issue contents

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296

November 2013 issue

Special issue on Pharmaceuticals, drug discovery and natural products

Guest Editor: Professor Christopher S. Frampton (Pharmorphix, Cambridge, England)

Highlighted illustration

Cover illustration: The structure of carbamazepine tri­fluoro­acetic acid monosol­vate overlaid on its difference Fourier map [see Eberlin, Eddleston & Frampton (2013). Acta Cryst. C69, 1260-1266]. The paper forms part of the special issue on Pharmaceuticals, drug discovery and natural products.

editorial


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An overview of current topics of interest in the field of solid-state pharmaceuticals and an introduction to papers featured in this special issue.

pharmaceuticals and natural products


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Density functional theory (DFT) NMR prediction, 1H–1H Total Correlated Spectroscopy (TOCSY) NMR and single-crystal X-ray crystallography were used to confirm the formation of a bis-cyclo­pentenyl-β-cyano­hydrin in preference to a 2,3,6,7-de­hydro­deca­lin-β-cyano­hydrin as the kinetic product upon subjecting tri- and tetra­ene substrates to Ru-catalyzed alkene metathesis.

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Glabridin is a species-specific biomarker from the roots Glycyrrhiza glabra L. (European licorice, Fabaceae). Stereochemical analysis, including circular dichroism, NMR data and an X-ray diffraction data set with Bijvoet differences, confirms that glabridin, purified from its natural source, is found only in a C3 R configuration.

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A new polymorph of the pharmaceutically active sulfa­pyridine derivative N-(6-methyl­pyridin-2-yl)mesityl­ene­sulfon­amide was obtained as a phase-pure product from methanol. The mol­ecules adopt the conformation which is predicted for an individual mol­ecule by force field calculations.

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High-resolution diffraction data support our interpretation that the title compound is coordinated by two ammine rather than by an ammine and an aqua ligand.

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The preparation, single-crystal X-ray structure and solution-state NMR analysis of (±)-threo-ritalinic acid, obtained from the hydrolysis of the methyl ester (±)-threo-methyl phenidate, are reported.

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The isostructural crystal structures of cefradine dihydrate and cefaclor dihydrate, based on experimental data where available and supplemented with dispersion-corrected density functional theory calculations, are presented. The crystal structures are typical examples of isolated-site hydrates.

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Gaboxadol hydrochloride (also known as THIP hydrochloride) undergoes a reversible single-crystal-to-single-crystal transformation at 221 K. Crystal structures have been determined at 298 and 220 K.

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(+)-6-Amino­penicillanic acid, a precursor of a variety of semi-synthetic penicillins, represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The complementary analysis of the crystal packing by the PIXEL method brings to light the nature and ranking of the energetically most stabilizing inter­molecular inter­action energies.

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This report illustrates the crystal structures of three new inhibitors targeting the mycobacterial regulator EthR which has previously been identified as a novel target for tuberculosis drug boosters. In addition, we describe how the results of our structure determination were used to develop a docking protocol using GOLD for future in silico screening.

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Solving pharmaceutical crystal structures from powder diffraction data is discussed in terms of both the various methodologies that have been applied and the complexity of the structures that have been solved.

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Methane­sulfonic acid salt forms of carbamazepine and 10,11-di­hydro­carbamazepine have been prepared and characterized by a number of analytical techniques, including single-crystal X-ray diffraction at 100 K. The structural data for these complexes were analysed in relation to data derived from other carbamazepine complexes and a redetermination of the apparently anomalous tri­fluoro­acetic acid solvate structure was undertaken.

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The mol­ecules in the title cocrystal are present in their neutral forms, and assemble a mol­ecular layer by means of hydrogen bonding. Differences in the environments of the isonicotinamide molecules were assessed by Hirshfeld surface analysis.

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The structure determination of loxapine succinate and its monohydrate is presented. Fixed cell geometry optimization using density functional theory in CASTEP was used as a complementary tool to locate the H-atom positions in the crystal structure determined from X-ray powder diffraction data.

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Proton transfer systematically producing mol­ecular salts is used in a study of nine mol­ecular complexes of bromanilic acid with methyl­pyridines, which show predictable synthons related to the stoichiometry and a common N—H⋯O charge-assisted hydrogen bond.

inorganic compounds


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The title compounds were prepared via a mechano­chemical reaction in the solid state. They crystallize in the NaSc(BH4)4 structure type composed of isolated [Yb(BH4)4] anions, with Yb coordinated tetra­hedrally by BH4 groups, surrounded by M+ cations (M = Na, K) which form distorted trigonal prisms.

