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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

September 2018 issue

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Cover illustration: A large number of structural determinations of compounds containing 2-hydroxy-3,5-dinitrobenzoic acid and its various deprotonated forms, 2-hydroxy-3,5-dinitrobenzoate or 2-carboxy-4,6-dinitrophenolate, are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intramolecular hydrogen bond between the neighbouring carboxylic/carboxylate and oxo/hydroxy groups. This hydrogen bond belongs to the category of resonance-assisted hydrogen bonds. The position of the bridging hydrogen seems to be dependent on the pKa(base), though with exceptions. A stronger basicity enhances the probability of the presence of a phenolate. The problem of the location and the refinement of such a bridging hydrogen as well as that of the hydrogen atoms involved in the hydroxy, and primary and secondary amine groups is discussed. It appears that the best model, in many cases, is obtained by fixing the hydrogen-atom position found in the difference electron-density map while refining its isotropic displacement parameter. See: Fabry [Acta Cryst. (2018). E74, 1344-1357].

research communications


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The crystal and mol­ecular structure of 1,1′-formyl­ruthenocene has been determined. The mol­ecules self-assemble in a two-dimensional structure by C—H⋯O and C—H⋯π inter­actions with cisoid relative orientations of the two formyl groups.

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The synthesis and structural properties of a series of chromium tricarbonyl `piano-stool' complexes bearing substituted penta­fulvene ligands were studied. Significant deviation of the exocyclic fulvene double bond from the cyclo­penta­diene plane accompanies coordination. Evidence of non-covalent π-π inter­actions was observed.

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The title mol­ecule is twisted with the dihedral angle between the N-bound 4-cyano­phenyl and C-bound acetyl groups of the 1,2,3-triazoyl ring being 60.82 (13)°. The mol­ecular packing is sustained by carbonyl-C=O⋯π(triazo­yl), cyano-C≡N⋯π(triazo­yl) and π–π stacking inter­actions.

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In the title compound, the 2,5-di­chloro­thio­phene and 2,4-di­chloro­phenyl rings, linked via a prop-2-en-1-one spacer, make a dihedral angle of 12.24 (15)°. Both the thio­phene and benzene rings of adjacent mol­ecules inter­act attractively in a face-to-face manner, forming zigzag sheets lying parallel to the (011) plane.

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The IrIII atom in the solvated title complex adopts a distorted octa­hedral geometry coordinated by two C,N-chelating 2,6-dimethyl-3-(pyridin-2-yl)pyridin-4-yl ligands and one O,O′-chelating 2,2,6,6-tetra­methylhepta­ne-3,5-dionate ligand. The title compound shows bright blue–green emission in solution at room temperature.

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In the crystal, classical N—H⋯N hydrogen bonds, weak C—H⋯O hydrogen bonds and weak C—H⋯π inter­actions link the mol­ecules into a three-dimensional supra­molecular network.

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The mol­ecular structure of the first orally active carbapenem agent tebipenem pivoxil is described.

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The structure of a deca­ahydro­acridine derivative with phenyl substituents at the 3- and 5-positions of the cyclo­hexenone rings is reported. An extensive range of O—H⋯O, C—H⋯O hydrogen bonds augmented by C—H⋯π(ring) hydrogen bonds an O⋯Br halogen bond and an unusual Br⋯π(ring) contact stabilizes the crystal packing.

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The new structural NiFe hydrogenase model [Ni(L′)FeCp*(CO)][PF6] [L′ = S—C(Me)=C(Me)—S—(CH2)3—S—C(Me)=C(Me)—S] is reported.

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In the title compound, the FeII cation is octa­hedrally coordinated by two dipa ligands and has crystallographic twofold symmetry. The nonplanar polynitrile tcpd2− anion is disordered about an inversion center.

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In hexa­aqua­zinc(II) dinitrate 5-(pyridinium-3-yl)tetra­zol-1-ide, the pyridinium and tetra­zolide rings in the zwitterion are nearly coplanar. Several O—H⋯N and N—H⋯O hydrogen-bonding inter­actions exist between the [Zn(H2O)6]2+ cation and the N atoms of the tetra­zolide ring, and between the nitrate anions and the N—H groups of the pyridinium ring, respectively, giving rise to a three-dimensional network.

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A crystal structure of the osmole complex (μ-η4-C4Ph4)Os2(CO)6 revealed an eclipsed sawhorse mol­ecular geometry with no bridging or semi-bridging carbonyl ligands.

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The title compound is a novel halogen-substituted hydrazine derivative. Intra­molecular N—H⋯O inter­actions form S(6) graph-set motifs, while C—H⋯O and C—H⋯N inter­actions form S(5) graph-set motifs.

