How we use drones  British Geological Survey

The Geography Olympiad: Bandung, Indonesia  British Geological Survey

Moving stones: faults, slopes and sediments  British Geological Survey

Visit by Indonesian Embassy representatives to BGS  British Geological Survey

The thio­nocarbonate of trans-cyclo­octenediol, C9H12O2S, crystallizes with a 9/1 disorder in the position of the R,R and S,S-enanti­omers. As a result of trans-annulation, both rings adopt a twist conformation.

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.

Recent advances in quantum crystallography have shown that, beyond conventional charge density refinement, a one-electron reduced density matrix (1-RDM) satisfying N-representability conditions can be reconstructed using jointly experimental X-ray structure factors and directional Compton profiles (DCP) through semidefinite programming. So far, such reconstruction methods for 1-RDM, not constrained to idempotency, have been tested only on a toy model system (CO2). In this work, a new method is assessed on crystalline urea [CO(NH2)2] using static (0 K) and dynamic (50 K) artificial experimental data. An improved model, including symmetry constraints and frozen core-electron contribution, is introduced to better handle the increasing system complexity. Reconstructed 1-RDMs, deformation densities and DCP anisotropy are analysed, and it is demonstrated that the changes in the model significantly improve the reconstruction quality, even when there is insufficient information and data corruption. The robustness of the model and the strategy are thus shown to be well adapted to address the reconstruction problem from actual experimental scattering data.

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.

The title compound is a non-liquid crystal mol­ecule. The mol­ecular crystal is consolidated by C—Br⋯O&z-dbnd;C type contacts running continuously along the [001] direction.

Bone material contains a hierarchical network of micro- and nano-cavities and channels, known as the lacuna-canalicular network (LCN), that is thought to play an important role in mechanobiology and turnover. The LCN comprises micrometer-sized lacunae, voids that house osteocytes, and submicrometer-sized canaliculi that connect bone cells. Characterization of this network in three dimensions is crucial for many bone studies. To quantify X-ray Zernike phase-contrast nanotomography data, deep learning is used to isolate and assess porosity in artifact-laden tomographies of zebrafish bones. A technical solution is proposed to overcome the halo and shade-off domains in order to reliably obtain the distribution and morphology of the LCN in the tomographic data. Convolutional neural network (CNN) models are utilized with increasing numbers of images, repeatedly validated by `error loss' and `accuracy' metrics. U-Net and Sensor3D CNN models were trained on data obtained from two different synchrotron Zernike phase-contrast transmission X-ray microscopes, the ANATOMIX beamline at SOLEIL (Paris, France) and the P05 beamline at PETRA III (Hamburg, Germany). The Sensor3D CNN model with a smaller batch size of 32 and a training data size of 70 images showed the best performance (accuracy 0.983 and error loss 0.032). The analysis procedures, validated by comparison with human-identified ground-truth images, correctly identified the voids within the bone matrix. This proposed approach may have further application to classify structures in volumetric images that contain non-linear artifacts that degrade image quality and hinder feature identification.

Accurate analysis of the rich information contained within X-ray spectra usually calls for detailed electronic structure theory simulations. However, density functional theory (DFT), time-dependent DFT and many-body perturbation theory calculations increasingly require the use of advanced codes running on high-performance computing (HPC) facilities. Consequently, many researchers who would like to augment their experimental work with such simulations are hampered by the compounding of nontrivial knowledge requirements, specialist training and significant time investment. To this end, we present Web-CONEXS, an intuitive graphical web application for democratizing electronic structure theory simulations. Web-CONEXS generates and submits simulation workflows for theoretical X-ray absorption and X-ray emission spectroscopy to a remote computing cluster. In the present form, Web-CONEXS interfaces with three software packages: ORCA, FDMNES and Quantum ESPRESSO, and an extensive materials database courtesy of the Materials Project API. These software packages have been selected to model diverse materials and properties. Web-CONEXS has been conceived with the novice user in mind; job submission is limited to a subset of simulation parameters. This ensures that much of the simulation complexity is lifted and preliminary theoretical results are generated faster. Web-CONEXS can be leveraged to support beam time proposals and serve as a platform for preliminary analysis of experimental data.

