ria 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
ria High-throughput and high-resolution powder X-ray diffractometer consisting of six sets of 2D CdTe detectors with variable sample-to-detector distance and innovative automation system By journals.iucr.org Published On :: 2024-06-20 The demand for powder X-ray diffraction analysis continues to increase in a variety of scientific fields, as the excellent beam quality of high-brightness synchrotron light sources enables the acquisition of high-quality measurement data with high intensity and angular resolution. Synchrotron powder diffraction has enabled the rapid measurement of many samples and various in situ/operando experiments in nonambient sample environments. To meet the demands for even higher throughput measurements using high-energy X-rays at SPring-8, a high-throughput and high-resolution powder diffraction system has been developed. This system is combined with six sets of two-dimensional (2D) CdTe detectors for high-energy X-rays, and various automation systems, including a system for automatic switching among large sample environmental equipment, have been developed in the third experimental hutch of the insertion device beamline BL13XU at SPring-8. In this diffractometer system, high-brilliance and high-energy X-rays ranging from 16 to 72 keV are available. The powder diffraction data measured under ambient and various nonambient conditions can be analysed using Rietveld refinement and the pair distribution function. Using the 2D CdTe detectors with variable sample-to-detector distance, three types of scan modes have been established: standard, single-step and high-resolution. A major feature is the ability to measure a whole powder pattern with millisecond resolution. Equally important, this system can measure powder diffraction data with high Q exceeding 30 Å−1 within several tens of seconds. This capability is expected to contribute significantly to new research avenues using machine learning and artificial intelligence by utilizing the large amount of data obtained from high-throughput measurements. Full Article text
ria The diamond–silicon carbide composite Skeleton® as a promising material for substrates of intense X-ray beam optics By journals.iucr.org Published On :: 2024-08-06 The paper considers the possibility of using the diamond-silicon carbide composite Skeleton® with a technological coating of polycrystalline silicon as a substrate for X-ray mirrors used with powerful synchrotron radiation sources (third+ and fourth generation). Samples were studied after polishing to provide the following surface parameters: root-mean-square flatness ≃ 50 nm, micro-roughness on the frame 2 µm × 2 µm σ ≃ 0.15 nm. The heat capacity, thermal conductivity and coefficient of linear thermal expansion were investigated. For comparison, a monocrystalline silicon sample was studied under the same conditions using the same methods. The value of the coefficient of linear thermal expansion turned out to be higher than that of monocrystalline silicon and amounted to 4.3 × 10−6 K−1, and the values of thermal conductivity (5.0 W cm−1 K−1) and heat capacity (1.2 J K−1 g−1) also exceeded the values for Si. Thermally induced deformations of both Skeleton® and monocrystalline silicon samples under irradiation with a CO2 laser beam have also been experimentally studied. Taking into account the obtained thermophysical constants, the calculation of thermally induced deformation under irradiation with hard (20 keV) X-rays showed almost three times less deformation of the Skeleton® sample than of the monocrystalline silicon sample. Full Article text
ria Hyperspectral full-field quick-EXAFS imaging at the ROCK beamline for monitoring micrometre-sized heterogeneity of functional materials under process conditions By journals.iucr.org Published On :: 2024-08-23 Full-field transmission X-ray microscopy has been recently implemented at the hard X-ray ROCK–SOLEIL quick-EXAFS beamline, adding micrometre spatial resolution to the second time resolution characterizing the beamline. Benefiting from a beam size versatility due to the beamline focusing optics, full-field hyperspectral XANES imaging has been successfully used at the Fe K-edge for monitoring the pressure-induced spin transition of a 150 µm × 150 µm Fe(o-phen)2(NCS)2 single crystal and the charge of millimetre-sized LiFePO4 battery electrodes. Hyperspectral imaging over 2000 eV has been reported for the simultaneous monitoring of Fe and Cu speciation changes during activation of a FeCu bimetallic catalyst along a millimetre-sized catalyst bed. Strategies of data acquisition and post-data analysis using Jupyter notebooks and multivariate data analysis are presented, and the gain obtained using full-field hyperspectral quick-EXAFS imaging for studies of functional materials under process conditions in comparison with macroscopic information obtained by non-spatially resolved quick-EXAFS techniques is discussed. Full Article text
ria (4-Butyl-1-ethyl-1,2,4-triazol-5-ylidene)[(1,2,5,6-η)-cycloocta-1,5-diene](triphenylphosphane)rhodium(I) tetrafluoridoborate By journals.iucr.org Published On :: 2024-01-26 In the title triazole-based N-heterocyclic carbene rhodium(I) cationic complex with a tetrafluoridoborate counter-anion, [Rh(C8H12)(C8H15N3)(C18H15P)]BF4, which crystallizes with two cations and two anions in the asymmetric unit, the Rh center has a distorted square-planar coordination geometry with expected bond distances. Several nonclassical C—H⋯F hydrogen-bonding interactions help to consolidate the packing. Two of the F atoms of one of the anions are disordered over adjacent sites in a 0.814 (4):0.186 (4) ratio. Full Article text
