Virtual issue on absolute structure

H. D. Flack

Acta Crystallographica Section C is pleased to announce the publication of its second virtual issue. The issue is dedicated to the subject of absolute structure and includes papers relating to this topic published in Section C between January 2011 and November 2012. Three additional recent related papers from other IUCr journals have been included to highlight recent developments in the field.

Analysing Friedel averages and differences

S. Parsons, P. Pattison and H. D. Flack

Various practical applications of the average (A) and difference (D) of Friedel opposites are described. Techniques based on the resonant-scattering contribution to Friedel differences are applied to see whether a crystal is centrosymmetric or not, and to determine the point group of the crystal. For the validation of a structural study, plots of A_obs against A_model, and D_obs against D_model are used extensively. Moreover, it is useful to display both plots on the same graph. Intensity measurements on a crystal of NaClO₃ were made at three different speeds, with two different radiations and two different diffractometers, and treated with two different software packages and four different absorption corrections. The evaluation of these numerous data sets reveals underlying deficiencies. For comparison, plots of A_obs against A_model, and D_obs against D_model are presented for two centrosymmetric crystals.

Applications of leverage analysis in structure refinement

S. Parsons, T. Wagner, O. Presly, P. A. Wood and R. I. Cooper

Leverages measure the influence that observations (intensity data and restraints) have on the fit obtained in crystal structure refinement. Further analysis enables the influence that observations have on specific parameters to be measured. The results of leverage analyses are discussed in the context of the amino acid alanine and an incomplete high-pressure data set of the complex bis(salicylaldoximato)copper(II). Leverage analysis can reveal situations where weak data are influential and allows an assessment of the influence of restraints. Analysis of the high-pressure refinement of the copper complex shows that the influence of the highest-leverage intensity observations increases when completeness is reduced, but low leverages stay low. The influence of restraints, notably those applying the Hirshfeld rigid-bond criterion, also increases dramatically. In alanine the precision of the Flack parameter is determined by medium-resolution data with moderate intensities. The results of a leverage analysis can be incorporated into a weighting scheme designed to optimize the precision of a selected parameter. This was applied to absolute structure refinement of light-atom crystal structures. The standard uncertainty of the Flack parameter could be reduced to around 0.1 even for a hydrocarbon.

Practical applications of averages and differences of Friedel opposites

H. D. Flack, M. Sadki, A. L. Thompson and D. J. Watkin

The practical use of the average and difference intensities of Friedel opposites at different stages of structure analysis has been investigated. It is shown how these values may be properly and practically used at the stage of space-group determination. At the stage of least-squares refinement, it is shown that increasing the weight of the difference intensities does not improve their fit to the model. The correct form of the coefficients for a difference electron-density calculation is given. In the process of structure validation, it is further shown that plots of the observed and model difference intensities provide an objective method to evaluate the fit of the data to the model and to reveal insufficiencies in the intensity measurements. As a further tool for the validation of structure determinations, the use of the Patterson functions of the average and difference intensities has been investigated and their clear advantage demonstrated.

The mixed diol-dithiol 2,2-bis(sulfanylmethyl)propane-1,3-diol: characterization of key intermediates on a new synthetic pathway

