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Characterization of the Pseudomonas aeruginosa T6SS PldB immunity proteins PA5086, PA5087 and PA5088 explains a novel stockpiling mechanism

The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.




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Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa

Factor for inversion stimulation (Fis) is a versatile bacterial nucleoid-associated protein that can directly bind and bend DNA to influence DNA topology. It also plays crucial roles in regulating bacterial virulence factors and in optimizing bacterial adaptation to various environments. Fis from Pseudomonas aeruginosa (PA4853, referred to as PaFis) has recently been found to be required for virulence by regulating the expression of type III secretion system (T3SS) genes. PaFis can specifically bind to the promoter region of exsA, which functions as a T3SS master regulator, to regulate its expression and plays an essential role in transcription elongation from exsB to exsA. Here, the crystal structure of PaFis, which is composed of a four-helix bundle and forms a homodimer, is reported. PaFis shows remarkable structural similarities to the well studied Escherichia coli Fis (EcFis), including an N-terminal flexible loop and a C-terminal helix–turn–helix (HTH) motif. However, the critical residues for Hin-catalyzed DNA inversion in the N-terminal loop of EcFis are not conserved in PaFis and further studies are required to investigate its exact role. A gel-electrophoresis mobility-shift assay showed that PaFis can efficiently bind to the promoter region of exsA. Structure-based mutagenesis revealed that several conserved basic residues in the HTH motif play essential roles in DNA binding. These structural and biochemical studies may help in understanding the role of PaFis in the regulation of T3SS expression and in virulence.




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Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway

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.




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Exploring the complex map of insulin polymorphism: a novel crystalline form in the presence of m-cresol

A novel monoclinic phase of human insulin co-crystallized with m-cresol was structurally characterized by means of powder and single-crystal X-ray diffraction.




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Crystal and solution structures of fragments of the human leucocyte common antigen-related protein

The crystal and solution SAXS structures of a fragment of human leucocyte common antigen-related protein show that it is less flexible than the homologous proteins tyrosine phosphatase receptors δ and σ.




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Structure of P46, an immunodominant surface protein from Mycoplasma hyopneumoniae: interaction with a monoclonal antibody

Structures of the immunodominant protein P46 from M. hyopneumoniae has been determined by X-ray crystallography and it is shown that P46 can bind a diversity of oligosaccharides, particularly xylose, which exhibits a very high affinity for this protein. Structures of a monoclonal antibody, both alone and in complex with P46, that was raised against M. hyopnemoniae cells and specifically recognizes P46 are also reported.




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Structural and thermodynamic analysis of interactions between death-associated protein kinase 1 and anthraquinones

Death-associated protein kinase 1 (DAPK1) was found to form a complex with purpurin and the crystal structure of the complex was determined. Purpurin may be a good lead compound for for the discovery of inhibitors of DAPK1.




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Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

The bond-valence method was performed on 51 crystal data sets from nitrogenase proteins, indicating the presence of molybdenum(III) in FeMo cofactors and vanadium(III) with more reduced iron complements in FeV cofactors.




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Macromolecular X-ray crystallography: soon to be a road less travelled?

From the perspective of a young(ish) structural biologist who currently specialises in macromolecular X-ray crystallography, are the best years of crystallography over? Some evidence and hopefully thought-provoking analysis is presented here on the subject.




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Structure of Thermococcus litoralis Δ1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline

The paper reports the structure of a Δ1-pyrroline-2-carboxylate reductase from the archaeon Thermococcus litoralis, a key enzyme involved in the second step of trans-4-Hydroxy-L-proline metabolism, conserved in archaea, bacteria and humans.




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6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetra­hydro­pyrimidin-5-aminium sulfate monohydrate

The title compound, C4H9N5O2+·SO42−·H2O, is the monohydrate of the commercially available compound `C4H7N5O·H2SO4·xH2O'. It is obtained by reprecipitation of C4H7N5O·H2SO4·xH2O from dilute sodium hydroxide solution with dilute sulfuric acid. The crystal structure of anhydrous 2,4,5-tri­amino-1,6-di­hydro­pyrimidin-6-one sulfate is known, although called by the authors 5-amminium-6-amino-isocytosinium sulfate [Bieri et al. (1993). Private communication (refcode HACDEU). CCDC, Cambridge, England]. In the structure, the sulfate group is deprotonated, whereas one of the amino groups is protonated (R2C—NH3+) and one is rearranged to a protonated imine group (R2C=NH2+). This arrangement is very similar to the known crystal structure of the anhydrate. Several tautomeric forms of the investigated mol­ecule are possible, which leads to questionable proton attributions. The measured data allowed the location of all hydrogen atoms from the residual electron density. In the crystal, ions and water mol­ecules are linked into a three-dimensional network by N—H⋯O and O—H⋯O hydrogen bonds.