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Crystals of MgCl2·8H2O, MgCl2·12H2O, MgBr2·6H2O, MgBr2·9H2O, MgI2·8H2O and MgI2·9H2O were grown from their aqueous solutions at temperatures below 298 K according to the solid–liquid phase diagrams. All structures are built up from Mg(H2O)6 octa­hedra. Dimensions and angles in the hexa­aqua cation complexes are very similar and variation is not systematic.

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Rietveld refinement of Na9Sc(MoO4)6 shows that its structure is made up of clusters formed from an ScO6 octa­hedron and three Na1O6 octa­hedra sharing total edges. The clusters are connected by sharing vertices with bridging MoO4 tetra­hedra, forming a three-dimensional framework.

metal-organic compounds


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In the title organic–inorganic hybrid material, the tetra­chlorido­zincate anions and 1-cyclo­hexyl­piperazine-1,4-diium dications are inter­connected via N—H⋯Cl and C—H⋯Cl hydrogen bonds to form layers parallel to the (001) plane. The cyclo­hexyl groups are located between these layers to form an infinite three-dimensional network.

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A novel cadmium complex consists of one-dimensional ladders constructed from [Cd2(COO)2] dimeric subunits. A combination of hydrogen bonding and π–π stacking inter­actions extend the one-dimensional ladders into a three-dimensional supra­molecular architecture.

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The title compound is a two-dimensional network containing an –Mn—O—C—O—Mn– chain. Each layer presents a herringbone pattern and interacts with neighbouring layers through intermolecular hydrogen bonds.

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A three-dimensional metallohelicate is constructed from one-dimensional metal–organic helices of purine-containing 3-(6-oxo-6,9-di­hydro-1H-purin-1-yl)propionate ligands and zinc(II) ions.

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3,4-Dihy­droxy-1,6-bis­(4-meth­oxy­phenyl)hexa-2,4-diene-1,6-dione exhibits the di-enol-dione tautomeric form and is compared with its 4-methyl­phenyl analogue. In a potassium salt of 2-hy­droxy-4-(4-meth­oxy­phenyl)-4-oxobut-2-enoic acid, the organic species are linked by a strong hydrogen bond between the carb­oxy­lic acid and carboxyl­ate groups.

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Two novel inorganic–organic coordination polymers, based on NaI cations with semi-rigid V-shaped di­carboxyl­ate ligands, have been prepared and structurally characterized.

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In a novel three-dimensional CdII complex prepared by hydro­thermal assembly of Cd(NO3)2·4H2O, 1,4-bis­[2-(pyridin-4-yl)ethenyl]benzene and 2,2′-(1,4-phenyl­ene)di­acetic acid, each CdII centre is located in a distorted penta­gonal bipyramidal coordination environment. The three-dimensional net can be regarded as a diamondoid network by treating the CdII atoms as nodes and the benzene and di­acetic acid ligands as linkers.

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A one-dimensional polymeric structure of CdII with sulfaquinoxaline is further stabilized by inter­molecular hydrogen bonding. The fluorescence spectrum reveals that the complex emits strong blue fluorescence. The thermal analysis shows that the framework is stable up to 663 K.

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A dinuclear tin(IV) complex of 2-[(2-oxido­benzyl­idene)amino]­ethanolate is disordered above 178 K. The crystal structure at 93 K contains two ordered mol­ecules. The phase transition corresponds to an order–disorder transition of a vinyl group bound to the SnIV atom.

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A novel anionic tubular CdII coordination polymer based on the 5-(carboxyl­atometh­oxy)benzene-1,3-di­carboxyl­ate ligand and containing 4-amino­pyridinium cations had been synthesized under hydro­thermal conditions. In the solid state, the 4-amino­pyridinium cation props up the structure through hydrogen bonds to the O-atom acceptors of ligands and solvent water mol­ecules.

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The layered polymeric structure of a benzene-1,2,4,5-tetra­carboxyl­ate–Cu complex forms parallelogram-shaped channels.

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In a dinuclear zinc(II) complex of acetate and 6-chloro-2-{(E)-[(pyridin-2-yl)methyl­imino]­methyl}phenolate, the ZnII cations differ in their five-coordinate geometries, with one adopting a distorted trigonal bipyramidal geometry and the other a square-pyramidal geometry.