T. R. Simmons, C. J. Pickett and J. A. Wright

A new synthetic route to 2,2-bis(sulfanylmethyl)propane-1,3-diol, (II), is described starting from the commercially available 2,2-bis(hydroxymethyl)propane-1,3-diol. The structures of two intermediates on this route are described. 5,5-Dimethenyl-2,2-dimethyl-1,3-dioxane bis(thiocyanate) (systematic name: {[5-(cyanosulfanyl)-2,2-dimethyl-1,3-dioxan-5-yl]sulfanyl}formonitrile), C₁₀H₁₄N₂O₂S₂, (X), crystallizes in the space group P2₁/c with no symmetry relationship between the two thiocyanate groups. There is a short intramolecular NS contact for one thiocyanate group, while the second group is positioned such that this type of interaction is not possible. 1,3-(Hydroxymethyl)propane-1,3-diyl bis(thiocyanate), C₇H₁₀N₂O₂S₂, (XI), also features a single short NS contact in the solid state. Hydrogen bonding between two molecules of compound (XI) results in the formation of dimers in the crystal, which are then linked together by a second hydrogen-bond interaction between the dimers. In addition, the structures of two intermediates from an unsuccessful alternative synthesis of (II) are reported. 2,2-Bis(chloromethyl)propane-1,3-diol, C₅H₁₀Cl₂O₂, (VI), crystallized as an inversion twin with a minor twin fraction of 0.43 (6). It forms a zigzag structure as a result of intermolecular hydrogen bonding. The structure of 9,9-dimethyl-2,4,8,10-tetraoxa-3⁴-thiaspiro[5.5]undecan-3-one, C₈H₁₄O₅S, (VII), shows evidence for a weak SO contact with a distance of 3.2529 (11) Å.

Planarity of heteroaryldithiocarbazic acid derivatives showing tuberculostatic activity. II. Crystal structures of 3-[amino(pyrazin-2-yl)methylidene]-2-methylcarbazic acid esters

A. Olczak, M. Szczesio, J. Golka, C. Orlewska, K. Gobis, H. Foks and M. L. Glówka

Four compounds showing moderate antituberculostatic activity have been studied to test the hypothesis that the planarity of the 2-[amino(pyrazin-2-yl)methylidene]dithiocarbazate fragment is crucial for activity. N'-Anilinopyrazine-2-carboximidamide, C₁₁H₁₁N₅, D1, and diethyl 2,2'-[({[amino(pyrazin-2-yl)methylidene]hydrazinylidene}methylidene)bis(sulfanediyl)]diacetate, C₁₄H₁₉N₅O₄S₂, B1, maintain planarity due to conjugation and attractive intramolecular hydrogen-bond contacts, while methyl 3-[amino(pyrazin-2-yl)methylidene]-2-methyldithiocarbazate, C₈H₁₁N₅S₂, C1, and benzyl 3-[amino(pyrazin-2-yl)methylidene]-2-methyldithiocarbazate, C₁₄H₁₅N₅S₂, C2, are not planar, due to methylation at one of the N atoms of the central N-N bond. The resulting twists of the two molecular halves (parts) of C1 and C2 are indicated by torsion angles of 116.5 (2) and -135.9 (2)°, respectively, compared with values of about 180° in the crystal structures of nonsubstituted compounds. As the methylated derivatives show similar activity against Mycobacterium tuberculosis to that of the nonsubstituted derivatives, maintaining planarity does not seem to be a prerequisite for activity.

Six two- and three-component ammonium carboxylate salt structures with a ladder-type hydrogen-bonding motif, three incorporating neutral carboxylic acid molecules

A. Lemmerer

Six ammonium carboxylate salts are synthesized and reported, namely 2-propylammonium benzoate, C₃H₁₀N⁺·C₇H₅O₂^-, (I), benzylammonium (R)-2-phenylpropionate, C₆H₁₀N⁺·C₉H₉O₂^-, (II), (RS)-1-phenylethylammonium naphthalene-1-carboxylate, C₈H₁₂N⁺·C₁₁H₇O₂^-, (III), benzylammonium-benzoate-benzoic acid (1/1/1), C₆H₁₀N⁺·C₇H₅O₂^-·C₇H₆O₂, (IV), cyclopropylammonium-benzoate-benzoic acid (1/1/1), C₃H₈N⁺·C₇H₅O₂^-·C₇H₆O₂, (V), and cyclopropylammonium-ea-cis-cyclohexane-1,4-dicarboxylate-ee-trans-cyclohexane-1,4-dicarboxylic acid (2/1/1), 2C₃H₈N⁺·C₈H₁₀O₄^2-·C₈H₁₂O₄, (VI). Salts (I)-(III) all have a 1:1 ratio of cation to anion and feature three N⁺-HO^- hydrogen bonds which form one-dimensional hydrogen-bonded ladders. Salts (I) and (II) have type II ladders, consisting of repeating R₄³(10) rings, while (III) has type III ladders, in this case consisting of alternating R₄²(8) and R₄⁴(12) rings. Salts (IV) and (V) have a 1:1:1 ratio of cation to anion to benzoic acid. They have type III ladders formed by three N⁺-HO^- hydrogen bonds, while the benzoic acid molecules are pendant to the ladders and hydrogen bond to them via O-HO^- hydrogen bonds. Salt (VI) has a 2:1:1 ratio of cation to anion to acid and does not feature any hydrogen-bonded ladders; instead, the ionized and un-ionized components form a three-dimensional network of hydrogen-bonded rings. The two-component 1:1 salts are formed from a 1:1 ratio of amine to acid. To create the three-component salts (IV)-(VI), the ratio of amine to acid was reduced so as to deprotonate only half of the acid molecules, and then to observe how the un-ionized acid molecules are incorporated into the ladder motif. For (IV) and (V), the ratio of amine to acid was reduced to 1:2, while for (VI) the ratio of amine to acid required to deprotonate only half the diacid molecules was 1:1.