In the title mol­ecule, C21H15N3OS, the C5=C6 double bond in the central enone group adopts a trans configuration. The dihedral angle between planes of the thia­zole and pyrazole rings is 6.6 (2)°. In the crystal, pairs of C—H⋯O hydrogen bonds generate inversion dimers and another pair of C—H⋯N hydrogen bonds link the dimers into chains propagating along a-axis direction.

The structure of the title complex, [Zn2(C2H3O2)4(C11H9N3O)2], is triclinic containing half of the mol­ecule in the asymmetric unit. Each zinc atom is coordinated to a pyridyl and oxime nitro­gen from one di-2-pyridyl ketone oxime (dpko) ligand and a third nitro­gen from the other dpko pyridyl ring. Additionally, each zinc is coordinated to two acetato anions, one of which is bidentate and the other monodentate. The uncoordinated oxygen of the monodentate acetato group is involved in a hydrogen bond with the oxime hydrogen. The packing in the crystal is assisted by weak C—H⋯O inter­actions between acetato groups and neighboring pyridyl rings.

The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C15H22O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022). Powder Diffr. 37, 98–104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the inter­molecular inter­actions of germacrone type II.

The title compound, C22H24N2O2, crystallizes in space group P21/n. The mol­ecular structure is almost planar except for a tilt of the phenyl rings. The allyl groups on both ends exhibit the trans-form and the connected N atoms show sp2 character. The mol­ecules are stacked and assembled along the c-axis direction by C—H⋯π inter­actions.

The title compound {systematic name: (2S)-2-aza­niumyl-3-[(2-carb­oxy­ethane)­sulfon­yl]propano­ate}, C6H11NO6S, forms enanti­opure crystals in the monoclinic space group P21 and exists as a zwitterion, with a protonated α-amino group and a deprotonated α-carboxyl group. Both the carboxyl groups and the amino group are involved in an extensive multicentered inter­molecular hydrogen-bonding scheme. In the crystal, the diperiodic network of hydrogen bonds propagates parallel to (101) and involves inter­connected heterodromic R43(10) rings. Electrostatic forces are major contributors to the structure energy, which was estimated by DFT calculations as Etotal = −333.5 kJ mol−1.

In the title compound, C26H22N2O3, the dihedral angle between the benzene and pyrazole rings of the chalcone unit is 88.3 (1)°. The pyrazole ring has two attached phenyl rings that form dihedral angles with the pyrazole ring of 22.6 (2) and 40.0 (1)°. In the crystal, pairwise C—H⋯O hydrogen bonds generate R22(20) inversion dimers.

In the title compound, C6H10N2O2, the piperazine-2,3-dione ring adopts a half-chair conformation. In the crystal, the mol­ecules are linked by weak C—H⋯O hydrogen bonds, forming (010) sheets.

The thio­nocarbonate of trans-cyclo­octenediol, C9H12O2S, crystallizes with a 9/1 disorder in the position of the R,R and S,S-enanti­omers. As a result of trans-annulation, both rings adopt a twist conformation.

α-d-2'-De­oxy­ribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-d-2'-de­oxy­adenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydro­gen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydro­gen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydro­gen bonds formed by the conformers. The formation of the supra­molecular assembly of α-dA is controlled by hydro­gen bonding and stacking inter­actions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydro­gen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydro­gen bonds involving the sugar moieties to form a sheet. A com­parison of the solid-state structures of the anomeric 2'-de­oxy­adenosines revealed significant differences of their conformational parameters.

