The di­hydro­imidazole ring in the title mol­ecule, C20H20N2O3S, is slightly distorted and the lone pair on the tri-coordinate nitro­gen atom is involved in intra-ring π bonding. The methyl­sulfanyl substituent lies nearly in the plane of the five-membered ring while the ester substituent is rotated well out of that plane. In the crystal, C—H⋯O hydrogen bonds form inversion dimers, which are connected along the a- and c-axis directions by additional C—H⋯O hydrogen bonds, forming layers parallel to the ac plane. The major contributors to the Hirshfeld surface are C⋯H/H⋯C, O⋯H/H⋯O and S⋯H/H⋯S contacts at 20.5%, 14.7% and 4.9%, respectively.

The crystal structure of hexa­glycinium tetra-μ-iodido-octa­iodido­triplumbate, (C2H6NO2)6[Pb3I12] or (GlyH)6[Pb3I12], is reported. The compound crystallizes in the triclinic space group Poverline{1}. The [Pb3I12]6− anion is discrete and located around a special position: the central Pb ion located on the inversion center is holodirected, while the other two are hemidirected. The supra­molecular nature is mainly based on C—H⋯I, N—H⋯I, O—H⋯I and N—H⋯O hydrogen bonds. Dimeric cations of type (A+⋯A+) for the amino acid glycine are observed for the first time.

The cyclic peptide cyclo(Val-Leu-Leu-d-Phe-Pro)2 (peptide 1) was specifically designed for structural chemistry investigations, drawing inspiration from Gramicidin S (GS). Previous studies have shown that Pro residues within 1 adopt a down-puckering conformation of the pyrrolidine ring. By incorporating fluoride-Pro with 4-trans/cis-isomers into 1, an up-puckering conformation was successfully induced. In the current investigation, introducing hy­droxy­prolines with 4-trans/cis-isomer configurations (tHyp/cHyp) into 1 gave cyclo(Val-Leu-Leu-d-Phe-tHyp)2 methanol disolvate monohydrate, C62H94N10O12·2CH4O·H2O (4), and cyclo(Val-Leu-Leu-d-Phe-cHyp)2 monohydrate, C62H94N10O12·H2O (5), respectively. However, the puckering of 4 and 5 remained in the down conformation, regardless of the geometric position of the hydroxyl group. Although the backbone structure of 4 with trans-substitution was asymmetric, the asymmetric backbone of 5 with cis-substitution was unexpected. It is speculated that the anti­cipated influence of stress from the geometric positioning, which was expected to affect the puckering, may have been mitigated by inter­actions between the hydroxyl groups of hy­droxy­proline, the solvent mol­ecules, and peptides.

In the structure of the title salt, {[Ba(μ3-C3H2N3O2)2(μ-H2O)(H2O)]·H2O}n, the barium ion and all three oxygen atoms of the water mol­ecules reside on a mirror plane. The hydrogen atoms of the bridging water and the solvate water mol­ecules are arranged across a mirror plane whereas all atoms of the monodentate aqua ligand are situated on this mirror plane. The distorted ninefold coord­ination of the Ba ions is completed with four nitroso-, two carbonyl- and three aqua-O atoms at the distances of 2.763 (3)–2.961 (4) Å and it is best described as tricapped trigonal prism. The three-dimensional framework structure is formed by face-sharing of the trigonal prisms, via μ-nitroso- and μ-aqua-O atoms, and also by the bridging coordination of the anions via carbonyl-O atoms occupying two out of the three cap positions. The solvate water mol­ecules populate the crystal channels and facilitate a set of four directional hydrogen bonds. The principal Ba–carbamoyl­cyano­nitro­somethanido linkage reveals a rare example of the inherently polar binodal six- and three-coordinated bipartite topology (three-letter notation sit). It suggests that small resonance-stabilized cyano­nitroso anions can be utilized as bridging ligands for the supra­molecular synthesis of MOF solids. Such an outcome may be anti­cipated for a broader range of hard Lewis acidic alkaline earth metal ions, which perfectly match the coordination preferences of highly nucleophilic nitroso-O atoms. Thermal analysis reveals two-stage dehydration of the title compound (383 and 473 K) followed by decomposition with release of CO2, HCN and H2O at 558 K.