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Di­chlorido­{N,N,N'-trimethyl-N'-(1H-pyrazol-1-yl-κN2)meth­yl]ethane-1,2-di­amine-κ2N,N'}copper(II) methanol monosolvate

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.




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6-Methyl­uracil: a redetermination of polymorph (II)

6-Methyluracil, C5H6N2O2, exists in two crystalline phases: form (I), monoclinic, space group P21/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, mol­ecules form ribbons approximately running parallel to the c-axis direction through N—H⋯O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms C—(O−)=N—H+ relative to the neutral canonical form C(=O)—N—H induced by hydrogen-bonding inter­actions.




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Di­bromido­[N-(1-di­ethyl­amino-1-oxo-3-phenyl­propan-2-yl)-N'-(pyridin-2-yl)imidazol-2-yl­idene]palladium(II) di­chloro­methane monosolvate

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.




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n-Decyl­tri­methyl­ammonium bromide

The title compound, C13H30N+·Br− (systematic name: N,N,N-trimethyl-1-deca­naminium bromide), forms crystals having a bilayer structure, comprised of layers of tri­methyl­ammonium cations and bromide anions separated by the inter-digitated n-decyl groups of the cation; close ammonium-methyl-C—H⋯Br contacts connect the ions. The n-decyl chain adopts a slightly distorted all-trans conformation. The n-decyl chain exhibits positional disorder with all atoms at half occupancy. The sample was a racemic twin.




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1,2,4,5-Tetra­chloro-3,6-di­iodo­benzene benzene monosolvate

The title compound, C6Cl4I2·C6H6, crystallizes from benzene solution as cube-shaped crystals in the triclinic space group Poverline{1} with Z = 1. The asymmetric unit of the crystal structure contains one half of each mol­ecule. In the crystal, the benzene ring is almost orthogonal to the perhalo­benzene ring and the mol­ecules are linked by C—I⋯π inter­actions, with a close contact between the iodine atom and the benzene ring of 3.412 (1) Å.




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(1,4,8,11-Tetra­aza­cyclo­tetra­deca­ne)palladium(II) diiodide monohydrate

In the title compound, [Pd(C10H24N4)]I2·H2O, the PdII ion is four-coordinated in a slightly distorted square-planar coordination environment defined by four N atoms from a 1,4,8,11-tetra­aza­cyclo­tetra­decane ligand. The cationic complex, two I− anions and the solvent water mol­ecule are linked through inter­molecular hydrogen bonds into a three-dimensional network structure.




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(Pyridine-2,6-di­carboxyl­ato-κ3O,N,O')(2,2':6',2''- terpyridine-κ3N,N',N'')nickel(II) di­methyl­formamide monosolvate monohydrate

In the title complex, [Ni(C7H3NO4)(C15H11N3)]·C3H7NO·H2O, the NiII ion is six-coordinated within an octa­hedral geometry defined by three N atoms of the 2,2':6',2''-terpyridine ligand, and two O atoms and the N atom of the pyridine-2,6-di­carboxyl­ate di-anion. In the crystal, the complex mol­ecules are stacked in columns parallel to the a axis being connected by π–π stacking [closest inter-centroid separation between pyridyl rings = 3.669 (3) Å]. The connections between columns and solvent mol­ecules to sustain a three-dimensional architecture are of the type water-O—H⋯O(carbon­yl) and pyridyl-, methyl-C—H⋯O(carbon­yl).




