Spotlight on BGS coastal erosion data  British Geological Survey

The crystal structure of a neo­pentyl­oxypillar[5]arene with two pyridine mol­ecules encapsulated in the macrocyclic cavity is reported.

Following the work of Day & Hawthorne [Acta Cryst. (2022), A78, 212–233] and Day et al. [Acta Cryst. (2024), A80, 258–281], the program GraphT–T has been developed to embed graphical representations of observed and hypothetical chains of (SiO4)4− tetrahedra into 2D and 3D Euclidean space. During embedding, the distance between linked vertices (T–T distances) and the distance between unlinked vertices (T⋯T separations) in the resultant unit-distance graph are restrained to the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is restrained to be equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. The notional interactions between vertices are described by a 3D spring-force algorithm in which the attractive forces between linked vertices behave according to Hooke's law and the repulsive forces between unlinked vertices behave according to Coulomb's law. Embedding parameters (i.e. spring coefficient, k, and Coulomb's constant, K) are iteratively refined during embedding to determine if it is possible to embed a given graph to produce a unit-distance graph with T–T distances and T⋯T separations that are compatible with the observed T–T distances and T⋯T separations in crystal structures. The resultant unit-distance graphs are denoted as compatible and may form crystal structures if and only if all distances between linked vertices (T–T distances) agree with the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. If the unit-distance graph does not satisfy these conditions, it is considered incompatible and the corresponding chain of tetrahedra is unlikely to form crystal structures. Using GraphT–T, Day et al. [Acta Cryst. (2024), A80, 258–281] have shown that several topological properties of chain graphs influence the flexibility (and rigidity) of the corresponding chains of Si tetrahedra and may explain why particular compatible chain arrangements (and the minerals in which they occur) are more common than others and/or why incompatible chain arrangements do not occur in crystals despite being topologically possible.

The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallo­graphic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.

The African Light Source (AfLS) project is now almost eight years old. This article assesses the history, current context and future of the project. There is by now considerable momentum in building the user community, including deep training, facilitating access to current facilities, growing the scientific output, scientific networks and growing the local laboratory-scale research infrastructure. The Conceptual Design Report for the AfLS is in its final editing stages. This document specifies the socio-economic and scientific rationales and the technical aspects amongst others. The AfLS is supported by many national and Pan-African scientific professional bodies and voluntary associates across many scientific disciplines, and there are stakeholders throughout the continent and beyond. The current roadmap phases have expanded to include national and Pan-African level conversations with policy makers through new Strategic Task Force groups. The document summarizes this progress and discusses the future of the project.

In recent years, China's advanced light sources have entered a period of rapid construction and development. As modern X-ray detectors and data acquisition technologies advance, these facilities are expected to generate massive volumes of data annually, presenting significant challenges in data management and utilization. These challenges encompass data storage, metadata handling, data transfer and user data access. In response, the Data Organization Management Access Software (DOMAS) has been designed as a framework to address these issues. DOMAS encapsulates four fundamental modules of data management software, including metadata catalogue, metadata acquisition, data transfer and data service. For light source facilities, building a data management system only requires parameter configuration and minimal code development within DOMAS. This paper firstly discusses the development of advanced light sources in China and the associated demands and challenges in data management, prompting a reconsideration of data management software framework design. It then outlines the architecture of the framework, detailing its components and functions. Lastly, it highlights the application progress and effectiveness of DOMAS when deployed for the High Energy Photon Source (HEPS) and Beijing Synchrotron Radiation Facility (BSRF).

The beamline optics and endstations at branch B of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source are described. B07-B provides medium-flux X-rays in the range 45–2200 eV from a bending magnet source, giving access to local electronic structure for atoms of all elements from Li to Y. It has an endstation for high-throughput X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) measurements under ultrahigh-vacuum (UHV) conditions. B07-B has a second endstation dedicated to NEXAFS at pressures from UHV to ambient pressure (1 atm). The combination of these endstations permits studies of a wide range of interfaces and materials. The beamline and endstation designs are discussed in detail, as well as their performance and the commissioning process.

To characterize an electron beam, visible synchrotron light is often used and dedicated beamlines at synchrotron sources are becoming a more common feature as instruments and methods for the diagnostics are, along with the accelerators, further developed. At KARA (Karlsruhe Research Accelerator), such a beamline exists and is based on a typical infrared/visible-light configuration. From experience at such beamlines no significant radiation was expected (dose rates larger than 0.5 µSv h−1). This was found not to be the case and a higher dose was measured which fortunately could be shielded to an acceptable level with 0.3 mm of aluminium foil or 2.0 mm of Pyrex glass. The presence of this radiation led to further investigation by both experiment and calculation. A custom setup using a silicon drift detector for energy-dispersive spectroscopy (Ketek GmbH) and attenuation experiments showed the radiation to be predominantly copper K-shell fluorescence and is confirmed by calculation. The measurement of secondary radiation from scattering of synchrotron and other radiation, and its calculation, is important for radiation protection, and, although a lot of experience exists and methods for radiation protection are well established, changes in machine, beamlines and experiments mean a constant appraisal is needed.

