Two new phenyl­sulfonyl­indole derivatives, namely, N-{[3-bromo-1-(phenyl­sulfon­yl)-1H-indol-2-yl]meth­yl}-N-(4-bromo-3-meth­oxy­phen­yl)benzene­sulfonamide, C28H22Br2N2O5S2, (I), and N,N-bis­{[3-bromo-1-(phenyl­sulfon­yl)-1H-indol-2-yl]meth­yl}benzene­sulfonamide, C36H27Br2N3O6S3, (II), reveal the impact of intra­molecular π–π inter­actions of the indole moieties as a factor not only governing the conformation of N,N-bis­(1H-indol-2-yl)meth­yl)amines, but also significantly influencing the crystal patterns. For I, the crystal packing is dominated by C—H⋯π and π–π bonding, with a particular significance of mutual indole–indole inter­actions. In the case of II, the mol­ecules adopt short intra­molecular π–π inter­actions between two nearly parallel indole ring systems [with the centroids of their pyrrole rings separated by 3.267 (2) Å] accompanied by a set of forced Br⋯O contacts. This provides suppression of similar inter­actions between the mol­ecules, while the importance of weak C—H⋯O hydrogen bonding to the packing naturally increases. Short contacts of the latter type [C⋯O = 3.389 (6) Å] assemble pairs of mol­ecules into centrosymmetric dimers with a cyclic R22(13) ring motif. These findings are consistent with the results of a Hirshfeld surface analysis and together they suggest a tool for modulating the supra­molecular behavior of phenyl­sulfonyl­ated indoles.

In the title compound, C10H8N2·2C6H5NO3, 4-nitro­phenol and 4,4'-bi­pyridine crystallized together in a 2:1 ratio in the space group P21/n. There is a hydrogen-bonding inter­action between the nitro­gen atoms on the 4,4'-bi­pyridine mol­ecule and the hydrogen atom on the hydroxyl group on the 4-nitro­phenol, resulting in trimolecular units. This structure is a polymorph of a previously reported structure [Nayak & Pedireddi (2016). Cryst. Growth Des. 16, 5966–5975], which differs mainly due to a twist in the 4,4'-bi­pyridine mol­ecule.

The absolute configuration of the title compound, C13H16O4, determined as 1S,2R,3S,4R based on the synthetic pathway, was confirmed by single-crystal X-ray diffraction. The mol­ecule is a relevant inter­mediary for the synthesis of speciosins, ep­oxy­quinoides or their analogues. The mol­ecule contains fused five- and six-membered rings with two free hydroxyl groups and two protected as an iso­propyl­idenedioxo ring. The packing is directed by hydrogen bonds that define double planes of mol­ecules laying along the ab plane and van der Waals inter­actions between aliphatic chains that point outwards of the planes.

Two different multi-component crystals consisting of papaverine [1-(3,4-di­meth­oxy­benz­yl)-6,7-di­meth­oxy­iso­quinoline, C20H21NO4] and fumaric acid [C4H4O4] were obtained. Single-crystal X-ray structure analysis revealed that one, C20H21NO4·1.5C4H4O4 (I), is a salt co-crystal composed of salt-forming and non-salt-forming mol­ecules, and the other, C20H21NO4·0.5C4H4O4 (II), is a salt–co-crystal inter­mediate (i.e., in an inter­mediate state between a salt and a co-crystal). In this study, one state (crystal structure at 100 K) within the salt–co-crystal continuum is defined as the ‘inter­mediate’.

In the title compound, C25H17NO3, the torsion angle associated with the phenyl benzoate group is −173.7 (2)° and that for the benz­yloxy group is −174.8 (2)° establishing an anti-type conformation. The dihedral angles between the ten-membered cyanona­phthalene ring and the aromatic ring of the phenyl benzoate and the benz­yloxy fragments are 40.70 (10) and 87.51 (11)°, respectively, whereas the dihedral angle between the aromatic phenyl benzoate and the benz­yloxy fragments is 72.30 (13)°. In the crystal, the mol­ecules are linked by weak C—H⋯O inter­actions forming S(4) chains propagating parallel to [010]. The packing is consolidated by three C—H⋯π inter­actions and two π–π stacking inter­actions between the aromatic rings of naphthalene and phenyl benzoate with centroid-to-centroid distances of 3.9698 (15) and 3.8568 (15) Å, respectively. Inter­molecular inter­actions were qu­anti­fied using Hirshfeld surface analysis. The mol­ecular structure was further optimized by density functional theory (DFT) at the B3LYP/6–311+ G(d,p) level, revealing that the energy gap between HOMO and LUMO is 3.17 eV. Mol­ecular docking studies were carried out for the title compound as a ligand and SARS-Covid-2(PDB ID:7QF0) protein as a receptor giving a binding affinity of −9.5 kcal mol−1.

