Scientific report published  British Geological Survey

Natural flood management: is geology more important than trees?  British Geological Survey

2024 Mine Water Energy Symposium  British Geological Survey

New research supports conservation of fallow deer across Europe  British Geological Survey

BGS scientist announced as Scottish Government policy fellow  British Geological Survey

Small earthquake recorded under Powys town  Powys County Times

Spotlight on BGS coastal erosion data  British Geological Survey

Responsible extraction in South America’s Lithium Triangle  British Geological Survey

Funding awarded for study on hydrogen storage potential in the East Midlands  British Geological Survey

BGS joins new initiative supporting technical career paths  British Geological Survey

New appointments to BGS Science Advisory Committee  British Geological Survey

Forty years and counting: new topsoil data provides most extensive snapshot of environmental pollution effects  British Geological Survey

What lies beneath Liverpool?  British Geological Survey

New community launched to support effective management of the subsurface  British Geological Survey

Crystal structure and topology of two new thiosulfates formed with mono- and diprotonated species of 1-methylpiperazine is reported.

Incommensurate phase of potassium guaninate monohydrate is the first example of a modulation in purine derivatives and of a high-pressure incommensurate crystal structure to be solved for an organic compound.

Tetragonal YxOs4B4 (x = 1.161) is an incommensurate composite of columns of Y atoms in a three-dimensional Os4B4 framework. The structure was refined using the superspace approach.

A new orthorhombic crystal Pb5(PO4)3OHδ of space-group symmetry Pnma significantly differs differing from the hexagonal apatite phases of Pb10(PO4)6O and Pb5(PO4)3OH.

Five multicomponent solid forms of an antifungal drug flucytosine are reported with a hygroscopic stability study. A detailed CSD search on the cocrystal/salts of flucytosine is evaluated and correlated the structures based on bond angles and bond distances.

The rotating substrate method of crystallite deposition is modeled, allowing computation of effective material coefficients of the layers resulting from the averaging. A worked numerical example particularized to 6mm ZnO is provided.

Low-concentration poly(ethylene oxide) exhibit the polymorph-dependent effects on both the surface and bulk crystal growth of carbamazepine polymorphs. These polymorph-dependent effects of PEO were mainly attributed to the polymer enrichment at the interface and different crystal surface-polymer interactions.

This study presents the first theoretical predictions of the phase transitions, elastic properties, and thermal behavior of AuMTe2 (M = Ga, In) chalcopyrite compounds. Using density functional theory and the quasi-harmonic Debye model, key mechanical and thermodynamic properties are analyzed, offering insights valuable for future experimental validation.

YxOs4B4 (x = 1.161) crystallizes as a tetragonal incommensurate composite of columns of Y atoms extending along [001] in an Os4B4 framework. The structure was refined using the superspace approach. The basic structure of the Y subsystem can be idealized as having I4/mmm symmetry, with a crystallographically unique Y atom located on the 4/mmm position. The actual superspace symmetry is P42/nmc(00σ3)s0s0. The Y atoms feature only subtle positional modulation in the [001] direction. The Os4B4 subsystem [P42/ncm(00σ3)00ss superspace symmetry] is built of columns of edge-sharing Os4 tetrahedra extending along [001] and B2 dumbbells. The Os4 tetrahedra feature pronounced positional modulation with a distinct variation of the Os—Os bond lengths. Modulation of the B2 dumbbells is best described as a rotation about the [001] axis.

The crystal structure of the incommensurate modulated phase of potassium guaninate monohydrate has been solved on the basis of high-pressure single-crystal X-ray diffraction data. The modulated structure was described as a `mosaic' sequence of three different local configurations of two neighbouring guaninate rings. In contrast to known examples of incommensurate modulated organic compounds, the modulation functions of all atoms are discontinuous. This is the first example of the experimental detection of an incommensurate modulated crystal structure that can be modelled using the special `soliton mode' modulation function proposed by Aramburu et al. [(1995), J. Phys. Condens. Matter, 7, 6187–6196].

The seventh blind test of crystal structure prediction (CSP) methods substantially increased the level of complexity of the target compounds relative to the previous tests organized by the Cambridge Crystallographic Data Centre. In this work, the performance of density-functional methods is assessed using numerical atomic orbitals and the exchange-hole dipole moment dispersion correction (XDM) for the energy-ranking phase of the seventh blind test. Overall, excellent performance was seen for the two rigid molecules (XXVII, XXVIII) and for the organic salt (XXXIII). However, for the agrochemical (XXXI) and pharmaceutical (XXXII) targets, the experimental polymorphs were ranked fairly high in energy amongst the provided candidate structures and inclusion of thermal free-energy corrections from the lattice vibrations was found to be essential for compound XXXI. Based on these results, it is proposed that the importance of vibrational free-energy corrections increases with the number of rotatable bonds.