The users of synchrotron light are now tens of thousands throughout the world. Paradoxically, many of them do not know much about the early history of their domain. This is regrettable, since education about the initial developments makes it easier to fully understand synchrotron radiation and effectively use its amazing features. Scarcely known, in particular, is the key role of scientists working in Frascati, Italy. Partly based on his personal experiences, the author reports here relevant aspects of this story, including a pioneering French–Italian experiment that started in the early 1960s, and the Frascati contributions in the 1970s and 1980s to the birth of synchrotron light research. Finally, the unwise strategic decisions that prevented Italy from achieving absolute leadership in this domain – in spite of its unique initial advantages – are analyzed.

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.

The Biomedical Imaging and Therapy facility of the Canadian Light Source comprises two beamlines, which together cover a wide X-ray energy range from 13 keV up to 140 keV. The beamlines were designed with a focus on synchrotron applications in preclinical imaging and veterinary science as well as microbeam radiation therapy. While these remain a major part of the activities of both beamlines, a number of recent upgrades have enhanced the versatility and performance of the beamlines, particularly for high-resolution microtomography experiments. As a result, the user community has been quickly expanding to include researchers in advanced materials, batteries, fuel cells, agriculture, and environmental studies. This article summarizes the beam properties, describes the endstations together with the detector pool, and presents several application cases of the various X-ray imaging techniques available to users.

Aerosol science is of utmost importance for both climate and public health research, and in recent years X-ray techniques have proven effective tools for aerosol-particle characterization. To date, such methods have often involved the study of particles collected onto a substrate, but a high photon flux may cause radiation damage to such deposited particles and volatile components can potentially react with the surrounding environment after sampling. These and many other factors make studies on collected aerosol particles challenging. Therefore, a new aerosol sample-delivery system dedicated to X-ray photoelectron spectroscopy studies of aerosol particles and gas molecules in-flight has been developed at the MAX IV Laboratory. The aerosol particles are brought from atmospheric pressure to vacuum in a continuous flow, ensuring that the sample is constantly renewed, thus avoiding radiation damage, and allowing measurements on the true unsupported aerosol. At the same time, available gas molecules can be used for energy calibration and to study gas-particle partitioning. The design features of the aerosol sample-delivery system and important information on the operation procedures are described in detail here. Furthermore, to demonstrate the experimental range of the aerosol sample-delivery system, results from aerosol particles of different shape, size and composition are presented, including inorganic atmospheric aerosols, secondary organic aerosols and engineered nanoparticles.

A state-of-the-art multilayer deposition system with a 4200 mm-long linear substrate translator housed within an ultra-high vacuum chamber has been developed. This instrument is engineered to produce single and multilayer coatings, accommodating mirrors up to 2000 mm in length through the utilization of eight rectangular cathodes. To ensure the quality and reliability of the coatings, the system incorporates various diagnostic tools for in situ thickness uniformity and stress measurement. Furthermore, the system features an annealing process capable of heating up to 700°C within the load-lock chamber. The entire operation, including pump down, deposition and venting processes, is automated through user-friendly software. In addition, all essential log data, power of sputtering source, working pressure and motion positions are automatically stored for comprehensive data analysis. Preliminary commissioning results demonstrate excellent lateral film thickness uniformity, achieving 0.26% along the translation direction over 1500 mm in dynamic mode. The multilayer deposition system is poised for use in fabricating periodic, lateral-graded and depth-graded multilayers, specifically catering to the beamlines for diverse scientific applications at Diamond Light Source.

The reaction between a racemic mixture of (R,S)-fixolide and 4-methyl­thio­semicarbazide in ethanol with a 1:1 stoichiometric ratio and catalysed with HCl, yielded the title compound, C20H31N3S [common name: (R,S)-fixolide 4-methyl­thio­semicarbazone]. There is one crystallographically independent mol­ecule in the asymmetric unit, which is disordered over the aliphatic ring [site-occupancy ratio = 0.667 (13):0.333 (13)]. The disorder includes the chiral C atom, the neighbouring methyl­ene group and the methyl H atoms of the methyl group bonded to the chiral C atom. The maximum deviations from the mean plane through the disordered aliphatic ring amount to 0.328 (6) and −0.334 (6) Å [r.m.s.d. = 0.2061 Å], and −0.3677 (12) and 0.3380 (12) Å [r.m.s.d. = 0.2198 Å] for the two different sites. Both fragments show a half-chair conformation. Additionally, the N—N—C(=S)—N entity is approximately planar, with the maximum deviation from the mean plane through the selected atoms being 0.0135 (18) Å [r.m.s.d. = 0.0100 Å]. The mol­ecule is not planar due to the dihedral angle between the thio­semicarbazone entity and the aromatic ring, which amounts to 51.8 (1)°, and due to the sp3-hybridized carbon atoms of the fixolide fragment. In the crystal, the mol­ecules are connected by H⋯S inter­actions with graph-set motif C(4), forming a mono-periodic hydrogen-bonded ribbon along [100]. The Hirshfeld surface analysis suggests that the major contributions for the crystal cohesion are [(R,S)-isomers considered separately] H⋯H (75.7%), H⋯S/S⋯H (11.6%), H⋯C/C⋯H (8.3% and H⋯N/N⋯H (4.4% for both of them).

