Single-crystal growth, differential thermal analysis (DTA), derivative thermogravimetry (DTG), differential scanning calorimetry (DSC), X-ray structural studies and polarized microscopy observations of bis(ethylenediammonium) tetrabromozincate(II) bromide [NH3(CH2)2NH3]2[ZnBr4]Br2 are presented. A reversible phase transition is described. At room temperature, the complex crystallizes in the monoclinic system. In some cases, the single crystals are twinned into two or more large domains of ferroelastic type with domain walls in the (100) crystallographic plane. DTA and DTG measurements show chemical stability of the crystal up to ∼538 K. In the DSC studies, a reversible isostructural phase transition was revealed at ∼526/522 K on heating/cooling run, respectively. Optical observation on the heating run reveals that at the phase transition the plane of twinning (domain wall) does not disappear and additionally the appearance of a new domain structure of ferroelastic type with domain walls in the planes (101), (101), (100) and (001) is observed. The domain structure pattern is preserved after cooling to the room-temperature phase and the symmetry of this phase is unchanged.

Nickel orthovanadate is a promising material with potential applications in energy storage and photocatalytic devices. The crystal structure of Ni3V2O8 at 299 (3) K and 1323 (8) K was studied using X-ray powder diffraction. The sample was a single-phase orthorhombic kagome-staircase-Ni3(VO4)2-type structure (space group Cmca) at both temperatures. The phase purity and morphology was studied using energy-dispersive X-ray spectroscopy and scanning electron microscopy. The refined unit-cell parameters at 299 (3) K are a = 5.93384 (4) Å, b = 11.38318 (7) Å and c = 8.23818 (5) Å, and at 1323 (8) K are a = 6.02077 (7) Å, b = 11.48838 (7) Å and c = 8.32611 (9) Å. The obtained results indicate thermal expansion anisotropy, with a largest expansivity along a. Variations in Ni—O and V—O bonds with temperature are observed. The variation in the Ni—O bond is about one order higher in magnitude than that of the V—O bond, signifying the high rigidity of V—O bonds. The unit-cell size variations with rising effective ionic volume of the divalent A ion in the A3B2O8 family [A = Ni, Mg, Zn, Co, Mn (experimental data) and also A = Cu, Cd (theoretical data), B = V or As] are analyzed. Based on experimental and theoretical data, trends within the family are observed and the unit-cell size for reported solid solution of nickel (87%) and copper (13%) mixture in (Ni1–xCux)3V2O8 are predicted. Predictions are also provided for some hypothetical A3B2O8 ternary compound and solid solutions.

The crystal structure of the incommensurate modulated phase of potassium guaninate monohydrate has been solved on the basis of high-pressure single-crystal X-ray diffraction data. The modulated structure was described as a `mosaic' sequence of three different local configurations of two neighbouring guaninate rings. In contrast to known examples of incommensurate modulated organic compounds, the modulation functions of all atoms are discontinuous. This is the first example of the experimental detection of an incommensurate modulated crystal structure that can be modelled using the special `soliton mode' modulation function proposed by Aramburu et al. [(1995), J. Phys. Condens. Matter, 7, 6187–6196].

The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox (CCTBX) and in Phenix as the default choice.

Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data.

Monoclinic ferroelectric phases are prevalent in various functional materials, most notably mixed-ion perovskite oxides. These phases can manifest as regularly ordered long-range crystallographic structures or as macroscopic averages of the self-assembled tetragonal/rhombohedral nanodomains. The structural and physical properties of monoclinic ferroelectric phases play a pivotal role when exploring the interplay between ferroelectricity, ferroelasticity, giant piezoelectricity and multiferroicity in crystals, ceramics and epitaxial thin films. However, the complex nature of this subject presents challenges, particularly in deciphering the microstructures of monoclinic domains. In Paper I [Biran & Gorfman (2024). Acta Cryst. A80, 112–128] the geometrical principles governing the connection of domain microstructures formed by pairing MAB type monoclinic domains were elucidated. Specifically, a catalog was established of `permissible domain walls', where `permissible', as originally introduced by Fousek & Janovec [J. Appl. Phys. (1969), 40, 135–142], denotes a mismatch-free connection between two monoclinic domains along the corresponding domain wall. The present article continues the prior work by elaborating on the formalisms of permissible domain walls to describe domain microstructures formed by pairing the MC type monoclinic domains. Similarly to Paper I, 84 permissible domain walls are presented for MC type domains. Each permissible domain wall is characterized by Miller indices, the transformation matrix between the crystallographic basis vectors of the domains and, crucially, the expected separation of Bragg peaks diffracted from the matched pair of domains. All these parameters are provided in an analytical form for easy and intuitive interpretation of the results. Additionally, 2D illustrations are provided for selected instances of permissible domain walls. The findings can prove valuable for various domain-related calculations, investigations involving X-ray diffraction for domain analysis and the description of domain-related physical properties.

