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 title complex, (1,4,7,10,13,16-hexa­oxa­cyclo­octa­decane-1κ6O)(μ-oxalato-1κ2O1,O2:2κ2O1',O2')triphenyl-2κ3C-potassium(I)tin(IV), [KSn(C6H5)3(C2O4)(C12H24O6)] or K[18-Crown-6][(C6H5)3SnO4C2], was synthesized. The complex consists of a potassium cation coordinated to the six oxygen atoms of a crown ether mol­ecule and the two oxygen atoms of the oxalatotri­phenyl­stannate anion. It crystallizes in the monoclinic crystal system within the space group P21. The tin atom is coordinated by one chelating oxalate ligand and three phenyl groups, forming a cis-trigonal–bipyramidal geometry around the tin atom. The cations and anions form ion pairs, linked through carbonyl coordination to the potassium atoms. The crystal structure features C—H⋯O hydrogen bonds between the oxygen atoms of the oxalate group and the hydrogen atoms of the phenyl groups, resulting in an infinite chain structure extending along a-axis direction. The primary inter-chain inter­actions are van der Waals forces.

Crystallization of 5-nona­noyl-8-hy­droxy­quinoline in the presence of InCl3 in aceto­nitrile yields a dinuclear InIII complex crystallizing in the space group Poverline{1}. In this complex, [In2(C18H22NO2)2Cl4(H2O)2], each indium ion is sixfold coordinated by two chloride ions, one water mol­ecule and two 8-quinolino­late ions. The crystal of the title complex is composed of two-dimensional supra­molecular aggregates, resulting from the linkage of the Owater—H⋯O=C and Owater—H⋯Cl hydrogen bonds as well as bifurcated Carene—H⋯Cl contacts.

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.

The mol­ecule of the title compound, [Ni(C5H7O2)2(C8H9N3)(H2O)]·C2H5OH, has triclinic (Poverline{1}) symmetry. This compound is of inter­est for its anti­microbial properties. The asymmetric unit comprises two independent complex mol­ecules, which are linked by N—H⋯O and O—H⋯O hydrogen bonds along [111]. Hirshfeld surface analysis indicates that 71.7% of inter­mol­ecular inter­actions come from H⋯H contacts, 17.7% from C⋯H/H⋯C contacts and 7.6% from O⋯H/H⋯O contacts, with the remaining contribution coming from N⋯H/H⋯N, C⋯N/N⋯C, C⋯C and O⋯O contacts.

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 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.

The crystal structure of the title compound, [Ni(C8H20N4)(NO3)]NO3, at room temperature, has monoclinic (P21/n) symmetry. The structure displays inter­molecular hydrogen bonding. The nickel displays a distorted bipyramidal geometry with the symmetric bidentate bonded nitrate occupying an equatorial site. The 1,4,7,10-tetra­aza­cyclo­dodecane (cyclen) backbone has the [4,8] configuration, with three nitro­gen-bound H atoms directed above the plane of the nitro­gen atoms towards the offset nickel atom with the fourth nitro­gen-bound hydrogen directed below from the plane of the nitro­gen atoms. The nitrate anion O atoms are seen to hydrogen bond to the H atoms bound to the N atoms of the ligand.

The structures of the title compounds 2-hy­droxy-N'-methyl­acetohydrazide, 1, and 2-hy­droxy-N-methyl­acetohydrazide, 2, both C3H8N2O2, as regioisomers differ in the position of the methyl group relative to the N atoms in 2-hy­droxy-acetohydrazide. In the structure of 1, the 2-hy­droxy-acetohydrazide core [OH—C—C(=O)—NH—NH] is almost planar and the methyl group is rotated relative to this plane. As opposed to 1, in the structure of 2 all non-hydrogen atoms lie in the same plane. The hydroxyl and carbonyl groups in structures 1 and 2 are in trans and cis positions, respectively. The methyl amino group and carbonyl group are in the cis position relative to the C—N bond in structure 1, while the amino group and carbonyl group are in the trans position relative to the C—N bond in stucture 2. In the crystal, mol­ecules of 1 are linked by N—H⋯O and O—H⋯N inter­molecular hydrogen bonds, forming layers parallel to the ab crystallographic plane. A Hirshfeld surface analysis showed that the H⋯H contacts dominate the crystal packing with a contribution of 55.3%. The contribution of the H⋯O/O⋯H inter­action is somewhat smaller, amounting to 30.8%. In the crystal, as a result of the inter­molecular O—H⋯O hydrogen bonds, mol­ecules of 2 form dimers, which are linked by N—H⋯O hydrogen bonds and a three-dimensional supra­molecular network The major contributors to the Hirshfeld surface are H⋯H (58.5%) and H⋯O/O⋯H contacts (31.7%).

