IV of barbituric acid as an example.An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross-correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross-correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product-moment correlation coefficient, using polymorph IV of barbituric acid as an example.texthttps://creativecommons.org/licenses/by/4.0/text/htmlComparison and evaluation of pair distribution functions, using a similarity measure based on cross-correlation functionsdoi:10.1107/S1600576721001722International Union of Crystallography2021-03-31Habermehl, S.Schlesinger, C.Prill, D.A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross-correlation functions is introduced and evaluated.urn:issn:1600-5767PAIR DISTRIBUTION FUNCTIONS; SIMILARITY MEASURES; TOTAL SCATTERING TECHNIQUES; CROSS-CORRELATION FUNCTIONS; R VALUESenresearch papers6232April 20216121600-576754https://creativecommons.org/licenses/by/4.0/2021-03-31Journal of Applied Crystallography1600-5767med@iucr.orgThe effect of polydispersity, shape fluctuations and curvature on small unilamellar vesicle small-angle X-ray scattering curves
http://scripts.iucr.org/cgi-bin/paper?vg5124
Small unilamellar vesicles (20–100 nm diameter) are model systems for strongly curved lipid membranes, in particular for cell organelles. Routinely, small-angle X-ray scattering (SAXS) is employed to study their size and electron-density profile (EDP). Current SAXS analysis of small unilamellar vesicles (SUVs) often employs a factorization into the structure factor (vesicle shape) and the form factor (lipid bilayer electron-density profile) and invokes additional idealizations: (i) an effective polydispersity distribution of vesicle radii, (ii) a spherical vesicle shape and (iii) an approximate account of membrane asymmetry, a feature particularly relevant for strongly curved membranes. These idealizations do not account for thermal shape fluctuations and also break down for strong salt- or protein-induced deformations, as well as vesicle adhesion and fusion, which complicate the analysis of the lipid bilayer structure. Presented here are simulations of SAXS curves of SUVs with experimentally relevant size, shape and EDPs of the curved bilayer, inferred from coarse-grained simulations and elasticity considerations, to quantify the effects of size polydispersity, thermal fluctuations of the SUV shape and membrane asymmetry. It is observed that the factorization approximation of the scattering intensity holds even for small vesicle radii (∼30 nm). However, the simulations show that, for very small vesicles, a curvature-induced asymmetry arises in the EDP, with sizeable effects on the SAXS curve. It is also demonstrated that thermal fluctuations in shape and the size polydispersity have distinguishable signatures in the SAXS intensity. Polydispersity gives rise to low-q features, whereas thermal fluctuations predominantly affect the scattering at larger q, related to membrane bending rigidity. Finally, it is shown that simulation of fluctuating vesicle ensembles can be used for analysis of experimental SAXS curves.Small unilamellar vesicles (20–100 nm diameter) are model systems for strongly curved lipid membranes, in particular for cell organelles. Routinely, small-angle X-ray scattering (SAXS) is employed to study their size and electron-density profile (EDP). Current SAXS analysis of small unilamellar vesicles (SUVs) often employs a factorization into the structure factor (vesicle shape) and the form factor (lipid bilayer electron-density profile) and invokes additional idealizations: (i) an effective polydispersity distribution of vesicle radii, (ii) a spherical vesicle shape and (iii) an approximate account of membrane asymmetry, a feature particularly relevant for strongly curved membranes. These idealizations do not account for thermal shape fluctuations and also break down for strong salt- or protein-induced deformations, as well as vesicle adhesion and fusion, which complicate the analysis of the lipid bilayer structure. Presented here are simulations of SAXS curves of SUVs with experimentally relevant size, shape and EDPs of the curved bilayer, inferred from coarse-grained simulations and elasticity considerations, to quantify the effects of size polydispersity, thermal fluctuations of the SUV shape and membrane asymmetry. It is observed that the factorization approximation of the scattering intensity holds even for small vesicle radii (∼30 nm). However, the simulations show that, for very small vesicles, a curvature-induced asymmetry arises in the EDP, with sizeable effects on the SAXS curve. It is also demonstrated that thermal fluctuations in shape and the size polydispersity have distinguishable signatures in the SAXS intensity. Polydispersity gives rise to low-q features, whereas thermal fluctuations predominantly affect the scattering at larger q, related to membrane bending rigidity. Finally, it is shown that simulation of fluctuating vesicle ensembles can be used for analysis of experimental SAXS curves.texthttps://creativecommons.org/licenses/by/4.0/text/htmlThe effect of polydispersity, shape fluctuations and curvature on small unilamellar vesicle small-angle X-ray scattering curvesdoi:10.1107/S1600576721001461International Union of Crystallography2021-03-25Chappa, V.Smirnova, Y.Komorowski, K.Müller, M.Salditt, T.It is a challenge to distinguish the effect of shape fluctuations and size polydispersity on experimental small-angle X-ray scattering curves of small unilamellar vesicles. Here it is shown that both effects have distinguishable spectral patterns, and an efficient simulation tool is presented for simulating and analysing experimental data. The importance of curvature-induced electron-density profile asymmetry for estimating the vesicle size from SAXS scattering curves is also demonstrated.urn:issn:1600-5767SMALL UNILAMELLAR VESICLES; COARSE-GRAINED SIMULATIONS; ELASTIC SIMULATIONS; SMALL-ANGLE X-RAY SCATTERING; SAXS CURVESenhttps://creativecommons.org/licenses/by/4.0/med@iucr.org1600-57672021-03-25Journal of Applied CrystallographyApril 2021research papers56821600-576754557The advanced treatment of hydrogen bonding in quantum crystallography