ria (4-Butyl-1-ethyl-1,2,4-triazol-5-ylidene)[(1,2,5,6-η)-cycloocta-1,5-diene](triphenylphosphane)iridium(I) tetrafluoridoborate By journals.iucr.org Published On :: 2024-06-07 The title compound, [Ir(C8H12)(C8H15N3)(C18H15P)]BF4, a new triazole-based N-heterocyclic carbene iridium(I) cationic complex with a tetrafluoridoborate counter-anion, crystallizes with two cations and two anions in the asymmetric unit of space group Pc. The Ir centers of the cations have distorted square-planar conformations, formed by a bidentate (η2 + η2) cycloocta-1,5-diene (COD) ligand, an N-heterocyclic carbene and a triphenylphosphane ligand with the NHC carbon atom and P atom being cis. In the extended structure, non-classical C–H⋯F hydrogen bonds, one of which is notably short (H⋯F = 2.21 Å), link the cations and anions. The carbon atoms of one of the COD ligands are disordered over adjacent sites in a 0.62:0.38 ratio. Full Article text
ria Triacetonitrile(1,4,7-trimethyl-1,4,7-triazacyclononane)cobalt(II) bis(tetraphenylborate) By journals.iucr.org Published On :: 2024-06-11 The title cobalt(II) complex, [Co(C2H3N)3(C9H21N3)](C24H20B)2 or [(tacn)Co(NCMe)3][BPh4]2, has been characterized by single-crystal X-ray diffraction. It incorporates the well-known macrocyclic tacn (1,4,7-trimethyl-1,4,7-triazacyclononane) ligand, which is coordinated facially to the metal center. The complex crystallizes in space group P21/c with Z = 4. The divalent cobalt ion exhibits a six-coordinate octahedral geometry by one tacn and three acetonitrile ligands. Two non-coordinating tetraphenylborate (BPh4−) anions are also present. Full Article text
ria Poly[[μ3-2-(benzotriazol-1-yl)acetato-κ3O:O':N3]chlorido(ethanol-κO)cobalt(II)] By journals.iucr.org Published On :: 2024-07-05 In the title compound, [Co(C8H6N3O2)Cl(C2H5OH)]n, the CoII atoms adopt octahedral trans-CoN2O4 and tetrahedral CoCl2O2 coordination geometries (site symmetries overline{1} and m, respectively). The bridging μ3-O:O:N 2-(benzotriazol-1-yl)acetato ligands connect the octahedral cobalt nodes into (010) sheets and the CoCl2 fragments link the sheets into a tri-periodic network. The structure displays O—H⋯O hydrogen bonding and the ethanol molecule is disordered over two orientations. Full Article text
ria Chlorido[(1,2,5,6-η)-cycloocta-1,5-diene](1-ethyl-4-isobutyl-1,2,4-triazol-5-ylidene)rhodium(I) By journals.iucr.org Published On :: 2024-07-23 A new neutral triazole-based N-heterocyclic carbene rhodium(I) complex [RhCl(C8H12)(C8H15N3)], has been synthesized and structurally characterized. The complex crystallizes with two molecules in the asymmetric unit. The central rhodium(I) atom has a distorted square-planar coordination environment, formed by a cycloocta-1,5-diene (COD) ligand, an N-heterocyclic carbene (NHC) ligand, and a chlorido ligand. The bond lengths are unexceptional. A weak intermolecular non-standard hydrogen-bonding interaction exists between the chlorido and NHC ligands. Full Article text
ria [(1,2,5,6-η)-Cycloocta-1,5-diene](1-ethyl-4-isobutyl-1,2,4-triazol-5-ylidene)(triphenylphosphane)rhodium(I) tetrafluoridoborate By journals.iucr.org Published On :: 2024-08-02 A new, cationic N-heterocyclic carbene RhI complex with a tetrafluoridoborate counter-anion, [Rh(C8H12)(C8H15N3)(C18H15P)]BF4, has been synthesized and structurally characterized. There are two independent ion pairs in the asymmetric unit. Each complex cation exhibits a distorted square-planar conformation around the RhI atom. Bond lengths and bond angles are as expected for an Rh–NHC complex. There are several close, non-standard C—H⋯F hydrogen-bonding interactions between the ions. One of the tetrafluoridoborate anions shows statistical disorder of the F atoms. Full Article text
ria [(1,2,5,6-η)-Cycloocta-1,5-diene](1-ethyl-4-isobutyl-1,2,4-triazol-5-ylidene)(triphenylphosphane)iridium(I) tetrafluoridoborate dichloromethane hemisolvate By journals.iucr.org Published On :: 2024-09-30 A new triazole-based N-heterocyclic carbene IrI cationic complex with a tetrafluoridoborate counter-anion and hemi-solvating dichloromethane, [Ir(C8H12)(C8H15N3)(C18H15P)]BF4·0.5CH2Cl2, has been synthesized and structurally characterized. There are two independent ion pairs in the asymmetric unit and one dichloromethane solvent molecule per two ion pairs. The cationic complex exhibits a distorted square-planar conformation around the IrI atom, formed by a bidentate cycloocta-1,5,diene (COD) ligand, a triphenylphosphane ligand, and an N-heterocyclic carbene (NHC). There are several close non-standard H⋯F hydrogen-bonding interactions that orient the tetrafluoridoborate anions with respect to the IrI complex molecules. The complex shows promising catalytic activity in transfer hydrogenation reactions. The structure was refined as a non-merohedral twin, and one of the COD molecules is statistically disordered. Full Article text