The title compound, [Zn2(C22H18ClN4O)Cl3], is a dinuclear zinc(II) complex with three chlorido ligands and one penta­dentate ligand containing quinolin-8-olato and bis­(pyridin-2-ylmeth­yl)amine groups. One of the two ZnII atom adopts a tetra­hedral geometry and coordinates two chlorido ligands with chelate coord­ination of the N and O atoms of the quinolin-8-olato group in the ligand. The other ZnII atom adopts a distorted trigonal–bipyramidal geometry, and coordinates one chlorido-O atom of the quinolin-8-olato group and three N atoms of the bis­(pyridin-2-ylmeth­yl)amine unit. In the crystal, two mol­ecules are associated through a pair of inter­molecular C—H⋯Cl hydrogen bonds, forming a dimer with an R22(12) ring motif. Another inter­molecular C—H⋯Cl hydrogen bond forms a spiral C(8) chain running parallel to the [010] direction. The dimers are linked by these two inter­molecular C—H⋯Cl hydrogen bonds, generating a ribbon sheet structure in ac plane. Two other inter­molecular C—H⋯Cl hydrogen bonds form a C(7) chain along the c-axis direction and another C(7) chain generated by a d-glide plane. The mol­ecules are cross-linked through the four inter­molecular C—H⋯Cl hydrogen bonds to form a three-dimensional network.

The asymmetric unit of the title compound, [Co(C8Br4O4)(C3H4N2)2(H2O)2]n or [Co(Br4bdc)(im)2(H2O)2]n, comprises half of CoII ion, tetra­bromo­benzene­dicarboxylate (Br4bdc2−), imidazole (im) and a water mol­ecule. The CoII ion exhibits a six-coordinated octa­hedral geometry with two oxygen atoms of the Br4bdc2− ligand, two oxygen atoms of the water mol­ecules, and two nitro­gen atoms of the im ligands. The carboxyl­ate group is nearly perpendicular to the benzene ring and shows monodentate coordination to the CoII ion. The CoII ions are bridged by the Br4bdc2− ligand, forming a one-dimensional chain. The carboxyl­ate group acts as an inter­molecular hydrogen-bond acceptor toward the im ligand and a coordinated water mol­ecule. The chains are connected by inter­chain N—H⋯O(carboxyl­ate) and O—H(water)⋯O(carboxyl­ate) hydrogen-bonding inter­actions and are not arranged in parallel but cross each other via inter­chain hydrogen bonding and π–π inter­actions, yielding a three-dimensional network.

Crystal growth of 2-(3,4,5-triphen­ylphen­yl)acetic acid (1) from aceto­nitrile yields a monosolvate, C26H20O2·CH3CN, of the space group P1. In the crystal, the title mol­ecule adopts a conformation in which the three phenyl rings are arranged in a paddlewheel-like fashion around the central arene ring and the carboxyl residue is oriented nearly perpendicular to the plane of this benzene ring. Inversion-symmetric dimers of O—H⋯O-bonded mol­ecules of 1 represent the basic supra­molecular entities of the crystal structure. These dimeric mol­ecular units are further linked by C—H⋯O=C bonds to form one-dimensional supra­molecular aggregates running along the crystallographic [111] direction. Weak Car­yl—H⋯N inter­actions occur between the mol­ecules of 1 and aceto­nitrile.

Lopinavir is a potent protease inhibitor that is used as a first-line pharmaceutical drug for the treatment of HIV. The multi-component solvated Lopinavir crystal, systematic name (2S)-N-[(2S,4S,5S)-5-[2-(2,6-di­methyl­phen­oxy)acetamido]-4-hy­droxy-1,6-di­phenyl­hexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide–ethane-1,2-diol–water (8/3/7) 8C37H48N4O5·3C2H6O2·7H2O, was prepared using evaporative methods. The crystalline material obtained from this experimental synthesis was characterized and elucidated by single-crystal X-ray diffraction (SC-XRD). The crystal structure is unusual in that the unit cell contains 18 mol­ecules. The stoichiometric ratio of this crystal is eight Lopinavir mol­ecules [8(C37H48N4O5)], three ethane-1,2-diol mol­ecules [3(C2H6O2)] and seven water mol­ecules [7(H2O)]. The crystal packing features both bi- and trifurcated hydrogen bonds between atoms.