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Synthesis and crystal structure of [Cs([2.2.2]crypt)]2[Mo(CO)5]

Reduction of the heteroleptic metal carbonyl complex Mo(CO)3(η5-Cp)H with the metallic salt Cs5Bi4 in the presence of [2.2.2]crypt (= 4,7,13,16,21,24-hexa­oxa-1,10-di­aza­bicyclo­[8.8.8]hexa­cosa­ne) in liquid ammonia led to single crystals of bis­[(4,7,13,16,21,24-hexa­oxa-1,10-di­aza­bicyclo­[8.8.8]hexa­cosa­ne)caesium] penta­carbonyl­molybdate, [Cs(C18H36N2O6)]2[Mo(CO)5] or [Cs([2.2.2]crypt)]2[Mo(CO)5]. The twofold negatively charged anionic complex corresponds to the 18 valence electron rule. It consists of an Mo atom coordinated by five carbonyl ligands in a shape inter­mediate between trigonal–bipyramidal and square-pyramidal. The Mo—C distances range from 1.961 (3) to 2.017 (3) Å, and the C≡O distances from 1.164 (3) to 1.180 (4) Å.




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3-Bromo­pyridine-2-carbo­nitrile

The title compound, C6H3BrN2, also known as 3-bromo­picolino­nitrile, was synthesized by cyanation of 2,3-di­bromo­pyridine. In the solid state, short inter­molecular Br⋯N contacts are observed. Additionally, the crystal packing is consolidated by π–π stacking inter­actions with centroid–centroid distances of 3.7893 (9) Å.




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9α-Hy­droxy-4,8-dimethyl-3'-phenyl-3,14-dioxatri­cyclo­[9.3.0.02,4]tetra­dec-7-en-13-one-12-spiro-5'-isoxazole monohydrate

In the title compound, C22H25NO5·H2O, the ten-membered ring displays an approximate chair–chair conformation, whereas the five-membered furan ring has an envelope conformation, with the C atom of the methine group adjacent to the spiro C atom as the flap. The isoxazole ring is almost planar and its plane is slightly inclined to the plane of the attached phenyl ring. The mean plane of the furan ring is nearly perpendicular to that of the isoxazole ring, as indicated by the dihedral angle between them of 89.39 (12)°. In the crystal, the organic mol­ecules are linked into [010] chains by O—H⋯O hydrogen bonds. The water mol­ecule forms O—H⋯O and O—H⋯N hydrogen bonds and a weak C—H⋯O inter­action is also observed. Together, these lead to a three-dimensional network.




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Bis(4-hy­droxy-N,N-di-n-propyl­tryptammonium) fumarate tetra­hydrate

The title compound (systematic name: bis­{[2-(4-hy­droxy-1H-indol-3-yl)eth­yl]bis­(propan-2-yl)aza­nium} but-2-enedioate tetra­hydrate), 2C16H25N2O+·C4H2O42−·4H2O, has a singly protonated DPT cation, one half of a fumarate dianion (completed by a crystallographic centre of symmetry) and two water mol­ecules of crystallization in the asymmetric unit. A series of N—H⋯O and O—H⋯O hydrogen bonds form a three-dimensional network in the solid state.




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(4-Carb­oxy­benz­yl)tri­phenyl­phospho­nium hexa­fluorido­phosphate tetra­hydro­furan monosolvate

The title compound, C26H22O2P+·PF6−·C4H7O, crystallizes as a cation-anion pair with a single solvent mol­ecule in the asymmetric unit. Hydrogen bonding occurs between the carb­oxy­lic acid group on the cation and the oxygen atom of the solvent mol­ecule. Longer hydrogen-bonding inter­actions are observed between fluorine atoms of the anion and H atoms on the phenyl rings of the cation.




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[Oxybis(ethane-1,2-di­yl)]bis­(di­methyl­ammonium) octa­molybdate dihydrate

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.




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Tetra­kis(2,3,5,6-tetra­fluoro­benzene­thiol­ato-κS)(tri­phenyl­phosphane-κP)osmium(IV): a monoclinic polymorph

The structure of the title compound, [Os(C6HF4S)4{P(C6H5)3}], has been previously reported [Arroyo et al. (1994). J. Chem. Soc. Dalton Trans. pp. 1819–1824], in the space group Poverline{1}. We have now obtained a monoclinic polymorph for this compound, crystallized from ethanol, while the previous form was obtained from a hexa­ne/chloro­form mixture. The mol­ecular structure is based on a trigonal–bipyramidal OsIV coordination geometry, close to that observed previously in the triclinic form.