The reaction of ethane-1,2-di­amine (en, C2H8N2), the sodium salt of naphthalene-1,5-di­sulfonic acid (H2NDS, C10H8O6S2), and nickel sulfate in an aqueous solution resulted in the formation of the title salt, [Ni(C2H8N2)(H2O)4](C10H6O6S2)·2H2O or [Ni(en)(H2O)4](NDS)·2H2O. In the asymmetric unit, one half of an [Ni(en)(H2O)4]2+ cation and one half of an NDS2− anion, and one water mol­ecule of crystallization are present. The Ni2+ cation in the complex is positioned on a twofold rotation axis and exhibits a slight tetra­gonal distortion of the cis-NiO4N2 octa­hedron, with an Ni—N bond length of 2.0782 (16) Å, and Ni—O bond lengths of 2.1170 (13) Å and 2.0648 (14) Å. The anion is completed by inversion symmetry. In the extended structure, the cations, anions, and non-coordinating water mol­ecules are connected by inter­molecular N—H⋯O and O—H⋯O hydrogen bonding, as well as C—H⋯π inter­actions, forming a three-dimensional network.

The title compound, C17H17BN3I, is a type of di­aza­borinane featuring substitution at the 1, 2, and 3 positions of the nitro­gen–boron six-membered heterocycle. The organic mol­ecule has a planar structure, the dihedral angle between the pyridyl ring and the fused ring system being 3.46 (4)°. In the crystal, mol­ecules are stacked in a head-to-tail manner. The iodide ion makes close contacts with three organic mol­ecules and supports the alternating stack.

The cation of the title hydrated salt, C17H17BN3+·I−·H2O, is a di­aza­borinane featuring substitution at the 1, 2, and 3 positions in the nitro­gen–boron six-membered heterocycle. The cation is approximately planar with a dihedral angle between the pyridyl ring and the di­aza­borinane ring system of 5.40 (5)°. In the crystal, the cations stack along [100] in an alternating head-to-tail manner, while the iodide ion and water mol­ecule form one-dimensional hydrogen-bonded chains beside the cation stack. The cation stacks and I−–water chains are crosslinked by N—H⋯I and N—H⋯O hydrogen bonds.

The inter­action between 8-hy­droxy­quinoline (8HQ, C9H7NO) and naphthalene-1,5-di­sulfonic acid (H2NDS, C10H8O6S2) in aqueous media results in the formation of the salt hydrate bis­(8-hy­droxy­quinolinium) naphthalene-1,5-di­sulfonate tetra­hydrate, 2C9H8NO+·C10H6O6S22−·4H2O. The asymmetric unit comprises one protonated 8HQ+ cation, half of an NDS2– dianion symmetrically disposed around a center of inversion, and two water mol­ecules. Within the crystal structure, these components are organized into chains along the [010] and [10overline{1}] directions through O—H⋯O and N—H⋯O hydrogen-bonding inter­actions, forming a di-periodic network parallel to (101). Additional stabilizing inter­actions such as C—H⋯O, C—H⋯π, and π–π inter­actions extend this arrangement into a tri-periodic network structure

The title compound, C15H12BN3, is a type of di­aza­borinane featuring substitution at 1, 2, and 3 positions in the nitro­gen–boron six-membered heterocycle. It is comprised of two almost planar units, the pyridyl ring and the Bdan (dan = 1,8-di­aminona­phtho) group, which subtend a dihedral angle of 24.57 (5)°. In the crystal, the mol­ecules are linked into R44(28) hydrogen-bonding networks around the fourfold inversion axis, giving cyclic tetra­mers. The mol­ecules form columnar stacks along the c axis.

The mol­ecular structure of C18H28O4, (+)-diplodiatoxin, is described, whereby the absolute configuration of the structure of diplodiatoxin has been confirmed by single-crystal X-ray diffraction. Diplodiatoxin crystallizes in the chiral P43212 space group with one mol­ecule in the asymmetric unit.

The crystal structure of 1,4-bis­(neopent­yloxy)pillar[5]arene, C95H140N2O10 (TbuP), featuring two encapsulated pyridine mol­ecules, reveals significant host–guest inter­actions. Inter­estingly, the pyridine guests are positioned near the neopent­yloxy substituents instead of the electron-rich aromatic core of the pillar[5]arene. This spatial arrangement suggests a preference for the pyridine mol­ecules to engage with the aliphatic regions of the host. Detailed analysis of the structural characteristics of this host–guest system (TbuP·2Py), as well as its packing pattern within the crystal network, is presented and discussed.

