Absolute-structure reports

A detailed analysis of the reporting of absolute structure has been undertaken on all the non-centrosymmetric crystal structures published in Acta Crystallographica Section C between January 2011 and November 2012.

Avoiding problems with hydrogen misplacement in reporting crystal structures

Some reported structures fail to include all possible donor–acceptor close contacts, or to seek H-atom electron densities associated with apparent D—H⋯A trios. The relevant issues are illustrated with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.

Bis{tris­[(1H-benzimidazol-3-ium-2-yl)methyl]amine} tetra­aqua­octa-μ₂-chlorido-octa­chlorido­penta­cadmate(II) monohydrate

The structure of the anion is a novel chloride-bridged penta­nuclear cluster. The five unique Cd^II centres have quite different coordination environments.

Poly[[μ-(1-aza­nium­ylethane-1,1-di­yl)bis­(hydrogen phosphon­ato)]sodium]: a powder X-ray diffraction study

The central Na⁺ cation exhibits distorted octa­hedral coordination geometry involving two deprotonated O atoms, two hy­droxy O atoms and two double-bonded O atoms of the bis­phosphon­ate anion. Pairs of sodium-centred octa­hedra share edges and the pairs are in turn connected to each other by the biphosphon­ate anion to form a two-dimensional network parallel to the (001) plane.

A three-dimensional coordination polymer of 3-(3,5-di­carb­oxy­benzyl­oxy)benzoic acid with zinc

Reaction of a newly synthesized 3-(3,5-dicarboxybenzyloxy)benzoic acid ligand with zinc ions yielded a single-framework metal–organic coordination polymer (MOF) of attractive architecture.

The supra­molecular structure of a cadmium complex with the new functionalized terpyridine ligand 4′-[4-(pyrimidin-5-yl)phen­yl]-2,2′:6′,2′′-terpyridine (L1): aqua­(L1-κ³N,N′,N′′)(nitrato-κ²O,O′)(nitrato-κO)cadmium(II) dihydrate

The coordinating properties of the novel ligand 4′-[4-(pyrimidin-5-yl)phenyl]-2,2′:6′,2′′-terpyridine were tested by reacting it with cadmium(II) nitrate. The resulting title complex presents a supramolecular motif dominated by a significant number of π–π interactions involving all the aromatic rings.

Poly[μ₇-sulfane­diyl­diacetato-disilver(I)]

In the title coordination polymer, each Ag^I cation has a distorted tetra­hedral geometry coordinated by three of the four carboxyl­ate O atoms and the S atom from symmetry-related sulfane­di­yl­di­acetate ligands. The bridging sulfane­di­yl­di­acetate groups lead to a two-dimensional layer structure and the layers are interconnected via Ag—S bonds.

A novel cadmium(II) coordination polymer containing two kinds of independent one-dimensional chain

The title structure con­tains two kinds of independent one-dimensional chain, viz. {[Cd(C₈H₁₅N₂O₂)Cl₂]⁺}_n and {[CdCl₃(H₂O)]⁻}_n, and uncoordinated water mol­ecules. Each Cd^II cation in the former chain is octa­hedrally coordinated by two pairs of bridging chloride ligands and two O atoms from different bridging carboxyl­ate groups, while Cd^II cations in the latter chain are octa­hedrally surrounded by four bridging chloride ligands, one terminal chloride ligand and one coordinated water mol­ecule.

catena-Poly[bis­(μ-2,2′-bipyridin-6-ol­ato)-κ³N,N′:O;O:N,N′-dicopper(I,II) [[tetra­fluorido­niobium(V)]-μ-oxido]]

The structural unit consists of one C₂-symmetric [NbOF₄]⁻ anion, where the Nb^V centre is five-coordinated by four F atoms and one O atom in the first coordination shell, forming a square-pyramidal coordination geometry, and of one centrosymmetric coordinated [Cu₂(obpy)₂]⁺ cation (obpy is 2,2′-bipyridin-6-olate), in which the oxidation state of each Cu site is disordered, which is confirmed by XPS results.

Triple ring contraction of a [2+2] macrocyclic ligand

Transmetallation of a barium [2+2] Schiff base macrocycle with copper(II) results in three successive ring contractions, reducing the ring size from 20 to 16 members. Unusually, the contraction does not appear to result in an improved `fit' for the copper(II) ion.