Two new zinc(II) complexes, tri­ethyl­ammonium di­chlorido­[2-(4-nitro­phen­yl)-4-phenyl­quinolin-8-olato]zinc(II), (C6H16N){Zn(C21H13N2O3)Cl2] (ZnOQ), and bis­(tri­ethyl­ammonium) {2,2'-[1,4-phenyl­enebis(nitrilo­methyl­idyne)]diphenolato}bis­[di­chlorido­zinc(II)], (C6H16N)2[Zn2(C20H14N2O2)Cl4] (ZnBS), were synthesized and their structures were determined using ESI–MS spectrometry, 1H NMR spectroscopy, and single-crystal X-ray diffraction. The results showed that the ligands 2-(4-nitro­phen­yl)-4-phenyl­quinolin-8-ol (HOQ) and N,N'-bis­(2-hy­droxy­benzyl­idene)benzene-1,4-di­amine (H2BS) were deprotonated by tri­ethyl-amine, forming the counter-ion Et3NH+, which inter­acts via an N—H⋯O hydrogen bond with the ligand. The ZnII atoms have a distorted trigonal–pyramidal (ZnOQ) and distorted tetra­hedral (ZnBS) geometries with a coord­ination number of four, coordinating with the ligands via N and O atoms. The N atoms coordinating with ZnII correspond to the heterocyclic nitro­gen for the HOQ ligand, while for the H2BS ligand, it is the nitro­gen of the imine (CH=N). The crystal packing of ZnOQ is characterized by C—H⋯π inter­actions, while that of ZnBS by C—H⋯Cl inter­actions. The emission spectra showed that ZnBS complex exhibits green fluorescence in the solid state with a small band-gap energy, and the ZnOQ complex does exhibit non-fluorescence.

The title organic–inorganic hybrid salt, C2H7IN+·I−, is isotypic with its bromine analog, C2H7BrN+·Br− [Semenikhin et al. (2024). Acta Cryst. E80, 738–741]. Its asymmetric unit consists of one 2-iodo­ethyl­ammonium cation and one iodide anion. The NH3+ group of the organic cation forms weak hydrogen bonds with four neighboring iodide anions, leading to the formation of supra­molecular layers propagating parallel to the bc plane. Hirshfeld surface analysis reveals that the most important contribution to the crystal packing is from N—H⋯I inter­actions (63.8%). The crystal under investigation was twinned by a 180° rotation around [001].

A new uranium metal–organic complex salt, [U(C10H9O2)2O2(C2H6O)], with benzoyl acetone, namely, bis­(benzoyl­acetonato)(ethanol)dioxidouranium(VI), was synthesized. The compound has monoclinic P21/n symmetry. The geometry of the seven-coordinate U atom is penta­gonal bipyramidal, with the uranyl oxygen atoms in apical positions. In the complex, the ligands bind to the metal through oxygen atoms. Additional weak O—H⋯O contacts between the cations and anions consolidate the three-dimensional arrangement of the structure. On the Hirshfeld surface, the largest contributions come from the short contacts such as van der Waals forces, including H⋯H, O⋯H and C⋯H. Inter­actions including C⋯C and O⋯C contacts were also observed; however, their contribution to the overall cohesion of the crystal structure is minor. A packing analysis was performed to check the strength of the crystal packing.

In the title compound, (C5H7N2)5[TeV9O28], the tellurium and vanadium atoms are statistically disordered over two of the ten metal-atom sites in the [TeV9O28]5– heteropolyanion. The anions stack along [100] and are extended into a three-dimensional supra­molecular network through N—H⋯O and weak C—H⋯O hydrogen bonds involving the self-assembled 2-amino­pyridinium penta­mers, which are linked by C—H⋯π and π–π stacking inter­actions. The most important contributions to the Hirshfeld surface arise from O⋯H/H⋯O (54.8%), H⋯H (17.8%) and C⋯H/H⋯C (13.4%) contacts.

Through numerical optimization of cooling lengths and cooling groove positions for the first reflection mirror of a free-electron laser [OK?], the root mean square of the height error of the mirror's thermal deformation was minimized. The optimized mirror design effectively mitigated stray light and enhanced the peak intensity of the focus spot at the sample, thereby enhancing the optical performance of the high-heat-load mirror under high repetition rates at beamline FEL-II of the SHINE facility.

The major principles and requirements of asymmetric and inclined double-crystal monochromators are re-examined and presented to guide their design and development for significantly reducing heat load density and gradient on the monochromators of fourth-generation synchrotron light sources and X-ray free-electron lasers.