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(2,2'-Bi­pyridine-κ2N,N')(pyridine-2,6-di­carboxyl­ato-κ2N,O)palladium(II) monohydrate

In the title compound, [Pd(C7H3NO4)(C10H8N2)]·H2O, the PdII cation is four-coordinated in a distorted square-planar coordination geometry defined by the two N atoms of the 2,2'-bi­pyridine ligand, one O atom and one N atom from the pyridine-2,6-di­carboxyl­ate anion. The complex and solvent water mol­ecule are linked by inter­molecular hydrogen bonds. In the crystal, the complex mol­ecules are stacked in columns along the a axis.




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6,6'-[(3,3'-Di-tert-butyl-5,5'-dimeth­oxy-1,1'-biphenyl-2,2'-di­yl)bis(oxy)]bis­(dibenzo[d,f][1,3,2]dioxaphosphepine) benzene monosolvate

The crystal structure of the benzene monosolvate of the well known organic diphosphite ligand BIPHEPHOS, C46H44O8P2·C6H6, is reported for the first time. Single crystals of BIPHEPHOS were obtained from a benzene solution after layering with n-heptane at room temperature. One specific property of this type of diphosphite structure is the twisting of the biphenyl units. In the crystal, C—H⋯π contacts and π–π stacking inter­actions [centroid-to-centroid distance = 3.8941 (15) Å] are observed.




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2-[4,5-Bis(4-bromo­phen­yl)-1-(4-tert-but­ylphen­yl)-1H-imidazol-2-yl]-4,6-di­chloro­phenol

In the title compound, C31H24Br2Cl2N2O, the dihedral angles subtended by the tert-butyl-phenyl, 4,6-di­chloro­phenol and 4-bromo­phenyl (×2) rings are 70.7 (3), 8.1 (3), 28.1 (3) and 84.2 (3)°, respectively. The orientations of the pendant rings may be related to intra­molecular O—H⋯N and C—H⋯π inter­actions. One of the tert-butyl methyl groups is disordered over two sets of sites in a 0.54 (3):0.46 (3) ratio. In the crystal, a weak C—H⋯π inter­action generates inversion dimers.




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N'-(2-Hy­droxy-3-meth­oxy­benzyl­idene)pyrazine-2-carbohydrazide monohydrate

In the title hydrated Schiff base, C13H12N4O3·H2O, the dihedral angle between the aromatic rings is 5.06 (11)° and an intra­molecular O—H⋯N hydrogen bond closes an S(6) ring. In the crystal, Ow—H⋯O and Ow—H⋯N (w = water) hydrogen bonds link the components into centrosymmetric tetra­mers (two Schiff bases and two water mol­ecules). Longer N—H⋯O hydrogen bonds link the tetra­mers into [010] chains. A weak C—H⋯O hydrogen bond and aromatic π–π stacking between the pyrazine and phenyl rings [centroid–centroid separations = 3.604 (2) and 3.715 (2) Å] are also observed.




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Di­chlorido­bis­[2-(pyridin-2-yl-κN)-1H-benzimidazole-κN3]nickel(II) monohydrate

In the title complex, [NiCl2(C12H9N3)2]·H2O, a divalent nickel atom is coordinated by two 2-(pyridin-2-yl)-1H-benzimidazole ligands in a slightly distorted octa­hedral environment defined by four N donors of two N,N'-chelating ligands, along with two cis-oriented anionic chloride donors. The title complex crystallized with a water mol­ecule disordered over two positions. In the crystal, a combination of O—H⋯Cl, O—H.·O and N—H⋯Cl hydrogen bonds, together with C—H⋯O, C—H⋯Cl and C—H⋯π inter­actions, links the complex mol­ecules and the water mol­ecules to form a supra­molecular three-dimensional framework. The title complex is isostructural with the cobalt(II) dichloride complex reported previously [Das et al. (2011). Org. Biomol. Chem. 9, 7097–7107].




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(3S,5R,6S)-Di­phenyl­methyl 1-oxo-6-bromo­penicillanate

In the title compound, C21H20BrNO4S, a key inter­mediate in the synthesis of the widely used β-lactamase inhibitor tazobactam, the five-membered thia­zolidine ring adopts an envelope conformation and the four-membered azetidine ring is in a distorted planar conformation. The crystal structure features C—H⋯O hydrogen bonds and a weak C—H⋯π inter­action.




