al Optimizing crucible geometry to improve the quality of AlN crystals by the physical vapor transport method By journals.iucr.org Published On :: 2024-10-16 In the conventional crucible structure for AlN crystal growth by physical vapor transport, owing to the long molecular transport path of Al vapor and the disruption of the gas flow by the presence of a deflector, the Al vapor easily forms polycrystals in the growth domain. The result is increased internal stress in the crystals and increased difficulty in growing large-sized crystals. On this basis, with the help of finite element simulations, a novel crucible structure is designed. This crucible not only optimizes the gas transport but also increases the radial gradient of the AlN crystal surface, making the enhanced growth rate in the central region more obvious. The thermal stresses between the deflector and the crystal are also reduced. High-quality AlN crystals with an FWHM of 79 arcsec were successfully grown with this structure, verifying the accuracy of finite element simulation of the growth of AlN crystals. Our work has important guiding significance for the growth of high-quality AlN crystals. Full Article text
al Duality of spaces and the origin of integral reflection conditions By journals.iucr.org Published On :: 2024-10-16 The dualism between direct and reciprocal space is at the origin of well known relations between basis vectors in the two spaces. It is shown that when a coordinate system corresponding to a non-primitive unit cell is adopted, this dualism has to be handled with care. In particular, the reciprocal of a non-primitive unit cell is not a unit cell but a region in reciprocal space that does not represent a unit of repetition by translation. The basis vectors do not correspond to reciprocal-space cell lengths, contrary to what is stated even in the core CIF dictionary. The corresponding unit cell is a multiple of this region. The broken correspondence between basis vectors and unit cell is at the origin of the integral reflection conditions. Full Article text
al Sheet-on-sheet fixed target data collection devices for serial crystallography at synchrotron and XFEL sources By journals.iucr.org Published On :: 2024-10-16 Serial crystallography (SX) efficiently distributes over many crystals the radiation dose absorbed during diffraction data acquisition, enabling structure determination of samples at ambient temperature. SX relies on the rapid and reliable replacement of X-ray-exposed crystals with fresh crystals at a rate commensurate with the data acquisition rate. `Solid supports', also known as `fixed targets' or `chips', offer one approach. These are microscopically thin solid panes into or onto which crystals are deposited to be individually interrogated by an X-ray beam. Solid supports are generally patterned using photolithography methods to produce a regular array of features that trap single crystals. A simpler and less expensive alternative is to merely sandwich the microcrystals between two unpatterned X-ray-transparent polymer sheets. Known as sheet-on-sheet (SOS) chips, these offer significantly more versatility. SOS chips place no constraint on the size or size distribution of the microcrystals or their growth conditions. Crystals ranging from true nanocrystals up to microcrystals can be investigated, as can crystals grown in media ranging from low viscosity (aqueous solution) up to high viscosity (such as lipidic cubic phase). Here, we describe our two SOS devices. The first is a compact and lightweight version designed specifically for synchrotron use. It incorporates a standard SPINE-type magnetic base for mounting on a conventional macromolecular crystallography goniometer. The second and larger chip is intended for both X-ray free-electron laser and synchrotron use and is fully compatible with the fast-scanning XY-raster stages developed for data collection with patterned chips. Full Article text
al Multi-scale and time-resolved structure analysis of relaxor ferroelectric crystals under an electric field By journals.iucr.org Published On :: 2024-10-29 Lead-based relaxor ferroelectrics exhibit giant piezoelectric properties owing to their heterogeneous structures. The average and local structures measured by single-crystal X-ray diffraction under DC and AC electric fields are reviewed in this article. The position-dependent local lattice strain and the distribution of polar nanodomains and nanoregions show strong electric field dependence, which contributes to the giant piezoelectric properties. Full Article text
al Periodic diffraction from an aperiodic monohedral tiling – the Spectre tiling. Addendum By journals.iucr.org Published On :: 2024-10-08 This article describes the diffraction pattern (2-periodic Fourier transform) from the vertices of a large patch of the recently discovered `Spectre' tiling – a strictly chiral aperiodic monotile. It was reported recently that the diffraction pattern of the related weakly chiral aperiodic `Hat' monotile was 2-periodic with chiral plane-group symmetry p6 [Kaplan et al. (2024). Acta Cryst. A80, 72–78]. The diffraction periodicity arises because the Hat tiling is a systematic aperiodic deletion of vertices from the 2-periodic hexagonal mta tiling. Despite the similarity of the Hat and Spectre tilings, the Spectre tiling is not aligned with a 2-periodic lattice, and its diffraction pattern is non-periodic with chiral point symmetry 6 about the origin. Full Article text
al Structure of face-centred icosahedral quasicrystals with cluster close packing By journals.iucr.org Published On :: 2024-09-30 A 6D structure model for face-centred icosahedral quasicrystals consisting of so-called pseudo-Mackay and mini-Bergman-type atomic clusters is proposed based on the structure model of the Al69.1Pd22Cr2.1Fe6.8 3/2 cubic approximant crystal (with space group Pa3, a = 40.5 Å) [Fujita et al. (2013). Acta Cryst. A69, 322–340]. The cluster centres form an icosahedral close sphere packing generated by the occupation domains similar to those in the model proposed by Katz & Gratias [J. Non-Cryst. Solids (1993), 153–154, 187–195], but their size is smaller by a factor τ2 [τ = (1 + (5)1/2)/2]. The clusters cover approximately 99.46% of the atomic structure, and the cluster arrangement exhibits 15 and 19 different local configurations, respectively, for the pseudo-Mackay and mini-Bergman-type clusters. The occupation domains that generate cluster shells are modelled and discussed in terms of structural disorder and local reorganization of the cluster arrangements (phason flip). Full Article text