The benzimidazole moiety in the title mol­ecule, C19H25N5O, is almost planar and oriented nearly perpendicular to the triazole ring. In the crystal, C—H⋯O hydrogen bonds link the mol­ecules into a network structure. There are no π–π inter­actions present but two weak C—H⋯π(ring) inter­actions are observed. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (62.0%), H⋯C/C⋯H (16.1%), H⋯N/N⋯H (13.7%) and H⋯O/O⋯H (7.5%) inter­actions. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via the dispersion energy contributions in the title compound.

This work describes the X-ray structure of orange–red crystals of 2-meth­oxy-5-nitro­aniline, C7H8N2O3. The compound displays concentration-dependent UV-Vis spectra, which is attributed to dipole-induced aggregation, and light absorption arising from an inter­molecular charge-transfer process that decreases in energy as the degree of aggregation increases. The crystals display π-stacking where the dipole moments align anti­parallel. Stacked mol­ecules inter­act with the next stack via hydrogen bonds, which is a state of maximum aggregation. Light absorption by charge transfer can be compared to colored inorganic semiconductors such as orange–red CdS, with a band gap of 2.0–2.5 eV.

The synthesis of the title compound, [Zn(C4H6N2)6](NO3)2, is described. This complex consists of a central zinc metal ion surrounded by six 1-methyl­imidazole ligands, charge balanced by two nitrate anions. The complex crystallizes in the space group Poverline{3}. In the crystal, the nitrate ions are situated within the cavities created by the [Zn(N-Melm)6]2+ cations, serving as counter-ions. The three oxygen atoms of the nitrate ion engage in weak C—H⋯O inter­actions. In addition to single-crystal X-ray diffraction analysis, the complex was characterized using elemental analysis, 1H NMR, 13C NMR, and FTIR spectroscopy.

A new pyridine-fused seleno­diazo­lium salt, 3-(phenyl­selan­yl)[1,2,4]selena­diazolo[4,5-a]pyridin-4-ylium chloride di­chloro­methane 0.352-solvate, C12H9N2Se2+·Cl−·0.352CH2Cl2, was obtained from the reaction between 2-pyridyl­selenenyl chloride and phenyl­seleno­cyanate. Single-crystal structural analysis revealed the presence of C—H⋯N, C—H⋯Cl−, C—H⋯Se hydrogen bonds as well as chalcogen–chalcogen (Se⋯Se) and chalcogen–halogen (Se⋯Cl−) inter­actions. Non-covalent inter­actions were explored by DFT calculations followed by topological analysis of the electron density distribution (QTAIM analysis). The structure consists of pairs of seleno­diazo­lium moieties arranged in a head-to-tail fashion surrounding disordered di­chloro­methane mol­ecules. The assemblies are connected by C—H⋯Cl− and C—H⋯N hydrogen bonds, forming layers, which stack along the c-axis direction connected by bifurcated Se⋯Cl−⋯H—C inter­actions.