http://scripts.iucr.org/cgi-bin/paper?in5039
Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.texthttps://creativecommons.org/licenses/by/4.0/text/htmlThe advanced treatment of hydrogen bonding in quantum crystallographydoi:10.1107/S1600576721001126International Union of Crystallography2021-04-16Malaspina, L.A.Genoni, A.Jayatilaka, D.Turner, M.J.Sugimoto, K.Nishibori, E.Grabowsky, S.Hydrogen-bonding parameters are modelled with different methods of quantum crystallography. The underlying model assumptions are analysed and related to the refinement results.urn:issn:1600-5767QUANTUM CRYSTALLOGRAPHY; HIRSHFELD ATOM REFINEMENT; X-RAY CONSTRAINED WAVEFUNCTION FITTING; ELECTRON DENSITY; HYDROGEN BONDINGen1600-576754718June 2021research papers7293med@iucr.org1600-57672021-04-16Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/In situ X-ray diffraction investigation of electric-field-induced switching in a hybrid improper ferroelectric
http://scripts.iucr.org/cgi-bin/paper?kc5124
Improper ferroelectric mechanisms are increasingly under investigation for their potential to expand the current catalogue of functional materials whilst promoting couplings between ferroelectricity and other technologically desirable properties such as ferromagnetism. This work presents the results of an in situ synchrotron X-ray diffraction experiment performed on samples of Ca2.15Sr0.85Ti2O7 in an effort to elucidate the mechanism of hybrid improper ferroelectric switching in this compound. By simultaneously applying an electric field and recording diffraction patterns, shifts in the intensity of superstructure peaks consistent with one of the switching mechanisms proposed by Nowadnick & Fennie [Phys. Rev. B, (2016), 94, 104105] are observed. While the experiment only achieves a partial response, comparison with simulated data demonstrates a preference for a one-step switching mechanism involving an unwinding of the octahedral rotation mode in the initial stages of switching. These results represent some of the first reported experimental diffraction-based evidence for a switching mechanism in an improper ferroelectric.Improper ferroelectric mechanisms are increasingly under investigation for their potential to expand the current catalogue of functional materials whilst promoting couplings between ferroelectricity and other technologically desirable properties such as ferromagnetism. This work presents the results of an in situ synchrotron X-ray diffraction experiment performed on samples of Ca2.15Sr0.85Ti2O7 in an effort to elucidate the mechanism of hybrid improper ferroelectric switching in this compound. By simultaneously applying an electric field and recording diffraction patterns, shifts in the intensity of superstructure peaks consistent with one of the switching mechanisms proposed by Nowadnick & Fennie [Phys. Rev. B, (2016), 94, 104105] are observed. While the experiment only achieves a partial response, comparison with simulated data demonstrates a preference for a one-step switching mechanism involving an unwinding of the octahedral rotation mode in the initial stages of switching. These results represent some of the first reported experimental diffraction-based evidence for a switching mechanism in an improper ferroelectric.texthttps://creativecommons.org/licenses/by/4.0/text/htmlIn situ X-ray diffraction investigation of electric-field-induced switching in a hybrid improper ferroelectricdoi:10.1107/S1600576721001096International Union of Crystallography2021-03-18Clarke, G.Ablitt, C.Daniels, J.Checchia, S.Senn, M.S.This article reports the first in situ diffraction result collected under applied electric field on a hybrid improper ferroelectric which shows a subtle yet robust preference for a switching mechanism that proceeds via an unwinding of the octahedral rotation mode.urn:issn:1600-5767HYBRID IMPROPER FERROELECTRICS; IN SITU DIFFRACTION; RUDDLESDEN-POPPERenApril 2021research papers25401600-576754533https://creativecommons.org/licenses/by/4.0/med@iucr.org1600-57672021-03-18Journal of Applied CrystallographyMitigating background caused by extraneous scattering in small-angle neutron scattering instrument design
http://scripts.iucr.org/cgi-bin/paper?in5049
Measurements, calculations and design ideas to mitigate background caused by extraneous scattering in small-angle neutron scattering (SANS) instruments are presented. Scattering includes processes such as incoherent scattering, inelastic scattering and Bragg diffraction. Three primary sources of this type of background are investigated: the beam stop located in front of the detector, the inside lining of the detector vessel and the environment surrounding the sample. SANS measurements were made where materials with different albedos were placed in all three locations. Additional measurements of the angle-dependent scattering over the angular range of 0.7π–0.95π rad were completed on 16 different shielding materials at five wavelengths. The data were extrapolated to cover scattering angles from π/2 to π rad in order to estimate the materials' albedos. Modifications to existing SANS instruments and sample environments to mitigate extraneous scattering from surfaces are discussed.Measurements, calculations and design ideas to mitigate background caused by extraneous scattering in small-angle neutron scattering (SANS) instruments are presented. Scattering includes processes such as