A confiscated package of street drugs was characterized by the usual mass spectral (MS) and FT–IR analyses. The confiscated powder material was highly crystalline and was found to consist of two very different species, accidentally of sizes convenient for X-ray diffraction. Thus, one each was selected and redundant com­plete sets of data were collected at 100 K using Cu Kα radiation. The selected crystals contained: (a) 1,2-diphenyl-2-(pyrrolidin-1-yl)ethanone hy­dro­chloride hemihydrate or 1-(2-oxo-1,2-di­phenyl­eth­yl)pyrrolidin-1-ium chloride hemihydrate, C18H20NO+·Cl−·0.5H2O, (I), a synthetic cathinone called `α-D2PV', and (b) the sugar myo-inositol, C6H12O6, (II), probably the only instance in which the drug and its diluent have been fully characterized from a single confiscated sample. Moreover, the structural details of both are rather attractive showing: (i) inter­esting hydrogen bonding observed in pairwise inter­actions by the drug mol­ecules, mediated by the chloride counter-anions and the waters of crystallization, and (ii) π–π inter­actions in the case of the phenyl rings of the drug which are of two different types, namely, π–π stacking and edge-to-π. Finally, the inositol crystallizes with Z' = 2 and the resulting diastereoisomers were examined by overlay techniques.

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.

Herein we report the crystal structures of two ben­zo­di­az­e­pines obtained by reacting N,N'-(4,5-di­amino-1,2-phenyl­ene)bis­(4-methyl­ben­zene­sul­fon­am­ide) (1) or 4,5-(4-methyl­ben­zene­sul­fon­am­ido)­ben­zene-1,2-diaminium dichloride (1·2HCl) with acetone, giving 2,2,4-trimethyl-8,9-bis­(4-methyl­ben­zene­sul­fon­am­ido)-2,3-di­hydro-5H-1,5-ben­zo­di­az­e­pine, C26H30N4O4S2 (2), and 2,2,4-tri­methyl-8,9-bis­(4-methyl­ben­zene­sul­fon­am­ido)-2,3-di­hydro-5H-1,5-ben­zo­di­az­e­pin-1-ium chloride 0.3-hydrate, C26H31N4O4S2+·Cl−·0.3H2O (3). Compounds 2 and 3 were first obtained in attempts to recrystallize 1 and 1·2HCl using acetone as solvent. This solvent reacted with the vicinal di­amines present in the mol­ecular structures, forming a 5H-1,5-ben­zo­di­az­e­pine ring. In the crystal structure of 2, the seven-membered ring of ben­zo­di­az­e­pine adopts a boat-like conformation, while upon protonation, observed in the crystal structure of 3, it adopts an envelope-like conformation. In both crystalline com­pounds, the tosyl­amide N atoms are not in resonance with the arene ring, mainly due to hy­dro­gen bonds and steric hindrance caused by the large vicinal groups in the aromatic ring. At a supra­molecular level, the crystal structure is maintained by a combination of hy­dro­gen bonds and hydro­phobic inter­actions. In 2, amine-to-tosyl N—H⋯O and amide-to-imine N—H⋯N hy­dro­gen bonds can be observed. In contrast, in 3, the chloride counter-ion and water mol­ecule result in most of the hy­dro­gen bonds being of the amide-to-chloride and ammonium-to-chloride N—H⋯Cl types, while the amine inter­acts with the tosyl group, as seen in 2. In conclusion, we report the synthesis of 1, 1·2HCl and 2, as well as their chemical characterization. For 2, two synthetic methods are described, i.e. solvent-mediated crystallization and synthesis via a more efficient and cleaner route as a polycrystalline material. Salt 3 was only obtained as presented, with only a few crystals being formed.

Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nɛ—H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1—H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C—H⋯O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C—H group. Consequently, Cα—H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cɛ1—H and Cδ2—H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1—H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1—H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5–3.0 kcal mol−1, depending on the specific stereochemistry.

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.