ria 3-[(Benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione: polymorphism and twinning of a precursor to an antimycobacterial squaramide By journals.iucr.org Published On :: 2024-07-05 The title compound, 3-[(benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione, C12H9NO5 (3), is a precursor to an antimycobacterial squaramide. Block-shaped crystals of a monoclinic form (3-I, space group P21/c, Z = 8, Z' = 2) and needle-shaped crystals of a triclinic form (3-II, space group P-1, Z = 4, Z' = 2) were found to crystallize concomitantly. In both crystal forms, R22(10) dimers assemble through N—H⋯O=C hydrogen bonds. These dimers are formed from crystallographically unique molecules in 3-I, but exhibit crystallographic Ci symmetry in 3-II. Twinning by pseudomerohedry was encountered in the crystals of 3-II. The conformations of 3 in the solid forms 3-I and 3-II are different from one another but are similar for the unique molecules in each polymorph. Density functional theory (DFT) calculations on the free molecule of 3 indicate that a nearly planar conformation is preferred. Full Article text
ria AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography By journals.iucr.org Published On :: 2024-03-07 Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement. Full Article text
ria The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria By journals.iucr.org Published On :: 2024-02-19 Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reductases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future antituberculosis drug development. Full Article text
ria A snapshot love story: what serial crystallography has done and will do for us By journals.iucr.org Published On :: 2024-07-10 Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique in structural biology. Initially pioneered at X-ray free-electron laser facilities, it has now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments in serial crystallography, emphasizing recent results in time-resolved crystallography, and discussing challenges and shortcomings. Full Article text
ria STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials By journals.iucr.org Published On :: 2024-01-01 Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25. Full Article text
ria Data reduction in protein serial crystallography By journals.iucr.org Published On :: 2024-02-08 Serial crystallography (SX) has become an established technique for protein structure determination, especially when dealing with small or radiation-sensitive crystals and investigating fast or irreversible protein dynamics. The advent of newly developed multi-megapixel X-ray area detectors, capable of capturing over 1000 images per second, has brought about substantial benefits. However, this advancement also entails a notable increase in the volume of collected data. Today, up to 2 PB of data per experiment could be easily obtained under efficient operating conditions. The combined costs associated with storing data from multiple experiments provide a compelling incentive to develop strategies that effectively reduce the amount of data stored on disk while maintaining the quality of scientific outcomes. Lossless data-compression methods are designed to preserve the information content of the data but often struggle to achieve a high compression ratio when applied to experimental data that contain noise. Conversely, lossy compression methods offer the potential to greatly reduce the data volume. Nonetheless, it is vital to thoroughly assess the impact of data quality and scientific outcomes when employing lossy compression, as it inherently involves discarding information. The evaluation of lossy compression effects on data requires proper data quality metrics. In our research, we assess various approaches for both lossless and lossy compression techniques applied to SX data, and equally importantly, we describe metrics suitable for evaluating SX data quality. Full Article text
ria Droplet microfluidics for time-resolved serial crystallography By journals.iucr.org Published On :: 2024-03-01 Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis. A seeding strategy was used to overcome the improbability of Pdx1 nucleation occurring with diminishing droplet volumes. Convection within droplets was exploited for rapid crystal mixing with ligands. Mixing times of <2 ms were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be utilized to advance time-resolved serial crystallography. Full Article text
ria Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography By journals.iucr.org Published On :: 2024-07-22 Light–oxygen–voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process. Full Article text
ria In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry By journals.iucr.org Published On :: 2024-07-15 The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons. Full Article text
ria Exploring serial crystallography for drug discovery By journals.iucr.org Published On :: 2024-07-29 Structure-based drug design is highly dependent on the availability of structures of the protein of interest in complex with lead compounds. Ideally, this information can be used to guide the chemical optimization of a compound into a pharmaceutical drug candidate. A limitation of the main structural method used today – conventional X-ray crystallography – is that it only provides structural information about the protein complex in its frozen state. Serial crystallography is a relatively new approach that offers the possibility to study protein structures at room temperature (RT). Here, we explore the use of serial crystallography to determine the structures of the pharmaceutical target, soluble epoxide hydrolase. We introduce a new method to screen for optimal microcrystallization conditions suitable for use in serial crystallography and present a number of RT ligand-bound structures of our target protein. From a comparison between the RT structural data and previously published cryo-temperature structures, we describe an example of a temperature-dependent difference in the ligand-binding mode and observe that flexible loops are better resolved at RT. Finally, we discuss the current limitations and potential future advances of serial crystallography for use within pharmaceutical drug discovery. Full Article text