incoherent scattering, inelastic scattering and Bragg diffraction. Three primary sources of this type of background are investigated: the beam stop located in front of the detector, the inside lining of the detector vessel and the environment surrounding the sample. SANS measurements were made where materials with different albedos were placed in all three locations. Additional measurements of the angle-dependent scattering over the angular range of 0.7π–0.95π rad were completed on 16 different shielding materials at five wavelengths. The data were extrapolated to cover scattering angles from π/2 to π rad in order to estimate the materials' albedos. Modifications to existing SANS instruments and sample environments to mitigate extraneous scattering from surfaces are discussed.texthttps://creativecommons.org/licenses/by/4.0/text/htmlMitigating background caused by extraneous scattering in small-angle neutron scattering instrument designdoi:10.1107/S1600576721001084International Union of Crystallography2021-03-03Barker, J.G.Cook, J.C.Chabot, J.P.Kline, S.R.Zhang, Z.Gagnon, C.Measurements and methods of mitigation for small-angle neutron scattering instrument background caused by extraneous scattering from surfaces are presented.urn:issn:1600-5767EXTRANEOUS SCATTERING; ALBEDO; BACKGROUND; SMALL-ANGLE NEUTRON SCATTERING; SANSen541600-5767461April 2021472research papers2med@iucr.org1600-5767Journal of Applied Crystallography2021-03-03https://creativecommons.org/licenses/by/4.0/Tomographic X-ray scattering based on invariant reconstruction: analysis of the 3D nanostructure of bovine bone
http://scripts.iucr.org/cgi-bin/paper?vg5128
Small-angle X-ray scattering (SAXS) is an effective characterization technique for multi-phase nanocomposites. The structural complexity and heterogeneity of biological materials require the development of new techniques for the 3D characterization of their hierarchical structures. Emerging SAXS tomographic methods allow reconstruction of the 3D scattering pattern in each voxel but are costly in terms of synchrotron measurement time and computer time. To address this problem, an approach has been developed based on the reconstruction of SAXS invariants to allow for fast 3D characterization of nanostructured inhomogeneous materials. SAXS invariants are scalars replacing the 3D scattering patterns in each voxel, thus simplifying the 6D reconstruction problem to several 3D ones. Standard procedures for tomographic reconstruction can be directly adapted for this problem. The procedure is demonstrated by determining the distribution of the nanometric bone mineral particle thickness (T parameter) throughout a macroscopic 3D volume of bovine cortical bone. The T parameter maps display spatial patterns of particle thickness in fibrolamellar bone units. Spatial correlation between the mineral nanostructure and microscopic features reveals that the mineral particles are particularly thin in the vicinity of vascular channels.Small-angle X-ray scattering (SAXS) is an effective characterization technique for multi-phase nanocomposites. The structural complexity and heterogeneity of biological materials require the development of new techniques for the 3D characterization of their hierarchical structures. Emerging SAXS tomographic methods allow reconstruction of the 3D scattering pattern in each voxel but are costly in terms of synchrotron measurement time and computer time. To address this problem, an approach has been developed based on the reconstruction of SAXS invariants to allow for fast 3D characterization of nanostructured inhomogeneous materials. SAXS invariants are scalars replacing the 3D scattering patterns in each voxel, thus simplifying the 6D reconstruction problem to several 3D ones. Standard procedures for tomographic reconstruction can be directly adapted for this problem. The procedure is demonstrated by determining the distribution of the nanometric bone mineral particle thickness (T parameter) throughout a macroscopic 3D volume of bovine cortical bone. The T parameter maps display spatial patterns of particle thickness in fibrolamellar bone units. Spatial correlation between the mineral nanostructure and microscopic features reveals that the mineral particles are particularly thin in the vicinity of vascular channels.texthttps://creativecommons.org/licenses/by/4.0/text/htmlTomographic X-ray scattering based on invariant reconstruction: analysis of the 3D nanostructure of bovine bonedoi:10.1107/S1600576721000881International Union of Crystallography2021-03-03De Falco, P.Weinkamer, R.Wagermaier, W.Li, C.Snow, T.Terrill, N.J.Gupta, H.S.Goyal, P.Stoll, M.Benner, P.Fratzl, P.A new tomographic approach using X-ray scattering is presented, allowing the characterization of the 3D nanostructure of hybrid materials.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; SAXS; TOMOGRAPHY; BOVINE BONE; FIBROLAMELLAR UNIT; T PARAMETER; SCATTERING TOMOGRAPHY; FIBROLAMELLAR BONEenhttps://creativecommons.org/licenses/by/4.0/2021-03-03Journal of Applied Crystallographymed@iucr.org1600-5767April 20212497research papers4861600-576754MATSAS: a small-angle scattering computing tool for porous systems
http://scripts.iucr.org/cgi-bin/paper?ge5087