The crystal structures of 16 boron sub­phthalo­cy­an­ines (BsubPcs) with structurally diverse axial groups were analyzed and com­pared to elucidate the impact of the axial group on the inter­molecular π–π inter­actions, axial-group inter­actions, axial bond length and BsubPc bowl depth. π–π inter­actions between the iso­indole units of adjacent BsubPc mol­ecules most often involve concave–concave packing, whereas axial-group inter­actions with adjacent BsubPc mol­ecules tend to favour the convex side of the BsubPc bowl. Furthermore, axial groups that contain O and/or F atoms tend to have significant hy­dro­gen-bonding inter­actions, while axial groups containing arene site(s) can participate in π–π inter­actions with the BsubPc bowl, both of which can strongly influence the crystal packing. Bulky axial groups did tend to disrupt the π–π inter­actions and/or axial-group inter­actions, preventing some of the close packing that is seen in BsubPcs with less bulky axial groups. The atomic radius of the heteroatom bonded to boron directly influences the axial bond length, whereas the axial group has minimal impact on the BsubPc bowl depth. Finally, the crystal growth method did not generally appear to have a significant impact on the solid-state arrangement, with the exception of water occasionally being incorporated into crystal structures when hygroscopic solvents were used. These insights can help with the design and fine-tuning of the solid-state structures of BsubPcs as they continue to be developed as functional materials in organic electronics.

Three 2,4-di­aryl­pyrroles were synthesized starting from 4-nitro­butano­nes and the crystal structures of two derivatives were analysed. These are 4-(4-meth­oxy­phen­yl)-2-(thio­phen-2-yl)-1H-pyrrole, C15H13NOS, and 3-(4-bromo­phen­yl)-2-nitroso-5-phenyl-1H-pyrrole, C16H11BrN2O. Although pyrroles without sub­stituents at the α-position with respect to the N atom are very air sensitive and tend to polymerize, we succeeded in growing an adequate crystal for X-ray diffraction analysis. Further derivatization using sodium nitrite afforded a nitrosyl pyrrole derivative, which crystallized in the triclinic space group Poverline{1} with Z = 6. Thus, herein we report the first crystal structure of a nitrosyl pyrrole. Inter­estingly, the co-operative hydrogen bonds in this NO-substituted pyrrole lead to a trimeric structure with bifurcated halogen bonds at the ends, forming a two-dimensional (2D) layer with inter­stitial voids having a radius of 5 Å, similar to some reported macrocyclic porphyrins.

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.

The widespread adoption of cryoEM technologies for structural biology has pushed the discipline to new frontiers. A significant worldwide effort has refined the single-particle analysis (SPA) workflow into a reasonably standardized procedure. Significant investments of development time have been made, particularly in sample preparation, microscope data-collection efficiency, pipeline analyses and data archiving. The widespread adoption of specific commercial microscopes, software for controlling them and best practices developed at facilities worldwide has also begun to establish a degree of standardization to data structures coming from the SPA workflow. There is opportunity to capitalize on this moment in the maturation of the field, to capture metadata from SPA experiments and correlate the metadata with experimental outcomes, which is presented here in a set of programs called EMinsight. This tool aims to prototype the framework and types of analyses that could lead to new insights into optimal microscope configurations as well as to define methods for metadata capture to assist with the archiving of cryoEM SPA data. It is also envisaged that this tool will be useful to microscope operators and facilities looking to rapidly generate reports on SPA data-collection and screening sessions.

Type VII secretion (T7S) systems, also referred to as ESAT-6 secretion (ESX) systems, are molecular machines that have gained great attention due to their implications in cell homeostasis and in host–pathogen interactions in mycobacteria. The latter include important human pathogens such as Mycobacterium tuberculosis (Mtb), the etiological cause of human tuberculosis, which constitutes a pandemic accounting for more than one million deaths every year. The ESX-5 system is exclusively found in slow-growing pathogenic mycobacteria, where it mediates the secretion of a large family of virulence factors: the PE and PPE proteins. The secretion driving force is provided by EccC5, a multidomain ATPase that operates using four globular cytosolic domains: an N-terminal domain of unknown function (EccC5DUF) and three FtsK/SpoIIIE ATPase domains. Recent structural and functional studies of ESX-3 and ESX-5 systems have revealed EccCDUF to be an ATPase-like fold domain with potential ATPase activity, the functionality of which is essential for secretion. Here, the crystal structure of the MtbEccC5DUF domain is reported at 2.05 Å resolution, which reveals a nucleotide-free structure with degenerated cis-acting and trans-acting elements involved in ATP binding and hydrolysis. This crystallographic study, together with a biophysical assessment of the interaction of MtbEccC5DUF with ATP/Mg2+, supports the absence of ATPase activity proposed for this domain. It is shown that this degeneration is also present in DUF domains from other ESX and ESX-like systems, which are likely to exhibit poor or null ATPase activity. Moreover, based on an in silico model of the N-terminal region of MtbEccC5DUF, it is hypothesized that MtbEccC5DUF is a degenerated ATPase domain that may have retained the ability to hexamerize. These observations draw attention to DUF domains as structural elements with potential implications in the opening and closure of the membrane pore during the secretion process via their involvement in inter-protomer interactions.