ria Bridging length scales in hard materials with ultra-small angle X-ray scattering – a critical review By journals.iucr.org Published On :: 2024-08-01 Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for in situ characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments. Full Article text
ria Crossing length scales: X-ray approaches to studying the structure of biological materials By journals.iucr.org Published On :: 2024-08-28 Biological materials have outstanding properties. With ease, challenging mechanical, optical or electrical properties are realised from comparatively `humble' building blocks. The key strategy to realise these properties is through extensive hierarchical structuring of the material from the millimetre to the nanometre scale in 3D. Though hierarchical structuring in biological materials has long been recognized, the 3D characterization of such structures remains a challenge. To understand the behaviour of materials, multimodal and multi-scale characterization approaches are needed. In this review, we outline current X-ray analysis approaches using the structures of bone and shells as examples. We show how recent advances have aided our understanding of hierarchical structures and their functions, and how these could be exploited for future research directions. We also discuss current roadblocks including radiation damage, data quantity and sample preparation, as well as strategies to address them. Full Article text
ria Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography By journals.iucr.org Published On :: 2024-10-29 OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates. Full Article text
ria Crystal structure solution and high-temperature thermal expansion in NaZr2(PO4)3-type materials By journals.iucr.org Published On :: 2024-03-22 The NaZr2P3O12 family of materials have shown low and tailorable thermal expansion properties. In this study, SrZr4P6O24 (SrO·4ZrO2·3P2O5), CaZr4P6O24 (CaO·4ZrO2·3P2O5), MgZr4P6O24 (MgO·4ZrO2·3P2O5), NaTi2P3O12 [½(Na2O·4TiO2·3P2O5)], NaZr2P3O12 [½(Na2O·4ZrO2·3P2O5)], and related solid solutions were synthesized using the organic–inorganic steric entrapment method. The samples were characterized by in-situ high-temperature X-ray diffraction from 25 to 1500°C at the Advanced Photon Source and National Synchrotron Light Source II. The average linear thermal expansion of SrZr4P6O24 and CaZr4P6O24 was between −1 × 10−6 per °C and 6 × 10−6 per °C from 25 to 1500°C. The crystal structures of the high-temperature polymorphs of CaZr4P6O24 and SrZr4P6O24 with R3c symmetry were solved by Fourier difference mapping and Rietveld refinement. This polymorph is present above ∼1250°C. This work measured thermal expansion coefficients to 1500°C for all samples and investigated the differences in thermal expansion mechanisms between polymorphs and between compositions. Full Article text
ria Importance of powder diffraction raw data archival in a curated database for materials science applications By journals.iucr.org Published On :: 2024-08-26 In recent years, there is a significant interest from the crystallographic and materials science communities to have access to raw diffraction data. The effort in archiving raw data for access by the user community is spearheaded by the International Union of Crystallography (IUCr) Committee on Data. In materials science, where powder diffraction is extensively used, the challenge in archiving raw data is different to that from single crystal data, owing to the very nature of the contributions involved. Powder diffraction (X-ray or neutron) data consist of contributions from the material under study as well as instrument specific parameters. Having raw powder diffraction data can be essential in cases of analysing materials with poor crystallinity, disorder, micro structure (size/strain) etc. Here, the initiative and progress made by the International Centre for Diffraction Data (ICDDR) in archiving powder X-ray diffraction raw data in the Powder Diffraction FileTM (PDFR) database is outlined. The upcoming 2025 release of the PDF-5+ database will have more than 20 800 raw powder diffraction patterns that are available for reference. Full Article text
ria Synthesis and properties of Sr2La2NiW2O12, a new S = 1 triangular lattice magnet By journals.iucr.org Published On :: 2024-08-30 Magnetic materials featuring triangular arrangements of spins are frequently investigated as platforms hosting magnetic frustration. Hexagonal perovskites with ordered vacancies serve as excellent candidates for two-dimensional triangular magnetism due to the considerable separation of the magnetic planes. In this work, the effects of chemical pressure on the ferromagnetic ground state of Ba2La2NiW2O12 by substitution of Ba2+ with Sr2+ to produce Sr2La2NiW2O12 are investigated. The two materials are characterized using synchrotron-based XRD, XANES and EXAFS in addition to magnetometry in order to correlate their crystal structures and magnetic properties. Both materials form in space group R3, yet as a result of the enhanced bending of key bond angles due to the effects of chemical pressure, the TC value of the magnetic Ni2+ sublattice is reduced from ∼6 K in Ba2La2NiW2O12 to 4 K in Sr2La2NiW2O12. Full Article text