The development of instrumentation as well as applications for megahertz X-ray phase contrast imaging at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL are introduced here.

This review focuses on low-dose near-field X-ray speckle phase imaging in the differential mode introducing the existing algorithms with their specifications and comparing their performances under various experimental conditions.

In this work, we showed that the use of ethanol to increase image contrast when imaging cardiac tissue with synchrotron X-ray phase-contrast imaging (X-PCI) leads to heterogeneous tissue shrinkage, which has an impact on the 3D organization of the myocardium.

A slit-less wavelength-dispersive spectrometer design using a single-bounce monocapillary that aligns the sample on the Rowland circle, enhancing photon throughput and maintaining resolution. The compact design supports flexibility and reconfiguration in facilities without complex beamline infrastructure, significantly improving detection efficiency.

This study characterizes the microstructure and mineralogy of 132 (ODP sample), 1000 and 1880 million-year-old chert samples. By using ultra-small-angle X-ray scattering (USAXS), wide-angle X-ray scattering and other techniques, the preservation of organic matter (OM) in these samples is studied. The scarce microstructural data reported on chert contrast with many studies addressing porosity evolution in other sedimentary rocks. The aim of this work is to solve the distribution of OM and silica in chert by characterizing samples before and after combustion to pinpoint the OM distribution inside the porous silica matrix. The samples are predominantly composed of alpha quartz and show increasing crystallite sizes up to 33 ± 5 nm (1σ standard deviation or SD). In older samples, low water abundances (∼0.03%) suggest progressive dehydration. (U)SAXS data reveal a porous matrix that evolves over geological time, including, from younger to older samples, (1) a decreasing pore volume down to 1%, (2) greater pore sizes hosting OM, (3) decreasing specific surface area values from younger (9.3 ± 0.1 m2 g−1) to older samples (0.63 ± 0.07 m2 g−1, 1σ SD) and (4) a lower background intensity correlated to decreasing hydrogen abundances. The pore-volume distributions (PVDs) show that pores ranging from 4 to 100 nm accumulate the greater volume fraction of OM. Raman data show aromatic organic clusters up to 20 nm in older samples. Raman and PVD data suggest that OM is located mostly in mesopores. Observed structural changes, silica–OM interactions and the hydro­phobicity of the OM could explain the OM preservation in chert.

The International Tables Symmetry Database (https://symmdb.iucr.org/), which is part of International Tables for Crystallography, is a collection of individual databases of crystallographic space-group and point-group information with associated programs. The programs let the user access and in some cases interactively visualize the data, and some also allow new data to be calculated `on the fly'. Together these databases and programs expand upon and complement the symmetry information provided in International Tables for Crystallography Volume A, Space-Group Symmetry, and Volume A1, Symmetry Relations between Space Groups. The Symmetry Database allows users to learn about and explore the space and point groups, and facilitates the study of group–subgroup relations between space groups, with applications in determining crystal-structure relationships, in studying phase transitions and in domain-structure analysis. The use of the International Tables Symmetry Database in all these areas is demonstrated using several examples.

Time-resolved high-energy X-ray diffraction was used during growth of ultrathin NixFe3−xO4 films with varying Ni content (0 ≤ x ≤ 1.5) deposited on MgO(001) substrates by reactive molecular beam epitaxy, providing an insight into the growth dynamics of these films. In order to obtain structural information, reciprocal-space maps were recorded and the temporal evolution of the Bragg peaks specific to the octahedral and tetrahedral lattice sites of the inverse spinel structure of NixFe3−xO4 was observed during growth of the films. A time delay, corresponding to a coverage of 1.2–1.8 nm, between the appearance of the Bragg reflections originating from octahedral sites and reflections originating exclusively from tetrahedral sites indicates that the ferrite films grow in two stages. In the initial growth phase, a rock salt interface layer is formed. Afterwards, a structural transition occurs and the films grow in an inverse spinel structure. The thickness of the initial rock salt phase was found to increase with Ni content and to be responsible for atypical strain in the thin films. Films with Ni contents x > 1 do not show a structural transition. These films remain in a (deficient) rock salt structure consisting of a mixed Ni–Fe oxide and do not form a spinel structure at all. They show an increased number of NiO clusters as detected by X-ray photoelectron spectroscopy of the valence band, accompanied by a significant roughening of the films.

In crystallographic texture analysis, ensuring that sample directions are preserved from experiment to the resulting orientation distribution is crucial to obtain physical meaning from diffraction data. This work details a procedure to ensure instrument and sample coordinates are consistent when analyzing diffraction data with a Rietveld refinement using the texture analysis software MAUD. A quartz crystal is measured on the HIPPO diffractometer at Los Alamos National Laboratory for this purpose. The methods described here can be applied to any diffraction instrument measuring orientation distributions in polycrystalline materials.