Fatty acid-derivative prodrugs have been utilized extensively to improve the physicochemical, biopharmaceutical and pharmacokinetic properties of active pharmaceutical ingredients. However, to our knowledge, the crystallization behavior of prodrugs modified with different fatty acids has not been explored. In the present work, a series of paliperidone aliphatic prodrugs with alkyl chain lengths ranging from C4 to C16 was investigated with respect to crystal structure, crystal morphology and crystallization kinetics. The paliperidone derivatives exhibited isostructural crystal packing, despite the different alkyl chain lengths, and crystallized with the dominant (100) face in both melt and solution. The rate of crystallization for paliperidone derivatives in the melt increases with alkyl chain length owing to greater molecular mobility. In contrast, the longer chains prolong the nucleation induction time and reduce the crystal growth kinetics in solution. The results show a correlation between difficulty of nucleation in solution and the interfacial energy. This work provides insight into the crystallization behavior of paliperidone aliphatic prodrugs and reveals that the role of alkyl chain length in the crystallization behavior has a strong dependence on the crystallization method.

Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB–TcC subcomplex that makes a hollow shell. This TcB–TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB–TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.

This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.

Sialic acids play crucial roles in cell surface glycans of both eukaryotic and prokaryotic organisms, mediating various biological processes, including cell–cell interactions, development, immune response, oncogenesis and host–pathogen interactions. This review focuses on the β-anomeric form of N-acetyl­neuraminic acid (Neu5Ac), particularly its binding affinity towards various proteins, as elucidated by solved protein structures. Specifically, we delve into the binding mechanisms of Neu5Ac to proteins involved in sequestering and transporting Neu5Ac in Gram-negative bacteria, with implications for drug design targeting these proteins as antimicrobial agents. Unlike the initial assumptions, structural analyses revealed significant variability in the Neu5Ac binding pockets among proteins, indicating diverse evolutionary origins and binding modes. By comparing these findings with existing structures from other systems, we can effectively highlight the intricate relationship between protein structure and Neu5Ac recognition, emphasizing the need for tailored drug design strategies to inhibit Neu5Ac-binding proteins across bacterial species.

Ultrafast, high-intensity X-ray free-electron lasers can perform diffraction imaging of single protein molecules. Various algorithms have been developed to determine the orientation of each single-particle diffraction pattern and reconstruct the 3D diffraction intensity. Most of these algorithms rely on the premise that all diffraction patterns originate from identical protein molecules. However, in actual experiments, diffraction patterns from multiple different molecules may be collected simultaneously. Here, we propose a predicted model-aided one-step classification–multireconstruction algorithm that can handle mixed diffraction patterns from various molecules. The algorithm uses predicted structures of different protein molecules as templates to classify diffraction patterns based on correlation coefficients and determines orientations using a correlation maximization method. Tests on simulated data demonstrated high accuracy and efficiency in classification and reconstruction.

The structures of three multicomponent crystals formed with imidazole-based drugs, namely metronidazole, ketoconazole and miconazole, in conjunction with tri­thio­cyanuric acid are characterized. Each of the obtained adducts represents a different category of crystalline molecular forms: a cocrystal, a salt and a cocrystal of salt. The structural analysis revealed that in all cases, the N—H⋯N hydrogen bond is responsible for the formation of acid–base pairs, regardless of whether proton transfer occurs or not, and these molecular pairs are combined to form unique supramolecular motifs by centrosymmetric N—H⋯S interactions between acid molecules. The complex intermolecular forces acting in characteristic patterns are discussed from the geometric and energetic perspectives, involving Hirshfeld surface analysis, pairwise energy estimation, and natural bond orbital calculations.

The title compound, C5H5NO2, is a hy­droxy­lated pyridine ring that has been studied for its involvement in microbial degradation of nicotinic acid. Here we describe its synthesis as a formic acid salt, rather than the standard hydro­chloride salt that is commercially available, and its spectroscopic and crystallographic characterization.

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.

In the title mol­ecule, C7H7N3O, the pyrimidine ring is essentially planar, with the propynyl group rotated out of this plane by 15.31 (4)°. In the crystal, a tri-periodic network is formed by N—H⋯O, N—H⋯N and C—H⋯O hydrogen-bonding and slipped π–π stacking inter­actions, leading to narrow channels extending parallel to the c axis. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (36.2%), H⋯C/C⋯H (20.9%), H⋯O/O⋯H (17.8%) and H⋯N/N⋯H (12.2%) inter­actions, showing that hydrogen-bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions. The mol­ecular structure optimized by density functional theory (DFT) calculations at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The HOMO–LUMO behaviour was also elucidated to determine the energy gap.