Molecular structures can be determined in vitro and in situ with cryo-electron microscopy (cryo-EM). Specimen preparation is a major obstacle in cryo-EM. Typical sample preparation is orders of magnitude slower than biological processes. Time-resolved cryo-EM (TR-cryo-EM) can capture short-lived states. Here, Cryo-EM sample preparation with light-activated molecules (C-SPAM) is presented, an open-source, photochemistry-coupled device for TR-cryo-EM that enables millisecond resolution and tunable timescales across broad biological applications.

Human peptidylarginine deiminase isoform VI (PAD6), which is predominantly limited to cytoplasmic lattices in the mammalian oocytes in ovarian tissue, is essential for female fertility. It belongs to the peptidylarginine deiminase (PAD) enzyme family that catalyzes the conversion of arginine residues to citrulline in proteins. In contrast to other members of the family, recombinant PAD6 was previously found to be catalytically inactive. We sought to provide structural insight into the human homologue to shed light on this observation. We report here the first crystal structure of PAD6, determined at 1.7 Å resolution. PAD6 follows the same domain organization as other structurally known PAD isoenzymes. Further structural analysis and size-exclusion chromatography show that PAD6 behaves as a homodimer similar to PAD4. Differential scanning fluorimetry suggests that PAD6 does not coordinate Ca2+ which agrees with acidic residues found to coordinate Ca2+ in other PAD homologs not being conserved in PAD6. The crystal structure of PAD6 shows similarities with the inactive state of apo PAD2, in which the active site conformation is unsuitable for catalytic citrullination. The putative active site of PAD6 adopts a non-productive conformation that would not allow protein–substrate binding due to steric hindrance with rigid secondary structure elements. This observation is further supported by the lack of activity on the histone H3 and cytokeratin 5 substrates. These findings suggest a different mechanism for enzymatic activation compared with other PADs; alternatively, PAD6 may exert a non-enzymatic function in the cytoplasmic lattice of oocytes and early embryos.

Immunodominant membrane protein (IMP) is a prevalent membrane protein in phytoplasma and has been confirmed to be an F-actin-binding protein. However, the intricate molecular mechanisms that govern the function of IMP require further elucidation. In this study, the X-ray crystallographic structure of IMP was determined and insights into its interaction with plant actin are provided. A comparative analysis with other proteins demonstrates that IMP shares structural homology with talin rod domain-containing protein 1 (TLNRD1), which also functions as an F-actin-binding protein. Subsequent molecular-docking studies of IMP and F-actin reveal that they possess complementary surfaces, suggesting a stable interaction. The low potential energy and high confidence score of the IMP–F-actin binding model indicate stable binding. Additionally, by employing immunoprecipitation and mass spectrometry, it was discovered that IMP serves as an interaction partner for the phytoplasmal effector causing phyllody 1 (PHYL1). It was then shown that both IMP and PHYL1 are highly expressed in the S2 stage of peanut witches' broom phytoplasma-infected Catharanthus roseus. The association between IMP and PHYL1 is substantiated through in vivo immunoprecipitation, an in vitro cross-linking assay and molecular-docking analysis. Collectively, these findings expand the current understanding of IMP interactions and enhance the comprehension of the interaction of IMP with plant F-actin. They also unveil a novel interaction pathway that may influence phytoplasma pathogenicity and host plant responses related to PHYL1. This discovery could pave the way for the development of new strategies to overcome phytoplasma-related plant diseases.

To date, accurate modelling of the solvation process is challenging, often over-simplifying the solvent–solute interactions. The interplay between the molecular arrangement associated with the solvation process and crystal nucleation has been investigated by analysis of the piezo-solvatochromic behaviour of Reichardt's dye, ET(1), in methanol, ethanol and acetone under high pressure. High-pressure single-crystal X-ray diffraction and UV–Vis spectroscopy reveal the impact of solute–solvent interactions on the optical properties of ET(1). The study underscores the intricate relationship between solvent properties, molecular conformation and crystal packing. The connection between liquid and solid phases emphasizes the capabilities of high-pressure methods for expanding the field of crystal engineering. The high-pressure environment allowed the determination of the crystal structures reported here that are built from organic molecules fourfold solvated with ethanol or methanol: ET(1)·4CH3OH and ET(1)·4C2H5OH·H2O. The observed piezo-solvatochromic effects highlight the potential of ET(1) in nonlinear optoelectronics and expand the application of solvatochromic chemical indicators to pressure sensors.