MATSAS is a script-based MATLAB program for analysis of X-ray and neutron small-angle scattering (SAS) data obtained from various facilities. The program has primarily been developed for sedimentary rock samples but is equally applicable to other porous media. MATSAS imports raw SAS data from .xls(x) or .csv files, combines small-angle and very small angle scattering data, subtracts the sample background, and displays the processed scattering curves in log–log plots. MATSAS uses the polydisperse spherical (PDSP) model to obtain structural information on the scatterers (scattering objects); for a porous system, the results include specific surface area (SSA), porosity (Φ), and differential and logarithmic differential pore area/volume distributions. In addition, pore and surface fractal dimensions (Dp and Ds, respectively) are obtained from the scattering profiles. The program package allows simultaneous and rapid analysis of a batch of samples, and the results are then exported to .xlsx and .csv files with separate spreadsheets for individual samples. MATSAS is the first SAS program that delivers a full suite of pore characterizations for sedimentary rocks. MATSAS is an open-source package and is freely available at GitHub (https://github.com/matsas-software/MATSAS).MATSAS is a script-based MATLAB program for analysis of X-ray and neutron small-angle scattering (SAS) data obtained from various facilities. The program has primarily been developed for sedimentary rock samples but is equally applicable to other porous media. MATSAS imports raw SAS data from .xls(x) or .csv files, combines small-angle and very small angle scattering data, subtracts the sample background, and displays the processed scattering curves in log–log plots. MATSAS uses the polydisperse spherical (PDSP) model to obtain structural information on the scatterers (scattering objects); for a porous system, the results include specific surface area (SSA), porosity (Φ), and differential and logarithmic differential pore area/volume distributions. In addition, pore and surface fractal dimensions (Dp and Ds, respectively) are obtained from the scattering profiles. The program package allows simultaneous and rapid analysis of a batch of samples, and the results are then exported to .xlsx and .csv files with separate spreadsheets for individual samples. MATSAS is the first SAS program that delivers a full suite of pore characterizations for sedimentary rocks. MATSAS is an open-source package and is freely available at GitHub (https://github.com/matsas-software/MATSAS).texthttps://creativecommons.org/licenses/by/4.0/text/htmlMATSAS: a small-angle scattering computing tool for porous systemsdoi:10.1107/S1600576721000674International Union of Crystallography2021-03-18Rezaeyan, A.Pipich, V.Busch, A.MATSAS analyses X-ray and neutron small-angle scattering data obtained from porous systems. MATSAS delivers a full suite of pore characterizations, including specific surface area, porosity, pore size distribution and fractal dimensions.urn:issn:1600-5767MATSAS; SMALL-ANGLE SCATTERING; POLYDISPERSE SPHERICAL MODEL; POROUS MEDIA; COMPUTER PROGRAMSenApril 20212computer programs706697541600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2021-03-18med@iucr.org1600-5767Upscaling X-ray nanoimaging to macroscopic specimens
http://scripts.iucr.org/cgi-bin/paper?jo5064
Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based `smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based `smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.texthttps://creativecommons.org/licenses/by/4.0/text/htmlUpscaling X-ray nanoimaging to macroscopic specimensdoi:10.1107/S1600576721000194International Union of Crystallography2021-02-19Du, M.Di, Z.Gürsoy, D.Xian, R.P.Kozorovitskiy, Y.Jacobsen, C.In the era of diffraction-limited storage rings, can X-ray nanoimaging be extended to millimetre- or even centimetre-sized specimens such as whole mouse brains? The authors believe so and provide size-dependent imaging time and resource estimates based on calculated flux requirements and recent method developments in related disciplines.urn:issn:1600-5767X-RAY MICROSCOPY; PHASE CONTRAST X-RAY IMAGINGen541600-5767386401lead articles2April 20211600-5767med@iucr.orgJournal of Applied Crystallography2021-02-19https://creativecommons.org/licenses/by/4.0/Evolution of the analytical scattering model of live Escherichia coli
http://scripts.iucr.org/cgi-bin/paper?vg5126
A previously reported multi-scale model for (ultra-)small-angle X-ray (USAXS/SAXS) and (very) small-angle neutron scattering (VSANS/SANS) of live Escherichia coli was revised on the basis of compositional/metabolomic and ultrastructural constraints. The cellular body is modeled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was replaced by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data of E. coli ATCC 25922 over four orders of magnitude in length scale. Specifically, this approach provides detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. The model was also successfully applied to E. coli K12, used for the authors' original modeling, as well as for two other E. coli strains. Significant differences were detected between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of the approach outlined here to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labeling agents.A previously reported multi-scale model for (ultra-)small-angle X-ray (USAXS/SAXS) and (very) small-angle neutron scattering (VSANS/SANS) of live Escherichia coli was revised on the basis of compositional/metabolomic and ultrastructural constraints. The cellular body is modeled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was replaced by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data of E. coli ATCC 25922 over four orders of magnitude in length scale. Specifically, this approach provides detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. The model was also successfully applied to E. coli K12, used for the authors' original modeling, as well as for two other E. coli strains. Significant differences were detected between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of the approach outlined here to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labeling agents.texthttps://creativecommons.org/licenses/by/4.0/text/htmlEvolution of the analytical scattering model of live Escherichia colidoi:10.1107/S1600576721000169International Union of Crystallography2021-03-03Semeraro, E.F.Marx, L.Mandl, J.Frewein, M.P.K.Scott, H.L.Prévost, S.Bergler, H.Lohner, K.Pabst, G.Structural and compositional information about Escherichia coli cells is summarized and translated into an analytical multi-length-scale scattering form factor model of live bacterial suspensions.urn:issn:1600-5767BACTERIAL ULTRASTRUCTURE; SMALL-ANGLE SCATTERING; ULTRA-SMALL-ANGLE X-RAY SCATTERING; USAXS; VERY SMALL ANGLE NEUTRON SCATTERING; VSANS; COMPOSITIONAL MODELINGenJournal of Applied Crystallography2021-03-03med@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/473541600-5767April 2021research papers4852Polo: an open-source graphical user interface for crystallization screening