A novel approach to computationally enhance the sampling of molecular crystal structures is proposed and tested. This method is based on the use of extended variables coupled to a Monte Carlo based crystal polymorph generator. Inspired by the established technique of quasi-random sampling of polymorphs using the rigid molecule constraint, this approach represents molecular clusters as extended variables within a thermal reservoir. Polymorph unit-cell variables are generated using pseudo-random sampling. Within this framework, a harmonic coupling between the extended variables and polymorph configurations is established. The extended variables remain fixed during the inner loop dedicated to polymorph sampling, enforcing a stepwise propagation of the extended variables to maintain system exploration. The final processing step results in a polymorph energy landscape, where the raw structures sampled to create the extended variable trajectory are re-optimized without the thermal coupling term. The foundational principles of this approach are described and its effectiveness using both a Metropolis Monte Carlo type algorithm and modifications that incorporate replica exchange is demonstrated. A comparison is provided with pseudo-random sampling of polymorphs for the molecule coumarin. The choice to test a design of this algorithm as relevant for enhanced sampling of crystal structures was due to the obvious relation between molecular structure variables and corresponding crystal polymorphs as representative of the inherent vapor to crystal transitions that exist in nature. Additionally, it is shown that the trajectories of extended variables can be harnessed to extract fluctuation properties that can lead to valuable insights. A novel thermodynamic variable is introduced: the free energy difference between ensembles of Z' = 1 and Z' = 2 crystal polymorphs.

The synthesis of a chiral isothiourea, namely, (4aR,8aR)-3-phenyl-4a,5,6,7,8,8a-hexahydrobenzo[4,5]imidazo[2,1-b]thiazol-9-ium bromide, C15H17N2S+·Br−, with potential organocatalytic and anti-inflammatory activity is reported. The preparation of the heterocycle of interest was carried out in two high-yielding steps. The hydrobromide salt of the isothiourea of interest provided suitable crystals for X-ray diffraction analysis, the results of which are reported. Salient observations from this analysis are the near perpendicular arrangement of the phenyl ring and the mean plane of the heterocycle. This conformational characteristic may be relevant with regard the stereoselectivity induced by the chiral isothiourea in asymmetric reactions. Furthermore, evidence was found for the existence of an S...Br− halogen bond.

In Part I of this series, all topologically possible 1-periodic infinite graphs (chain graphs) representing chains of tetrahedra with up to 6–8 vertices (tetrahedra) per repeat unit were generated. This paper examines possible restraints on embedding these chain graphs into Euclidean space such that they are compatible with the metrics of chains of tetrahedra in observed crystal structures. Chain-silicate minerals with T = Si4+ (plus P5+, V5+, As5+, Al3+, Fe3+, B3+, Be2+, Zn2+ and Mg2+) have a grand nearest-neighbour 〈T–T〉 distance of 3.06±0.15 Å and a minimum T⋯T separation of 3.71 Å between non-nearest-neighbour tetrahedra, and in order for embedded chain graphs (called unit-distance graphs) to be possible atomic arrangements in crystals, they must conform to these metrics, a process termed equalization. It is shown that equalization of all acyclic chain graphs is possible in 2D and 3D, and that equalization of most cyclic chain graphs is possible in 3D but not necessarily in 2D. All unique ways in which non-isomorphic vertices may be moved are designated modes of geometric modification. If a mode (m) is applied to an equalized unit-distance graph such that a new geometrically distinct unit-distance graph is produced without changing the lengths of any edges, the mode is designated as valid (mv); if a new geometrically distinct unit-distance graph cannot be produced, the mode is invalid (mi). The parameters mv and mi are used to define ranges of rigidity of the unit-distance graphs, and are related to the edge-to-vertex ratio, e/n, of the parent chain graph. The program GraphT–T was developed to embed any chain graph into Euclidean space subject to the metric restraints on T–T and T⋯T. Embedding a selection of chain graphs with differing e/n ratios shows that the principal reason why many topologically possible chains cannot occur in crystal structures is due to violation of the requirement that T⋯T > 3.71 Å. Such a restraint becomes increasingly restrictive as e/n increases and indicates why chains with stoichiometry TO<2.5 do not occur in crystal structures.

Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops.