Characterization of a material structure with pair distribution function (PDF) analysis typically involves refining a structure model against an experimental data set, but finding or constructing a suitable atomic model for PDF modelling can be an extremely labour-intensive task, requiring carefully browsing through large numbers of possible models. Presented here is POMFinder, a machine learning (ML) classifier that rapidly screens a database of structures, here polyoxometallate (POM) clusters, to identify candidate structures for PDF data modelling. The approach is shown to identify suitable POMs from experimental data, including in situ data collected with fast acquisition times. This automated approach has significant potential for identifying suitable models for structure refinement to extract quantitative structural parameters in materials chemistry research. POMFinder is open source and user friendly, making it accessible to those without prior ML knowledge. It is also demonstrated that POMFinder offers a promising modelling framework for combined modelling of multiple scattering techniques.

The observation of neutron interference using a triple Laue interferometer formed by two separate crystals opens the way to the construction and operation of skew-symmetric interferometers with extended arm separation and length. The specifications necessary for their successful operation are investigated here: most importantly, how the manufacturing tolerance and crystal alignments impact the interference visibility. In contrast with previous studies, both incoherent sources and the three-dimensional operation of the interferometer are considered. It is found that, with a Gaussian Schell model of an incoherent source, the integrated density of the particles leaving the interferometer is the same as that yielded by a coherent Gaussian source having a radius equal to the coherence length.

Low-energy electron diffraction patterns contain precise information about the structure of the surface studied. However, retrieving the real space lattice periodicity from complex diffraction patterns is challenging, especially when the modeled patterns originate from superlattices with large unit cells composed of several symmetry-equivalent domains without a simple relation to the substrate. This work presents ProLEED Studio software, built to provide simple, intuitive and precise modeling of low-energy electron diffraction patterns. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results.

X-ray absorption spectroscopy (XAS) is a promising technique for determining structural information from sensitive biological samples, but high-accuracy X-ray absorption fine structure (XAFS) requires corrections of systematic errors in experimental data. Low-temperature XAS and room-temperature X-ray absorption spectro-electrochemical (XAS-EC) measurements of N-truncated amyloid-β samples were collected and corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumber (k). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing.

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and Dmax finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

An implementation of Slater-type spherical scattering factors for X-ray and electron diffraction for elements in the range Z = 1–103 is presented within the software Olex2. Both high- and low-angle Fourier behaviour of atomic electron density and electrostatic potential can thus be addressed, in contrast to the limited flexibility of the four Gaussian plus constant descriptions which are currently the most widely used method for calculating atomic scattering factors during refinement. The implementation presented here accommodates the increasing complexity of the electronic structure of heavier elements by using complete atomic wavefunctions without any interpolation between precalculated tables or intermediate fitting functions. Atomic wavefunctions for singly charged ions are implemented and made accessible, and these show drastic changes in electron diffraction scattering factors compared with the neutral atom. A comparison between the two different spherical models of neutral atoms is presented as an example for four different kinds of X-ray and two electron diffraction structures, and comparisons of refinement results using the existing diffraction data are discussed. A systematic but slight improvement in R values and residual densities can be observed when using the new scattering factors, and this is discussed relative to effects on the atomic displacement parameters and atomic positions, which are prominent near the heavier elements in a structure.

Rietveld refinements are widely used for many purposes in the physical sciences. Conducting a Rietveld refinement typically requires expert input because correct results may require that parameters be added to the fit in the proper order. This order will depend on the nature of the data and the initial parameter values. A mechanism for computing the next parameter to add to the refinement is shown. The fitting function is evaluated with the current parameter value set and each parameter incremented and decremented by a small offset. This provides the partial derivatives with respect to each parameter, along with information to discriminate meaningful values from numerical computational errors. The implementation of this mechanism in the open-source GSAS-II program is discussed. This new method is discussed as an important step towards the development of automated Rietveld refinement technology.

INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets.

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.

Hendrickson & Lattman [Acta Cryst. (1970), B26, 136–143] introduced a method for representing crystallographic phase probabilities defined on the unit circle. Their approach could model the bimodal phase probability distributions that can result from experimental phase determination procedures. It also provided simple and highly effective means to combine independent sources of phase information. The present work discusses the equivalence of the Hendrickson–Lattman distribution and the generalized von Mises distribution of order two, which has been studied in the statistical literature. Recognizing this connection allows the Hendrickson–Lattman distribution to be expressed in an alternative form which is easier to interpret, as it involves the location and concentration parameters of the component von Mises distributions. It also allows clarification of the conditions for bimodality and access to a simplified analytical method for evaluating the trigonometric moments of the distribution, the first of which is required for computing the best Fourier synthesis in the presence of phase, but not amplitude, uncertainty.