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.

In the title compound, C19H20Cl2N2O, the seven-membered 1,4-diazepane ring adopts a chair conformation while the 4-chloro­phenyl substituents adopt equatorial orientations. The chloro­phenyl ring at position 7 is disordered over two positions [site occupancies 0.480 (16):0.520 (16)]. The dihedral angle between the two benzene rings is 63.0 (4)°. The methyl groups at position 3 have an axial and an equatorial orientation. The compound exists as a dimer exhibiting inter­molecular N—H⋯O hydrogen bonding with R22(8) graph-set motifs. The crystal structure is further stabilized by C—H⋯O hydrogen bonds together with two C—Cl⋯π (ring) inter­actions. The geometry was optimized by DFT using the B3LYP/6–31 G(d,p) level basis set. In addition, the HOMO and LUMO energies, chemical reactivity parameters and mol­ecular electrostatic potential were calculated at the same level of theory. Hirshfeld surface analysis indicated that the most important contributions to the crystal packing are from H⋯H (45.6%), Cl⋯H/H⋯Cl (23.8%), H⋯C/C⋯H (12.6%), H⋯O/O⋯H (8.7%) and C⋯Cl/Cl⋯C (7.1%) inter­actions. Analysis of the inter­action energies showed that the dispersion energy is greater than the electrostatic energy. A crystal void volume of 237.16 Å3 is observed. A mol­ecular docking study with the human oestrogen receptor 3ERT protein revealed good docking with a score of −8.9 kcal mol−1.

In the structure of the title compound, C19H19N3O5S·C4H8O2, the two independent dioxane mol­ecules each display inversion symmetry. The pyrazole ring is approximately parallel to the aromatic ring of the oxy-ethanone group and approximately perpendicular to the tolyl ring of the sulfonyl substituent. An extensive system of classical and `weak' hydrogen bonds connects the residues to form a layer structure parallel to (201), within which dimeric subunits are conspicuous; neighbouring layers are connected by classical hydrogen bonds to dioxanes and by `weak' hydrogen bonds from Htol­yl donors.

Syntheses of the acyclic amidinium salts, morpholino­formamidinium hexa­fluorido­phosphate [OC4H8N—CH=NH2]PF6 or C5H11N2O+·PF6−, 1, and pyrrolidinoformamidinium hexa­fluorido­phosphate [C4H8N—CH= NH2]PF6 or C5H11N2+·PF6−, 2, were carried out by heating either morpholine or pyrrolidine with triethyl orthoformate and ammonium hexa­fluorido­phosphate. Crystals of 1 obtained directly from the reaction mixture contain one cation and one anion in the asymmetric unit. The structure involves cations linked in chains parallel to the b axis by N—H⋯O hydrogen bonds in space group Pbca, with glide-related chains pointing in opposite directions. Crystals of 1 obtained by recrystallization from ethanol, however, showed a similar unit cell and the same basic structure, but unexpectedly, there was positional disorder [occupancy ratio 0.639 (4):0.361 (4)] in one of the cation chains, which lowered the crystal symmetry to the non-centrosymmetric space group Pca21, with two cations and anions in the asymmetric unit. In the pyrrolidino compound, 2, cations and anions are ordered and are stacked separately, with zigzag N—H⋯F hydrogen-bonding between stacks, forming ribbons parallel to (101), extended along the b-axis direction. Slight differences in the delocalized C=N distances between the two cations may reflect the inductive effect of the oxygen atom in the morpholino compound.

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, C13H11NO, adopts an E configuration about the C=C double bond. The pyrrole ring is inclined to the phenyl ring at an angle of 44.94 (8)°. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming ribbons parallel to (020) in zigzag C(7) chains along the a axis. These ribbons are connected via C—H⋯π inter­actions, forming a three-dimensional network. No significant π–π inter­actions are observed.