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The crystal structures of hydro­thermally synthesized RbGa(HAsO4)2 and RbGa2As(HAsO4)6 were solved by single-crystal X-ray diffraction. They both crystallize in related R\overline{3}c structure types, one of which contains AsO6 octa­hedra assuming the topological role of M3+O6 octa­hedra.

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The dinuclear complex [(bpy)(Cl)Ru(tppz)Ru(Cl)(bpy)](PF6)2 has been synthesized as a catalyst precursor and characterized by X-ray crystallography and cyclic voltammetry.

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The title mol­ecule adopts the shape of the letter L as the dihedral angle between the pyridyl rings is 78.37 (5)°. Linear supra­molecular chains are found in the crystal mediated by weak carbonyl-C=O⋯π(triazol­yl) inter­actions.

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The compound [(bdippza)2Zn], where bdippza is bis­(3,5-diiso­propyl­pyrazol-1-yl)acetate, possesses inversion symmetry and the ZnII atom is located on the special position of the P21/c space group. The zinc atom is coordinated by two bdippza ligands resulting in a six-coordinate distorted octa­hedral geometry.

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In the crystal, the fumarate dianions bridge the NiII cations into polymeric chains propagating along the [101] direction; these polymeric chains are further linked by O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds, forming a three-dimensional supra­molecular architecture.

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The influence of the substituents in the crystals of the title compounds has not made any significant effect on the crystal packing and inter­molecular hydrogen bonds. The validity of chlorine–methyl exchange rule is confirmed.

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The asymmetric unit of the title disubstituted 2,3′-bi­pyridine, contains four independent mol­ecules (namely, A, B, C and D). The conformations of the mol­ecules differ, as seen from the dihedral angles between the two pyridine rings in each mol­ecule. They vary from 5.51 (9)° for mol­ecule B to 25.25 (8)° for mol­ecule A.

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The crystal structures of two aromatic amines are presented: a hydrogen-bonded brominated aniline, and a piperizine derivative.

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A new macrocycle obtained by the Michael reaction of aza­crown ether with dimethyl acetyl­enedi­carboxyl­ate was studied by X-ray diffraction, and its potential bioactivity was estimated from the structural data.

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The synthesis and crystal structure of 5,10,15,20-tetra­kis α,α,α,α 2-amino­phenyl zinc(II) porphyrin is reported, which is a potent starting material for the synthesis of several other picket fence porphyrins.

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In the crystal structure of the title salt, the cations, anions and water mol­ecules are linked into a three-dimensional network, which forms cross layers parallel to the (120) and (\overline{1}20) planes via O—H⋯Br, N—H⋯Br and N—H⋯N hydrogen bonds. C—H⋯π inter­actions also help in the stabilization of the mol­ecular packing.

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Two of the constituent mol­ecules in bis­(3-carbamoylpyridin-1-ium) phosphite monohydrate, i.e. the phosphite anion and the water mol­ecule, are situated on the symmetry plane. The mol­ecules are held together by moderate N—H⋯O and O—H⋯N, and weak O—H⋯O and C—H⋯Ocarbon­yl hydrogen bonds in which the primary and secondary amine and water H atoms are involved. The H atom directly bonded to the P atom avoids hydrogen bonding, as usual.

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The mol­ecular and crystal structures of methyl 4-methyl-2,2-dioxo-1H-2λ6,1-benzo­thia­zine-3-carboxyl­ate, which possesses analgesic properties, have been determined

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Two chalcones were synthesized in Claisen–Schmidt condensation reactions. In the crystals, π–π inter­actions and weak C—H⋯O and C—H⋯π inter­actions are observed. The effect of these inter­molecular inter­actions in the solid state can be seen inthe difference between the experimental and theoretical optimized geometrical parameters.

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The asymmetric unit of the adduct contains a neodymium(III) cation, three coordinated nitrate anions, four coordinated water mol­ecules and three uncoordinated neutraltriazine mol­ecules. The crystal structure consists of a three-dimensional supra­molecular framework held together by a network of O—H⋯O and O—H⋯N hydrogen bonds between the coordinated water mol­ecules, nitrate ions and triazine mol­ecules. The uncoordinated neutral triazine moieties form N—H⋯N hydrogen bonds. Hirshfeld surface and fingerprint plots identify the major contributors to the inter­molecular inter­actions.

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The title salt, Na+·C6H13O9S [systematic name: sodium (1S,2S,3S,4R,5R)-1,2,3,4,5,6-hexa­hydroxy­hexane-1-sulfonate], is formed by reaction of D-mannose with sodium bis­ulfite (sodium hydrogen sulfite) in water. The carbohydrate anions are arranged in a head (–SO3) to head (–SO3) arrangement, thereby forming two parallel sheets linked through coordination to sodium ions, with each component sheet containing inter­molecular hydrogen bonds between the anionic residues. Unusually, the double sheets are not connected to neighbouring sets of double sheets, either by ion coordination or inter­molecular hydrogen bonding.