The suitability of point focus X-ray beam and area detector techniques for the determination of the uniaxial symmetry axis (fibre texture) of the natural mineral satin spar is demonstrated. Among the various diffraction techniques used in this report, including powder diffraction, 2D pole figures, rocking curves looped on φ and 2D X-ray diffraction, a single simple symmetric 2D scan collecting the reciprocal plane perpendicular to the apparent fibre axis provided sufficient information to determine the crystallographic orientation of the fibre axis. A geometrical explanation of the `wing' feature formed by diffraction spots from the fibre-textured satin spar in 2D scans is provided. The technique of wide-range reciprocal space mapping restores the `wing' featured diffraction spots on the 2D detector back to reciprocal space layers, revealing the nature of the fibre-textured samples.

NdGa hydride and deuteride phases were prepared from high-quality NdGa samples and their structures characterized by powder and single-crystal X-ray diffraction and neutron powder diffraction. NdGa with the orthorhombic CrB-type structure absorbs hydrogen at hydrogen pressures ≤ 1 bar until reaching the composition NdGaH(D)1.1, which maintains a CrB-type structure. At elevated hydrogen pressure additional hydrogen is absorbed and the maximum composition recovered under standard temperature and pressure conditions is NdGaH(D)1.6 with the Cmcm LaGaH1.66-type structure. This structure is a threefold superstructure with respect to the CrB-type structure. The hydrogen atoms are ordered and distributed on three fully occupied Wyckoff positions corresponding to tetrahedral (4c, 8g) and trigonal–bipyramidal (8g) voids in the parent structure. The threefold superstructure is maintained in the H-deficient phases NaGaH(D)x until 1.6 ≥ x ≥ 1.2. At lower H concentrations, coinciding with the composition of the hydride obtained from hydrogenation at atmospheric pressure, the unit cell of the CrB-type structure is resumed. This phase can also display H deficiency, NdGaH(D)y (1.1 ≥ y ≥ 0.9), with H(D) exclusively situated in partially empty tetrahedral voids. The phase boundary between the threefold superstructure (LaGaH1.66 type) and the onefold structure (NdGaH1.1 type) is estimated on the basis of phase–composition isotherms and neutron powder diffraction to be x = 1.15.

In cellulo crystallization is a rare event in nature. Recent advances that have made use of heterologous overexpression can promote the intracellular formation of protein crystals, but new tools are required to detect and characterize these targets in the complex cell environment. The present work makes use of Mask R-CNN, a convolutional neural network (CNN)-based instance segmentation method, for the identification of either single or multi-shaped crystals growing in living insect cells, using conventional bright field images. The algorithm can be rapidly adapted to recognize different targets, with the aim of extracting relevant information to support a semi-automated screening pipeline, in order to aid the development of the intracellular protein crystallization approach.

The maximum range of perpendicular momentum transfer (qz) has been tripled for X-ray scattering from liquid surfaces when using a double-crystal deflector setup to tilt the incident X-ray beam. This is achieved by employing a higher-energy X-ray beam to access Miller indices of reflecting crystal atomic planes that are three times higher than usual. The deviation from the exact Bragg angle condition induced by misalignment between the X-ray beam axis and the main rotation axis of the double-crystal deflector is calculated, and a fast and straightforward procedure to align them is deduced. An experimental method of measuring scattering intensity along the qz direction on liquid surfaces up to qz = 7 Å−1 is presented, with liquid copper serving as a reference system for benchmarking purposes.

A multi-slit very small angle neutron scattering (MS-VSANS) instrument has been finally accepted at the China Spallation Neutron Source (CSNS). It is the first spallation neutron source based VSANS instrument. MS-VSANS has a good signal-to-noise ratio and can cover a wide scattering vector magnitude range from 0.00028 to 1.4 Å−1. In its primary flight path, a combined curved multichannel beam bender and sections of rotary exchange drums are installed to minimize the background downstream of the instrument. An exchangeable multi-slit beam focusing system is integrated into the primary flight path, enabling access to a minimum scattering vector magnitude of 0.00028 Å−1. MS-VSANS has three modes, namely conventional SANS, polarizing SANS and VSANS modes. In the SANS mode, three motorized high-efficiency 3He tube detectors inside the detector tank cover scattering angles from 0.12 to 35° simultaneously. In the polarizing SANS mode, a double-V cavity provides highly polarized neutrons and a high-efficiency 3He polarization analyser allows full polarization analysis. In the VSANS mode, an innovative high-resolution gas electron multiplier detector covers scattering angles from 0.016 to 0.447°. The absolute scattering intensities of a selection of standard samples are obtained using the direct-beam technique; the effectiveness of this method is verified by testing the standard samples and comparing the results with those from a benchmark instrument. The MS-VSANS instrument is designed to be flexible and versatile and all the design goals have been achieved.