In Part I of this series, all topologically possible 1-periodic infinite graphs (chain graphs) representing chains of tetrahedra with up to 6–8 vertices (tetrahedra) per repeat unit were generated. This paper examines possible restraints on embedding these chain graphs into Euclidean space such that they are compatible with the metrics of chains of tetrahedra in observed crystal structures. Chain-silicate minerals with T = Si4+ (plus P5+, V5+, As5+, Al3+, Fe3+, B3+, Be2+, Zn2+ and Mg2+) have a grand nearest-neighbour 〈T–T〉 distance of 3.06±0.15 Å and a minimum T⋯T separation of 3.71 Å between non-nearest-neighbour tetrahedra, and in order for embedded chain graphs (called unit-distance graphs) to be possible atomic arrangements in crystals, they must conform to these metrics, a process termed equalization. It is shown that equalization of all acyclic chain graphs is possible in 2D and 3D, and that equalization of most cyclic chain graphs is possible in 3D but not necessarily in 2D. All unique ways in which non-isomorphic vertices may be moved are designated modes of geometric modification. If a mode (m) is applied to an equalized unit-distance graph such that a new geometrically distinct unit-distance graph is produced without changing the lengths of any edges, the mode is designated as valid (mv); if a new geometrically distinct unit-distance graph cannot be produced, the mode is invalid (mi). The parameters mv and mi are used to define ranges of rigidity of the unit-distance graphs, and are related to the edge-to-vertex ratio, e/n, of the parent chain graph. The program GraphT–T was developed to embed any chain graph into Euclidean space subject to the metric restraints on T–T and T⋯T. Embedding a selection of chain graphs with differing e/n ratios shows that the principal reason why many topologically possible chains cannot occur in crystal structures is due to violation of the requirement that T⋯T > 3.71 Å. Such a restraint becomes increasingly restrictive as e/n increases and indicates why chains with stoichiometry TO<2.5 do not occur in crystal structures.

Analytical calculations of absorption corrections for X-ray powder diffraction experiments on non-ideal samples with surface roughness, porosity or absorption contrasts from multiple phases require complex mathematical models to represent their material distribution. In a computational approach to this problem, a practicable ray-tracing algorithm is formulated which is capable of simulating angle-dependent absorption corrections in reflection geometry for any given rasterized sample model. Single or multiphase systems with arbitrary surface roughness, porosity and spatial distribution of the phases in any combination can be modeled on a voxel grid by assigning respective values to each voxel. The absorption corrections are calculated by tracing the attenuation of X-rays along their individual paths via a modified shear-warp algorithm. The algorithm is presented in detail and the results of simulated absorption corrections on samples with various surface modulations are discussed in the context of published experimental results.

The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB6 from measurements made in different-sized capillaries.

Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops.

Human tRNA (uracil-5-)-methyltransferase 2 homolog A (TRMT2A) is the dedicated enzyme for the methylation of uridine 54 in transfer RNA (tRNA). Human TRMT2A has also been described as a modifier of polyglutamine (polyQ)-derived neuronal toxicity. The corresponding human polyQ pathologies include Huntington's disease and constitute a family of devastating neuro­degenerative diseases. A polyQ tract in the corresponding disease-linked protein causes neuronal death and symptoms such as impaired motor function, as well as cognitive impairment. In polyQ disease models, silencing of TRMT2A reduced polyQ-associated cell death and polyQ protein aggregation, suggesting this protein as a valid drug target against this class of disorders. In this paper, the 1.6 Å resolution crystal structure of the RNA-recognition motif (RRM) from Drosophila melanogaster, which is a homolog of human TRMT2A, is described and analysed.