X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump–probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light–oxygen–voltage domain 1 (LOV1) from Chlamydomonas reinhardtii were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump–probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δt = 10 µs a covalent thio­ether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.

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.

A pressure-induced triclinic-to-monoclinic phase transition has been caught `in the act' over a wider series of high-pressure synchrotron diffraction experiments conducted on a large, photoluminescent organo-gold(I) compound. Here, we describe the mechanism of this single-crystal-to-single-crystal phase transition, the onset of which occurs at ∼0.6 GPa, and we report a high-quality structure of the new monoclinic phase, refined using aspherical atomic scattering factors. Our case illustrates how conducting a fast series of diffraction experiments, enabled by modern equipment at synchrotron facilities, can lead to overestimation of the actual pressure of a phase transition due to slow transformation kinetics.

A polycrystalline sample LuCrO3 has been characterized by neutron powder diffraction (NPD) and magnetization measurements. Its crystal structure has been Rietveld refined from NPD data in space group Pnma; this perovskite contains strongly tilted CrO6 octahedra with extremely bent Cr—O—Cr superexchange angles of ∼142°. The NPD data show that below Néel temperature (TN ≃ 131 K), the magnetic structure can be defined as an A-type antiferromagnetic arrangement of Cr3+ magnetic moments, aligned along the b axis, with a canting along the c axis. A noticeable magneto­strictive effect is observed in the unit-cell parameters and volume upon cooling down across TN. The AC magnetic susceptibility indicates the onset of magnetic ordering below 112.6 K; the magnetization isotherms below TN show a nonlinear behaviour that is associated with the described canting of the Cr3+ magnetic moments. From the Curie–Weiss law, the effective moment of the Cr3+ sublattice is found to be μeff = 3.55 μB (calculated 3.7 μB) while the ΘCW parameter yields a value of −155 K, indicating antiferromagnetic interactions. There is a conspicuous increase of TN upon the application of external pressure, which must be due to shortening of the Cr—O bond length under compression that increases the orbital overlap integral.

The reaction between the (R,S)-fixolide 4-methyl­thio­semicarbazone and PdII chloride yielded the title compound, [Pd(C20H30N3S)2]·C2H6O {common name: trans-bis­[(R,S)-fixolide 4-methyl­thio­semicarbazonato-κ2N2S]palladium(II) ethanol monosolvate}. The asymmetric unit of the title compound consists of one bis-thio­semicarbazonato PdII complex and one ethanol solvent mol­ecule. The thio­semicarbazononato ligands act as metal chelators with a trans configuration in a distorted square-planar geometry. A C—H⋯S intra­molecular inter­action, with graph-set motif S(6), is observed and the coordination sphere resembles a hydrogen-bonded macrocyclic environment. Additionally, one C—H⋯Pd anagostic inter­action can be suggested. Each ligand is disordered over the aliphatic ring, which adopts a half-chair conformation, and two methyl groups [s.o.f. = 0.624 (2):0.376 (2)]. The disorder includes the chiral carbon atoms and, remarkably, one ligand has the (R)-isomer with the highest s.o.f. value atoms, while the other one shows the opposite, the atoms with the highest s.o.f. value are associated with the (S)-isomer. The N—N—C(=S)—N fragments of the ligands are approximately planar, with the maximum deviations from the mean plane through the selected atoms being 0.0567 (1) and −0.0307 (8) Å (r.m.s.d. = 0.0403 and 0.0269 Å) and the dihedral angle with the respective aromatic rings amount to 46.68 (5) and 50.66 (4)°. In the crystal, the complexes are linked via pairs of N—H⋯S inter­actions, with graph-set motif R22(8), into centrosymmetric dimers. The dimers are further connected by centrosymmetric pairs of ethanol mol­ecules, building mono-periodic hydrogen-bonded ribbons along [011]. The Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are [atoms with highest/lowest s.o.f.s considered separately]: H⋯H (81.6/82.0%), H⋯C/C⋯H (6.5/6.4%), H⋯N/N⋯H (5.2/5.0%) and H⋯S/S⋯H (5.0/4.9%).

A novel o-phenyl­enedi­amine (opda)-based cadmium complex, bis­(benzene-1,2-di­amine-κ2N,N')bis­(benzene-1,2-di­amine-κN)cadmium(II) naphthalene-1,5-di­sulfonate, [Cd(C6H8N2)4](C10H6O6S2), was synthesized. The complex salt crystallizes in the monoclinic space group C2/c. The Cd atom occupies a special position and coordinates six nitro­gen atoms from four o-phenyl­enedi­amine mol­ecules, two as chelating ligands and two as monodentate ligands. The amino H atoms of opda inter­act with two O atoms of the naphthalene-1,5-di­sulfonate anions. The anions act as bridges between [Cd(opda)4]2+ cations, forming a two-dimensional network in the [010] and [001] directions. The Hirshfeld surface analysis shows that the primary factors contributing to the supramolecular inter­actions are short contacts, particularly van der Waals forces of the type H⋯H, O⋯H and C⋯H.