al An alternative method to the Takagi–Taupin equations for studying dark-field X-ray microscopy of deformed crystals By journals.iucr.org Published On :: 2024-09-26 This study introduces an alternative method to the Takagi–Taupin equations for investigating the dark-field X-ray microscopy (DFXM) of deformed crystals. In scenarios where dynamical diffraction cannot be disregarded, it is essential to assess the potential inaccuracies of data interpretation based on the kinematic diffraction theory. Unlike the Takagi–Taupin equations, this new method utilizes an exact dispersion relation, and a previously developed finite difference scheme with minor modifications is used for the numerical implementation. The numerical implementation has been validated by calculating the diffraction of a diamond crystal with three components, wherein dynamical diffraction is applicable to the first component and kinematic diffraction pertains to the remaining two. The numerical convergence is tested using diffraction intensities. In addition, the DFXM image of a diamond crystal containing a stacking fault is calculated using the new method and compared with the experimental result. The new method is also applied to calculate the DFXM image of a twisted diamond crystal, which clearly shows a result different from those obtained using the Takagi–Taupin equations. Full Article text
al Influence of device configuration and noise on a machine learning predictor for the selection of nanoparticle small-angle X-ray scattering models By journals.iucr.org Published On :: 2024-09-23 Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202–212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality. Full Article text
al Symmetries and symmetry-generated averages of elastic constants up to the sixth order of nonlinearity for all crystal classes, isotropy and transverse isotropy By journals.iucr.org Published On :: 2024-10-15 Algebraic expressions for averaging linear and nonlinear stiffness tensors from general anisotropy to different effective symmetries (11 Laue classes elastically representing all 32 crystal classes, and two non-crystalline symmetries: isotropic and cylindrical) have been derived by automatic symbolic computations of the arithmetic mean over the set of rotational transforms determining a given symmetry. This approach generalizes the Voigt average to nonlinear constants and desired approximate symmetries other than isotropic, which can be useful for a description of textured polycrystals and rocks preserving some symmetry aspects. Low-symmetry averages have been used to derive averages of higher symmetry to speed up computations. Relationships between the elastic constants of each symmetry have been deduced from their corresponding averages by resolving the rank-deficient system of linear equations. Isotropy has also been considered in terms of generalized Lamé constants. The results are published in the form of appendices in the supporting information for this article and have been deposited in the Mendeley database. Full Article text
al Crystal structures of two polymorphs for fac-bromidotricarbonyl[4-(4-methoxyphenyl)-2-(pyridin-2-yl)thiazole-κ2N,N']rhenium(I) By journals.iucr.org Published On :: 2024-11-08 Crystallization of the title compound, fac-[ReBr(ppt-OMe)(CO)3] (ppt-OMe = C15H12N2OS), from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and orthorhombic (Pna21; β form) space groups. The ReI complex molecules in either polymorph adopt a six-coordinate octahedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitrogen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds. In polymorph α, two types of hydrogen bonds (C—H...O) are found while, in polymorph β, four types of hydrogen bonds (C—H...O and C—H...Br) exist. Full Article text
al Crystal structure of AlPCl8 By journals.iucr.org Published On :: 2024-11-08 The crystal structure of aluminium phosphorus chloride (systematic name: phosphorus tetrachloride tetrachloridoaluminate), (PCl4)[AlCl4] or AlPCl8, was determined and refined using single-crystal X-ray diffraction data. The compound crystallizes in the orthorhombic space group Pbcm. The asymmetric unit comprises one Al atom, one P atom, and five Cl atoms. The structure is characterized by isolated AlCl4 and PCl4 tetrahedra, isostructural with FePCl8 and GaPCl8. Full Article text
al Crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies of ethyl 5-amino-2-bromoisonicotinate By journals.iucr.org Published On :: 2024-11-08 In the title compound, C8H9BrN2O2, the C—O—C—C torsion angle between isonicotine and the ethyl group is 180.0 (2)°. Intramolecular N—H...O and C—H...O interactions consolidate the molecular structure. In the crystal, N—H...N interaction form S(5) zigzag chains along [010]. The most significant contributions to the Hirshfeld surface arise from H...H (33.2%), Br...H/H...Br (20.9%), O...H/H...O (11.2%), C...H/H...C (11.1%) and N...H/H...N (10%) contacts. The topology of the three-dimensional energy frameworks was generated using the B3LYP/6–31 G(d,p) model to calculate the total interaction energy. The net interaction energies for the title compound are Eele = 59.2 kJ mol−1, Epol = 15.5 kJ mol−1, Edis = 140.3 kJ mol−1 and Erep = 107.2 kJ mol−1 with a total interaction energy Etot of 128.8 kJ mol−1. The molecular structure was optimized by density functional theory (DFT) at the B3LYP/6–311+G(d,p) level and the theoretical and experimentally obtained parameters were compared. The frontier molecular orbitals HOMO and LUMO were generated, giving an energy gap ΔE of 4.0931 eV. The MEP was generated to identify active sites in the molecule and molecular docking studies carried out with the title compound (ligand) and the covid-19 main protease PDB ID: 6LU7, revealing a moderate binding affinity of −5.4 kcal mol−1. Full Article text
al Crystal structure and Hirshfeld-surface analysis of an etoxazole metabolite designated R13 By journals.iucr.org Published On :: 2024-11-08 The etoxazole metabolite R13, systematic name 4-(4-tert-butyl-2-ethoxyphenyl)-2-(2,6-difluorophenyl)oxazole (C21H21F2NO2), results from the oxidation of etoxazole, a chitin synthesis inhibitor belonging to the oxazoline class, widely used as an insecticide/acaricide since 1998. The structure of R13 features a central oxazole ring with attached 2,6-difluorophenyl and 4-t-butyl-2-ethoxyphenyl moieties. The overall conformation gives dihedral angles between these rings and the oxazole of 24.91 (5)° (with difluorophenyl) and 15.30 (6)° (with t-butyl-ethoxyphenyl), indicating an overall deviation from planarity. Additionally, torsion angles of the ethoxy and t-butyl groups define the orientation of these substituents relative to their benzene ring. In the crystal packing, no significant hydrogen bonds are present, but a Hirshfeld surface analysis highlights weak intermolecular contacts leading to π–π-stacked dimers linked by weak C—H...N contacts. The packing analysis confirms that most intermolecular interactions involve hydrogen atoms. Full Article text
