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The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and l-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.

In the title compound, [CuCl2(C9H18N4)]·CH3OH, the central CuII ion is coordinated by three N atoms from the pyrazole derivative ligand and two chloride co-ligands. The coordination geometry around the CuII ion is distorted trigonal–bipyramidal. In the crystal, the mol­ecules are linked by C—H⋯O, C—H⋯Cl and O—H⋯Cl hydrogen bonds, forming a three-dimensional framework with the lattice solvent mol­ecule.

In the mol­ecule of the title N,N'-disubstituted imidazol-2-yl­idene palladium(II) complex, [PdBr2(C21H24N4O)]·CH2Cl2, the palladium(II) atom adopts a slightly distorted square-planar coordination (r.m.s. deviation = 0.0145 Å), and the five-membered chelate ring is almost planar [maximum displacement = 0.015 (8) Å]. The mol­ecular conformation is enforced by intra­molecular C—H⋯Br hydrogen bonds. In the crystal, complex mol­ecules and di­chloro­methane mol­ecules are linked into a three-dimensional network by C—H⋯O and C—H⋯Br hydrogen bonds.

The complete mol­ecule of the title compound, C32H22F12N4O2, is generated by a crystallographic twofold axis aligned parallel to [010]. The F atoms of one of the CF3 groups are disordered over three orientations in a 0.6: 0.2: 0.2 ratio. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming zigzag chains propagating along the a-axis direction. In addition, weak C—H⋯O and C—H⋯F bonds are observed. The contribution of the disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] of PLATON. The solvent contribution is not included in the reported mol­ecular weight and density.

In the title compound, C8H5ClF3NO, the F—C—C=O grouping shows a syn conformation [torsion angle = 1.1 (3)°] and an intra­molecular N—H⋯O hydrogen bond generates an S(6) ring. In the crystal, N—H⋯F and N—H⋯O hydrogen bonds link the mol­ecules into [010] chains.

Trinuclear copper–pyrazolate entities are present in various Cu-based enzymes and nanojar supra­molecular arrangements. The reaction of copper(II) chloride with pyrazole (pzH) and sodium benzoate (benzNa) assisted by microwave radiation afforded a neutral centrosymmetric hexa­nuclear copper(II) complex, [Cu6(C7H5O2)4(OH)2(C3H3N2)6(C2H5OH)2]·2C2H5OH. Half a mol­ecule is present in the asymmetric unit that comprises a [Cu3(μ3-OH)(pz)3]2+ core with the copper(II) atoms arranged in an irregular triangle. The three copper(II) atoms are bridged by an O atom of the central hydroxyl group and by three bridging pyrazolate ligands on each of the sides. The carboxyl­ate groups show a chelating mode to one and a bridging syn,syn mode to the other two CuII atoms. The coordination environment of one CuII atom is square-planar while it is distorted square-pyramidal for the other two. Two ethanol mol­ecules are present in the asymmetric unit, one binding to one of the CuII atoms, one as a solvent mol­ecule. In the crystal, stabilization arises from inter­molecular O—H⋯O hydrogen-bonding inter­actions.

The title compound, C16H16N2O6, lies about an inversion centre at the mid-point of the N—N bond. The mol­ecule features two intra­molecular O—H⋯N and two C—H⋯O hydrogen bonds, each of which forms an S(6) ring motif. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds into infinite zigzag chains propagating along the c-axis direction. π–π stacking inter­actions between the pyrone rings [centroid–centroid distances = 3.975 (2) Å] stack the mol­ecules along b.

The title com­pound, C34H24O4S·0.5CH2Cl2, crystallizes with two independent mol­ecules and one di­chloro­methane solvent mol­ecule in the asymmetric unit. The crystal packing is consolidated by C—H⋯O hydrogen bonds.

The title magnesium complex, [Mg(C21H20NO2)2(C4H8O)]n, exhibits two N,O-bidentate 2-(di­methyl­amino)-α,α-di­phenyl­benzene­methano­late ligands, form­ing two six-membered chelate rings. The distorted square-pyramidal coordination sphere of the MgII atom is completed by the O atom of a tetra­hydro­furan ligand, with its O atom in the apical position. The O and N atoms are in a mutual trans arrangement. Except for two C—H⋯π inter­actions, no significant inter­molecular inter­actions are observed in the crystal.