Mycobacterium tuberculosis can reside and persist in deep tissues; latent tuberculosis can evade immune detection and has a unique mechanism to convert it into active disease through reactivation. M. tuberculosis Rv1421 (MtRv1421) is a hypothetical protein that has been proposed to be involved in nucleotide binding-related metabolism in cell-growth and cell-division processes. However, due to a lack of structural information, the detailed function of MtRv1421 remains unclear. In this study, a truncated N-terminal domain (NTD) of MtRv1421, which contains a Walker A/B-like motif, was purified and crystallized using PEG 400 as a precipitant. The crystal of MtRv1421-NTD diffracted to a resolution of 1.7 Å and was considered to belong to either the C-centered monoclinic space group C2 or the I-centered orthorhombic space group I222, with unit-cell parameters a = 124.01, b = 58.55, c = 84.87 Å, β = 133.12° or a = 58.53, b = 84.86, c = 90.52 Å, respectively. The asymmetric units of the C2 or I222 crystals contained two or one monomers, respectively. In terms of the binding ability of MtRv1421-NTD to various ligands, uridine diphosphate (UDP) and UDP-N-acetylglucosamine significantly increased the melting temperature of MtRv1421-NTD, which indicates structural stabilization through the binding of these ligands. Altogether, the results reveal that a UDP moiety may be required for the interaction of MtRv1421-NTD as a nucleotide-binding protein with its ligand.

Pseudoalteromonas fuliginea sp. PS47 is a recently identified marine bacterium that has extensive enzymatic machinery to metabolize polysaccharides, including a locus that targets pectin-like substrates. This locus contains a gene (locus tag EU509_03255) that encodes a pectin-degrading lyase, called PfPL1, that belongs to polysaccharide lyase family 1 (PL1). The 2.2 Å resolution X-ray crystal structure of PfPL1 reveals the compact parallel β-helix fold of the PL1 family. The back side of the core parallel β-helix opposite to the active site is a meandering set of five α-helices joined by lengthy loops. A comparison of the active site with those of other PL1 enzymes suggests a catalytic mechanism that is independent of metal ions, such as Ca2+, but that substrate recognition may require metal ions. Overall, this work provides the first structural insight into a pectinase of marine origin and the first structure of a PL1 enzyme in subfamily 2.

Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9–5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.

This review summarizes the methodological aspects of laboratory X-ray powder micro-diffraction and demonstrates the assets of the method in the research of painted artworks for evaluation of their provenance or diagnosing their degradation.

The growth quality of AlN single crystals was improved by optimizing the crucible structure for Al vapor transport with the help of finite element simulation.

New software capabilities in RMCProfile allow researchers to study the structure of materials by combining machine learning interatomic potentials and reverse Monte Carlo.

The effect of boron in BxGa1−xN/SiC heteroepitaxy was established by X-ray diffraction reciprocal-space maps on symmetric 0002 and asymmetric 11 {overline 2} 4 reflections. The density of screw and edge threading dislocations was quantified in the framework of the mosaic model.

This study examines the quality of charge density obtained by fitting the multipole model to wavefunctions in different basis sets. The complex analysis reveals that changing the basis set quality from double- to triple-zeta can notably improve the charge density related properties of a multipole model.

The performance of a high-Z photon-counting detector for powder diffraction measurements at high (>50 keV) energies is characterized, and the appropriate corrections are described in order to obtain data of higher quality than have previously been obtained from 2D detectors in these energy ranges.

Combined 100 ms resolved grazing-incidence small/wide-angle X-ray scattering and optical interferometry reveal that the additive diiodooctane can significantly double the solvent evaporation rate, thereby effectively suppressing the rapid spinodal decomposition process in the early stage of spin-coasting, favouring slow phase segregation kinetics with nucleation and growth.

The position- and time-resolved monitoring of a mechanochemical reaction using synchrotron powder X-ray diffraction revealed a position-independent increase rate of product in the jar of a shaker mill.

RAPID (RAtio method Pattern InDexing) is an ImageJ macro script developed for the quick determination of sample orientation and indexing of calibrated and uncalibrated zone axis aligned electron diffraction patterns from materials with a cubic crystal structure. In addition to SAED and NBED patterns, the program is also capable of handling zone axis TEM Kikuchi patterns and FFTs derived from HR(S)TEM images. The software enables users to rapidly determine whether materials are cubic, pseudo-cubic, or non-cubic, and to distinguish between P, I, and F Bravais lattices. It can also provide lattice parameters for material verification and aid in determining the camera constant of the instrument, thus making the program a convenient tool for on-site crystallographic analysis in the TEM laboratory.

This study proposes an operation optimization framework for impurity-free recycling of spent lithium-ion batteries. Using a hybrid population balance equation integrated with a data-driven condition classifier, the study firstly identifies the optimal batch and semi-batch operation conditions that significantly reduce the operation time with 100% purity of product; detailed guidelines are given for industrial applications.

For the first time, a multimodal reconstruction of a magnetic thin-film structure has been found using polarised neutron reflectivity. This has been achieved by implementing the Bayesian approach in combination with error correction based on the maximum likelihood method and instrument function optimization.