Dirubidium hexa­aqua­cobalt(II) tetra­kis­(hydrogen phthalate) tetra­hydrate and coordination modes of the hydrogen phthalate anion

The Rb⁺ cation is surrounded by nine O atoms from Hpht⁻ anions and water mol­ecules, with a strongly deformed penta­gonal–bipyramidal geometry and one apex split into three positions. The crystal packing is governed by numerous hydrogen bonds involving all water mol­ecules and Hpht⁻ anions.

Positional and compositional disorder in a ruthenium(II) piano-stool complex

This paper gives an account of a procedure to establish the identity of a ligand in an Ru complex and to refine two instances of positional and compositional disorder in the ligand and a counter-ion.

Bis{2-[(phenyl­imino)­eth­yl]-1H-pyrrol-1-ido-κ²N,N′}nickel(II): a supra­molecular structure formed by C—H⋯π hydrogen bonds

The title complex is composed of two deprotonated N,N′-bidentate 2-[(phenyl­imino)­ethyl]-1H-pyrrol-1-ide ligands around a central Ni^II cation, with the pyrrolide rings and imine groups lying trans to each other. Mol­ecules are linked into simple chains by two C—H⋯π hydrogen bonds, one of which is inter­molecular with a phenyl β-C atom as donor, while the other is intra­molecular with a pyrrole β-C atom as donor.

Two polymorphs of tris­(ethyl­ene­diamine)­cobalt(III) tetra­thio­anti­monate(V)

Two polymorphs contain octa­hedral [Co(en)₃]³⁺ cations (en is ethyl­ene­diamine) and tetra­hedral [SbS₄]³⁻ anions, which are inter­connected via various N—H⋯S hydrogen bonds to form two different types of three-dimensional network.

A mixed chloride/tri­fluoro­methane­sulfonate ligand species in a ruthenium(II) complex

The crystal structure determination of this complex revealed the presence of two different anionic species which other spectroscopic methods failed to characterize. The reduced catalytic activity was not fully understood until the crystallographic data provided evidence for the mixed anionic species. The crystal structure of this Ru^II complex clearly shows that the majority of the synthesized material has a chloride anion present.

Three transition-metal complexes with the macrocyclic ligand meso-5,7,7,12,14,14-hexa­methyl-1,4,8,11-tetra­aza­cyclo­tetra­decane (L): [Cu(ClO₄)₂(L)], [Zn(NO₃)₂(L)] and [CuCl(L)(H₂O)]Cl

The three title transition-metal complexes display a distorted 4+2 octahedral environment for the cation, with the macrocycle defining the base. The effect of the different axial ligands in the intra- and intermolecular hydrogen bonding is discussed.

Psuedosymmetry and pseudomerodry or nonmerohedral twinning for the known structure of di­aqua­bis­(quinolin-8-olato-κ²N,O)zinc(II)

A structure evaluation is presented of a known structure from a merohedrally twinned crystal, together with a re-examination of the previously published models.

Poly[bis­[μ₂-3-(pyridin-4-yl)benzoato-κ³N:O,O′]lead(II)]

In the title compound, the Pb atom sits on a crystallographic C₂ axis and is six-coordinate, ligated by two chelating carboxyl­ate groups from two 3-(pyridin-4-yl)benzoate ligands and by two N atoms from another two benzoate ligands. Each ligand is conformationally chiral and bridges two Pb^II centres, extending the structure into a corrugated two-dimensional (4,4) net.

A novel three-dimensional Ag^I coordination polymer based on mixed naphthalene-1,5-di­sulfonate and amino­acetate ligands

The title Ag^I coordination polymer is a novel three-dimensional framework involving mixed naphthalene-1,5-disulfonate and aminoacetate ligands. In the crystal structure, each of the three different functional groups (carboxylate, amino and sulfonate) is coordinated to the Ag^I atoms.

3a-Phenyl-2,3,3a,4-tetra­hydro-1H-benzo[d]pyrrolo­[1,2-a]imidazol-1-one, a potential plant-growth regulator

Mol­ecules of the title compound are linked into chains by inter­molecular C=O⋯H—N hydrogen bonds and the chains are weakly inter­connected by π–π stacking inter­actions. A comparison of the geometric parameters of the title mol­ecule and several related benzimid­azoles and pyrrolidones is presented.