al Crystal structure of a solvated dinuclear CuII complex derived from 3,3,3',3'-tetraethyl-1,1'-(furan-2,5-dicarbonyl)bis(thiourea) By journals.iucr.org Published On :: 2024-11-08 Reaction between equimolar amounts of 3,3,3',3'-tetraethyl-1,1'-(furan-2,5-dicarbonyl)bis(thiourea) (H2L) and CuCl2·2H2O in methanol in the presence of the supporting base Et3N gave rise to a neutral dinuclear complex bis[μ-3,3,3',3'-tetraethyl-1,1'-(furan-2,5-dicarbonyl)bis(thioureato)]dicopper(II) dichloromethane disolvate, [Cu2(C16H22N4O3S2)2]·2CH2Cl2 or [Cu2(L)2]·2CH2Cl2. The aroylbis(thioureas) are doubly deprotonated and the resulting anions {L2–} bond to metal ions through (S,O)-chelating moieties. The copper atoms adopt a virtually cis-square-planar environment. In the crystal, adjacent [Cu2(L)2]·2CH2Cl2 units are linked into polymeric chains along the a-axis direction by intermolecular coordinative Cu...S interactions. The co-crystallized solvent molecules play a vital role in the crystal packing. In particular, weak C—Hfuran...Cl and C—Hethyl...Cl contacts consolidate the three-dimensional supramolecular architecture. Full Article text
al Crystal structures and circular dichroism of {2,2'-[(1S,2S)-1,2-diphenylethane-1,2-diylbis(nitrilophenylmethanylylidene)]diphenolato}nickel(II) and its ethanol solvate By journals.iucr.org Published On :: 2024-11-08 The title compound, [Ni(C40H30N2O2)] (1), with an optically active Schiff base ligand derived from 2-hydroxybenzophenone and (1S,2S)-1,2-diphenylethylenediamine, was crystallized as the solvent-free and ethanol solvate forms (1 and 1·2C2H5OH). In both structures, the two phenyl groups on the stereogenic centers of the O,N,N,O-tetradentate ligand are axially oriented, and the conformation of the central diamine chelate ring is λ. The circular dichroism (CD) spectra of 1 and the analogous nickel(II) complex [Ni(C30H26N2O2)] (2) in solution show partially similar patterns in the 350–450 nm range, but are mirror images in the longer wavelength region (450–650 nm). In the latter region, the sign of CD for these complexes is sensitive to the substituents on the C=N carbon atoms (phenyl for 1 and methyl for 2) rather than the diamine chelate ring conformation. Full Article text
al Similarity score for screening phase-retrieved maps in X-ray diffraction imaging – characterization in reciprocal space By journals.iucr.org Published On :: 2024-01-01 X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed. Full Article text
al Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging By journals.iucr.org Published On :: 2024-01-01 In X-ray diffraction imaging (XDI), electron density maps of a targeted particle are reconstructed computationally from the diffraction pattern alone using phase-retrieval (PR) algorithms. However, the PR calculations sometimes fail to yield realistic electron density maps that approximate the structure of the particle. This occurs due to the absence of structure amplitudes at and near the zero-scattering angle and the presence of Poisson noise in weak diffraction patterns. Consequently, the PR calculation becomes a bottleneck for XDI structure analyses. Here, a protocol to efficiently yield realistic maps is proposed. The protocol is based on the empirical observation that realistic maps tend to yield low similarity scores, as suggested in our prior study [Sekiguchi et al. (2017), J. Synchrotron Rad. 24, 1024–1038]. Among independently and concurrently executed PR calculations, the protocol modifies all maps using the electron-density maps exhibiting low similarity scores. This approach, along with a new protocol for estimating particle shape, improved the probability of obtaining realistic maps for diffraction patterns from various aggregates of colloidal gold particles, as compared with PR calculations performed without the protocol. Consequently, the protocol has the potential to reduce computational costs in PR calculations and enable efficient XDI structure analysis of non-crystalline particles using synchrotron X-rays and X-ray free-electron laser pulses. Full Article text
al Heitt Mjölnir: a heated miniature triaxial apparatus for 4D synchrotron microtomography By journals.iucr.org Published On :: 2024-01-01 Third- and fourth-generation synchrotron light sources with high fluxes and beam energies enable the use of innovative X-ray translucent experimental apparatus. These experimental devices access geologically relevant conditions whilst enabling in situ characterization using the spatial and temporal resolutions accessible at imaging beamlines. Here, Heitt Mjölnir is introduced, a heated miniature triaxial rig based on the design of Mjölnir, but covering a wider temperature range and larger sample volume at similar pressure capacities. This device is designed to investigate coupled thermal, chemical, hydraulic and mechanical processes from grain to centimetre scales using cylindrical samples of 10 mm × 20 mm (diameter × length). Heitt Mjölnir can simultaneously reach confining (hydraulic) pressures of 30 MPa and 500 MPa of axial stress with independently controlled sample pore fluid pressure < 30 MPa. This internally heated apparatus operates to temperatures up to 573 K with a minimal vertical thermal gradient in the sample of <0.3 K mm−1. This new apparatus has been deployed in operando studies at the TOMCAT (Swiss Light Source), I12 JEEP (Diamond Light Source) and PSICHÉ (Synchrotron SOLEIL) beamlines for 4D X-ray microtomography with scan intervals of a few minutes. Heitt Mjölnir is portable and modular, allowing a wide range of 4D characterizations of low-grade metamorphism and deformational processes. It enables spatially and temporally resolved fluid–rock interaction studies at conditions of crustal reservoirs and is suitable for characterization of material properties in geothermal, carbonation or subsurface gas storage applications. Technical drawings and an operation guide are included in this publication. Full Article text
al Angle-resolved X-ray emission spectroscopy facility realized by an innovative spectrometer rotation mechanism at SPring-8 BL07LSU By journals.iucr.org Published On :: 2024-02-01 The X-ray emission spectrometer at SPring-8 BL07LSU has recently been upgraded with advanced modifications that enable the rotation of the spectrometer with respect to the scattering angle. This major upgrade allows the scattering angle to be flexibly changed within the range of 45–135°, which considerably simplifies the measurement of angle-resolved X-ray emission spectroscopy. To accomplish the rotation system, a sophisticated sample chamber and a highly precise spectrometer rotation mechanism have been developed. The sample chamber has a specially designed combination of three rotary stages that can smoothly move the connection flange along the wide scattering angle without breaking the vacuum. In addition, the spectrometer is rotated by sliding on a flat metal surface, ensuring exceptionally high accuracy in rotation and eliminating the need for any further adjustments during rotation. A control system that integrates the sample chamber and rotation mechanism to automate the measurement of angle-resolved X-ray emission spectroscopy has also been developed. This automation substantially streamlines the process of measuring angle-resolved spectra, making it far easier than ever before. Furthermore, the upgraded X-ray emission spectrometer can now also be utilized in diffraction experiments, providing even greater versatility to our research capabilities. Full Article text