ria Synthesis, structure and Hirshfeld surface analysis of 1,3-bis[(1-octyl-1H-1,2,3-triazol-4-yl)methyl]-1H-benzo[d]imidazol-2(3H)-one By journals.iucr.org Published On :: 2023-11-21 The title molecule, C29H44N8O, adopts a conformation resembling a two-bladed fan with the octyl chains largely in fully extended conformations. In the crystal, C—H⋯O hydrogen bonds form chains of molecules extending along the b-axis direction, which are linked by weak C—H⋯N hydrogen bonds and C—H⋯π interactions to generate a three-dimensional network. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (68.3%), H⋯N/N⋯H (15.7%) and H⋯C/C⋯H (10.4%) interactions. Full Article text
ria Crystal structure and antimycobacterial evaluation of 2-(cyclohexylmethyl)-7-nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-one By journals.iucr.org Published On :: 2023-11-30 The title compound, C15H15F3N2O3S, crystallizes in the monoclinic system, space group I2/a, with Z = 8. As expected, the nine-membered heterobicyclic system is virtually planar and the cyclohexyl group adopts a chair conformation. There is structural evidence for intramolecular N—S⋯O chalcogen bonding between the benzisothiazolinone S atom and one O atom of the nitro group, approximately aligned along the extension of the covalent N—S bond [N—S⋯O = 162.7 (1)°]. In the crystal, the molecules form centrosymmetric dimers through C—H⋯O weak hydrogen bonding between a C—H group of the electron-deficient benzene ring and the benzothiazolinone carbonyl O atom with an R22(10) motif. In contrast to the previously described N-acyl 7-nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-ones, the title N-cyclohexylmethyl analogue does not inhibit growth of Mycobacterium aurum and Mycobacterium smegmatis in vitro. Full Article text
ria Crystal structure and Hirshfeld-surface analysis of diaquabis(5-methyl-1H-1,2,4-triazole-3-carboxylato)copper(II) By journals.iucr.org Published On :: 2024-01-01 The title compound, [Cu(HL)2(H2O)2] or [Cu(C4H4N3O2)2(H2O)2], is a mononuclear octahedral CuII complex based on 5-methyl-1H-1,2,4-triazole-3-carboxylic acid (H2L). [Cu(HL)2(H2O)2] was synthesized by reaction of H2L with copper(II) nitrate hexahydrate (2:1 stoichiometric ratio) in water under ambient conditions to produce clear light-blue crystals. The central Cu atom exhibits an N2O4 coordination environment in an elongated octahedral geometry provided by two bidentate HL− anions in the equatorial plane and two water molecules in the axial positions. Hirshfeld surface analysis revealed that the most important contributions to the surface contacts are from H⋯O/O⋯H (33.1%), H⋯H (29.5%) and H⋯N/N⋯H (19.3%) interactions. Full Article text
ria JUAMI, the joint undertaking for an African materials institute: building materials science research collaborations and capabilities between continents By journals.iucr.org Published On :: 2024-01-26 JUAMI, the joint undertaking for an African materials institute, is a project to build collaborations and materials research capabilities between PhD researchers in Africa, the United States, and the world. Focusing on research-active universities in the East African countries of Kenya, Ethiopia, Tanzania and Uganda, the effort has run a series of schools focused on materials for sustainable energy and materials for sustainable development. These bring together early-career researchers from Africa, the US, and beyond, for two weeks in a close-knit environment. The program includes lectures on cutting-edge research from internationally renowned speakers, highly interactive tutorial lectures on the science behind the research, also from internationally known researchers, and hands-on practicals and team-building exercises that culminate in group proposals from self-formed student teams. The schools have benefited more than 300 early-career students and led to proposals that have received funding and have led to research collaborations and educational non-profits. JUAMI continues and has an ongoing community of alumni who share resources and expertise, and is open to like-minded people who want to join and develop contacts and collaborations internationally. Full Article text
ria An unexpected tautomer: synthesis and crystal structure of N-[6-amino-4-(methylsulfanyl)-1,2-dihydro-1,3,5-triazin-2-ylidene]benzenesulfonamide By journals.iucr.org Published On :: 2024-01-09 The title compound, C10H11N5O2S2, consists of an unexpected tautomer with a protonated nitrogen atom in the triazine ring and a formal exocyclic double bond C=N to the sulfonamide moiety. The ring angles at the unsubstituted nitrogen atoms are narrow, at 115.57 (12) and 115.19 (12)°, respectively, whereas the angle at the carbon atom between these N atoms is very wide, 127.97 (13)°. The interplanar angle between the two rings is 79.56 (5)°. The molecules are linked by three classical hydrogen bonds, forming a ribbon structure. There are also unusual linkages involving three short contacts (< 3 Å) from a sulfonamide oxygen atom to the C—NH—C part of a triazine ring. Full Article text