When reacted in dry, degassed toluene, [Ir(COD)Cl]2 (COD = cyclo­octa-1,5-diene) and 2 equivalents of 2-(di-tert-butyl­phosphinito)anthra­quinone (tBuPOAQH) were found to form a unique tri-iridium compound consisting of one monoanionic dinuclear tri-μ-chlorido complex bearing one bidentate tBuPOAQ ligand per iridium, which was charge-balanced by an outer sphere [Ir(toluene)(COD)]+ ion, the structure of which has not previously been reported. This product, which is a toluene solvate, namely, (η2:η2-cyclo­octa-1,5-diene)(η6-toluene)­iridium(I) tri-μ-chlorido-bis­({3-[(di-tert-butyl­phosphan­yl)­oxy]-9,10-dioxoanthracen-2-yl}hydridoiridium(III)) toluene monosolvate, [Ir(C7H8)(C8H12)][Ir2H2(C22H24O3P)2Cl3]·C7H8 or [Ir(toluene)(COD)][Ir(κ-P,C-tBuPOAQ)(H)]2(μ-Cl)3]·toluene, formed as small orange platelets at room temperature, crystallizing in the triclinic space group Poverline{1}. The cation and anion are linked via weak C—H⋯O inter­actions. The stronger inter­molecular attractions are likely the offset parallel π–π inter­actions, which occur between the toluene ligands of pairs of inverted cations and between pairs of inverted anthra­quinone moieties, the latter of which are capped by toluene solvate mol­ecules, making for π-stacks of four mol­ecules each. The related ligand, 2-(di-tert-butyl­phosphinometh­yl)-anthra­quinone (tBuPCAQH), did not form crystals suitable for X-ray diffraction under analogous reaction conditions. However, when the reaction was conducted in chloro­form, yellow needles readily formed following addition of 1 atm of carbon monoxide. Diffraction studies revealed a neutral, dinuclear, di-μ-chlorido complex, di-μ-chlorido-bis­(carbon­yl{3-[(di-tert-butyl­phosphan­yl)­oxy]-9,10-dioxoanthracen-2-yl}hydridoiridium(I)), [Ir2H2(C23H26O2P)2Cl2(CO)2] or [Ir(κ-P,C-tBuPCAQ)(H)(CO)(μ-Cl)]2, Ir2C48H54Cl2O6P2, again crystallizing in space group Poverline{1}. Offset parallel π–π inter­actions between anthra­quinone groups of adjacent mol­ecules link the mol­ecules in one dimension.

Reaction of 4-methyl­pyridine N-oxide and Co(NCS)2 in ethanol as solvent accidentally leads to the formation of single crystals of Co(NCS)2(4-methyl­pyridine N-oxide)(ethanol) or [Co(NCS)2(C6H7NO)(C2H6O)]n. The asymmetric unit of the title compound consists of one CoII cation, two crystallographically independent thio­cyanate anions, one 4-methyl­pyridine N-oxide coligand and one ethanol mol­ecule on general positions. The cobalt cations are sixfold coordinated by one terminal and two bridging thio­cyanate anions, two bridging 4-methyl­pyridine N-oxide coligands and one ethanol mol­ecule, with a slightly distorted octa­hedral geometry. The cobalt cations are linked by single μ-1,3(N,S)-bridging thio­cyanate anions into corrugated chains, that are further connected into layers by pairs of μ-1,1(O,O)-bridging 4-methyl­pyridine N-oxide coligands. The layers are parallel to the bc plane and are separated by the methyl groups of the 4-methyl­pyridine N-oxide coligands. Within the layers, intra­layer hydrogen bonding is observed.

The title compound, [Cd(C14H16N3S)Cl] or [CdLCl] (1), where LH = 2-[bis­(pyridin-2-ylmeth­yl)amino]­ethane-1-thiol, was prepared and structurally characterized. The Cd2+ complex crystallizes in P21/c with a distorted trigonal–bipyramidal metal coordination geometry. Supra­molecular inter­actions in 1 include parallel offset face-to-face inter­actions between inversion-related pyridyl rings and potential hydrogen bonds with chlorine or sulfur as the acceptor. Additional cooperative pyrid­yl–pyridyl inter­actions with roughly 45° tilt angles and centroid–centroid distances of less than 5.5 Å likely also contribute to the overall solid-state stability. Hirshfeld surface analysis indicates that H⋯H (51.2%), Cl⋯H/H⋯Cl (13.9%), C⋯H/H⋯C (12.3%) and S⋯H/H⋯S (11.8%) inter­actions are dominant in the solid state.

The title mol­ecule, C25H23BrN2O2, adopts a cup shaped conformation with the distinctly ruffled imidazolidine ring as the base. In the crystal, weak C—H⋯O hydrogen bonds and C—H⋯π(ring) inter­actions form helical chains of mol­ecules extending along the b-axis direction that are linked by additional weak C—H⋯π(ring) inter­actions across inversion centres. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (51.0%), C⋯H/H⋯C (21.3%), Br⋯H/H⋯Br (12.8%) and O⋯H/H⋯O (12.4%) inter­actions. The volume of the crystal voids and the percentage of free space were calculated to be 251.24 Å3 and 11.71%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy.