X-ray diffraction from dislocation half-loops consisting of a misfit segment with two threading arms extending from it to the surface is calculated by the Monte Carlo method. The diffraction profiles and reciprocal space maps are controlled by the ratio of the total lengths of the misfit and the threading segments of the half-loops. A continuous transformation from the diffraction characteristic of misfit dislocations to that of threading dislocations with increasing thickness of epitaxial film is studied. Diffraction from dislocations with edge- and screw-type threading arms is considered and the contributions of the two types of dislocations are compared.

Fluctuation X-ray scattering (FXS) offers a complementary approach for nano- and bioparticle imaging with an X-ray free-electron laser (XFEL), by extracting structural information from correlations in scattered XFEL pulses. Here a workflow is presented for single-particle structure determination using FXS. The workflow includes procedures for extracting the rotational invariants from FXS patterns, performing structure reconstructions via iterative phasing of the invariants, and aligning and averaging multiple reconstructions. The reconstruction pipeline is implemented in the open-source software xFrame and its functionality is demonstrated on several simulated structures.

This work introduces X-Ray Calc (XRC), an open-source software package designed to simulate X-ray reflectivity (XRR) and address the inverse problem of reconstructing film structures on the basis of measured XRR curves. XRC features a user-friendly graphical interface that facilitates interactive simulation and reconstruction. The software employs a recursive approach based on the Fresnel equations to calculate XRR and incorporates specialized tools for modeling periodic multilayer structures. This article presents the latest version of the X-Ray Calc software (XRC3), with notable improvements. These enhancements encompass an automatic fitting capability for XRR curves utilizing a modified flight particle swarm optimization algorithm. A novel cost function was also developed specifically for fitting XRR curves of periodic structures. Furthermore, the overall user experience has been enhanced by developing a new single-window interface.

Dark-field X-ray microscopy (DFXM) is a full-field imaging technique that non-destructively maps the structure and local strain inside deeply embedded crystalline elements in three dimensions. In DFXM, an objective lens is placed along the diffracted beam to generate a magnified projection image of the local diffracted volume. This work explores contrast methods and optimizes the DFXM setup specifically for the case of mapping dislocations. Forward projections of detector images are generated using two complementary simulation tools based on geometrical optics and wavefront propagation, respectively. Weak and strong beam contrast and the mapping of strain components are studied. The feasibility of observing dislocations in a wall is elucidated as a function of the distance between neighbouring dislocations and the spatial resolution. Dislocation studies should be feasible with energy band widths of 10−2, of relevance for fourth-generation synchrotron and X-ray free-electron laser sources.

X-ray reflectometry (XRR) is a powerful tool for probing the structural characteristics of nanoscale films and layered structures, which is an important field of nanotechnology and is often used in semiconductor and optics manufacturing. This study introduces a novel approach for conducting quantitative high-resolution millisecond monochromatic XRR measurements. This is an order of magnitude faster than in previously published work. Quick XRR (qXRR) enables real time and in situ monitoring of nanoscale processes such as thin film formation during spin coating. A record qXRR acquisition time of 1.4 ms is demonstrated for a static gold thin film on a silicon sample. As a second example of this novel approach, dynamic in situ measurements are performed during PMMA spin coating onto silicon wafers and fast fitting of XRR curves using machine learning is demonstrated. This investigation primarily focuses on the evolution of film structure and surface morphology, resolving for the first time with qXRR the initial film thinning via mass transport and also shedding light on later thinning via solvent evaporation. This innovative millisecond qXRR technique is of significance for in situ studies of thin film deposition. It addresses the challenge of following intrinsically fast processes, such as thin film growth of high deposition rate or spin coating. Beyond thin film growth processes, millisecond XRR has implications for resolving fast structural changes such as photostriction or diffusion processes.

A systematic procedure is introduced for modeling charge-neutral non-polar surfaces of ionic minerals containing polyatomic anions. By integrating distance- and charge-based clustering to identify chemical species within the mineral bulk, our pipeline, PolyCleaver, renders a variety of theoretically viable surface terminations. As a demonstrative example, this approach was applied to forsterite (Mg2SiO4), unveiling a rich interface landscape based on interactions with formaldehyde, a relevant multifaceted molecule, and more particularly in prebiotic chemistry. This high-throughput method, going beyond techniques traditionally applied in the modeling of minerals, offers new insights into the potential catalytic properties of diverse surfaces, enabling a broader exploration of synthetic pathways in complex mineral systems.