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[1–9-NαC]-Linusorb B3 (Cyclo­linopeptide A) dimethyl sulfoxide monosolvate

Crystals of the dimethyl sulfoxide (DMSO) solvate of [1–9-NαC]-linusorb B3 (Cyclo­linopeptide A; CLP-A; C57H84N9O9·C2H6OS), a cyclic polypeptide were obtained following peptide extraction and purification from flaxseed oil. There are four intramolecular N—H⋯O hydrogen bonds. In the crystal, the mol­ecules are linked in chains along the a axis by N—H⋯O hydrogen bonds. Each DMSO O atom accepts a hydrogen bond from an NH group at the Phe6 location in the CLP-A mol­ecule.




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Tris­(4,4'-di-tert-butyl-2,2'-bi­pyridine)(trans-4-tert-butyl­cyclo­hexa­nolato)­deca-μ-oxido-hepta­oxido­hepta­vanadium aceto­nitrile monosolvate including another unknown solvent mol­ecule

The title hepta­nuclear alkoxido(oxido)vanadium(V) oxide cluster complex, [V7(C10H19O)O17(C18H24N2)3]·CH3CN, was obtained by the reaction of [V8O20(C18H24N2)4] with 4-tert-butyl­cyclo­hexa­nol (mixture of cis and trans) in a mixed CHCl3/CH3CN solvent. The complex has a V7O18N6 core with approximately Cs symmetry, which is composed of two VO4 tetra­hedra, two VO6 octa­hedra and three VO4N2 octa­hedra. In the crystal, these complexes are linked together by weak inter­molecular C—H⋯O hydrogen bonds between the 4,4'-di-tert-butyl-2,2'-bi­pyridine ligand and the V7O18N6 core, forming a one-dimensional network along the c-axis direction. Besides the complex, the asymmetric unit contains one CH3CN solvent mol­ecule. The contribution of other disordered solvent mol­ecules to the scattering was removed using the SQUEEZE option in PLATON [Spek (2015). Acta Cryst. C71, 9–18]. The unknown solvent mol­ecules are not considered in the chemical formula and other crystal data.




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Redetermination of di­ammonium trivanadate, (NH4)2V3O8

The crystal structure of (NH4)2V3O8 has been reported twice using single-crystal X-ray data [Theobald et al. (1984). J. Phys. Chem. Solids, 45, 581–587; Range et al. (1988). Z. Naturforsch. Teil B, 43, 309–317]. In both cases, the orientation of the ammonium cation in the asymmetric unit was poorly defined: in Theobald's study, the shape and dimensions were constrained for NH4+, while in Range's study, H atoms were not included. In the present study, we collected a highly redundant data set for this ternary oxide, at 0.61 Å resolution, using Ag Kα radiation. These accurate data reveal that the NH4+ cation is disordered by rotation around a non-crystallographic axis. The rotation axis coincides with one N—H bond lying in the mirror m symmetry element of space-group type P4bm, and the remaining H sites were modelled over two disordered positions, with equal occupancy. It therefore follows that the NH4+ cations filling the space available in the (001) layered structure formed by (V3O8)2– ions do not form strong N—H⋯O hydrogen bonds with the mixed-valent oxidovanadate(IV,V) anions. This feature could have consequences for the Li-ion inter­calation properties of this material, which is used as a cathode for supercapacitors.




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Crystal structure and Hirshfeld surface analysis of 4-[4-(1H-benzo[d]imidazol-2-yl)phen­oxy]phthalo­nitrile dimethyl sulfoxide monosolvate

This work presents the synthesis and structural characterization of [4-(1H-benzo[d]imidazol-2-yl)phen­oxy]phthalo­nitrile, a phthalo­nitrile derivative carrying a benzimidazole moiety. The compound crystallizes as its dimethyl sulfoxide monosolvate, C21H12N4O·(CH3)2SO. The dihedral angle between the two fused rings in the heterocyclic ring system is 2.11 (1)°, while the phenyl ring attached to the imidazole moiety is inclined by 20.7 (1)° to the latter. In the crystal structure, adjacent mol­ecules are connected by pairs of weak inter­molecular C—H⋯N hydrogen bonds into inversion dimers. N—H⋯O and C—H⋯O hydrogen bonds with R21(7) graph-set motifs are also formed between the organic mol­ecule and the disordered dimethyl sulfoxide solvent [occupancy ratio of 0.623 (5):0.377 (5) for the two sites of the sulfur atom]. Hirshfeld surface analysis and fingerprint plots were used to investigate the inter­molecular inter­actions in the crystalline state.