al Combination of XEOL, TR-XEOL and HB-T interferometer at the TPS 23A X-ray nanoprobe for exploring quantum materials By journals.iucr.org Published On :: 2024-01-19 In this study, a combination of X-ray excited optical luminescence (XEOL), time-resolved XEOL (TR-XEOL) and the Hanbury-Brown and Twiss (HB-T) interferometer at the Taiwan Photon Source (TPS) 23A X-ray nanoprobe beamline for exploring quantum materials is demonstrated. On the basis of the excellent spatial resolution rendered using a nano-focused beam, emission distributions of artificial micro-diamonds can be obtained by XEOL maps, and featured emission peaks of a selected local area can be obtained by XEOL spectra. The hybrid bunch mode of the TPS not only provides a sufficiently high peak power density for experiments at each beamline but also permits high-quality temporal domain (∼200 ns) measurements for investigating luminescence dynamics. From TR-XEOL measurements, the decay lifetime of micro-diamonds is determined to be approximately 16 ns. Furthermore, the XEOL spectra of artificial micro-diamonds can be investigated by the HB-T interferometer to identify properties of single-photon sources. The unprecedented strategy of combining XEOL, TR-XEOL and the HB-T interferometer at the X-ray nanoprobe beamline will open new avenues with significant characterization abilities for unraveling the emission mechanisms of single-photon sources for quantum materials. Full Article text
al Correlation of refractive index based and THz streaking arrival time tools for a hard X-ray free-electron laser By journals.iucr.org Published On :: 2024-01-22 To fully exploit ultra-short X-ray pulse durations routinely available at X-ray free-electron lasers to follow out-of-equilibrium dynamics, inherent arrival time fluctuations of the X-ray pulse with an external perturbing laser pulse need to be measured. In this work, two methods of arrival time measurement were compared to measure the arrival time jitter of hard X-ray pulses. The methods were photoelectron streaking by a THz field and a transient refractive index change of a semiconductor. The methods were validated by shot-to-shot correction of a pump–probe transient reflectivity measurement. An ultimate shot-to-shot full width at half-maximum error between the devices of 19.2 ± 0.1 fs was measured. Full Article text
al Finback: a web-based data collection system at SSRF biological macromolecular crystallography beamlines By journals.iucr.org Published On :: 2024-01-19 An integrated computer software system for macromolecular crystallography (MX) data collection at the BL02U1 and BL10U2 beamlines of the Shanghai Synchrotron Radiation Facility is described. The system, Finback, implements a set of features designed for the automated MX beamlines, and is marked with a user-friendly web-based graphical user interface (GUI) for interactive data collection. The Finback client GUI can run on modern browsers and has been developed using several modern web technologies including WebSocket, WebGL, WebWorker and WebAssembly. Finback supports multiple concurrent sessions, so on-site and remote users can access the beamline simultaneously. Finback also cooperates with the deployed experimental data and information management system, the relevant experimental parameters and results are automatically deposited to a database. Full Article text
al A thermal deformation optimization method for cryogenically cooled silicon crystal monochromators under high heat load By journals.iucr.org Published On :: 2024-01-22 A method to optimize the thermal deformation of an indirectly cryo-cooled silicon crystal monochromator exposed to intense X-rays at a low-emittance diffraction-limited synchrotron radiation source is presented. The thermal-induced slope error of the monochromator crystal has been studied as a function of heat transfer efficiency, crystal temperature distribution and beam footprint size. A partial cooling method is proposed, which flattens the crystal surface profile within the beam footprint by modifying the cooling contact area to optimize the crystal peak temperature. The optimal temperature varies with different photon energies, which is investigated, and a proper cooling strategy is obtained to fulfil the thermal distortion requirements over the entire photon energy range. At an absorbed power up to 300 W with a maximum power density of 44.8 W mm−2 normal incidence beam from an in-vacuum undulator, the crystal thermal distortion does not exceed 0.3 µrad at 8.33 keV. This method will provide references for the monochromator design on diffraction-limited synchrotron radiation or free-electron laser light sources. Full Article text
al xrdPlanner: exploring area detector geometries for powder diffraction and total scattering experiments By journals.iucr.org Published On :: 2024-02-02 xrdPlanner is a software package designed to aid in the planning and preparation of powder X-ray diffraction and total scattering beam times at synchrotron facilities. Many modern beamlines provide a flexible experimental setup and may have several different detectors available. In combination with a range of available X-ray energies, it often makes it difficult for the user to explore the available parameter space relevant for a given experiment prior to the scheduled beam time. xrdPlanner was developed to provide a fast and straightforward tool that allows users to visualize the accessible part of reciprocal space of their experiment at a given combination of photon energy and detector geometry. To plan and communicate the necessary geometry not only saves time but also helps the beamline staff to prepare and accommodate for an experiment. The program is tailored toward powder X-ray diffraction and total scattering experiments but may also be useful for other experiments that rely on an area detector and for which detector placement and achievable momentum-transfer range are important experimental parameters. Full Article text