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Double nitrile⋯π interactions are relevant for the crystal packing of charge-diffuse conjugated tetracyanopropenide anions when combined with common heteroaromatic tris-chelate octahedral complexes, [Fe(phen)3]2−.

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The Cu atoms in the title complexes are five-coordinated in distorted trigonal bipyramidal environments by four N atoms of two 5,5′-dimethyl-2,2′-bi­pyridine ligands and one N atom of a dicyanamide anion, which is coordinated in a monodentate manner in the equatorial plane. The structures are stabilized by C—H⋯N and C—H⋯X hydrogen bonds (X = F and O) and π–π inter­actions between pyridine rings.

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Two five-coordinated aqua­copper(II) centres chelated to pyridine-2,6-di­carboxyl­ate terminal ligands are bridged by a 1,2-bis­(pyridin-3-yl­oxy)ethane spacer. The structure includes a well-resolved cyclic water tetra­mer, which acts as a subunit to form a larger aggregate.

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The crystal structures of bis­(4-methyl­anilinium) and bis­(4-iodo­anilinium) penta­molybdates were determined using laboratory X-ray data and refined by total energy minimization methods. The obtained structures present alternating organic cation and inorganic polyanion layers bound by weak bonding (apart from ionic inter­actions).

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A novel infinite one-dimensional coordination polymer involving N′-(2-hy­droxy­benzyl­idene)-2-(naphthalen-2-yl­oxy)aceto­hydrazide, and a trinuclear nickel complex of 2-hy­droxy-N′-(2-oxo-2-phen­oxy­ethyl)benzo­hydrazide with a one-dimensional network structure constructed by hydrogen-bonding inter­actions, are reported.

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In a mononuclear NdIII complex, three chelating 2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate ligands and three aqua ligands build up a distorted monocapped square anti­prism around the cation. A complex hydrogen-bonding network results in a densely packed structure (packing index = 77.7%)

organic compounds


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A series of N-(2-phenyl­ethyl)nitro­aniline derivatives is presented, demonstrating that modest changes in the functional groups cause significant differences in mol­ecular conformation, inter­molecular inter­actions and packing.

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Proline (Pro) exists in its neutral form in N-acetyl-L-proline monohydrate and is zwitterionic in N-benzyl-L-proline. The presence of a water molecule in the neutral form and the difference in the ionization states between the two forms have effected significant changes in the respective intermolecular schemes.

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Three N-[2-(pyridin-2-yl)ethyl]-substituted sulfonamides are almost structurally identical, the most dramatic different being seen for the N—C—C—C torsion angle with the introduction of a methyl group in the para position of the sulfonamide moiety. These compounds are prospective ligands for the formation of new metal complexes.

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The structures of two 6-amino­uracil di­methyl­acetamide monosolvates and a 1-methyl­pyrrolidin-2-one monosolvate display N—H⋯O hydrogen-bonding patterns that link the uracil mol­ecules to their respective solvent mol­ecules. The formation of R_{2}^{2}(8) N—H⋯O hydrogen-bond motifs between 6-amino­uracil mol­ecules can only be found in two-dimensional frameworks, whereas R_{3}^{3}(14) N—H⋯O patterns are present when zigzag chains of 6-amino­uracil mol­ecules are formed.

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The crystal structure of a potent glycogen phospho­rylase a (GPa) inhibitor (IC50 of 6.3 µM) consists of four distinct conjugated π systems separated by rotatable bonds around the Csp3 atoms. The mol­ecules are linked into dimers disposed about a crystallographic centre of symmetry through a cyclic N—H⋯O hydrogen-bonding motif.

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The absolute configuration of the enantio­pure anti-head-to-head cyclo­dimer of anthracene-2-carb­oxy­lic acid was determined. The dimer inter­acts with L-prolinol through a nine-membered hydrogen-bonded ring [R_{2}^{2}(9)], while a di­chloro­methane mol­ecule is incorporated to fill the void space.

addenda and errata


Special and virtual issues

Acta Crystallographica Section C is planning special issues on

The Structural Chemistry of Homogeneous and Heterogeneous Catalysts

NMR Crystallography

Full details are available on the special issues page.

The latest virtual issue, featuring Coordination polymers and with an introduction by Len Barbour, was published in July 2014.

What are the 'most read' articles from the recent special issues?

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