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

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.

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

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

A general formalism is presented for the isotropically averaged single-chain scattering function (form factor) of single, double, triple and higher-order helices, as well as twisted fibres consisting of concentric layers of strands. Form factors for double and triple helices with differently sized grooves have also been derived. The formulas include the longitudinal and transverse interference over the pitch and radius of the helices, respectively. The results may be useful for the analysis of small-angle scattering data of (bio)macromolecules or molecular assemblies exhibiting a helical arrangement.

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.

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

Recently, we introduced the liquid application method for time-resolved analyses (LAMA). The time-consuming cleaning cycles required for the substrate solution exchange and storage of the sensitive droplet-dispenser nozzles present practical challenges. In this work, a dispenser cleaning system for the semi-automated cleaning of the piezo-actuator-driven picolitre-droplet dispensers required for LAMA is introduced to streamline typical workflows.

Van Vleck modes describe all possible displacements of octahedrally coordinated ligands about a core atom. They are a useful analytical tool for analysing the distortion of octahedra, particularly for first-order Jahn–Teller distortions, but determination of the Van Vleck modes of an octahedron is complicated by the presence of angular distortion of the octahedron. This problem is most commonly resolved by calculating the bond distortion modes (Q2, Q3) along the bond axes of the octahedron, disregarding the angular distortion and losing information on the octahedral shear modes (Q4, Q5 and Q6) in the process. In this paper, the validity of assuming bond lengths to be orthogonal in order to calculate the Van Vleck modes is discussed, and a method is described for calculating Van Vleck modes without disregarding the angular distortion. A Python package for doing this, VanVleckCalculator, is introduced and some examples of its use are given. Finally, it is shown that octahedral shear and angular distortion are often, but not always, correlated, and a parameter η is proposed as the shear fraction. It is demonstrated that η can be used to predict whether the values will be correlated when varying a tuning parameter such as temperature or pressure.

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.

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.

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

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

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

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.

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.

Processing of single-crystal X-ray diffraction data from area detectors can be separated into two steps. First, raw intensities are obtained by integration of the diffraction images, and then data correction and reduction are performed to determine structure-factor amplitudes and their uncertainties. The second step considers the diffraction geometry, sample illumination, decay, absorption and other effects. While absorption is only a minor effect in standard macromolecular crystallography (MX), it can become the largest source of uncertainty for experiments performed at long wavelengths. Current software packages for MX typically employ empirical models to correct for the effects of absorption, with the corrections determined through the procedure of minimizing the differences in intensities between symmetry-equivalent reflections; these models are well suited to capturing smoothly varying experimental effects. However, for very long wavelengths, empirical methods become an unreliable approach to model strong absorption effects with high fidelity. This problem is particularly acute when data multiplicity is low. This paper presents an analytical absorption correction strategy (implemented in new software AnACor) based on a volumetric model of the sample derived from X-ray tomography. Individual path lengths through the different sample materials for all reflections are determined by a ray-tracing method. Several approaches for absorption corrections (spherical harmonics correction, analytical absorption correction and a combination of the two) are compared for two samples, the membrane protein OmpK36 GD, measured at a wavelength of λ = 3.54 Å, and chlorite dismutase, measured at λ = 4.13 Å. Data set statistics, the peak heights in the anomalous difference Fourier maps and the success of experimental phasing are used to compare the results from the different absorption correction approaches. The strategies using the new analytical absorption correction are shown to be superior to the standard spherical harmonics corrections. While the improvements are modest in the 3.54 Å data, the analytical absorption correction outperforms spherical harmonics in the longer-wavelength data (λ = 4.13 Å), which is also reflected in the reduced amount of data being required for successful experimental phasing.

This paper introduces a new 2D representation of the orientation distribution function for an arbitrary material texture. The approach is based on the isometric square torus mapping of the Clifford torus, which allows for points on the unit quaternion hypersphere (each corresponding to a 3D orientation) to be represented in a periodic 2D square map. The combination of three such orthogonal mappings into a single RGB (red–green–blue) image provides a compact periodic representation of any set of orientations. Square torus representations of five different orientation sampling methods are compared and analyzed in terms of the Riesz s energies that quantify the uniformity of the samplings. The effect of crystallographic symmetry on the square torus map is analyzed in terms of the Rodrigues fundamental zones for the rotational symmetry groups. The paper concludes with example representations of important texture components in cubic and hexagonal materials. The new RGB representation provides a convenient and compact way of generating training data for the automated analysis of material textures by means of neural networks.