al Extracting the electronic structure signal from X-ray and electron scattering in the gas phase By journals.iucr.org Published On :: 2024-02-22 X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) and ab initio electronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total, i.e. energy-integrated, scattering from three molecules, fluoroform (CHF3), 1,3-cyclohexadiene (C6H8) and naphthalene (C10H8), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q ≤ 8 Å−1) in the scattering signal, with a maximum percent difference contribution at 2 ≤ q ≤ 3 Å−1. A procedure to determine the molecular geometry from the large-q scattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediate q and to provide a measure of the effect of valence electronic structure on the scattering signal. Full Article text
al Open-source electrochemical cell for in situ X-ray absorption spectroscopy in transmission and fluorescence modes By journals.iucr.org Published On :: 2024-02-02 X-ray spectroscopy is a valuable technique for the study of many materials systems. Characterizing reactions in situ and operando can reveal complex reaction kinetics, which is crucial to understanding active site composition and reaction mechanisms. In this project, the design, fabrication and testing of an open-source and easy-to-fabricate electrochemical cell for in situ electrochemistry compatible with X-ray absorption spectroscopy in both transmission and fluorescence modes are accomplished via windows with large opening angles on both the upstream and downstream sides of the cell. Using a hobbyist computer numerical control machine and free 3D CAD software, anyone can make a reliable electrochemical cell using this design. Onion-like carbon nanoparticles, with a 1:3 iron-to-cobalt ratio, were drop-coated onto carbon paper for testing in situ X-ray absorption spectroscopy. Cyclic voltammetry of the carbon paper showed the expected behavior, with no increased ohmic drop, even in sandwiched cells. Chronoamperometry was used to apply 0.4 V versus reversible hydrogen electrode, with and without 15 min of oxygen purging to ensure that the electrochemical cell does not provide any artefacts due to gas purging. The XANES and EXAFS spectra showed no differences with and without oxygen, as expected at 0.4 V, without any artefacts due to gas purging. The development of this open-source electrochemical cell design allows for improved collection of in situ X-ray absorption spectroscopy data and enables researchers to perform both transmission and fluorescence simultaneously. It additionally addresses key practical considerations including gas purging, reduced ionic resistance and leak prevention. Full Article text
al ProSPyX: software for post-processing images of X-ray ptychography with spectral capabilities By journals.iucr.org Published On :: 2024-02-09 X-ray ptychography is a coherent diffraction imaging technique based on acquiring multiple diffraction patterns obtained through the illumination of the sample at different partially overlapping probe positions. The diffraction patterns collected are used to retrieve the complex transmittivity function of the sample and the probe using a phase retrieval algorithm. Absorption or phase contrast images of the sample as well as the real and imaginary parts of the probe function can be obtained. Furthermore, X-ray ptychography can also provide spectral information of the sample from absorption or phase shift images by capturing multiple ptychographic projections at varying energies around the resonant energy of the element of interest. However, post-processing of the images is required to extract the spectra. To facilitate this, ProSPyX, a Python package that offers the analysis tools and a graphical user interface required to process spectral ptychography datasets, is presented. Using the PyQt5 Python open-source module for development and design, the software facilitates extraction of absorption and phase spectral information from spectral ptychographic datasets. It also saves the spectra in file formats compatible with other X-ray absorption spectroscopy data analysis software tools, streamlining integration into existing spectroscopic data analysis pipelines. To illustrate its capabilities, ProSPyX was applied to process the spectral ptychography dataset recently acquired on a nickel wire at the SWING beamline of the SOLEIL synchrotron. Full Article text
al Investigation of structural and reflective characteristics of short-period Mo/B4C multilayer X-ray mirrors By journals.iucr.org Published On :: 2024-02-09 The results of a study of the structural and reflective characteristics of short-period multilayer X-ray mirrors based on Mo/B4C at wavelengths 1.54 Å, 9.89 Å and 17.59 Å are presented. The period of the samples varied in the range 8–35 Å. The average widths of the interfaces were ∼3.5 and 2.2 Å at one and the other boundaries, with a tendency for weak growth with any decrease in the period. The interlayer roughness was ∼1 Å. The research results indicate promising prospects for the use of multilayer Mo/B4C mirrors for synchrotron applications. Full Article text
al The role of carboxylate ligand orbitals in the breathing dynamics of a metal-organic framework by resonant X-ray emission spectroscopy By journals.iucr.org Published On :: 2024-02-16 Metal-organic frameworks (MOFs) exhibit structural flexibility induced by temperature and guest adsorption, as demonstrated in the structural breathing transition in certain MOFs between narrow-pore and large-pore phases. Soft modes were suggested to entropically drive such pore breathing through enhanced vibrational dynamics at high temperatures. In this work, oxygen K-edge resonant X-ray emission spectroscopy of the MIL-53(Al) MOF was performed to selectively probe the electronic perturbation accompanying pore breathing dynamics at the ligand carboxylate site for metal–ligand interaction. It was observed that the temperature-induced vibrational dynamics involves switching occupancy between antisymmetric and symmetric configurations of the carboxylate oxygen lone pair orbitals, through which electron density around carboxylate oxygen sites is redistributed and metal–ligand interactions are tuned. In turn, water adsorption involves an additional perturbation of π orbitals not observed in the structural change solely induced by temperature. Full Article text