Hydrogen-bonded bilayers in 7-benzyl-3-tert-butyl-1-phenyl-4,5,6,7-tetra­hydro-1H-spiro[pyrazolo­[3,4-b]pyridine-5,2′-indan]-1′,3′-dione

The molecules contain an intramolecular π–π stacking interaction, and C—H⋯O and C—H⋯N hydrogen bonds link the molecules to form a bilayer having tert-butyl groups on both faces.

An unexpected tetra­gonal unit cell for N-(L-2-amino­butyr­yl)-L-serine

The title dipeptide, incorporating the nonproteinogenic amino acid residue L-2-aminobutyric acid, forms an extensively disordered, compact crystal packing arrangement in the tetragonal space group I4.

1,7-Dide­aza-2′-de­oxy-6-nitro­nebularine: a pyrrolo­[2,3-b]pyridine nucleoside with an intra­molecular hydrogen bond stabilizing the syn conformation

In the title nucleoside, the N-glycosylic bond exhibits a syn conformation and the pento­furanosyl residue adopts a C2′-endo envelope conformation. The orientation of the exocyclic C4′—C5′ bond is +sc (gauche, gauche). The nucleoside forms an ordered and stacked three-dimensional network.

A new polymorph of bis­(2-amino­pyridinium) fumarate–fumaric acid (1/1) from powder X-ray diffraction

A new polymorph of bis(2-aminopyridinium) fumarate–fumaric acid (1/1), determined using powder X-ray diffraction data, is described. The similarities and differences in hydrogen bonds between the new and previous polymorph are discussed in order to understand the polymorphism of the title salt.

N-tert-Butyl-N′-[5-cyano-2-(4-methyl­phen­oxy)phenyl­sulfon­yl]urea, a new TXA₂ receptor antagonist

The conformation of a new TXA₂ receptor antagonist, mainly determined by an intramolecular N—H⋯O hydrogen bond, is further explored using the Cambridge Structural Database.

N—H⋯O, O—H⋯O hydrogen-bonded supra­molecular sheet formation in the bis­(2-amino­anilinium) fumarate, 3-methyl­anilinium hydrogen fumarate and 4-chloro­anilinium hydrogen fumarate salts

The crystal structures of three fumarate salts with different substituted anilines are reported. 3-Methyl­anilinium hydrogen fumarate and 4-chloro­anilinium hydrogen fumarate are isostructural resulting in the formation of similar supramolecular architectures.

Determination of the electron density in methyl (±)-(1S,2S,3R)-2-methyl-1,3-di­phenyl­cyclo­propane­carboxyl­ate using refinements with X-ray scattering factors from wavefunction calculations of the whole mol­ecule

The electron density in the title substituted cyclo­propane has been determined by refining single-crystal X-ray data using scattering factors derived from quantum mechanical calculations. Topological analysis of the electron densities in the three cyclo­propane C—C bonds was carried out and shows the effects of substitution on these C—C bonds.

Two methyl 3-(1H-pyrazol-4-yl)octa­hydro­pyrrolo­[3,4-c]pyrrole-1-carboxyl­ates form different hydrogen-bonded sheets

Two very closely related pyrrolo[3,4-c]pyrrole derivatives form hydrogen-bonded sheets using a different combination of C—H⋯N, C—H⋯O and C—H⋯π interactions.

Comparison of the structure of (E)-2-(2-benzylidenehydrazinyl­idene)quin­oxaline with those of its chloro- and bromo­benzyl­idene analogues

The structures of (E)-2-(2-(phenylidene)hydrazinyl)quinoxaline and six Cl and Br derivatives have similar supramolecular structures involving an N—H⋯N hydrogen bond and π–π stacking interactions.

Two polymorphs of N-(2-meth­oxy­phen­yl)-4-oxo-4H-chromone-3-car­box­amide

Two polymorphs of N-(2-meth­oxy­phen­yl)-4-oxo-4H-chromone-3-car­box­amide crystallise in the monoclinic space group P2₁/c, each with two molecules in the asymmetric unit. The conformations of all four molecules are similar, the main differences being in their supramolecular interactions.

The zwitterionic structure of 2-hy­droxy-4-[(2-hy­droxy­benzyl­idene)amino]­benzoic acid

The title compound exists in a zwitterionic form. There is a strong intra­molecular N—H⋯O hydrogen bond, an intra­molecular O—H⋯O hydrogen bond, an inter­molecular C—H⋯O contact and π–π stacking inter­actions, resulting in a three-dimensional network.