Serial crystallography experiments at synchrotron and X-ray free-electron laser (XFEL) sources are producing crystallographic data sets of ever-increasing volume. While these experiments have large data sets and high-frame-rate detectors (around 3520 frames per second), only a small percentage of the data are useful for downstream analysis. Thus, an efficient and real-time data classification pipeline is essential to differentiate reliably between useful and non-useful images, typically known as `hit' and `miss', respectively, and keep only hit images on disk for further analysis such as peak finding and indexing. While feature-point extraction is a key component of modern approaches to image classification, existing approaches require computationally expensive patch preprocessing to handle perspective distortion. This paper proposes a pipeline to categorize the data, consisting of a real-time feature extraction algorithm called modified and parallelized FAST (MP-FAST), an image descriptor and a machine learning classifier. For parallelizing the primary operations of the proposed pipeline, central processing units, graphics processing units and field-programmable gate arrays are implemented and their performances compared. Finally, MP-FAST-based image classification is evaluated using a multi-layer perceptron on various data sets, including both synthetic and experimental data. This approach demonstrates superior performance compared with other feature extractors and classifiers.

Proteins are well known `shapeshifters' which change conformation to function. In crystallography, multiple conformational states are often present within the crystal and the resulting electron-density map. Yet, explicitly incorporating alternative states into models to disentangle multi-conformer ensembles is challenging. We previously reported the tool FLEXR, which, within a few minutes, automatically separates conformational signal from noise and builds the corresponding, often missing, structural features into a multi-conformer model. To make the method widely accessible for routine multi-conformer building as part of the computational toolkit for macromolecular crystallography, we present a graphical user interface (GUI) for FLEXR, designed as a plugin for Coot 1. The GUI implementation seamlessly connects FLEXR models with the existing suite of validation and modeling tools available in Coot. We envision that FLEXR will aid crystallographers by increasing access to a multi-conformer modeling method that will ultimately lead to a better representation of protein conformational heterogeneity in the Protein Data Bank. In turn, deeper insights into the protein conformational landscape may inform biology or provide new opportunities for ligand design. The code is open source and freely available on GitHub at https://github.com/TheFischerLab/FLEXR-GUI.

This work presents observations of symmetry breakages in the intensity distributions of near-zone-axis convergent-beam electron diffraction (CBED) patterns that can only be explained by the symmetry of the specimen and not the symmetry of the unit cell describing the atomic structure of the material. The specimen is an aluminium–copper–tin alloy containing voids many tens of nanometres in size within continuous single crystals of the aluminium host matrix. Several CBED patterns where the incident beam enters and exits parallel void facets without the incident beam being perpendicular to these facets are examined. The symmetries in their intensity distributions are explained by the specimen morphology alone using a geometric argument based on the multislice theory. This work shows that it is possible to deduce nanoscale morphological information about the specimen in the direction of the electron beam – the elusive third dimension in transmission electron microscopy – from the inspection of CBED patterns.

In addressing the challenges faced by laboratories and universities with limited (or no) cryo-electron microscopy (cryo-EM) infrastructure, the ESRF, in collaboration with the Grenoble Institute for Structural Biology (IBS), has implemented the cryo-EM Solution-to-Structure (SOS) pipeline. This inclusive process, spanning grid preparation to high-resolution data collection, covers single-particle analysis and cryo-electron tomography (cryo-ET). Accessible through a rolling access route, proposals undergo scientific merit and technical feasibility evaluations. Stringent feasibility criteria demand robust evidence of sample homogeneity. Two distinct entry points are offered: users can either submit purified protein samples for comprehensive processing or initiate the pipeline with already vitrified cryo-EM grids. The SOS pipeline integrates negative stain imaging (exclusive to protein samples) as a first quality step, followed by cryo-EM grid preparation, grid screening and preliminary data collection for single-particle analysis, or only the first two steps for cryo-ET. In both cases, if the screening steps are successfully completed, high-resolution data collection will be carried out using a Titan Krios microscope equipped with a latest-generation direct electron counting detector coupled to an energy filter. The SOS pipeline thus emerges as a comprehensive and efficient solution, further democratizing access to cryo-EM research.

Analysis of small-angle scattering (SAS) data requires intensive modeling to infer and characterize the structures present in a sample. This iterative improvement of models is a time-consuming process. Presented here is Scattering Equation Builder (SEB), a C++ library that derives exact analytic expressions for the form factors of complex composite structures. The user writes a small program that specifies how the sub-units should be linked to form a composite structure and calls SEB to obtain an expression for the form factor. SEB supports e.g. Gaussian polymer chains and loops, thin rods and circles, solid spheres, spherical shells and cylinders, and many different options for how these can be linked together. The formalism behind SEB is presented and simple case studies are given, such as block copolymers with different types of linkage, as well as more complex examples, such as a random walk model of 100 linked sub-units, dendrimers, polymers and rods attached to the surfaces of geometric objects, and finally the scattering from a linear chain of five stars, where each star is built up of four diblock copolymers. These examples illustrate how SEB can be used to develop complex models and hence reduce the cost of analyzing SAS data.