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The naphtho­quinone unit in 2-hy­droxy-3-(prop-2-yn-1-yl)naphthalene-1,4-dione is essentially planar and the linear propargyl group is nearly perpendicular to the naphthalene ring system. In the crystal, O—H⋯O and C—H⋯O hydrogen bonds form an infinite tape structure.

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Metathesis of 2-, 3- and 4-cyano-1-methyl­pyridinium iodide with KPF6 in water generated the corresponding hexa­fluorido­phosphate salts, C7H7N2+·PF6, whose crystal structures were determined. They feature a variety of weak inter­actions (C—H⋯F hydrogen bonds and P—F⋯π inter­actions). Dispersion-corrected density functional theory (DFT-D) calculations were carried out in order to elucidate some of the energetic aspects of the solid-state structures.

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The structures and absolute stereochemistry of two pairs of diastereomeric nitro­gen mustards related to the chemotherapeutic cyclo­phosphamide were determined to test 31P NMR chemical shift trends proposed based on the spatial relationship of the bis­(2-chloro­eth­yl)amine moiety and the chiral substituent of the amino alcohol.

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The structure of the pseudopolymorph of 3-(tri­phenyl­phospho­ranyl­idene)-2,5-di­hydro­furan-2,5-dione with a THF solvent mol­ecule is described. The compound has a hydrogen-bonded layer structure, and displays C—H⋯O hydrogen bonds connecting mol­ecules of the di­hydro­furan-2,5-dione derivative into chains.

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In the crystal, the CdII atom, located on a twofold rotation axis, is coordinated by three chelating ligands, leading to a distorted octa­hedral CdN4O2 coordination sphere.

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A large number of structural determinations of compounds containing 2-hy­droxy-3,5-di­nitro­benzoic acid and its various deprotonated forms, 2-hy­droxy-3,5-di­nitro­benzoate or 2-carb­oxy-4,6-di­nitro­phenolate, are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intra­molecular hydrogen bond between the neighbouring carb­oxy­lic/carboxyl­ate and oxo/hy­droxy groups. The present article examines the problem of the location and refinement of such a bridging hydrogen in a number of reported compounds. The analysis of the intra­molecular hydrogen bonding is also discussed.

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The two orthophosphates, Na1.85Mg1.85In1.15(PO4)3 and Ag1.69Mg1.69In1.31(PO4)3 adopt alluaudite-type structures. Edge-sharing [(In,Mg)O6] octa­hedra are linked together by PO4 tetra­hedra, leaving channels in which the Na+ or Ag+ cations are situated..

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The mol­ecular and crystal structure of trimethyl citrate is reported. The formation of inversion is the principal contributor to the crystal packing.

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Single crystals of Ti8Bi9O0.25 were grown by using a Bi flux and were investigated in order to clarify the structural changes by O atom occupation at the inter­stital site in the Ti4 tetra­hedron.

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The title complex is assumed to have formed via the insertion of formaldehyde into the copper–carbon bond in an N-heterocyclic carbene complex of copper(I) chloride·The Cu—O bond lengths are shorter than those previously reported in structures with the same central Cu2O2 motif. The complex displays C—H⋯Cl inter­actions involving the H atoms of the heterocycle backbone and the chloride ligands of a neighbouring mol­ecule.

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In the triclinic crystal form, the mol­ecules are linked by hydrogen bonds into an infinite assembly propagating along the a axis; hydro­phobic tert-butyl and phenyl groups form an external coating of the assembly.

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The structure is reported of a complex containing a trinuclear Zn cation lying on a crystallographic twofold axis. It consists of a tetra­hedral ZnII atom bridging two six-coordinate ZnII atoms in which the two terminal ZnII cations adopt distorted octa­hedral geometries and the central ZnII cation adopts a distorted tetra­hedral geometry.

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The mononuclear discrete complex [Cu(pivHA)2] contains two pivaloyl hydroxamates (pivHA) coordinated to a copper(II) ion in a centrosymmetric trans mode through hydroxamate and carbonyl O atoms. The copper(II) O4 coordination is square planar.

Research communications

Research communications are designed to help authors bring out the science behind their structure determinations. Authors are encouraged to report more than one structure in the same communication and also to include the results of investigations with other techniques. The Research communications format makes Acta E the natural home for structure determinations with interesting science to report.

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Acta E is included in the Emerging Sources Citation Index.

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