ria Synthesis and crystal structure of a cadmium(II) coordination polymer based on 4,4'-(1H-1,2,4-triazole-3,5-diyl)dibenzoate By journals.iucr.org Published On :: 2024-01-09 The asymmetric unit of the title compound, catena-poly[[[aquabis(pyridine-κN)cadmium(II)]-μ2-4,4'-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ4O,O':O'',O'''] 4.5-hydrate], {[Cd(C16H9N3O4)(C5H5N)2(H2O)]·4.5H2O}n or {[Cd(bct)(py)2(H2O)]·4.5H2O}n (I), consists of a Cd2+ cation coordinated to one bct2– carboxylate dianion, two molecules of pyridine and a water molecule as well as four and a half water molecules of crystallization. The metal ion in I possesses a pentagonal–bipyramidal environment with the four O atoms of the two bidentately coordinated carboxylate groups and the N atom of a pyridine molecule forming the O4N equatorial plane, while the N atom of another pyridine ligand and the O atom of the water molecule occupy the axial positions. The bct2– bridging ligand connects two metal ions via its carboxylic groups, resulting in the formation of a parallel linear polymeric chain running along the [1overline{1}1] direction. The coordinated water molecule of one chain forms a strong O—H⋯O hydrogen bond with the carboxylate O atom of a neighboring chain, leading to the formation of double chains with a closest distance of 5.425 (7) Å between the cadmium ions belonging to different chains. Aromatic π–π stacking interactions between the benzene fragments of the anions as well as between the coordinated pyridine molecules belonging to different chains results in the formation of sheets oriented parallel to the (overline{1}01) plane. As a result of hydrogen-bonding interactions involving the water molecules of crystallization, the sheets are joined together in a three-dimensional network. Full Article text
ria Synthesis, crystal structure and Hirshfeld surface analysis of 2-({5-[(naphthalen-1-yl)methyl]-4-phenyl-4H-1,2,4-triazol-3-yl}sulfanyl)-1-(4-nitrophenyl)ethanone By journals.iucr.org Published On :: 2024-01-26 The title compound, C27H20N4O3S, crystallizes in the monoclinic system, space group P21/n, with Z = 4. The global shape of the molecule is determined by the orientation of the substituents on the central 4H-1,2,4-triazole ring. The nitrophenyl ring, phenyl ring, and naphthalene ring system are oriented at dihedral angles of 82.95 (17), 77.14 (18) and 89.46 (15)°, respectively, with respect to the triazole ring. The crystal packing features chain formation in the b-axis direction by S⋯O interactions. A Hirshfeld surface analysis indicates that the highest contributions to surface contacts arise from contacts in which H atoms are involved. Full Article text
ria Structure of the five-coordinate CoII complex (1H-imidazole){tris[(1-benzyltriazol-4-yl-κN3)methyl]amine-κN}cobalt(II) bis(tetrafluoroborate) By journals.iucr.org Published On :: 2024-04-18 The title compound, [Co(C3H4N2)(C30H30N10)](BF4)2, is a five-coordinate CoII complex based on the neutral ligands tris[(1-benzyltriazol-4-yl)methyl]amine (tbta) and imidazole. It exhibits a distorted trigonal bipyramidal geometry in which the equatorial positions are occupied by the three N-atom donors from the triazole rings of the tripodal tbta ligand. The apical amine N-atom donor of tbta and the N-atom donor of the imidazole ligand occupy the axial positions of the coordination sphere. Two tetrafluoroborate anions provide charge balance in the crystal. Full Article text
ria Crystal structure of bis{2-[5-(3,4,5-trimethoxyphenyl)-4H-1,2,4-triazol-3-yl]pyridine}palladium(II) bis(trifluoroacetate) trifluoroacetic acid disolvate By journals.iucr.org Published On :: 2024-05-03 The new palladium(II) complex, [Pd(C16H16N4O3)2](CF3COO)2·2CF3COOH, crystallizes in the triclinic space group Poverline{1} with the asymmetric unit containing half the cation (PdII site symmetry Ci), one trifluoroactetate anion and one co-crystallized trifluoroacetic acid molecule. Two neutral chelating 2-[5-(3,4,5-trimethoxyphenyl)-4H-1,2,4-triazol-3-yl]pyridine ligands coordinate to the PdII ion through the triazole-N and pyridine-N atoms in a distorted trans-PdN4 square-planar configuration [Pd—N 1.991 (2), 2.037 (2) Å; cis N—Pd—N 79.65 (8), 100.35 (8)°]. The complex cation is quite planar, except for the methoxo groups (δ = 0.117 Å for one of the C atoms). The planar configuration is supported by two intramolecular C—H⋯N hydrogen bonds. In the crystal, the π–π-stacked cations are arranged in sheets parallel to the ab plane that are flanked on both sides by the trifluoroacetic acid–trifluoroacetate anion pairs. Apart from classical N/O—H⋯O hydrogen-bonding interactions, weak C—H⋯F/N/O contacts consolidate the three-dimensional architecture. Both trifluoroacetic moieties were found to be disordered over two resolvable positions with a refined occupancy ratio of 0.587 (1):0.413 (17) and 0.530 (6):0.470 (6) for the protonated and deprotonated forms, respectively. Full Article text
ria Crystal structure, Hirshfeld surface analysis, calculations of intermolecular interaction energies and energy frameworks and the DFT-optimized molecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)methyl]-3-(prop-1-en-2-yl)-1H-b By journals.iucr.org Published On :: 2024-05-14 The benzimidazole entity of the title molecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C—H⋯O hydrogen bonds link individual molecules into layers extending parallel to the ac plane. Two weak C—H⋯π(ring) interactions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) interactions. Hydrogen bonding and van der Waals interactions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The molecular structure optimized by density functional theory (DFT) at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined molecular structure in the solid state. Full Article text