The in­do­line portion of the title mol­ecule, C16H13NO2, is planar. In the crystal, a layer structure is generated by C—H⋯O hydrogen bonds and C—H⋯π(ring), π-stacking and C=O⋯π(ring) inter­actions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (43.0%), H⋯C/C⋯H (25.0%) and H⋯O/O⋯H (22.8%) inter­actions. Hydrogen bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 120.52 Å3 and 9.64%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311G(d,p) level is compared with the experimentally determined mol­ecular structure in the solid state.

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.

In the crystal of the title compound, C6H9ClN2O, mol­ecular pairs form dimers with an R22(8) motif through N—H⋯O hydrogen bonds. These dimers are connect into ribbons parallel to the (100) plane with R44(10) motifs by N—H⋯O hydrogen bonds along the c-axis direction. In addition, π–π [centroid-to-centroid distance = 3.4635 (9) Å] and C—Cl⋯π inter­actions between the ribbons form layers parallel to the (100) plane. The three-dimensional consolidation of the crystal structure is also ensured by Cl⋯H and Cl⋯Cl inter­actions between these layers. According to a Hirshfeld surface study, H⋯H (43.3%), Cl⋯H/H⋯Cl (22.1%) and O⋯H/H⋯O (18.7%) inter­actions are the most significant contributors to the crystal packing.

In the title compound, C12H11N3OS, the inter­planar angle between the pyrazole and benzo­thia­zole rings is 3.31 (7)°. In the three-dimensional mol­ecular packing, the carbonyl oxygen acts as acceptor to four C—H donors (with one H⋯O as short as 2.25 Å), while one methyl hydrogen is part of the three-centre system H⋯(S, O). A double layer structure parallel to (overline{1}01) can be recognized as a subsection of the packing.

A CuII coordination polymer, catena-poly[[[aqua­copper(II)]-bis­(μ-4-amino­benz­o­ato)-κ2N:O;κ2O:N] monohydrate], {[Cu(pABA)2(H2O)]·H2O}n (pABA = p-amino­benzoate, C7H4NO2−), was synthesized and characterized. It exhibits a one-dimensional chain structure extended into a three-dimensional supra­molecular assembly through hydrogen bonds and π–π inter­actions. While the twinned crystal shows a metrically ortho­rhom­bic lattice and an apparent space group Pbcm, the true symmetry is monoclinic (space group P2/c), with disordered Cu atoms and mixed roles of water mol­ecules (aqua ligand/crystallization water). The luminescence spectrum of the complex shows an emission at 345 nm, cf. 349 nm for pABAH.

The crystal structure of the sodium salt of mesotrione, namely, catena-poly[[sodium-μ3-2-[(4-methane­sulfonyl-2-nitro­phen­yl)carbon­yl]-3-oxo­cyclo­hex-1-en-1-olato] ethanol monosolvate], {[Na(C14H12NO7S)]C2H5OH}n, is described. The X-ray structural analysis results reveal that the coordination sphere is established by two chelating O atoms, the O atom of the coordinated ethanol mol­ecule, and an O atom from the methyl­sulfonyl group of a neighboring mol­ecule. Simultaneously, an O atom of the cyclo­hexane fragment serves as a bridge to a neighboring sodium ion, forming a flat Na–O–Na–O quadrangle, thereby forming a mono-periodic polymer. The structure displays O—H⋯O hydrogen bonds and C—H⋯O short contacts. Thermogravimetric analysis (TGA) data indicate that the sodium salt of mesotrione decomposes in four stages.

In the title compound, C31H24N4O2, the quinoxaline units are distinctly non-planar and twisted end-to-end. In the crystal, C—H⋯O and C—H⋯N hydrogen bonds link the mol­ecules into chains extending along the a-axis direction. The chains are linked through π-stacking inter­actions between inversion-related quinoxaline moieties.

The structure of (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone, C13H13ClFNO4, at 100 K has monoclinic (P21) symmetry. The compound has a polymeric structure propagated by a screw axis parallel to the b axis with N—H⋯O hydrogen bonding. It is of inter­est with respect to efforts in the synthesis of a candidate anti­cancer drug, parsaclisib.