http://scripts.iucr.org/cgi-bin/paper?ei5066
Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to efficiently inspect their crystallization experiments. Polo aims to increase efficiency, reducing time spent manually reviewing crystallization images, and to improve the potential of identifying positive crystallization conditions. Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes (MARCO) convolutional neural network for automated image classification, as well as powerful tools to view and score crystallization images, to compare crystallization conditions, and to facilitate collaborative review of crystallization screening results. Crystallization images need not have been captured at HWI to utilize Polo's basic functionality. Polo is free to use and modify for both academic and commercial use under the terms of the copyleft GNU General Public License v3.0.Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to efficiently inspect their crystallization experiments. Polo aims to increase efficiency, reducing time spent manually reviewing crystallization images, and to improve the potential of identifying positive crystallization conditions. Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes (MARCO) convolutional neural network for automated image classification, as well as powerful tools to view and score crystallization images, to compare crystallization conditions, and to facilitate collaborative review of crystallization screening results. Crystallization images need not have been captured at HWI to utilize Polo's basic functionality. Polo is free to use and modify for both academic and commercial use under the terms of the copyleft GNU General Public License v3.0.texthttps://creativecommons.org/licenses/by/4.0/text/htmlPolo: an open-source graphical user interface for crystallization screeningdoi:10.1107/S1600576721000108International Union of Crystallography2021-02-19Holleman, E.T.Duguid, E.Keefe, L.J.Bowman, S.E.J.A multi-platform open-source Python-based graphical user interface has been developed to provide access to automated classification and data management tools for biomolecular crystallization screening.urn:issn:1600-5767CRYSTALLIZATION; CRYSTAL IMAGING; MACHINE LEARNING; OPEN-SOURCE GRAPHICAL USER INTERFACESen6731600-5767542computer programs679April 20212021-02-19Journal of Applied Crystallography1600-5767med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Validation of the Crystallography Open Database using the Crystallographic Information Framework
http://scripts.iucr.org/cgi-bin/paper?yr5065
Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. A set of programs intended to aid in the dictionary migration from DDL1 to DDLm is also presented.Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. A set of programs intended to aid in the dictionary migration from DDL1 to DDLm is also presented.texthttps://creativecommons.org/licenses/by/4.0/text/htmlValidation of the Crystallography Open Database using the Crystallographic Information Frameworkdoi:10.1107/S1600576720016532International Union of Crystallography2021-02-14Vaitkus, A.Merkys, A.Gražulis, S.Data curation practices of the Crystallography Open Database are described with greater focus being placed on the cif_validate program, capable of validating crystallographic information files against both DDL1 and DDLm dictionaries.urn:issn:1600-5767CRYSTALLOGRAPHY OPEN DATABASE; CRYSTALLOGRAPHIC INFORMATION FRAMEWORK; CIF VALIDATION; CIF DICTIONARY; DDLMenhttps://creativecommons.org/licenses/by/4.0/2021-02-14Journal of Applied Crystallography1600-5767med@iucr.org672CIF applications2April 20216611600-576754Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates
http://scripts.iucr.org/cgi-bin/paper?gj5257
In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low-cost device is presented that functions as a cover for 96-well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi-crystal screening campaigns.In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low-cost device is presented that functions as a cover for 96-well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi-crystal screening campaigns.texthttps://creativecommons.org/licenses/by/4.0/text/htmlFacilitated crystal handling using a simple device for evaporation reduction in microtiter platesdoi:10.1107/S1600576720016477International Union of Crystallography2021-02-01Barthel, T.Huschmann, F.U.Wallacher, D.Feiler, C.G.Klebe, G.Weiss, M.S.Wollenhaupt, J.A simple and low-cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting.urn:issn:1600-5767EVAPORATION REDUCTION; CRYSTAL HANDLING; CRYSTAL HARVESTING; CRYSTALLOGRAPHIC FRAGMENT SCREENINGen382laboratory notes1February 20213761600-576754https://creativecommons.org/licenses/by/4.0/2021-02-01Journal of Applied Crystallography1600-5767med@iucr.orgcrystIT: complexity and configurational entropy of crystal structures via information theory
http://scripts.iucr.org/cgi-bin/paper?oc5005