Scintillator-based ZnS:Ag/6LiF neutron detectors have been under development at ISIS for more than three decades. Continuous research and development aim to improve detector capabilities, achieve better performance and meet the increasingly demanding requirements set by neutron instruments. As part of this program, a high-efficiency 2D position-sensitive scintillator detector with wavelength-shifting fibres has been developed for neutron-diffraction applications. The detector consists of a double scintillator-fibre layer to improve detection efficiency. Each layer is made up of two orthogonal fibre planes placed between two ZnS:Ag/6LiF scintillator screens. Thin reflective foils are attached to the front and back scintillators of each layer to minimize light cross-talk between layers. The detector has an active area of 192 × 192 mm with a square pixel size of 3 × 3 mm. As part of the development process of the double-layer detector, a single-layer detector was built, together with a prototype detector in which the two layers of the detector could be read out separately. Efficiency calculations and measurements of all three detectors are discussed. The novel double-layer detector has been installed and tested on the SXD diffractometer at ISIS. The detector performance is compared with the current scintillator detectors employed on SXD by studying reference crystal samples. More than a factor of 3 improvement in efficiency is achieved with the double-layer wavelength-shifting-fibre detector. Software routines for further optimizations in spatial resolution and uniformity of response have been implemented and tested for 2D detectors. The methods and results are discussed in this manuscript.

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages (Dozor and DIALS), demonstrating that this is an appropriate framework to support future extensions and improvements.

Polymer-derived ceramics (PDCs) remain at the forefront of research for a variety of applications including ultra-high-temperature ceramics, energy storage and functional coatings. Despite their wide use, questions remain about the complex structural transition from polymer to ceramic and how local structure influences the final microstructure and resulting properties. This is further complicated when nanofillers are introduced to tailor structural and functional properties, as nanoparticle surfaces can interact with the matrix and influence the resulting structure. The inclusion of crystalline nanofiller produces a mixed crystalline–amorphous composite, which poses characterization challenges. With this study, we aim to address these challenges with a local-scale structural study that probes changes in a polysiloxane matrix with incorporated copper nanofiller. Composites were processed at three unique temperatures to capture mixing, pyrolysis and initial crystallization stages for the pre-ceramic polymer. We observed the evolution of the nanofiller with electron microscopy and applied synchrotron X-ray diffraction with differential pair distribution function (d-PDF) analysis to monitor changes in the matrix's local structure and interactions with the nanofiller. The application of the d-PDF to PDC materials is novel and informs future studies to understand interfacial interactions between nanofiller and matrix throughout PDC processing.

Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (i.e. their orientation determined), integrated and merged. Introduced here is TORO (Torch-powered robust optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In tests, TORO outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like DIALS real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). Acta Cryst. D70, 2652–2666] and XGandalf [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). Acta Cryst. A75, 694–704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, TORO consistently matches, and in certain instances outperforms, established algorithms such as XGandalf and MOSFLM [Powell (1999). Acta Cryst. D55, 1690–1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of TORO and the versatility of PyTorch code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX.

It is demonstrated that high-resolution energy-dispersive X-ray fluorescence mapping devices based on a micro-focused beam are not restricted to high-speed analyses of element distributions or to the detection of different grains, twins and subgrains in crystalline materials but can also be used for the detection of dislocations in high-quality single crystals. Si single crystals with low dislocation densities were selected as model materials to visualize the position of dis­locations by the spatially resolved measurement of Bragg-peak intensity fluctuations. These originate from the most distorted planes caused by the stress fields of dislocations. The results obtained by this approach are compared with laboratory-based Lang X-ray topographs. The presented methodology yields comparable results and it is of particular interest in the field of crystal growth, where fast chemical and microstructural characterization feedback loops are indispensable for short and efficient development times. The beam divergence was reduced via an aperture management system to facilitate the visualization of dislocations for virtually as-grown, non-polished and non-planar samples with a very pronounced surface profile.

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

A deep-learning algorithm is proposed for the inpainting of Bragg coherent diffraction imaging (BCDI) patterns affected by detector gaps. These regions of missing intensity can compromise the accuracy of reconstruction algorithms, inducing artefacts in the final result. It is thus desirable to restore the intensity in these regions in order to ensure more reliable reconstructions. The key aspect of the method lies in the choice of training the neural network with cropped sections of diffraction data and subsequently patching the predictions generated by the model along the gap, thus completing the full diffraction peak. This approach enables access to a greater amount of experimental data for training and offers the ability to average overlapping sections during patching. As a result, it produces robust and dependable predictions for experimental data arrays of any size. It is shown that the method is able to remove gap-induced artefacts on the reconstructed objects for both simulated and experimental data, which becomes essential in the case of high-resolution BCDI experiments.