al Optimization of synchrotron radiation parameters using swarm intelligence and evolutionary algorithms By journals.iucr.org Published On :: 2024-02-22 Alignment of each optical element at a synchrotron beamline takes days, even weeks, for each experiment costing valuable beam time. Evolutionary algorithms (EAs), efficient heuristic search methods based on Darwinian evolution, can be utilized for multi-objective optimization problems in different application areas. In this study, the flux and spot size of a synchrotron beam are optimized for two different experimental setups including optical elements such as lenses and mirrors. Calculations were carried out with the X-ray Tracer beamline simulator using swarm intelligence (SI) algorithms and for comparison the same setups were optimized with EAs. The EAs and SI algorithms used in this study for two different experimental setups are the Genetic Algorithm (GA), Non-dominated Sorting Genetic Algorithm II (NSGA-II), Particle Swarm Optimization (PSO) and Artificial Bee Colony (ABC). While one of the algorithms optimizes the lens position, the other focuses on optimizing the focal distances of Kirkpatrick–Baez mirrors. First, mono-objective evolutionary algorithms were used and the spot size or flux values checked separately. After comparison of mono-objective algorithms, the multi-objective evolutionary algorithm NSGA-II was run for both objectives – minimum spot size and maximum flux. Every algorithm configuration was run several times for Monte Carlo simulations since these processes generate random solutions and the simulator also produces solutions that are stochastic. The results show that the PSO algorithm gives the best values over all setups. Full Article text
al Novel correction procedure for compensating thermal contraction errors in the measurement of the magnetic field of superconducting undulator coils in a liquid helium cryostat By journals.iucr.org Published On :: 2024-02-22 Superconducting undulators (SCUs) can offer a much higher on-axis undulator field than state-of-the-art cryogenic permanent-magnet undulators with the same period and vacuum gap. The development of shorter-period and high-field SCUs would allow the free-electron laser and synchrotron radiation source community to reduce both the length of undulators and the dimensions of the accelerator. Magnetic measurements are essential for characterizing the magnetic field quality of undulators for operation in a modern light source. Hall probe scanning is so far the most mature technique for local field characterization of undulators. This article focuses on the systematic error caused by thermal contraction that influences Hall probe measurements carried out in a liquid helium cryostat. A novel procedure, based on the redundant measurement of the magnetic field using multiple Hall probes at known relative distance, is introduced for the correction of such systematic error. Full Article text
al ForMAX – a beamline for multiscale and multimodal structural characterization of hierarchical materials By journals.iucr.org Published On :: 2024-02-22 The ForMAX beamline at the MAX IV Laboratory provides multiscale and multimodal structural characterization of hierarchical materials in the nanometre to millimetre range by combining small- and wide-angle X-ray scattering with full-field microtomography. The modular design of the beamline is optimized for easy switching between different experimental modalities. The beamline has a special focus on the development of novel fibrous materials from forest resources, but it is also well suited for studies within, for example, food science and biomedical research. Full Article text
al Determination of optimal experimental conditions for accurate 3D reconstruction of the magnetization vector via XMCD-PEEM By journals.iucr.org Published On :: 2024-02-19 This work presents a detailed analysis of the performance of X-ray magnetic circular dichroism photoemission electron microscopy (XMCD-PEEM) as a tool for vector reconstruction of magnetization. For this, 360° domain wall ring structures which form in a synthetic antiferromagnet are chosen as the model to conduct the quantitative analysis. An assessment is made of how the quality of the results is affected depending on the number of projections that are involved in the reconstruction process, as well as their angular distribution. For this a self-consistent error metric is developed which allows an estimation of the optimum azimuthal rotation angular range and number of projections. This work thus proposes XMCD-PEEM as a powerful tool for vector imaging of complex 3D magnetic structures. Full Article text
al Development of the multiplex imaging chamber at PAL-XFEL By journals.iucr.org Published On :: 2024-03-22 Various X-ray techniques are employed to investigate specimens in diverse fields. Generally, scattering and absorption/emission processes occur due to the interaction of X-rays with matter. The output signals from these processes contain structural information and the electronic structure of specimens, respectively. The combination of complementary X-ray techniques improves the understanding of complex systems holistically. In this context, we introduce a multiplex imaging instrument that can collect small-/wide-angle X-ray diffraction and X-ray emission spectra simultaneously to investigate morphological information with nanoscale resolution, crystal arrangement at the atomic scale and the electronic structure of specimens. Full Article text
al Increased spatial coherence length from an asymmetric crystal reflection at grazing exit By journals.iucr.org Published On :: 2024-03-26 Coherent X-ray imaging is an active field at synchrotron sources. The images rely on the available coherent flux over a limited field of view. At many synchrotron beamlines a double-crystal monochromator (DCM) is employed in a standard nondispersive arrangement. For coherent diffraction imaging it is advantageous to increase the available field of view by increasing the spatial coherence length (SCL) of a beam exiting such a DCM. Here, Talbot interferometry data together with ray-tracing simulations for a (+ − − +) four-reflection experimental arrangement are presented, wherein the first two reflections are in the DCM and the final fourth reflection is asymmetric at grazing exit. Analyses of the interferometry data combined with the simulations show that compared with the beam exiting the DCM a gain of 76% in the SCL was achieved, albeit with a factor of 20 reduction in flux density, which may not be a severe penalty at a synchrotron beamline. Previous efforts reported in the literature to increase the SCL that employed asymmetric crystal diffraction at grazing incidence are also discussed. A much reduced SCL is found presently in simulations wherein the same asymmetric crystal is set for grazing incidence instead of grazing exit. In addition, the present study is compared and contrasted with two other means of increasing the SCL. These are (i) focusing the beam onto an aperture to act as a secondary source, and (ii) allowing the beam to propagate in vacuum an additional distance along the beamline. Full Article text