Brucella ovis is an etiologic agent of ovine epididymitis and brucellosis that causes global devastation in sheep, rams, goats, small ruminants and deer. There are no cost-effective methods for the worldwide eradication of ovine brucellosis. B. ovis and other protein targets from various Brucella species are currently in the pipeline for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), with the aim of identifying new therapeutic targets. Furthermore, the wealth of structures generated are effective tools for teaching scientific communication, structural science and biochemistry. One of these structures, B. ovis leucine-, isoleucine-, valine-, threonine- and alanine-binding protein (BoLBP), is a putative periplasmic amino acid-binding protein. BoLBP shares less than 29% sequence identity with any other structure in the Protein Data Bank. The production, crystallization and high-resolution structures of BoLBP are reported. BoLBP is a prototypical bacterial periplasmic amino acid-binding protein with the characteristic Venus flytrap topology of two globular domains encapsulating a large central cavity containing the peptide-binding region. The central cavity contains small molecules usurped from the crystallization milieu. The reported structures reveal the conformational flexibility of the central cavity in the absence of bound peptides. The structural similarity to other LBPs can be exploited to accelerate drug repurposing.

Proliferating cell nuclear antigen (PCNA) plays a critical role in DNA replication by enhancing the activity of various proteins involved in replication. In this study, the crystal structure of ApePCNA1, one of three PCNAs from the thermophilic archaeon Aeropyrum pernix, was elucidated. ApePCNA1 was cloned and expressed in Escherichia coli and the protein was purified and crystallized. The resulting crystal structure determined at 2.00 Å resolution revealed that ApePCNA1 does not form a trimeric ring, unlike PCNAs from other domains of life. It has unique structural features, including a long interdomain-connecting loop and a PIP-box-like sequence at the N-terminus, indicating potential interactions with other proteins. These findings provide insights into the functional mechanisms of PCNAs in archaea and their evolutionary conservation across different domains of life. A modified medium and protocol were used to express recombinant protein containing the lac operon. The expression of the target protein increased and the total incubation time decreased when using this system compared with those of previous expression protocols.

Animations, videos and 3D models have been designed to visualize the effects of symmetry operators on selected cases of crystal structures, pointing out the relationship with the diagrams published in International Tables for Crystallography, Vol. A.

The correct determination of X-ray transmission at X-ray nanoprobes equipped with small beamstops for small- and wide-angle X-ray scattering collection is an unsolved problem with huge implications for data correction pipelines. We present a cost-effective solution to detect the transmission via the X-ray fluorescence of the beamstop with an avalanche photodiode.

New software capabilities in RMCProfile allow researchers to study the structure of materials by combining machine learning interatomic potentials and reverse Monte Carlo.

Rotations of small- and wide-angle X-ray scattering samples during acquisition are shown to give a drastic improvement in the reliability of the characterization of anisotropic precipitates in metallic alloys.

A new processing technique for synchrotron scanning 3D X-ray diffraction data is introduced, utilizing symmetric Bragg reflections hkl and hkl, known as Friedel pairs. This technique is designed to tackle the difficulties associated with large, highly deformed, polyphase materials, especially geological samples.

Here, an open-source Python library for identifying and screening potential stacking fault models in crystalline materials with planar disorder is presented.

The article presents a non-invasive nanoscale imaging technique that can be used in screening crystallization conditions for protein micro- and nanocrystals.

The L-edge EXAFS of the entire set of lanthanide oxides were collected and modeled, taking into consideration the aggregation of inequivalent absorbing sites, geometric parameterization of the crystal lattice and multielectron excitation removal.

Here we describe TOMOMAN (TOMOgram MANager), an extensible open-sourced software package for handling cryo-electron tomography data preprocessing. TOMOMAN streamlines interoperability between a wide range of external packages and provides tools for project sharing and archival.

The impact of sample thickness and experimental noise on angular correlation analysis from scanning electron nanobeam diffraction patterns of disordered carbon are investigated and analyzed regarding the interpretability of the analysis results.

In the complex, the ligand binds to the metal through an oxygen atom. The geometry of the seven-coordinate U atom is penta­gonal bipyramidal, with the uranyl O atoms in apical positions.

In the title compound, the tellurium(VI) and vanadium(V) atoms are statistically disordered over two of the ten metal-atom sites in the unprotonated [TeV9O28]5– heteropolyanion.

A chiral nickel(II) Schiff base complex derived from 2-hy­droxy­benzo­phenone and (1S,2S)-1,2-di­phenyl­ethyl­enedi­amine shows a λ conformation of the central di­amine chelate ring. The substituents on the C&z-dbnd;N carbon atoms significantly affect the circular dichroism spectra.