Using the well known Rn ratio method, a protocol has been elaborated for determining the lattice direction for the 15 most common cubic zone axis spot patterns. The method makes use of the lengths of the three shortest reciprocal-lattice vectors in each pattern and the angles between them. No prior pattern calibration is required for the method to work, as the Rn ratio method is based entirely on geometric relationships. In the first step the pattern is assigned to one of three possible pattern types according to the angles that are measured between the three reciprocal-lattice vectors. The lattice direction [uvw] and possible Bravais type(s) and Laue indices of the corresponding reflections can then be determined by using lookup tables. In addition to determining the lattice direction, this simple geometric analysis allows one to distinguish between the P, I and F Bravais lattices for spot patterns aligned along [013], [112], [114] and [233]. Moreover, the F lattice can always be uniquely identified from the [011] and [123] patterns.

Neutron diffraction beamlines have traditionally relied on deploying large detector arrays of 3He tubes or neutron-sensitive scintillators coupled with photomultipliers to efficiently probe crystallographic and microstructure information of a given material. Given the large upfront cost of custom-made data acquisition systems and the recent scarcity of 3He, new diffraction beamlines or upgrades to existing ones demand innovative approaches. This paper introduces a novel Timepix3-based event-mode imaging neutron diffraction detector system as well as first results of a silicon powder diffraction measurement made at the HIPPO neutron powder diffractometer at the Los Alamos Neutron Science Center. Notably, these initial measurements were conducted simultaneously with the 3He array on HIPPO, enabling direct comparison. Data reduction for this type of data was implemented in the MAUD code, enabling Rietveld analysis. Results from the Timepix3-based setup and HIPPO were benchmarked against McStas simulations, showing good agreement for peak resolution. With further development, systems such as the one presented here may substantially reduce the cost of detector systems for new neutron instrumentation as well as for upgrades of existing beamlines.

Portland cements (PCs) and cement blends are multiphase materials of different fineness, and quantitatively analysing their hydration pathways is very challenging. The dissolution (hydration) of the initial crystalline and amorphous phases must be determined, as well as the formation of labile (such as ettringite), reactive (such as portlandite) and amorphous (such as calcium silicate hydrate gel) components. The microstructural changes with hydration time must also be mapped out. To address this robustly and accurately, an innovative approach is being developed based on in situ measurements of pastes without any sample conditioning. Data are sequentially acquired by Mo Kα1 laboratory X-ray powder diffraction (LXRPD) and microtomography (µCT), where the same volume is scanned with time to reduce variability. Wide capillaries (2 mm in diameter) are key to avoid artefacts, e.g. self-desiccation, and to have excellent particle averaging. This methodology is tested in three cement paste samples: (i) a commercial PC 52.5 R, (ii) a blend of 80 wt% of this PC and 20 wt% quartz, to simulate an addition of supplementary cementitious materials, and (iii) a blend of 80 wt% PC and 20 wt% limestone, to simulate a limestone Portland cement. LXRPD data are acquired at 3 h and 1, 3, 7 and 28 days, and µCT data are collected at 12 h and 1, 3, 7 and 28 days. Later age data can also be easily acquired. In this methodology, the amounts of the crystalline phases are directly obtained from Rietveld analysis and the amorphous phase contents are obtained from mass-balance calculations. From the µCT study, and within the attained spatial resolution, three components (porosity, hydrated products and unhydrated cement particles) are determined. The analyses quantitatively demonstrate the filler effect of quartz and limestone in the hydration of alite and the calcium aluminate phases. Further hydration details are discussed.

Small-angle X-ray tensor tomography and the related wide-angle X-ray tensor tomography are X-ray imaging techniques that tomographically reconstruct the anisotropic scattering density of extended samples. In previous studies, these methods have been used to image samples where the scattering density depends slowly on the direction of scattering, typically modeling the directionality, i.e. the texture, with a spherical harmonics expansion up until order ℓ = 8 or lower. This study investigates the performance of several established algorithms from small-angle X-ray tensor tomography on samples with a faster variation as a function of scattering direction and compares their expected and achieved performance. The various algorithms are tested using wide-angle scattering data from an as-drawn steel wire with known texture to establish the viability of the tensor tomography approach for such samples and to compare the performance of existing algorithms.