A host–guest supra­molecular inclusion complex was obtained from the co-crystallization of A1/A2-bromo­but­oxy-hy­droxy difunctionalized pillar[5]arene (PilButBrOH) with adipo­nitrile (ADN), C47H53.18Br0.82O10·C6H8N2. The adipo­nitrile guest is stabilized within the electron-rich cavity of the pillar[5]arene host via multiple C—H⋯O and C—H⋯π inter­actions. Both functional groups on the macrocyclic rim are engaged in supra­molecular inter­actions with an adjacent inclusion complex via hydrogen-bonding (O—H⋯N or C—H⋯Br) inter­actions, resulting in the formation of a supra­molecular dimer in the crystal structure.

The reaction of Zn(ClO4)2·6H2O with Na3SbS4·9H2O in a water/aceto­nitrile mixture leads to the formation of the title compound, (μ-tetra­thio­anti­monato-κ2S:S')bis­[(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4N)zinc(II)] perchlorate 0.8-hydrate, [Zn2(SbS4)(C10H24N4)2]ClO4·0.8H2O or [(Zn-cyclam)2(SbS4)]+[ClO4]−·0.8H2O. The asymmetric unit consists of two crystallographically independent [SbS4]3– anions, two independent perchlorate anions and two independent water mol­ecules as well as four crystallographically independent Zn(cyclam)2+ cations that are located in general positions. Both perchlorate anions and one cyclam ligand are disordered and were refined with a split mode using restraints. The water mol­ecules are partially occupied. Two Zn(cyclam)2+ cations are linked via the [SbS4]3– anions into [Zn2(cyclam)2SbS4]+ cations that are charged-balanced by the [ClO4]− anions. The water mol­ecules of crystallization are hydrogen bonded to the [SbS4]3– anions. The cations, anions and water mol­ecules are linked by N—H⋯O, N—H⋯S and O—H⋯S hydrogen bonds into a three-dimensional network. Powder X-ray diffraction proves that a pure sample had been obtained that was additionally investigated for its spectroscopic properties.

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.

The title compound, catena-poly[[tri­aqua­sodium]-di-μ-aqua-[tri­aqua­sodium]-μ-(ethane-1,2-di­yl)bis­[(3-meth­oxy­prop­yl)phosphinodi­thiol­ato]], [Na2(C10H22O2P2S4)(H2O)8]n, crystallizes in the triclinic space group P1. The dianionic [CH3O(CH2)3P(=S)(S—)CH2CH2P(=S)(S—)(CH2)3OCH3]2− ligand fragments are joined by a dicationic [Na2(H2O)8]2+ cluster that includes the oxygen of the meth­oxy­propyl unit of the ligand to form infinite chains.

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.

Reaction of 2-amino-5-iodo­pyridine (5IAP) with concentrated HBr at room temperature yielded 2-amino-5-iodo­pyridinium bromide, C5H6IN2+·Br− or (5IAPH)Br. The complex formed pale-yellow crystals, which exhibit significant hydrogen bonding between the amino and pyridinium N—H donors and bromide ion acceptors. Halogen bonding is also observed. Similarly, reaction of 5IAP with cobalt(II) chloride in mixed HCl/HBr in 1-propanol yielded 2-amino-5-iodo­pyridinium (2-amino-5-iodo­pyridine-κN1)bromido/chlorido­(0.51/2.48)cobalt(II), (C5H6IN2)[CoBr0.51Cl2.48(C5H5IN2)] or (5-IAPH)[(5IAP)CoCl2.48Br0.51], as blue block-shaped crystals. Two of the three halide positions exhibit mixed occupancy [Cl/Br = 0.797 (5):0.203 (5) and 0.689 (6):0.311 (6)], while the third position is occupied solely by a chloride ion. Extensive hydrogen and halogen bonding is observed.

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.

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.

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.

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.

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.

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.

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.