The strong metal–support interaction (SMSI) is a phenomenon observed in supported metal catalyst systems in which reducible metal oxide supports can form overlayers over the surface of active metal nanoparticles (NPs) under a hydrogen (H2) environment at elevated temperatures. SMSI has been shown to affect catalyst performance in many reactions by changing the type and number of active sites on the catalyst surface. Laboratory methods for the analysis of SMSI at the nanoparticle-ensemble level are lacking and mostly based on indirect evidence, such as gas chemisorption. Here, we demonstrate the possibility to detect and characterize SMSIs in Co/TiOx model catalysts using the laboratory X-ray standing wave (XSW) technique for a large ensemble of NPs at the bulk scale. We designed a thermally stable MoNx/SiNx periodic multilayer to retain XSW generation after reduction with H2 gas at 600°C. The model catalyst system was synthesized here by deposition of a thin TiOx layer on top of the periodic multilayer, followed by Co NP deposition via spare ablation. A partial encapsulation of Co NPs by TiOx was identified by analyzing the change in Ti atomic distribution. This novel methodological approach can be extended to observe surface restructuring of model catalysts in situ at high temperature (up to 1000°C) and pressure (≤3 mbar), and can also be relevant for fundamental studies in the thermal stability of membranes, as well as metallurgy.

X-ray Laue microdiffraction aims to characterize microstructural and mechanical fields in polycrystalline specimens at the sub-micrometre scale with a strain resolution of ∼10−4. Here, a new and unique Laue microdiffraction setup and alignment procedure is presented, allowing measurements at temperatures as high as 1500 K, with the objective to extend the technique for the study of crystalline phase transitions and associated strain-field evolution that occur at high temperatures. A method is provided to measure the real temperature encountered by the specimen, which can be critical for precise phase-transition studies, as well as a strategy to calibrate the setup geometry to account for the sample and furnace dilation using a standard α-alumina single crystal. A first application to phase transitions in a polycrystalline specimen of pure zirconia is provided as an illustrative example.

This article describes a correction procedure for the removal of indirect background contributions to measured small-angle X-ray scattering patterns. The high scattering power of a sample in the ultra-small-angle region may serve as a secondary source for a window placed in front of the detector. The resulting secondary scattering appears as a sample-dependent background in the measured pattern that cannot be directly subtracted. This is an intricate problem in measurements at ultra-low angles, which can significantly reduce the useful dynamic range of detection. Two different procedures are presented to retrieve the real scattering profile of the sample.

Due to the ambiguity related to the lack of phase information, determining the physical parameters of multilayer thin films from measured neutron and X-ray reflectivity curves is, on a fundamental level, an underdetermined inverse problem. This ambiguity poses limitations on standard neural networks, constraining the range and number of considered parameters in previous machine learning solutions. To overcome this challenge, a novel training procedure has been designed which incorporates dynamic prior boundaries for each physical parameter as additional inputs to the neural network. In this manner, the neural network can be trained simultaneously on all well-posed subintervals of a larger parameter space in which the inverse problem is underdetermined. During inference, users can flexibly input their own prior knowledge about the physical system to constrain the neural network prediction to distinct target subintervals in the parameter space. The effectiveness of the method is demonstrated in various scenarios, including multilayer structures with a box model parameterization and a physics-inspired special parameterization of the scattering length density profile for a multilayer structure. In contrast to previous methods, this approach scales favourably when increasing the complexity of the inverse problem, working properly even for a five-layer multilayer model and a periodic multilayer model with up to 17 open parameters.

X-ray crystallography is an established tool to probe the structure of macromolecules with atomic resolution. Compared with alternative techniques such as single-particle cryo-electron microscopy and micro-electron diffraction, X-ray crystallography is uniquely suited to room-temperature studies and for obtaining a detailed picture of macromolecules subjected to an external electric field (EEF). The impact of an EEF on proteins has been extensively explored through single-crystal X-ray crystallography, which works well with larger high-quality protein crystals. This article introduces a novel design for a 3D-printed in situ crystallization plate that serves a dual purpose: fostering crystal growth and allowing the concurrent examination of the effects of an EEF on crystals of varying sizes. The plate's compatibility with established X-ray crystallography techniques is evaluated.