The title compound, (C8H22N2O)2[Mo8O26]·H2O, (cis-H2L)2[β-Mo8O26]·H2O, where L = (bis­[2-N,N-di­methyl­amino)­eth­yl] ether), was synthesized from bis­[2-(di­methyl­amino)­eth­yl] ether and MoO3 under solvothermal conditions and characterized by multinuclear NMR and single-crystal X-ray diffraction techniques. The structure displays two [oxybis(ethane-1,2-di­yl)]bis­(di­methyl­ammonium), or [cis-H2L]2+, cations, a central [β-Mo8O26]4− anionic cluster consisting of eight distorted MoO6 octa­hedra, and two water mol­ecules in their deuterated form. The central anion lies across an inversion center. The [cis-H2L]2+ cations are hydrogen bonded to the central [β-Mo8O26]4− cluster via bridging water mol­ecules. In the crystal, O—H⋯O hydrogen bonds link the components into chains along [010]. Weak C—H⋯O hydrogen bonds link these chains into a three-dimensional network.

In the title compound, [Cu2(C7HF4O2)4(C12H8N2)2(CH3OH)], the mol­ecule lies on a twofold rotation axis in space group C2/c. The Cu2+ ion exhibits a distorted octa­hedral sphere with two N atoms from the phenanthroline ligand, three O atoms from the 2,3,4,5-tetra­fluoro­benzoate ligands and one O atom from a methanol mol­ecule. The distortion from an octa­hedral shape is a consequence of the Jahn–Teller effect of CuII and the small bite angle for the bidentate fluoro­benzoate ligand [54.50 (11)°]. The methanol mol­ecule bridges two symmetry-related CuII atoms to form the complete mol­ecule. In the bidentate fluoro­benzoate ligand, one F atom is disordered over two positions of equal occupancy. In the crystal structure, only weak inter­molecular inter­actions are observed.

The title compound, C12H10N2O2S, was synthesized via the acid-catalyzed condensation of 4-nitro­aniline and 5-methyl-2-thio­phene­carboxaldehyde in a methanol–water solution. The dihedral angle between the benzene and thio­phene rings is 54.62 (3)°. No directional inter­actions could be identified in the extended structure.

In the title compound, [Cd4Cl8(C6H16N2)4], the Cd2+ cations and Cl− anions form M4Cl8 clusters with six of the Cl− ions bridging Cd2+ cations and two being pendant. Each Cd2+ cation has distorted octa­hedral coordination completed by four Cl− ions and two N atoms of the asymmetrical bidentate amino ligand. The cluster consists of pairs of face-sharing hexa­hedra linked by a shared edge.

In the title compound, C18H16N2O2, the dihedral angle between the pyrrole rings is 79.47 (9)°, with the N—H groups approximately orthogonal (H—N⋯N—H pseudo torsion angle = −106°). In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into [11overline{1}] chains. A C—H⋯O inter­action is also observed.

The structure of the title compound, H3O+·C2F6NO4S2−·C12H24O6 or [H3O+·C12H24O6][N(SO2CF3)2−], which is an ionic liquid with a melting point of 341–343 K, has been determined at 113 K. The asymmetric unit consists of two crystallographically independent 18-crown-6 mol­ecules, two hydro­nium ions and two bis­(tri­fluoro­methane­sulfon­yl)amide anions; each 18-crown-6 mol­ecule complexes with a hydro­nium ion. In one 18-crown-6 mol­ecule, a part of the ring exhibits conformational disorder over two sets of sites with an occupancy ratio of 0.533 (13):0.467 (13). One hydro­nium ion is complexed with the ordered 18-crown-6 mol­ecule via O—H⋯O hydrogen bonds with H2OH⋯OC distances of 1.90 (6)–2.19 (7) Å, and the other hydro­nium ion with the disordered crown mol­ecule with distances of 1.85 (6)–2.36 (6) Å. The hydro­nium ions are also linked to the anions via O—H⋯F hydrogen bonds. The crystal studied was found to be a racemic twin with a component ratio of 0.55 (13):0.45 (13).