Theoretical and experimental structural studies of the title compound were undertaken using X-ray and DFT methods. The inter­actions present in the crystal were analyzed using Hirshfeld surface and MEP surface analysis. Docking studies with a covid-19 main protease (PDB ID: 6LU7) as the target receptor indicate that the synthesized compound may be a potential candidate for pharmaceutical applications.

The crystal structure of the co-crystal salt solvate 1,10-phenanthrolinium violurate violuric acid penta­hydrate features a tri-periodic hydrogen-bonded network with the violurate and violuric acid residues each assembled into tapes and the phenanthrolinium cations residing in channels.

Crystallization of the title compound from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and ortho­rhom­bic (Pna21; β form) space groups. The ReI complex mol­ecules in either polymorph adopt a six-coordinate octa­hedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitro­gen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds.

Quantitative X-ray diffraction approaches require careful correction for sample transmission. Though this is a routine task at state-of-the-art small-angle X-ray scattering (SAXS), wide-angle X-ray scattering (WAXS) or diffraction beamlines at synchrotron facilities, the transmission signal cannot be recorded concurrently with SAXS/WAXS when using the small, sub-millimetre beamstops at many X-ray nanoprobes during SAXS/WAXS experiments due to the divergence-limited size of the beamstop and the generally tight geometry. This is detrimental to the data quality and often the only solution is to re-scan the sample with a PIN photodiode as a detector to obtain transmission values. In this manuscript, we present a simple yet effective solution to this problem in the form of a small beamstop with an inlaid metal target for optimal fluorescence yield. This fluorescence can be detected with a high-sensitivity avalanche photodiode and provides a linear counter to determine the sample transmission.

A series of animations, videos and 3D models that were developed, filmed or built to teach the symmetry properties of crystals are described. At first, these resources were designed for graduate students taking a basic crystallography course, coming from different careers, at the National Autonomous University of Mexico. However, the COVID-19 pandemic had the effect of accelerating the generation of didactic material. Besides our experience with postgraduate students, we have noted that 3D models attract the attention of children, and therefore we believe that these models are particularly useful for teaching children about the assembled arrangements of crystal structures.

The present study introduces a processing strategy for synchrotron scanning 3D X-ray diffraction (s3DXRD) data, aimed at addressing the challenges posed by large, highly deformed, polyphase materials such as crystalline rocks. Leveraging symmetric Bragg reflections known as Friedel pairs, our method enables diffraction events to be precisely located within the sample volume. This method allows for fitting the phase, crystal structure and unit-cell parameters at the intra-grain scale on a voxel grid. The processing workflow incorporates several new modules, designed to (i) efficiently match Friedel pairs in large s3DXRD datasets containing up to 108 diffraction peaks; (ii) assign phases to each pixel or voxel, resolving potential ambiguities arising from overlap in scattering angles between different crystallographic phases; and (iii) fit the crystal orientation and unit cell locally on a point-by-point basis. We demonstrate the effectiveness of our technique on fractured granite samples, highlighting the ability of the method to characterize complex geological materials and show their internal structure and mineral composition. Additionally, we include the characterization of a metal gasket made of a commercial aluminium alloy, which surrounded the granite sample during experiments. The results show the effectiveness of the technique in recovering information about the internal texture and residual strain of materials that have undergone high levels of plastic deformation.

Nanometric precipitates in metallic alloys often have highly anisotropic shapes. Given the large grain size and non-random texture typical of these alloys, performing small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on such samples for determining their characteristics (typically size and volume fraction) results in highly anisotropic and irreproducible data. Rotations of flat samples during SAXS/WAXS acquisitions are presented here as a solution to these anisotropy issues. Two aluminium alloys containing anisotropic precipitates are used as examples to validate the approach with a −45°/45° angular range. Clear improvements can be seen on the SAXS I(q) fitting and the consistency between the different SAXS/WAXS measurements. This methodology results in more reliable measurements of the precipitate's characteristics, and thus allows for time- and space-resolved measurements with higher accuracy.

Structure refinement with reverse Monte Carlo (RMC) is a powerful tool for interpreting experimental diffraction data. To ensure that the under-constrained RMC algorithm yields reasonable results, the hybrid RMC approach applies interatomic potentials to obtain solutions that are both physically sensible and in agreement with experiment. To expand the range of materials that can be studied with hybrid RMC, we have implemented a new interatomic potential constraint in RMCProfile that grants flexibility to apply potentials supported by the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics code. This includes machine learning interatomic potentials, which provide a pathway to applying hybrid RMC to materials without currently available interatomic potentials. To this end, we present a methodology to use RMC to train machine learning interatomic potentials for hybrid RMC applications.