The title compound, C16H11N2OF, is a member of the azo dye family. The dihedral angle subtended by the benzene ring and the naphthalene ring system measures 18.75 (7)°, indicating that the compound is not perfectly planar. An intra­molecular N—H⋯O hydrogen bond occurs between the imino and carbonyl groups. In the crystal, the mol­ecules are linked into inversion dimers by C—H⋯O inter­actions. Aromatic π–π stacking between the naphthalene ring systems lead to the formation of chains along [001]. A Hirshfeld surface analysis was undertaken to investigate and qu­antify the inter­molecular inter­actions. In addition, energy frameworks were used to examine the cooperative effect of these inter­molecular inter­actions across the crystal, showing dispersion energy to be the most influential factor in the crystal organization of the compound.

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.

A new lanthanide coordination polymer, poly[[tri­aqua­bis­(μ4-phthalato)(μ3-pyridine-2,5-di­carboxyl­ato)dipraseodymium] monohydrate], {[Pr2(C7H3NO4)2(C8H4O4)(H2O)3]·H2O}n or {[Pr2(phth)2(pydc)(H2O)3]·H2O}n, (pydc2− = pyridine-2,5-di­carboxyl­ate and phth2− = phthalate) was synthesized and characterized, revealing the structure to be an assembly of di-periodic {Pr2(pydc)(phth)2(H2O)3}n layers. Each layer is built up by edge-sharing {Pr2N2O14} and {Pr2O16} dimers, which are connected through a new coordin­ation mode of pydc2− and phth2−. These layers are stabilized by inter­nal hydrogen bonds and π–π inter­actions. In addition, a three-dimensional supra­molecular framework is built by inter­layer hydrogen-bonding inter­actions involving the non-coordinated water mol­ecule. Thermogravimetric analysis shows that the title compound is thermally stable up to 400°C.

The title compound, C14H12N2O4, was obtained from 2-acetyl-6-amino­naphthalene through two-step reactions of acetyl­ation and nitration. The mol­ecule comprises the naphthalene ring system consisting of functional systems bearing a acetyl group (C-2), a nitro group (C-5), and an acetyl­amino group (C-6). In the crystal, the mol­ecules are assembled into two-dimensional sheet-like structures by inter­molecular N—H⋯O and C—H⋯O hydrogen-bonding inter­actions. Hirshfeld surface analysis illustrates that the most important contributions to the crystal packing are from O⋯H/H⋯O (43.7%), H⋯H (31.0%), and C⋯H/H⋯C (8.5%) contacts.

The title compound, C12H10N2O3, was obtained by the de­acetyl­ation reaction of 1-(6-amino-5-nitro­naphthalen-2-yl)ethanone in a concentrated sulfuric acid methanol solution. The mol­ecule comprises a naphthalene ring system bearing an acetyl group (C-3), an amino group (C-7), and a nitro group (C-8). In the crystal, the mol­ecules are assembled into a two-dimensional network by N⋯H/H⋯N and O⋯H/H⋯O hydrogen-bonding inter­actions. n–π and π–π stacking inter­actions are the dominant inter­actions in the three-dimensional crystal packing. Hirshfeld surface analysis indicates that the most important contributions are from O⋯H/H⋯O (34.9%), H⋯H (33.7%), and C⋯H/H⋯C (11.0%) contacts. The energies of the frontier mol­ecular orbitals were computed using density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-TZVP level of theory and the LUMO–HOMO energy gap of the mol­ecule is 3.765 eV.

In the racemic title compound, C28H30O2, the naphthyl ring systems subtend a dihedral angle of 68.59 (1)° and the mol­ecular conformation is consolidated by a pair of intra­molecular C—H⋯π contacts. The crystal packing features a weak C—H⋯π contact and van der Waals forces. A Hirshfeld surface analysis of the crystal structure reveals that the most significant contributions are from H⋯H (73.2%) and C⋯H/H⋯C (21.2%) contacts.