The information content of a crystal structure as conceived by information theory has recently proved an intriguing approach to calculate the complexity of a crystal structure within a consistent concept. Given the relatively young nature of the field, theory development is still at the core of ongoing research efforts. This work provides an update to the current theory, enabling the complexity analysis of crystal structures with partial occupancies as frequently found in disordered systems. To encourage wider application and further theory development, the updated formulas are incorporated into crystIT (crystal structure and information theory), an open-source Python-based program that allows for calculating various complexity measures of crystal structures based on a standardized *.cif file.The information content of a crystal structure as conceived by information theory has recently proved an intriguing approach to calculate the complexity of a crystal structure within a consistent concept. Given the relatively young nature of the field, theory development is still at the core of ongoing research efforts. This work provides an update to the current theory, enabling the complexity analysis of crystal structures with partial occupancies as frequently found in disordered systems. To encourage wider application and further theory development, the updated formulas are incorporated into crystIT (crystal structure and information theory), an open-source Python-based program that allows for calculating various complexity measures of crystal structures based on a standardized *.cif file.texthttps://creativecommons.org/licenses/by/4.0/text/htmlcrystIT: complexity and configurational entropy of crystal structures via information theorydoi:10.1107/S1600576720016386International Union of Crystallography2021-02-01Kaussler, C.Kieslich, G.Information theory provides an intriguing framework for evaluating the complexity of a crystal structure. This article provides an improvement to the current theory and describes the integration of the updated formulas into an open-source Python-based program called crystIT.urn:issn:1600-5767INFORMATION THEORY; CRYSTAL STRUCTURE COMPLEXITY; OPEN SOURCE COMPUTER PROGRAMSenhttps://creativecommons.org/licenses/by/4.0/2021-02-01Journal of Applied Crystallographymed@iucr.org1600-5767February 20211research papers3163061600-576754The anisotropy in the optical constants of quartz crystals for soft X-rays
http://scripts.iucr.org/cgi-bin/paper?te5071
The refractive index of a y-cut SiO2 crystal surface is reconstructed from orientation-dependent soft X-ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near-edge regions.The refractive index of a y-cut SiO2 crystal surface is reconstructed from orientation-dependent soft X-ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near-edge regions.texthttps://creativecommons.org/licenses/by/4.0/text/htmlThe anisotropy in the optical constants of quartz crystals for soft X-raysdoi:10.1107/S1600576720016325International Union of Crystallography2021-02-19Andrle, A.Hönicke, P.Vinson, J.Quintanilha, R.Saadeh, Q.Heidenreich, S.Scholze, F.Soltwisch, V.The refractive index of a y-cut SiO2 crystal surface is reconstructed from polarization-dependent soft X-ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge.urn:issn:1600-5767OPTICAL CONSTANTS; QUARTZ; ANISOTROPY; SOFT X-RAY REFLECTOMETRYenJournal of Applied Crystallography2021-02-19med@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/402541600-5767April 20212research papers408A simulational study of the indirect-geometry neutron spectrometer BIFROST at the European Spallation Source, from neutron source position to detector position
http://scripts.iucr.org/cgi-bin/paper?ge5093
The European Spallation Source (ESS) is intended to become the most powerful spallation neutron source in the world and the flagship of neutron science in upcoming decades. The exceptionally high neutron flux will provide unique opportunities for scientific experiments but also set high requirements for the detectors. One of the most challenging aspects is the rate capability and in particular the peak instantaneous rate capability, i.e. the number of neutrons hitting the detector per channel or cm2 at the peak of the neutron pulse. The primary purpose of this paper is to estimate the incident rates that are anticipated for the BIFROST instrument planned for ESS, and also to demonstrate the use of powerful simulation tools for the correct interpretation of neutron transport in crystalline materials. A full simulation model of the instrument from source to detector position, implemented with the use of multiple simulation software packages, is presented. For a single detector tube, instantaneous incident rates with a maximum of 1.7 GHz for a Bragg peak from a single crystal and 0.3 MHz for a vanadium sample are found. This paper also includes the first application of a new pyrolytic graphite model and a comparison of different simulation tools to highlight their strengths and weaknesses.The European Spallation Source (ESS) is intended to become the most powerful spallation neutron source in the world and the flagship of neutron science in upcoming decades. The exceptionally high neutron flux will provide unique opportunities for scientific experiments but also set high requirements for the detectors. One of the most challenging aspects is the rate capability and in particular the peak instantaneous rate capability, i.e. the number of neutrons hitting the detector per channel or cm2 at the peak of the neutron pulse. The primary purpose of this paper is to estimate the incident rates that are anticipated for the BIFROST instrument planned for ESS, and also to demonstrate the use of powerful simulation tools for the correct interpretation of neutron transport in crystalline materials. A full simulation model of the instrument from source to detector