The structure of the tertiary amine tris­(1H-benzimidazol-2-ylmeth­yl)amine (C24H21N7, abbreviated ntb) has been previously reported twice as solvates, namely the monohydrate and the aceto­nitrile–methanol–water (1/0.5/1.5) solvate, both with the tripodal conformation formed via multiple hydrogen bonds. Now, we report the tri­methanol adduct, ntb·3CH3OH, where the amine has the stair conformation featuring one benzimidazole group oriented in the opposite direction from the other two. The asymmetric unit contains one-half amine, completed through the mirror plane m in space group Pmn21 to form the ntb mol­ecule, with the H atom for each imidazole moiety equally disordered between both N sites available in the imidazole ring. The asymmetric unit also contains one and a half methanol mol­ecules, one being placed in general position with the hy­droxy H atom disordered over two sites with occupancy ratio 1:1, while the other lies on the m mirror plane, and has thus its hy­droxy H atom disordered by symmetry. As in the previously reported solvates, all imine and amine groups of the ntb mol­ecules and the methanol mol­ecules are involved in N—H⋯O and O—H⋯N hydrogen bonds. In the title compound, however, the involved H atom is systematically a disordered H atom provided by an imidazole group or a methanol mol­ecule.

The title compound, C15H13BrO2S, comprises three different substituents bound to a central (and chiral) methine-C atom, i.e. (4-bromo­phen­yl)sulfanyl, benzaldehyde and meth­oxy residues: crystal symmetry generates a racemic mixture. A twist in the mol­ecule is evident about the methine-C—C(carbon­yl) bond as evidenced by the O—C—C—O torsion angle of −20.8 (7)°. The dihedral angle between the bromo­benzene and phenyl rings is 43.2 (2)°, with the former disposed to lie over the oxygen atoms. The most prominent feature of the packing is the formation of helical supra­molecular chains as a result of methyl- and methine-C—H⋯O(carbon­yl) inter­actions. The chains assemble into a three-dimensional architecture without directional inter­actions between them. The nature of the weak points of contacts has been probed by a combination of Hirshfeld surface analysis, non-covalent inter­action plots and inter­action energy calculations. These point to the importance of weaker H⋯H and C—H⋯C inter­actions in the consolidation of the structure.

The title binuclear CoIII complex, [Co2(C9H8BrNOS)2(C18H16Br2N2O2S2)]·C3H7NO, with a Schiff base ligand formed in situ from cyste­amine (2-amino­ethane­thiol) and 5-bromo­salicyl­aldehyde crystallizes in the space group P21. It was found that during the synthesis the ligand undergoes spontaneous oxidation, forming the new ligand H2L' having an S—S bond. Thus, the asymmetric unit consists of one Co2(L)2(L') mol­ecule and one DMF solvent mol­ecule. Each CoIII ion has a slightly distorted octa­hedral S2N2O2 coordination geometry. In the crystal, the components are linked into a three-dimensional network by several S⋯ Br, C⋯ Br, C—H⋯Br, short S⋯C (essentially shorter than the sum of the van der Waals radii for the atoms involved) contacts as well by weak C—H⋯O hydrogen bonds. The crystal studied was refined as an inversion twin.

The asymmetric unit of the title compound, [Ni(C52H34Cl4N4O4)]·CH2Cl2, consists of two discrete complexes, which show significant differences in the conformation of the side chain. Each NiII cation is coordinated by four nitro­gen atoms of a porphyrin mol­ecule within a square-planar coordination environment. Weak intra­molecular C—H⋯Cl and C—H⋯O inter­actions stabilize the mol­ecular conformation. In the crystal structure, discrete complexes are linked by C—H⋯Cl hydrogen-bonding inter­actions. In addition, the two unique di­chloro­methane solvate mol­ecules (one being disordered) are hydrogen-bonded to the Cl atoms of the chloro­phenyl groups of the porphyrin mol­ecules, thus stabilizing the three-dimensional arrangement. The crystal exhibits pseudo-ortho­rhom­bic metrics, but structure refinements clearly show that the crystal system is monoclinic and that the crystal is twinned by pseudo-merohedry.