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Crystal structure, Hirshfeld surface analysis and HOMO–LUMO analysis of (E)-N'-(3-hy­droxy-4-meth­oxy­benzyl­idene)nicotinohydrazide monohydrate

The mol­ecule of the title Schiff base compound, C14H13N3O3·H2O, displays a trans configuration with respect to the C=N bond. The dihedral angle between the benzene and pyridine rings is 29.63 (7)°. The crystal structure features inter­molecular N—H⋯O, C—H⋯O, O—H⋯O and O—H⋯N hydrogen-bonding inter­actions, leading to the formation of a supramolecular framework. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (37.0%), O⋯H/H⋯O (23.7%)), C⋯H/H⋯C (17.6%) and N⋯H/H⋯N (11.9%) inter­actions. The title compound has also been characterized by frontier mol­ecular orbital analysis.




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Crystal structure and Hirshfeld surface analysis of a conformationally unsymmetrical bis­chalcone: (1E,4E)-1,5-bis­(4-bromo­phen­yl)penta-1,4-dien-3-one

In the title bis­chalcone, C17H12Br2O, the olefinic double bonds are almost coplanar with their attached 4-bromo­phenyl rings [torsion angles = −10.2 (4) and −6.2 (4)°], while the carbonyl double bond is in an s-trans conformation with with respect to one of the C=C bonds and an s-cis conformation with respect to the other [C=C—C=O = 160.7 (3) and −15.2 (4)°, respectively]. The dihedral angle between the 4-bromo­phenyl rings is 51.56 (2)°. In the crystal, mol­ecules are linked into a zigzag chain propagating along [001] by weak C—H⋯π inter­actions. The conformations of related bis­chalcones are surveyed and a Hirshfeld surface analysis is used to investigate and qu­antify the inter­molecular contacts.




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2-[(4-Bromo­phen­yl)sulfan­yl]-2-meth­oxy-1-phenyl­ethan-1-one: crystal structure, Hirshfeld surface analysis and computational chemistry

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.




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Crystal structure and Hirshfeld surface analysis of new polymorph of racemic 2-phenyl­butyramide

A new polymorph of the title compound, C10H13NO, was obtained by recrystallization of the commercial product from a water/ethanol mixture (1:1 v/v). Crystals of the previously reported racemic and homochiral forms of 2-phenyl­butyramide were grown from water–aceto­nitrile solution in 1:1 volume ratio [Khrustalev et al. (2014). Cryst. Growth Des. 14, 3360–3369]. While the previously reported racemic and enanti­opure forms of the title compound adopt very similar supra­molecular structures (hydrogen-bonded ribbons), the new racemic polymorph is stabilized by a single N—H⋯O hydrogen bond that links mol­ecules into chains along the c-axis direction with an anti­parallel (centrosymmetric) packing in the crystal. Hirshfeld mol­ecular surface analysis was employed to compare the inter­molecular inter­actions in the polymorphs of the title compound.




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Crystal structure of methyl α-l-rhamno­pyranosyl-(1→2)-α-l-rhamno­pyran­oside monohydrate

The title compound, C13H24O9·H2O, a structural model for part of bacterial O-anti­gen polysaccharides from Shigella flexneri and Escherichia coli, crystallizes with four independent disaccharide mol­ecules and four water mol­ecules in the asymmetric unit. The conformation at the glycosidic linkage joining the two rhamnosyl residues is described by the torsion angles φH of 39, 30, 37 and 37°, and ψH of −32, −35, −31 and −32°, which are the major conformation region known to be populated in an aqueous solution. The hexo­pyran­ose rings have the 1C4 chair conformation. In the crystal, the disaccharide and water mol­ecules are associated through O—H⋯O hydrogen bonds, forming a layer parallel to the bc plane. The layers stack along the a axis via hydro­phobic inter­actions between the methyl groups.