Crystallization of the title compound from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and ortho­rhom­bic (Pna21; β form) space groups. The ReI complex mol­ecules in either polymorph adopt a six-coordinate octa­hedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitro­gen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds.

We investigated the position and time dependence of a mechanochemical reaction induced by ball milling using in situ synchrotron powder X-ray diffraction with changing X-ray irradiation position. The mechanochemical reduction of AgCl with Cu was monitored in situ with the X-rays incident at two different vertical positions on the jar. Our previously developed multi-distance Rietveld method was applied to analyze the in situ diffraction data with a 1 min resolution. Both the vertical and the horizontal sample positions were determined using the sample-to-detector distances from the in situ data. Position dependence was found in the powder spreading and induction time. We reveal that the increase rate of the product is independent of the sample position when measured with a 1 min time resolution, confirming the validity of in situ monitoring of part of the space in a milling jar for a gradual mechanochemical reaction.

BGaN epilayers with boron contents up to 5.6% were grown on SiC substrates by metal–organic chemical vapor deposition. The effects of boron incorporation on the structural and optical properties were studied by high-resolution X-ray diffraction (XRD), atomic force microscopy (AFM), Raman spectroscopy and photoluminescence (PL) spectroscopy. XRD reciprocal-space maps around the symmetric 0002 and asymmetric 11 {overline 2} 4 reflections allowed evaluation of the lattice constants and lattice mismatch with respect to the underlying substrate. XRD rocking curves and AFM measurements indicated the mosaic microstructure of the epilayer. The impact of boron content on crystallite size, tilt and twist is evaluated and the correlation with threading dislocation density is discussed. The deterioration of optical properties with increasing boron content was assessed by Raman and PL spectroscopy.

Structure refinement with reverse Monte Carlo (RMC) is a powerful tool for interpreting experimental diffraction data. To ensure that the under-constrained RMC algorithm yields reasonable results, the hybrid RMC approach applies interatomic potentials to obtain solutions that are both physically sensible and in agreement with experiment. To expand the range of materials that can be studied with hybrid RMC, we have implemented a new interatomic potential constraint in RMCProfile that grants flexibility to apply potentials supported by the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics code. This includes machine learning interatomic potentials, which provide a pathway to applying hybrid RMC to materials without currently available interatomic potentials. To this end, we present a methodology to use RMC to train machine learning interatomic potentials for hybrid RMC applications.

In the conventional crucible structure for AlN crystal growth by physical vapor transport, owing to the long molecular transport path of Al vapor and the disruption of the gas flow by the presence of a deflector, the Al vapor easily forms polycrystals in the growth domain. The result is increased internal stress in the crystals and increased difficulty in growing large-sized crystals. On this basis, with the help of finite element simulations, a novel crucible structure is designed. This crucible not only optimizes the gas transport but also increases the radial gradient of the AlN crystal surface, making the enhanced growth rate in the central region more obvious. The thermal stresses between the deflector and the crystal are also reduced. High-quality AlN crystals with an FWHM of 79 arcsec were successfully grown with this structure, verifying the accuracy of finite element simulation of the growth of AlN crystals. Our work has important guiding significance for the growth of high-quality AlN crystals.

Painted artworks represent a significant group of cultural heritage artifacts, which are primarily admired because of their aesthetic quality. Nevertheless, the value of each particular painting depends also on what is known about it. Material investigation of paintings is one of the most reliable sources of information. Materials in painted artworks (i.e. panel, easel and miniature paintings, wall paintings, polychromed sculptures etc.) represent an extensive set of inorganic and organic phases, which are often present in complicated mixtures and exhibit characteristics reflecting their geological genesis (mineral pigments), manufacturing technology (artificial pigments), diverse biological nature (binders or dyes) or secondary changes (degradation or intentional later interventions). The analyses of paintings are often made challenging by the heterogeneous nature and minute size of micro-samples or, in some cases, even by the impossibility of sampling due to the preciousness, fragility or small dimensions of the artwork. This review demonstrates the successful implementation of laboratory X-ray powder micro-diffraction for material investigation of paintings, illustrating its efficiency for mineralogical analysis of (i) earth-based materials indicating the provenance of paintings, (ii) copper-based pigments pointing to their origin, and (iii) products of both salt corrosion and saponification enabling one to reveal the deterioration and probable original appearance of artworks.

In powder diffraction, lattice symmetry relaxation causes a peak to split into several components which are not resolved if the degree of desymmetrization is small (pseudosymmetry). Here the equations which rule peak splitting are elaborated for the six minimal symmetry transitions, showing that the resulting split peaks are generally broader and asymmetric, and suffer an hkl-dependent displacement with respect to the high-symmetry parent peak. These results will be of help in Rietveld refinement of pseudosymmetric structures where an exact interpretation of peak deformation is required.