al Improving sensitivity of XANES structural fit to the bridged metal–metal coordination By journals.iucr.org Published On :: 2024-03-26 Hard X-ray absorption spectroscopy is a valuable in situ probe for non-destructive diagnostics of metal sites. The low-energy interval of a spectrum (XANES) contains information about the metal oxidation state, ligand type, symmetry and distances in the first coordination shell but shows almost no dependency on the bridged metal–metal bond length. The higher-energy interval (EXAFS), on the contrary, is more sensitive to the coordination numbers and can decouple the contribution from distances in different coordination shells. Supervised machine-learning methods can combine information from different intervals of a spectrum; however, computational approaches for the near-edge region of the spectrum and higher energies are different. This work aims to keep all benefits of XANES and extend its sensitivity towards the interatomic distances in the first and second coordination shells. Using a binuclear bridged copper complex as a case study and cross-validation analysis as a quantitative tool it is shown that the first 170 eV above the edge are already sufficient to balance the contributions of Cu–O/N scattering and Cu–Cu scattering. As a more general outcome this work highlights the trivial but often overlooked importance of using `longer' energy intervals of XANES for structural refinement and machine-learning predictions. The first 200 eV above the absorption edge still do not require parametrization of Debye–Waller damping and can be calculated within full multiple scattering or finite difference approximations with only moderately increased computational costs. Full Article text
al Modelling the power threshold and optimum thermal deformation of indirectly liquid-nitrogen cryo-cooled Si monochromators By journals.iucr.org Published On :: 2024-04-09 Maximizing the performance of crystal monochromators is a key aspect in the design of beamline optics for diffraction-limited synchrotron sources. Temperature and deformation of cryo-cooled crystals, illuminated by high-power beams of X-rays, can be estimated with a purely analytical model. The analysis is based on the thermal properties of cryo-cooled silicon crystals and the cooling geometry. Deformation amplitudes can be obtained, quickly and reliably. In this article the concept of threshold power conditions is introduced and defined analytically. The contribution of parameters such as liquid-nitrogen cooling efficiency, thermal contact conductance and interface contact area of the crystal with the cooling base is evaluated. The optimal crystal illumination and the base temperature are inferred, which help minimize the optics deformation. The model has been examined using finite-element analysis studies performed for several beamlines of the Diamond-II upgrade. Full Article text
al Iterative Bragg peak removal on X-ray absorption spectra with automatic intensity correction By journals.iucr.org Published On :: 2024-04-09 This study introduces a novel iterative Bragg peak removal with automatic intensity correction (IBR-AIC) methodology for X-ray absorption spectroscopy (XAS), specifically addressing the challenge of Bragg peak interference in the analysis of crystalline materials. The approach integrates experimental adjustments and sophisticated post-processing, including an iterative algorithm for robust calculation of the scaling factor of the absorption coefficients and efficient elimination of the Bragg peaks, a common obstacle in accurately interpreting XAS data, particularly in crystalline samples. The method was thoroughly evaluated on dilute catalysts and thin films, with fluorescence mode and large-angle rotation. The results underscore the technique's effectiveness, adaptability and substantial potential in improving the precision of XAS data analysis. While demonstrating significant promise, the method does have limitations related to signal-to-noise ratio sensitivity and the necessity for meticulous angle selection during experimentation. Overall, IBR-AIC represents a significant advancement in XAS, offering a pragmatic solution to Bragg peak contamination challenges, thereby expanding the applications of XAS in understanding complex materials under diverse experimental conditions. Full Article text
al Development of dual-beamline photoelectron momentum microscopy for valence orbital analysis By journals.iucr.org Published On :: 2024-04-15 The soft X-ray photoelectron momentum microscopy (PMM) experimental station at the UVSOR Synchrotron Facility has been recently upgraded by additionally guiding vacuum ultraviolet (VUV) light in a normal-incidence configuration. PMM offers a very powerful tool for comprehensive electronic structure analyses in real and momentum spaces. In this work, a VUV beam with variable polarization in the normal-incidence geometry was obtained at the same sample position as the soft X-ray beam from BL6U by branching the VUV beamline BL7U. The valence electronic structure of the Au(111) surface was measured using horizontal and vertical linearly polarized (s-polarized) light excitations from BL7U in addition to horizontal linearly polarized (p-polarized) light excitations from BL6U. Such highly symmetric photoemission geometry with normal incidence offers direct access to atomic orbital information via photon polarization-dependent transition-matrix-element analysis. Full Article text
al A new experimental setup for combined fast differential scanning calorimetry and X-ray photon correlation spectroscopy By journals.iucr.org Published On :: 2024-04-24 Synchrotron-radiation-based techniques are a powerful tool for the investigation of materials. In particular, the availability of highly brilliant sources has opened the possibility to develop techniques sensitive to dynamics at the atomic scale such as X-ray photon correlation spectroscopy (XPCS). XPCS is particularly relevant in the study of glasses, which have been often investigated at the macroscopic scale by, for example, differential scanning calorimetry. Here, we show how to adapt a Flash calorimeter to combine XPCS and calorimetric scans. This setup paves the way to novel experiments requiring dynamical and thermodynamic information, ranging from the study of the crystallization kinetics to the study of the glass transition in systems that can be vitrified thanks to the high cooling rates reachable with an ultrafast calorimeter. Full Article text
al Evaluation of the X-ray/EUV Nanolithography Facility at AS through wavefront propagation simulations By journals.iucr.org Published On :: 2024-04-17 Synchrotron light sources can provide the required spatial coherence, stability and control to support the development of advanced lithography at the extreme ultraviolet and soft X-ray wavelengths that are relevant to current and future fabricating technologies. Here an evaluation of the optical performance of the soft X-ray (SXR) beamline of the Australian Synchrotron (AS) and its suitability for developing interference lithography using radiation in the 91.8 eV (13.5 nm) to 300 eV (4.13 nm) range are presented. A comprehensive physical optics model of the APPLE-II undulator source and SXR beamline was constructed to simulate the properties of the illumination at the proposed location of a photomask, as a function of photon energy, collimation and monochromator parameters. The model is validated using a combination of experimental measurements of the photon intensity distribution of the undulator harmonics. It is shown that the undulator harmonics intensity ratio can be accurately measured using an imaging detector and controlled using beamline optics. Finally, the photomask geometric constraints and achievable performance for the limiting case of fully spatially coherent illumination are evaluated. Full Article text