ria Synthesis, structural studies and Hirshfeld surface analysis of 2-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]pyridin-1-ium hexakis(nitrato-κ2O,O')thorate(IV) By journals.iucr.org Published On :: 2024-07-05 Reaction of thorium(IV) nitrate with 2-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]pyridine (L) yielded (LH)2[Th(NO3)6] or (C14H13N4)2[Th(NO3)6] (1), instead of the expected mixed-ligand complex [Th(NO3)4L2], which was detected in the mass spectrum of 1. In the structure, the [Th(NO3)6]2− anions display an icosahedral coordination geometry and are connected by LH+ cations through C—H⋯O hydrogen bonds. The LH+ cations interact via N—H⋯N hydrogen bonds. Hirshfeld surface analysis indicates that the most important interactions are O⋯H/H⋯O hydrogen-bonding interactions, which represent a 55.2% contribution. Full Article text
ria Crystal structure of catena-poly[[methanoldioxidouranium(VI)]-μ-2-[5-(2-oxidophenyl)-1H-1,2,4-triazol-3-yl]acetato-κ2O:O'] By journals.iucr.org Published On :: 2024-07-12 In the title complex, [U(C10H7N3O3)O2(CH3OH)]n, the UVI cation has a typical pentagonal–bipyramidal environment with the equatorial plane defined by one N and two O atoms of one doubly deprotonated 2-[5-(2-hydroxyphenyl)-1H-1,2,4-triazol-3-yl]acetic acid ligand, a carboxylate O atom of the symmetry-related ligand and the O atom of the methanol molecule [U—N/Oeq 2.256 (4)–2.504 (5) Å]. The axial positions are occupied by two oxide O atoms. The equatorial atoms are almost coplanar, with the largest deviation from the mean plane being 0.121 Å for one of the O atoms. The benzene and triazole rings of the tetradentate chelating–bridging ligand are twisted by approximately 21.6 (2)° with respect to each other. The carboxylate group of the ligand bridges two uranyl cations, forming a neutral zigzag chain reinforced by a strong O—H⋯O hydrogen bond. In the crystal, adjacent chains are linked into two-dimensional sheets parallel to the ac plane by C/N—H⋯N/O hydrogen bonding and π–π interactions. Further weak C—H⋯O contacts consolidate the three-dimensional supramolecular architecture. In the solid state, the compound shows a broad medium intensity LMCT transition centred around 463 nm, which is responsible for its red colour. Full Article text
ria Synthesis, crystal structure and Hirshfeld surface analysis of [1-(4-bromophenyl)-1H-1,2,3-triazol-4-yl]methyl 2-(4-nitrophenoxy)acetate By journals.iucr.org Published On :: 2024-07-31 The title compound, C17H13BrN4O5, was synthesized by a Cu2Br2-catalysed Meldal–Sharpless reaction between 4-nitrophenoxyacetic acid propargyl ether and para-bromophenylazide, and characterized by X-ray structure determination and 1H NMR spectroscopy. The molecules, with a near-perpendicular orientation of the bromophenyl-triazole and nitrophenoxyacetate fragments, are connected into a three-dimensional network by intermolecular C—H⋯O and C—H⋯N hydrogen bonds (confirmed by Hirshfeld surface analysis), π–π and Br–π interactions. Full Article text
ria Synthesis, crystal structure and Hirshfeld surface analysis of 1-[(1-octyl-1H-1,2,3-triazol-4-yl)methyl]-3-phenyl-1,2-dihydroquinoxalin-2(1H)-one By journals.iucr.org Published On :: 2024-08-09 In the title molecule, C25H29N5O, the dihydroquinoxaline unit is not quite planar (r.m.s. deviation = 0.030 Å) as there is a dihedral angle of 2.69 (3)° between the mean planes of the constituent rings and the molecule adopts a hairpin conformation. In the crystal, the polar portions of the molecules are associated through C—H⋯O and C—H⋯N hydrogen bonds and C—H⋯π(ring) and C=O⋯π(ring) interactions, forming thick layers parallel to the bc plane and with the n-octyl groups on the outside surfaces. Full Article text
ria Crystal structure and Hirshfeld surface analysis of dichlorido[2-(3-cyclopentyl-1,2,4-triazol-5-yl-κN4)pyridine-κN]palladium(II) dimethylformamide monosolvate By journals.iucr.org Published On :: 2024-08-16 This study presents the synthesis, characterization and Hirshfeld surface analysis of the title mononuclear complex, [PdCl2(C12H14N4)]·C3H7NO. The compound crystalizes in the P21/c space group of the monoclinic system. The asymmetric unit contains one neutral complex Pd(HLc-Pe)Cl2 [HLc-Pe is 2-(3-cyclopentyl-1,2,4-triazol-5-yl)pyridine] and one molecule of DMF as a solvate. The Pd atom has a square-planar coordination. In the crystal, molecules are linked by intermolecular N—H⋯O and C—H⋯N hydrogen bonds, forming layers parallel to the bc plane. A Hirshfeld surface analysis showed that the H⋯H contacts dominate the crystal packing with a contribution of 41.4%. The contribution of the N⋯H/H⋯N and H⋯O/O⋯H interactions is somewhat smaller, amounting to 12.4% and 5%, respectively. Full Article text