The crystal structure uniformity is numerically estimated as the standard deviation of the crystal space quantizer 〈G3〉. This criterion has been applied to explore the uniformity of ionic sublattices in 21465 crystal structures of inorganic ionic compounds. In most cases, at least one kind of sublattice (whole ionic lattice, cationic or anionic sublattice) was found to be highly uniform with a small 〈G3〉 value. Non-uniform structures appeared to be either erroneous or essentially non-ionic. As a result, a set of uniformity criteria is proposed for the estimation of the stability of ionic crystal structures.

In powder diffraction, lattice symmetry relaxation causes a peak to split into several components which are not resolved if the degree of desymmetrization is small (pseudosymmetry). Here the equations which rule peak splitting are elaborated for the six minimal symmetry transitions, showing that the resulting split peaks are generally broader and asymmetric, and suffer an hkl-dependent displacement with respect to the high-symmetry parent peak. These results will be of help in Rietveld refinement of pseudosymmetric structures where an exact interpretation of peak deformation is required.

Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202–212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.

Crystallization of the title compound, fac-[ReBr(ppt-OMe)(CO)3] (ppt-OMe = C15H12N2OS), from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and orthorhombic (Pna21; β form) space groups. The ReI complex molecules in either polymorph adopt a six-coordinate octahedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitrogen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds. In polymorph α, two types of hydrogen bonds (C—H...O) are found while, in polymorph β, four types of hydrogen bonds (C—H...O and C—H...Br) exist.

In the title compound, C8H9BrN2O2, the C—O—C—C torsion angle between isonicotine and the ethyl group is 180.0 (2)°. Intramolecular N—H...O and C—H...O interactions consolidate the molecular structure. In the crystal, N—H...N interaction form S(5) zigzag chains along [010]. The most significant contributions to the Hirshfeld surface arise from H...H (33.2%), Br...H/H...Br (20.9%), O...H/H...O (11.2%), C...H/H...C (11.1%) and N...H/H...N (10%) contacts. The topology of the three-dimensional energy frameworks was generated using the B3LYP/6–31 G(d,p) model to calculate the total interaction energy. The net interaction energies for the title compound are Eele = 59.2 kJ mol−1, Epol = 15.5 kJ mol−1, Edis = 140.3 kJ mol−1 and Erep = 107.2 kJ mol−1 with a total interaction energy Etot of 128.8 kJ mol−1. The molecular structure was optimized by density functional theory (DFT) at the B3LYP/6–311+G(d,p) level and the theoretical and experimentally obtained parameters were compared. The frontier molecular orbitals HOMO and LUMO were generated, giving an energy gap ΔE of 4.0931 eV. The MEP was generated to identify active sites in the molecule and molecular docking studies carried out with the title compound (ligand) and the covid-19 main protease PDB ID: 6LU7, revealing a moderate binding affinity of −5.4 kcal mol−1.

The title compound, [Ni(C40H30N2O2)] (1), with an optically active Schiff base ligand derived from 2-hydroxybenzophenone and (1S,2S)-1,2-diphenylethylenediamine, was crystallized as the solvent-free and ethanol solvate forms (1 and 1·2C2H5OH). In both structures, the two phenyl groups on the stereogenic centers of the O,N,N,O-tetradentate ligand are axially oriented, and the conformation of the central diamine chelate ring is λ. The circular dichroism (CD) spectra of 1 and the analogous nickel(II) complex [Ni(C30H26N2O2)] (2) in solution show partially similar patterns in the 350–450 nm range, but are mirror images in the longer wavelength region (450–650 nm). In the latter region, the sign of CD for these complexes is sensitive to the substituents on the C=N carbon atoms (phenyl for 1 and methyl for 2) rather than the diamine chelate ring conformation.