In the title compound, the asymmetric unit comprises an N,N,N-trimethyl-1-(4-vinyl­phen­yl)methanaminium cation and a 4-vinyl­benzene­sulfonate anion, C12H18N+·C8H7O3S−. The salt has a polymerizable vinyl group attached to both the cation and the anion. The methanaminium and vinyl substituents on the benzene ring of the cation subtend angles of 86.6 (3) and 10.5 (9)° to the ring plane, while the anion is planar excluding the sulfonate O atoms. The vinyl substituent on the benzene ring of the cation is disordered over two sites with a refined occupancy ratio of 0.542 (11):0.458 (11). In the crystal, C—H⋯O hydrogen bonds dominate the packing and combine with a C—H⋯π(ring) contact to stack the cations and anions along the a-axis direction. Hirshfeld surface analysis of the salt and of the individual cation and anion components is also reported.

Phenanthroline ligands are important metal-binding mol­ecules which have been extensively researched for applications in both material science and medicinal chemistry. Azo­benzene and its derivatives have received significant attention because of their ability to be reversibly switched between the E and Z forms and so could have applications in optical memory and logic devices or as mol­ecular machines. Herein we report the formation and crystal structure of a highly unusual novel diazo-diphenanthroline compound, C24H14N6O2·2CHCl3.

The asymmetric unit of the centrosymmetric title salt solvate, 2C17H17F6N2O+· C4H4O42−·CH3CH2OH, (systematic name: 2-{[2,8-bis­(tri­fluoro­meth­yl)quinolin-4-yl](hy­droxy)meth­yl}piperidin-1-ium butane­dioate ethanol monosolvate) comprises two independent cations, with almost superimposable conformations and each approximating the shape of the letter L, a butane­dioate dianion with an all-trans conformation and an ethanol solvent mol­ecule. In the crystal, supra­molecular chains along the a-axis direction are sustained by charge-assisted hy­droxy-O—H⋯O(carboxyl­ate) and ammonium-N—H⋯O(carboxyl­ate) hydrogen bonds. These are connected into a layer via C—F⋯π(pyrid­yl) contacts and π–π stacking inter­actions between quinolinyl-C6 and –NC5 rings of the independent cations of the asymmetric unit [inter-centroid separations = 3.6784 (17) and 3.6866 (17) Å]. Layers stack along the c-axis direction with no directional inter­actions between them. The analysis of the calculated Hirshfeld surface reveals the significance of the fluorine atoms in surface contacts. Thus, by far the greatest contribution to the surface contacts, i.e. 41.2%, are of the type F⋯H/H⋯F and many of these occur in the inter-layer region. However, these contacts occur at separations beyond the sum of the van der Waals radii for these atoms. It is noted that H⋯H contacts contribute 29.8% to the overall surface, with smaller contributions from O⋯H/H⋯O (14.0%) and F⋯F (5.7%) contacts.

The syntheses and crystal structures of the title compounds, C14H8F4N2O2 and C14H8F4N2O3, are reported. In each crystal, the packing is driven by C—H⋯F inter­tactions, along with a variety of C—H⋯O, C—O⋯π, and C—F⋯π contacts. Hirshfeld surface analysis was conducted to aid in the visualization of these various influences on the packing: they showed that the largest contributions to the surface contacts arise from H⋯F/F⋯H inter­actions, followed by H⋯H and O⋯H/H⋯O.

The asymmetric unit of the title compound, C12H22N+·CH3O3S−, consists of three (3,5-di­methyl­adamantan-1-yl)ammonium cations, C12H22N+, and three methane­sulfonate anions, CH3O3S−. In the crystal, the cations and anions associate via N—H⋯O hydrogen bonds into layers, parallel to the (001) plane, which include large supra­molecular hydrogen-bonded rings.