The mercury(II) halide complex [1,3-di-tert-butyl-2,4-bis­(tert-butyl­amino)-1,3,2λ5,4λ5-di­aza­diphosphetidine-2,4-diselone-κ2Se,Se']di­iodido­mercury(II) N,N-di­methyl­formamide monosolvate, [HgI2(C16H38N4P2Se2)]·C3H7NO or (1)HgI2, 2, containing cis-[(tBuNH)(Se)P(μ-NtBu)2P(Se)(NHtBu)] (1) was synthesized and structurally characterized. The crystal structure of 2 confirms the chelation of chalcogen donors to HgI2 with a natural bite angle of 112.95 (2)°. The coordination geometry around mercury is distorted tetra­hedral as indicated by the τ4 geometry index parameter (τ4 = 0.90). In the mercury complex, the exocyclic tert-butyl­amido substituents are arranged in an (endo, endo) fashion, whereas in the free ligand (1), the exocyclic substituents are arranged in an (exo, endo) pattern. Compound 2 displays non-classical N—H⋯O hydrogen-bonding inter­actions with the solvent N,N-di­methyl­formamide. These inter­actions may introduce geometrical distortion and deviation from an ideal geometry. An isostructural HgBr2 analogue containing cis-[(tBuNH)(S)P(μ-NtBu)2P(S)(NHtBu)] was also synthesized and structurally characterized, CIF data for the compound being presented as supporting information.

In the title compound, C25H17NO3, the torsion angle associated with the phenyl benzoate group is −173.7 (2)° and that for the benz­yloxy group is −174.8 (2)° establishing an anti-type conformation. The dihedral angles between the ten-membered cyanona­phthalene ring and the aromatic ring of the phenyl benzoate and the benz­yloxy fragments are 40.70 (10) and 87.51 (11)°, respectively, whereas the dihedral angle between the aromatic phenyl benzoate and the benz­yloxy fragments is 72.30 (13)°. In the crystal, the mol­ecules are linked by weak C—H⋯O inter­actions forming S(4) chains propagating parallel to [010]. The packing is consolidated by three C—H⋯π inter­actions and two π–π stacking inter­actions between the aromatic rings of naphthalene and phenyl benzoate with centroid-to-centroid distances of 3.9698 (15) and 3.8568 (15) Å, respectively. Inter­molecular inter­actions were qu­anti­fied using Hirshfeld surface analysis. The mol­ecular structure was further optimized by density functional theory (DFT) at the B3LYP/6–311+ G(d,p) level, revealing that the energy gap between HOMO and LUMO is 3.17 eV. Mol­ecular docking studies were carried out for the title compound as a ligand and SARS-Covid-2(PDB ID:7QF0) protein as a receptor giving a binding affinity of −9.5 kcal mol−1.

This study characterizes the microstructure and mineralogy of 132 (ODP sample), 1000 and 1880 million-year-old chert samples. By using ultra-small-angle X-ray scattering (USAXS), wide-angle X-ray scattering and other techniques, the preservation of organic matter (OM) in these samples is studied. The scarce microstructural data reported on chert contrast with many studies addressing porosity evolution in other sedimentary rocks. The aim of this work is to solve the distribution of OM and silica in chert by characterizing samples before and after combustion to pinpoint the OM distribution inside the porous silica matrix. The samples are predominantly composed of alpha quartz and show increasing crystallite sizes up to 33 ± 5 nm (1σ standard deviation or SD). In older samples, low water abundances (∼0.03%) suggest progressive dehydration. (U)SAXS data reveal a porous matrix that evolves over geological time, including, from younger to older samples, (1) a decreasing pore volume down to 1%, (2) greater pore sizes hosting OM, (3) decreasing specific surface area values from younger (9.3 ± 0.1 m2 g−1) to older samples (0.63 ± 0.07 m2 g−1, 1σ SD) and (4) a lower background intensity correlated to decreasing hydrogen abundances. The pore-volume distributions (PVDs) show that pores ranging from 4 to 100 nm accumulate the greater volume fraction of OM. Raman data show aromatic organic clusters up to 20 nm in older samples. Raman and PVD data suggest that OM is located mostly in mesopores. Observed structural changes, silica–OM interactions and the hydro­phobicity of the OM could explain the OM preservation in chert.

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

INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets.

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

A neutron time-of-flight (TOF) powder diffractometer with a continuous wide-angle array of detectors can be electronically focused to make a single pseudo-constant wavelength diffraction pattern, thus facilitating angle-dependent intensity corrections. The resulting powder diffraction peak profiles are affected by the neutron source emission profile and resemble the function currently used for TOF diffraction.

VMXm joins the suite of operational macromolecular crystallography beamlines at Diamond Light Source. It has been designed to optimize rotation data collections from protein crystals less than 10 µm and down to below 1 µm in size. The beamline has a fully focused beam of 0.3 × 2.3 µm (vertical × horizontal) with a tuneable energy range (6–28 keV) and high flux (1.6 × 1012 photons s−1 at 12.5 keV). The crystals are housed within a vacuum chamber to minimize background scatter from air. Crystals are plunge-cooled on cryo-electron microscopy grids, allowing much of the liquid surrounding the crystals to be removed. These factors improve the signal-to-noise during data collection and the lifetime of the microcrystals can be prolonged by exploiting photoelectron escape. A novel in vacuo sample environment has been designed which also houses a scanning electron microscope to aid with sample visualization. This combination of features at VMXm allows measurements at the physical limits of X-ray crystallography on biomacromolecules to be explored and exploited.