In the realm of X-ray ptychography experiments, a considerable amount of ptychography scans are typically performed within a field of view encompassing the target sample. While it is crucial to obtain overlapping scans in small increments over the region of interest for achieving high-resolution sample reconstruction, a significant number of these scans often redundantly measure the empty background within the wide field of view. To address this inefficiency, an innovative algorithm is proposed that introduces automatic guidance for data acquisition. The algorithm first directs the scan point to actively search for the object of interest within the field of view. Subsequently, it intelligently scans along the perimeter of the sample, strategically acquiring measurements exclusively within the boundary of the region of interest. By employing this approach, a reduction in the number of measurements required to obtain high-resolution reconstruction images is demonstrated, as compared with conventional raster scanning methods. Furthermore, the automatic guidance provided by the algorithm offers the added advantage of saving valuable time during the reconstruction process. Through practical implementation on real experiments, these findings showcase the efficacy of the proposed algorithm in enhancing the efficiency and accuracy of X-ray ptychography experiments. This novel approach holds immense potential for advancing sample analysis and imaging techniques in various scientific disciplines.

X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed.

Bone material contains a hierarchical network of micro- and nano-cavities and channels, known as the lacuna-canalicular network (LCN), that is thought to play an important role in mechanobiology and turnover. The LCN comprises micrometer-sized lacunae, voids that house osteocytes, and submicrometer-sized canaliculi that connect bone cells. Characterization of this network in three dimensions is crucial for many bone studies. To quantify X-ray Zernike phase-contrast nanotomography data, deep learning is used to isolate and assess porosity in artifact-laden tomographies of zebrafish bones. A technical solution is proposed to overcome the halo and shade-off domains in order to reliably obtain the distribution and morphology of the LCN in the tomographic data. Convolutional neural network (CNN) models are utilized with increasing numbers of images, repeatedly validated by `error loss' and `accuracy' metrics. U-Net and Sensor3D CNN models were trained on data obtained from two different synchrotron Zernike phase-contrast transmission X-ray microscopes, the ANATOMIX beamline at SOLEIL (Paris, France) and the P05 beamline at PETRA III (Hamburg, Germany). The Sensor3D CNN model with a smaller batch size of 32 and a training data size of 70 images showed the best performance (accuracy 0.983 and error loss 0.032). The analysis procedures, validated by comparison with human-identified ground-truth images, correctly identified the voids within the bone matrix. This proposed approach may have further application to classify structures in volumetric images that contain non-linear artifacts that degrade image quality and hinder feature identification.

Third- and fourth-generation synchrotron light sources with high fluxes and beam energies enable the use of innovative X-ray translucent experimental apparatus. These experimental devices access geologically relevant conditions whilst enabling in situ characterization using the spatial and temporal resolutions accessible at imaging beamlines. Here, Heitt Mjölnir is introduced, a heated miniature triaxial rig based on the design of Mjölnir, but covering a wider temperature range and larger sample volume at similar pressure capacities. This device is designed to investigate coupled thermal, chemical, hydraulic and mechanical processes from grain to centimetre scales using cylindrical samples of 10 mm × 20 mm (diameter × length). Heitt Mjölnir can simultaneously reach confining (hydraulic) pressures of 30 MPa and 500 MPa of axial stress with independently controlled sample pore fluid pressure < 30 MPa. This internally heated apparatus operates to temperatures up to 573 K with a minimal vertical thermal gradient in the sample of <0.3 K mm−1. This new apparatus has been deployed in operando studies at the TOMCAT (Swiss Light Source), I12 JEEP (Diamond Light Source) and PSICHÉ (Synchrotron SOLEIL) beamlines for 4D X-ray microtomography with scan intervals of a few minutes. Heitt Mjölnir is portable and modular, allowing a wide range of 4D characterizations of low-grade metamorphism and deformational processes. It enables spatially and temporally resolved fluid–rock interaction studies at conditions of crustal reservoirs and is suitable for characterization of material properties in geothermal, carbonation or subsurface gas storage applications. Technical drawings and an operation guide are included in this publication.

The X-ray emission spectrometer at SPring-8 BL07LSU has recently been upgraded with advanced modifications that enable the rotation of the spectrometer with respect to the scattering angle. This major upgrade allows the scattering angle to be flexibly changed within the range of 45–135°, which considerably simplifies the measurement of angle-resolved X-ray emission spectroscopy. To accomplish the rotation system, a sophisticated sample chamber and a highly precise spectrometer rotation mechanism have been developed. The sample chamber has a specially designed combination of three rotary stages that can smoothly move the connection flange along the wide scattering angle without breaking the vacuum. In addition, the spectrometer is rotated by sliding on a flat metal surface, ensuring exceptionally high accuracy in rotation and eliminating the need for any further adjustments during rotation. A control system that integrates the sample chamber and rotation mechanism to automate the measurement of angle-resolved X-ray emission spectroscopy has also been developed. This automation substantially streamlines the process of measuring angle-resolved spectra, making it far easier than ever before. Furthermore, the upgraded X-ray emission spectrometer can now also be utilized in diffraction experiments, providing even greater versatility to our research capabilities.