ria Synthesis, crystal structure and Hirshfeld surface analysis of a new copper(II) complex based on diethyl 2,2'-(4H-1,2,4-triazole-3,5-diyl)diacetate By journals.iucr.org Published On :: 2024-08-30 The title compound, bis[μ-2,2'-(4H-1,2,4-triazole-3,5-diyl)diacetato]bis[diaquacopper(II)] dihydrate, [Cu2(C6H5N3O4)2(H2O)4]·2H2O, is a dinuclear octahedral CuII triazole-based complex. The central copper atoms are hexa-coordinated by two nitrogen atoms in the equatorial positions, two equatorial oxygen atoms of two carboxylate substituents in position 3 and 5 of the 1,2,4-triazole ring, and two axial oxygen atoms of two water molecules. Two additional solvent water molecules are linked to the title molecule by O—H⋯N and O⋯H—O hydrogen bonds. The crystal structure is built up from the parallel packing of discrete supramolecular chains running along the a-axis direction. Hirshfeld surface analysis suggests that the most important contributions to the surface contacts are from H⋯O/O⋯H (53.5%), H⋯H (28.1%), O⋯O (6.3%) and H⋯C/C⋯H (6.2%) interactions. The crystal studied was twinned by a twofold rotation around [100]. Full Article text
ria Crystal structure, Hirshfeld surface analysis, and calculations of intermolecular interaction energies and energy frameworks of 1-[(1-hexyl-1H-1,2,3-triazol-4-yl)methyl]-3-(1-methylethenyl)-benzimidazol-2-one By journals.iucr.org Published On :: 2024-09-30 The benzimidazole moiety in the title molecule, C19H25N5O, is almost planar and oriented nearly perpendicular to the triazole ring. In the crystal, C—H⋯O hydrogen bonds link the molecules into a network structure. There are no π–π interactions present but two weak C—H⋯π(ring) interactions are observed. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (62.0%), H⋯C/C⋯H (16.1%), H⋯N/N⋯H (13.7%) and H⋯O/O⋯H (7.5%) interactions. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via the dispersion energy contributions in the title compound. Full Article text
ria Synthesis and crystal structure of 1H-1,2,4-triazole-3,5-diamine monohydrate By journals.iucr.org Published On :: 2024-10-11 The title compound, a hydrate of 3,5-diamino-1,2,4-triazole (DATA), C2H5N5·H2O, was synthesized in the presence of sodium perchlorate. The evaporation of H2O from its aqueous solution resulted in anhydrous DATA, suggesting that sodium perchlorate was required to precipitate the DATA hydrate. The DATA hydrate crystallizes in the P21/c space group in the form of needle-shaped crystals with one DATA and one water molecule in the asymmetric unit. The water molecules form a three-dimensional network in the crystal structure. Hirshfeld surface analysis revealed that 8.5% of the intermolecular interactions originate from H⋯O contacts derived from the incorporation of the water molecules. Full Article text
ria Synthesis and crystal structure of 1,3,5-tris[(1H-benzotriazol-1-yl)methyl]-2,4,6-triethylbenzene By journals.iucr.org Published On :: 2024-10-31 In the crystal structure of the title compound, C33H33N9, the tripodal molecule exists in a conformation in which the substituents attached to the central arene ring are arranged in an alternating order above and below the ring plane. The three benzotriazolyl moieties are inclined at angles of 88.3 (1), 85.7 (1) and 82.1 (1)° with respect to the mean plane of the benzene ring. In the crystal, only weak molecular cross-linking involving C—H⋯N hydrogen bonds is observed. Full Article text
ria Crystal structure of bis{5-(4-chlorophenyl)-3-[6-(1H-pyrazol-1-yl)pyridin-2-yl]-1H-1,2,4-triazol-1-ido}nickel(II) methanol disolvate By journals.iucr.org Published On :: 2024-10-31 The unit cell of the title compound, [Ni(C16H10ClN6)2]·2CH3OH, consists of a neutral complex and two methanol molecules. In the complex, the two tridentate 2-(3-(4-chlorophenyl)-1H-1,2,4-triazol-5-yl)-6-(1H-pyrazol-1-yl)pyridine ligands coordinate to the central NiII ion through the N atoms of the pyrazole, pyridine and triazole groups, forming a pseudooctahedral coordination sphere. Neighbouring tapered molecules are linked through weak C—H(pz)⋯π(ph) interactions into monoperiodic chains, which are further linked through weak C—H⋯N/C interactions into diperiodic layers. The intermolecular contacts were quantified using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative contributions of the contacts to the crystal packing to be H⋯H 32.8%, C⋯H/H⋯C 27.5%, N⋯H/H⋯N 15.1%, and Cl⋯H/H⋯Cl 14.0%. The average Ni—N bond distance is 2.095 Å. Energy framework analysis at the HF/3–21 G theory level was performed to quantify the interaction energies in the crystal structure. Full Article text
ria A workflow for single-particle structure determination via iterative phasing of rotational invariants in fluctuation X-ray scattering By journals.iucr.org Published On :: 2024-03-15 Fluctuation X-ray scattering (FXS) offers a complementary approach for nano- and bioparticle imaging with an X-ray free-electron laser (XFEL), by extracting structural information from correlations in scattered XFEL pulses. Here a workflow is presented for single-particle structure determination using FXS. The workflow includes procedures for extracting the rotational invariants from FXS patterns, performing structure reconstructions via iterative phasing of the invariants, and aligning and averaging multiple reconstructions. The reconstruction pipeline is implemented in the open-source software xFrame and its functionality is demonstrated on several simulated structures. Full Article text
ria Robust image descriptor for machine learning based data reduction in serial crystallography By journals.iucr.org Published On :: 2024-03-26 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. Full Article text
ria Applications of the Clifford torus to material textures By journals.iucr.org Published On :: 2024-04-15 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. Full Article text