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Crystal structure of zymonic acid and a redetermination of its precursor, pyruvic acid

The structure of zymonic acid (systematic name: 4-hy­droxy-2-methyl-5-oxo-2,5-di­hydro­furan-2-carb­oxy­lic acid), C6H6O5, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra­molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo­propanoic acid), C3H4O3, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977). Acta Cryst. B33, 210–212]. In zymonic acid, the hy­droxy­lactone ring is close to planar (r.m.s. deviation = 0.0108 Å) and the dihedral angle between the ring and the plane formed by the bonds of the methyl and carb­oxy­lic acid carbon atoms to the ring is 88.68 (7)°. The torsion angle of the carb­oxy­lic acid group relative to the ring is 12.04 (16)°. The pyruvic acid mol­ecule is almost planar, having a dihedral angle between the carb­oxy­lic acid and methyl-ketone groups of 3.95 (6)°. Inter­molecular inter­actions in both crystal structures are dominated by hydrogen bonding. The common R22(8) hydrogen-bonding motif links carb­oxy­lic acid groups on adjacent mol­ecules in both structures. In zymonic acid, this results in dimers about a crystallographic twofold of space group C2/c, which forces the carb­oxy­lic acid group to be disordered exactly 50:50, which scrambles the carbonyl and hydroxyl groups and gives an apparent equalization of the C—O bond lengths [1.2568 (16) and 1.2602 (16) Å]. The other hydrogen bonds in zymonic acid (O—H⋯O and weak C—H⋯O), link mol­ecules across a 21-screw axis, and generate an R22(9) motif. These hydrogen-bonding inter­actions propagate to form extended pleated sheets in the ab plane. Stacking of these zigzag sheets along c involves only van der Waals contacts. In pyruvic acid, inversion-related mol­ecules are linked into R22(8) dimers, with van der Waals inter­actions between dimers as the only other inter­molecular contacts.




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Crystal structure of bis(μ-{2-[(5-bromo-2-oxido­benzyl­idene)amino]­eth­yl}sulfanido-κ3N,O,S){2,2'-[(3,4-di­thia­hexane-1,6-di­yl)bis­(nitrilo­methanylyl­idene)]bis­(4-bromo­phenolato)-κ4O,N,N',O

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.




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Bis(4-acet­oxy-N,N-di­methyl­tryptammonium) fumarate: a new crystalline form of psilacetin, an alternative to psilocybin as a psilocin prodrug

The title compound (systematic name: bis­{2-[4-(acet­yloxy)-1H-indol-3-yl]ethan-1-aminium} but-2-enedioate), 2C14H19N2O2+·C4H2O42−, has a single protonated psilacetin cation and one half of a fumarate dianion in the asymmetric unit. There are N—H⋯O hydrogen bonds between the ammonium H atoms and the fumarate O atoms, as well as N—H⋯O hydrogen bonds between the indole H atoms and the fumarate O atoms. The hydrogen bonds hold the ions together in infinite one-dimensional chains along [111].




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Crystal structure of 210,220-bis­(2,6-di­chloro­phen­yl)-4,7,12,15-tetra­oxa-2(5,15)-nickel(II)porpyhrina-1,3(1,2)-dibenzena-cyclo­hepta­deca­phane-9-yne di­chloro­methane monosolvate

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.




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Crystal structure of a polymorph of μ-oxido-bis­[(5,10,15,20-tetra­phenyl­porphyrinato)iron(III)]

The title compound, [Fe2(C44H28N4O)2O], was obtained as a by-product during the synthesis of FeIII tetra­phenyl­porphyrin perchlorate. It crystallizes as a new polymorphic modification in addition to the ortho­rhom­bic form previously reported [Hoffman et al. (1972). J. Am. Chem. Soc. 94, 3620–3626; Swepston & Ibers (1985) Acta Cryst. C41, 671–673; Kooijmann et al. (2007). Private Communication (refcode 667666). CCDC, Cambridge, England]. In its crystal structure, the two crystallographically independent FeIII cations are coordinated in a square-planar environment by the four N atoms of a tetra­phenyl­porphyrin ligand. The FeIII-tetra­phenyl­porphyrine units are linked by a μ2-oxido ligand into a dimer with an Fe—O—Fe angle close to linearity. The final coordination sphere for each FeIII atom is square-pyramidal with the μ2-oxido ligand in the apical position. The crystal under investigation consisted of two domains in a ratio of 0.691 (3): 0.309 (3).