A method to optimize the thermal deformation of an indirectly cryo-cooled silicon crystal monochromator exposed to intense X-rays at a low-emittance diffraction-limited synchrotron radiation source is presented. The thermal-induced slope error of the monochromator crystal has been studied as a function of heat transfer efficiency, crystal temperature distribution and beam footprint size. A partial cooling method is proposed, which flattens the crystal surface profile within the beam footprint by modifying the cooling contact area to optimize the crystal peak temperature. The optimal temperature varies with different photon energies, which is investigated, and a proper cooling strategy is obtained to fulfil the thermal distortion requirements over the entire photon energy range. At an absorbed power up to 300 W with a maximum power density of 44.8 W mm−2 normal incidence beam from an in-vacuum undulator, the crystal thermal distortion does not exceed 0.3 µrad at 8.33 keV. This method will provide references for the monochromator design on diffraction-limited synchrotron radiation or free-electron laser light sources.

X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) and ab initio electronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total, i.e. energy-integrated, scattering from three molecules, fluoroform (CHF3), 1,3-cyclohexadiene (C6H8) and naphthalene (C10H8), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q ≤ 8 Å−1) in the scattering signal, with a maximum percent difference contribution at 2 ≤ q ≤ 3 Å−1. A procedure to determine the molecular geometry from the large-q scattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediate q and to provide a measure of the effect of valence electronic structure on the scattering signal.

This work investigates the performance of the electrospray aerosol generator at the European X-ray Free Electron Laser (EuXFEL). This generator is, together with an aerodynamic lens stack that transports the particles into the X-ray interaction vacuum chamber, the method of choice to deliver particles for single-particle coherent diffractive imaging (SPI) experiments at the EuXFEL. For these experiments to be successful, it is necessary to achieve high transmission of particles from solution into the vacuum interaction region. Particle transmission is highly dependent on efficient neutralization of the charged aerosol generated by the electrospray mechanism as well as the geometry in the vicinity of the Taylor cone. We report absolute particle transmission values for different neutralizers and geometries while keeping the conditions suitable for SPI experiments. Our findings reveal that a vacuum ultraviolet ionizer demonstrates a transmission efficiency approximately seven times greater than the soft X-ray ionizer used previously. Combined with an optimized orifice size on the counter electrode, we achieve >40% particle transmission from solution into the X-ray interaction region. These findings offer valuable insights for optimizing electrospray aerosol generator configurations and data rates for SPI experiments.

Metal-organic frameworks (MOFs) exhibit structural flexibility induced by temperature and guest adsorption, as demonstrated in the structural breathing transition in certain MOFs between narrow-pore and large-pore phases. Soft modes were suggested to entropically drive such pore breathing through enhanced vibrational dynamics at high temperatures. In this work, oxygen K-edge resonant X-ray emission spectroscopy of the MIL-53(Al) MOF was performed to selectively probe the electronic perturbation accompanying pore breathing dynamics at the ligand carboxyl­ate site for metal–ligand interaction. It was observed that the temperature-induced vibrational dynamics involves switching occupancy between antisymmetric and symmetric configurations of the carboxyl­ate oxygen lone pair orbitals, through which electron density around carboxyl­ate oxygen sites is redistributed and metal–ligand interactions are tuned. In turn, water adsorption involves an additional perturbation of π orbitals not observed in the structural change solely induced by temperature.

Maximizing the performance of crystal monochromators is a key aspect in the design of beamline optics for diffraction-limited synchrotron sources. Temperature and deformation of cryo-cooled crystals, illuminated by high-power beams of X-rays, can be estimated with a purely analytical model. The analysis is based on the thermal properties of cryo-cooled silicon crystals and the cooling geometry. Deformation amplitudes can be obtained, quickly and reliably. In this article the concept of threshold power conditions is introduced and defined analytically. The contribution of parameters such as liquid-nitro­gen cooling efficiency, thermal contact conductance and interface contact area of the crystal with the cooling base is evaluated. The optimal crystal illumination and the base temperature are inferred, which help minimize the optics deformation. The model has been examined using finite-element analysis studies performed for several beamlines of the Diamond-II upgrade.