al Wavefront analysis and phase correctors design using SHADOW By journals.iucr.org Published On :: 2024-04-23 Knife-edge imaging is a successful method for determining the wavefront distortion of focusing optics such as Kirkpatrick–Baez mirrors or compound refractive lenses. In this study, the wavefront error of an imperfect elliptical mirror is predicted by developing a knife-edge program using the SHADOW/OASYS platform. It is shown that the focusing optics can be aligned perfectly by minimizing the parabolic and cubic coefficients of the wavefront error. The residual wavefront error provides precise information about the figure/height errors of the focusing optics suggesting it as an accurate method for in situ optical metrology. A Python program is developed to design a customized wavefront refractive corrector to minimize the residual wavefront error. Uniform beam at and out of focus and higher peak intensity are achieved by the wavefront correction in comparison with ideal focusing. The developed code provides a quick way for wavefront error analysis and corrector design for non-ideal optics especially for the new-generation diffraction-limited sources, and saves considerable experimental time and effort. Full Article text
al Infrared spectroscopy across scales in length and time at BESSY II By journals.iucr.org Published On :: 2024-04-23 The infrared beamline at BESSY II storage ring was upgraded recently to extend the capabilities of infrared microscopy. The endstations available at the beamline are now facilitating improved characterization of molecules and materials at different length scales and time resolutions. Here, the current outline of the beamline is reported and an overview of the endstations available is given. In particular, the first results obtained by using a new microscope for nano-spectroscopy that was implemented are presented. The capabilities of the scattering-type near-field optical microscope (s-SNOM) are demonstrated by investigating cellulose microfibrils, representing nanoscopic objects of a hierarchical structure. It is shown that the s-SNOM coupled to the beamline allows imaging to be performed with a spatial resolution of less than 30 nm and infrared spectra to be collected from an effective volume of less than 30 nm × 30 nm × 12 nm. Potential steps for further optimization of the beamline performance are discussed. Full Article text
al Developing an in situ LED irradiation system for small-angle X-ray scattering at B21, Diamond Light Source By journals.iucr.org Published On :: 2024-05-31 Beamline B21 at the Diamond Light Source synchrotron in the UK is a small-angle X-ray scattering (SAXS) beamline that specializes in high-throughput measurements via automated sample delivery systems. A system has been developed whereby a sample can be illuminated by a focused beam of light coincident with the X-ray beam. The system is compatible with the highly automated sample delivery system at the beamline and allows a beamline user to select a light source from a broad range of wavelengths across the UV and visible spectrum and to control the timing and duration of the light pulse with respect to the X-ray exposure of the SAXS measurement. The intensity of the light source has been characterized across the wavelength range enabling experiments where a quantitative measure of dose is important. Finally, the utility of the system is demonstrated via measurement of several light-responsive samples. Full Article text
al Enhanced X-ray free-electron laser performance with optical klystron and helical undulators By journals.iucr.org Published On :: 2024-06-11 This article presents a demonstration of the improved performance of an X-ray free-electron laser (FEL) using the optical klystron mechanism and helical undulator configuration, in comparison with the common planar undulator configuration without optical klystron. The demonstration was carried out at Athos, the soft X-ray beamline of SwissFEL. Athos has variable-polarization undulators, and small magnetic chicanes placed between every two undulators to fully exploit the optical klystron. It was found that, for wavelengths of 1.24 nm and 3.10 nm, the required length to achieve FEL saturation is reduced by about 35% when using both the optical klystron and helical undulators, with each effect accounting for about half of the improvement. Moreover, it is shown that a helical undulator configuration provides a 20% to 50% higher pulse energy than planar undulators. This work represents an important step towards more compact and high-power FELs, rendering this key technology more efficient, affordable and accessible to the scientific community. Full Article text
al First X-ray spectral ptychography and resonant ptychographic computed tomography experiments at the SWING beamline from Synchrotron SOLEIL By journals.iucr.org Published On :: 2024-05-21 X-ray ptychography and ptychographic computed tomography have seen a rapid rise since the advent of fourth-generation synchrotrons with a high degree of coherent radiation. In addition to quantitative multiscale structural analysis, ptychography with spectral capabilities has been developed, allowing for spatial-localized multiscale structural and spectral information of samples. The SWING beamline of Synchrotron SOLEIL has recently developed a nanoprobe setup where the endstation's first spectral and resonant ptychographic measurements have been successfully conducted. A metallic nickel wire sample was measured using 2D spectral ptychography in XANES mode and resonant ptychographic tomography. From the 2D spectral ptychography measurements, the spectra of the components of the sample's complex-valued refractive index, δ and β, were extracted, integrated along the sample thickness. By performing resonance ptychographic tomography at two photon energies, 3D maps of the refractive index decrement, δ, were obtained at the Ni K-edge energy and another energy above the edge. These maps allowed the detection of impurities in the Ni wire. The significance of accounting for the atomic scattering factor is demonstrated in the calculation of electron density near a resonance through the use of the δ values. These results indicate that at the SWING beamline it is possible to conduct state-of-the-art spectral and resonant ptychography experiments using the nanoprobe setup. Full Article text