position, implemented with the use of multiple simulation software packages, is presented. For a single detector tube, instantaneous incident rates with a maximum of 1.7 GHz for a Bragg peak from a single crystal and 0.3 MHz for a vanadium sample are found. This paper also includes the first application of a new pyrolytic graphite model and a comparison of different simulation tools to highlight their strengths and weaknesses.texthttps://creativecommons.org/licenses/by/4.0/text/htmlA simulational study of the indirect-geometry neutron spectrometer BIFROST at the European Spallation Source, from neutron source position to detector positiondoi:10.1107/S1600576720016192International Union of Crystallography2021-02-01Klausz, M.Kanaki, K.Kittelmann, T.Toft-Petersen, R.Birk, J.O.Olsen, M.A.Zagyvai, P.Hall-Wilton, R.J.The incident detector rates that are anticipated for the indirect-geometry cold-neutron spectrometer BIFROST at the European Spallation Source are estimated, and the use of powerful simulation tools for the correct interpretation of neutron transport in crystalline materials is demonstrated.urn:issn:1600-5767GEANT4; MCSTAS; NEUTRON DETECTORS; NEUTRON SPECTROSCOPYenhttps://creativecommons.org/licenses/by/4.0/2021-02-01Journal of Applied Crystallographymed@iucr.org1600-5767February 20211279research papers2631600-576754On the structural formula of smectites: a review and new data on the influence of exchangeable cations
http://scripts.iucr.org/cgi-bin/paper?vb5011
The understanding of the structural formula of smectite minerals is basic to predicting their physicochemical properties, which depend on the location of the cation substitutions within their 2:1 layer. This implies knowing the correct distribution and structural positions of the cations, which allows assigning the source of the layer charge of the tetrahedral or octahedral sheet, determining the total number of octahedral cations and, consequently, knowing the type of smectite. However, sometimes the structural formula obtained is not accurate. A key reason for the complexity of obtaining the correct structural formula is the presence of different exchangeable cations, especially Mg. Most smectites, to some extent, contain Mg2+ that can be on both octahedral and interlayer positions. This indeterminacy can lead to errors when constructing the structural formula. To estimate the correct position of the Mg2+ ions, that is their distribution over the octahedral and interlayer positions, it is necessary to substitute the interlayer Mg2+ and work with samples saturated with a known cation (homoionic samples). Seven smectites of the dioctahedral and trioctahedral types were homoionized with Ca2+, substituting the natural exchangeable cations. Several differences were found between the formulae obtained for the natural and Ca2+ homoionic samples. Both layer and interlayer charges increased, and the calculated numbers of octahedral cations in the homoionic samples were closer to four and six in the dioctahedral and trioctahedral smectites, respectively, with respect to the values calculated in the non-homoionic samples. This change was not limited to the octahedral sheet and interlayer, because the tetrahedral content also changed. For both dioctahedral and trioctahedral samples, the structural formulae improved considerably after homoionization of the samples, although higher accuracy was obtained the more magnesic and trioctahedral the smectites were. Additionally, the changes in the structural formulae sometimes resulted in changing the classification of the smectite.The understanding of the structural formula of smectite minerals is basic to predicting their physicochemical properties, which depend on the location of the cation substitutions within their 2:1 layer. This implies knowing the correct distribution and structural positions of the cations, which allows assigning the source of the layer charge of the tetrahedral or octahedral sheet, determining the total number of octahedral cations and, consequently, knowing the type of smectite. However, sometimes the structural formula obtained is not accurate. A key reason for the complexity of obtaining the correct structural formula is the presence of different exchangeable cations, especially Mg. Most smectites, to some extent, contain Mg2+ that can be on both octahedral and interlayer positions. This indeterminacy can lead to errors when constructing the structural formula. To estimate the correct position of the Mg2+ ions, that is their distribution over the octahedral and interlayer positions, it is necessary to substitute the interlayer Mg2+ and work with samples saturated with a known cation (homoionic samples). Seven smectites of the dioctahedral and trioctahedral types were homoionized with Ca2+, substituting the natural exchangeable cations. Several differences were found between the formulae obtained for the natural and Ca2+ homoionic samples. Both layer and interlayer charges increased, and the calculated numbers of octahedral cations in the homoionic samples were closer to four and six in the dioctahedral and trioctahedral smectites, respectively, with respect to the values calculated in the non-homoionic samples. This change was not limited to the octahedral sheet and interlayer, because the tetrahedral content also changed. For both dioctahedral and trioctahedral samples, the structural formulae improved considerably after homoionization of the samples, although higher accuracy was obtained the more magnesic and trioctahedral the smectites were. Additionally, the changes in the structural formulae sometimes resulted in changing the classification of the smectite.texthttps://creativecommons.org/licenses/by/4.0/text/htmlOn the structural formula of smectites: a review and new data on the influence of exchangeable cationsdoi:10.1107/S1600576720016040International Union of Crystallography2021-02-01García-Romero, E.Lorenzo, A.García-Vicente, A.Morales, J.García-Rivas, J.Suárez, M.The fit of the smectite structural formula is reviewed. In addition, a group of samples, both dioctahedral and trioctahedral, are studied, demonstrating the influence of interlaminar Mg that can lead to the erroneous classification of smectite if it is not considered.urn:issn:1600-5767STRUCTURAL FORMULA; HOMOIONIZATION; SMECTITE; MONTMORILLONITE; BEIDELLITE; SAPONITE; STEVENSITE; KEROLITEen2021-02-01Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/2511600-576754February 2021262research papers1Elastic stiffness coefficients of thiourea from thermal diffuse scattering
http://scripts.iucr.org/cgi-bin/paper?vb5005
The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high-energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X-ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high-energy photons extends the applicability of the TDS-based approach to organic compounds which would suffer from radiation damage at lower photon energies.The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high-energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X-ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high-energy photons extends the applicability of the TDS-based approach to organic compounds which would suffer from radiation damage at lower photon energies.texthttps://creativecommons.org/licenses/by/4.0/text/htmlElastic stiffness coefficients of thiourea from thermal diffuse scatteringdoi:10.1107/S1600576720016039International Union of Crystallography2021-02-01Büscher, J.Mirone, A.Stękiel, M.Spahr, D.Morgenroth, W.Haussühl, E.Milman, V.Bosak, A.Ivashko, O.Zimmermann, M. vonDippel, A.-C.Winkler, B.The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering.urn:issn:1600-5767THERMAL DIFFUSE SCATTERING; ELASTIC STIFFNESS; THIOUREAenFebruary 2021research papers1294541600-5767287https://creativecommons.org/licenses/by/4.0/med@iucr.org1600-5767Journal of Applied Crystallography2021-02-01Evolution of dislocation microstructure in irradiated Zr alloys determined by X-ray peak profile analysis
http://scripts.iucr.org/cgi-bin/paper?nb5292
During neutron irradiation of metals, owing to the enhanced number of vacancies and interstitial atoms, the climb motion of dislocations becomes significant at room temperature, leading to a recrystallization of the material. Moreover, the vacancies and interstitial atoms tend to form prismatic dislocation loops that play a crucial role in the plastic properties of the materials. X-ray peak profile analysis is an efficient nondestructive method to determine the properties of dislocation microstructure. In the first half of this article, the foundation of the asymptotic peak broadening theory and the related restricted-moments peak-evaluation method is summarized. After this, the microstructural parameters obtained by X-ray peak profile analysis are reported for irradiated E110 and E110G Zr alloys used as cladding material in the nuclear industry.During neutron irradiation of metals, owing to the enhanced number of vacancies and interstitial atoms, the climb motion of dislocations becomes significant at room temperature, leading to a recrystallization of the material. Moreover, the vacancies and interstitial atoms tend to form prismatic dislocation loops that play a crucial role in the plastic properties of the materials. X-ray peak profile analysis is an efficient nondestructive method to determine the properties of dislocation microstructure. In the first half of this article, the foundation of the asymptotic peak broadening theory and the related restricted-moments peak-evaluation method is summarized. After this, the microstructural parameters obtained by X-ray peak profile analysis are reported for irradiated E110 and E110G Zr alloys used as cladding material in the nuclear industry.texthttps://creativecommons.org/licenses/by/4.0/text/htmlEvolution of dislocation microstructure in irradiated Zr alloys determined by X-ray peak profile analysisdoi:10.1107/S1600576720015885International Union of Crystallography2021-02-01Groma, I.Szenthe, I.Ódor, É.Jóni, B.Zilahi, G.Dankházi, Z.Ribárik, G.Hózer, Z.The dislocation microstructure developing during neutron irradiation is determined by X-ray line profile analysis.urn:issn:1600-5767NUCLEAR MATERIALS; X-RAY LINE PROFILE ANALYSIS; DISLOCATION DENSITY; NEUTRON IRRADIATION; VACANCIES; INTERSTITIAL ATOMSen2801600-576754February 2021research papers28612021-02-01Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/Determining paracrystallinity in mixed-tacticity polyhydroxybutyrates
http://scripts.iucr.org/cgi-bin/paper?fs5194
Recently, the authors reported on the development of crystallinity in mixed-tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X-ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.Recently, the authors reported on the development of crystallinity in mixed-tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X-ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.texthttps://creativecommons.org/licenses/by/4.0/text/htmlDetermining paracrystallinity in mixed-tacticity polyhydroxybutyratesdoi:10.1107/S1600576720015794International Union of Crystallography2021-02-01Van Opdenbosch, D.Haslböck, M.Zollfrank, C.A method to robustly determine paracrystalline contents from Rietveld-refined powder X-ray data is presented and discussed for the example of mixed-tacticity polyhydroxybutyrates.urn:issn:1600-5767POLYHYDROXYBUTYRATES; MIXED TACTICITY; PARACRYSTALLINITY; RIETVELD REFINEMENT; THERMAL FACTORSen2171600-576754February 2021research papers22712021-02-01Journal of Applied Crystallographymed@iucr.org1600-5767https://creativecommons.org/licenses/by/4.0/