Racemic (1,4-dioxan-2-yl)diphenylmethanol

T. Hsiao, R. M. Buchanan and M. S. Mashuta

The title compound, C₁₇H₁₈O₃, prepared by microwave irradiation of benzophenone and dioxane, crystallizes in a racemic mixture that forms one-dimensional chains via strong hydrogen bonding of the hydroxy group to the adjacent symmetry-generated 1,4-dioxan-2-yl group; the O-HO distance is 1.99 (3) Å and the O-HO angle is 160 (2)°.

Bis(4-methylbenzylammonium) tetrachloridozincate: a new noncentrosymmetric structure characterized by ¹³C CP-MAS NMR spectroscopy

R. Kefi, E. Jeanneau, F. Lefebvre and C. Ben Nasr

A new noncentrosymmetric organic-inorganic hybrid material, (C₈H₁₂N)₂[ZnCl₄], has been synthesized as single crystals at room temperature and characterized by X-ray diffraction and solid-state NMR spectroscopy. Its novel structure consists of two 4-methylbenzylammonium cations and one [ZnCl₄]^2- anion connected by N-HCl and C-HCl hydrogen bonds, two of which are three-centre interactions. The Zn^II metal centre has a slightly distorted tetrahedral coordination geometry. Results from ¹³C CP-MAS NMR spectroscopy are in good agreement with the X-ray structure. Density functional theory calculations allow the assignment of the carbon peaks to the independent crystallographic sites.

Pseudopolymorphs of 2,6-diaminopyrimidin-4-one and 2-amino-6-methylpyrimidin-4-one: one or two tautomers present in the same crystal

V. Gerhardt, M. Tutughamiarso and M. Bolte

The derivatives of pyrimidin-4-one can adopt either a 1H- or a 3H-tautomeric form, which affects the hydrogen-bonding interactions in cocrystals with compounds containing complementary functional groups. In order to study their tautomeric preferences, we crystallized 2,6-diaminopyrimidin-4-one and 2-amino-6-methylpyrimidin-4-one. During various crystallization attempts, four structures of 2,6-diaminopyrimidin-4-one were obtained, namely solvent-free 2,6-diaminopyrimidin-4-one, C₄H₆N₄O, (I), 2,6-diaminopyrimidin-4-one-dimethylformamide-water (3/4/1), C₄H₆N₄O·1.33C₃H₇NO·0.33H₂O, (Ia), 2,6-diaminopyrimidin-4-one dimethylacetamide monosolvate, C₄H₆N₄O·C₄H₉NO, (Ib), and 2,6-diaminopyrimidin-4-one-N-methylpyrrolidin-2-one (3/2), C₄H₆N₄O·1.5C₅H₉NO, (Ic). The 2,6-diaminopyrimidin-4-one molecules exist only as 3H-tautomers. They form ribbons characterized by R²₂(8) hydrogen-bonding interactions, which are further connected to form three-dimensional networks. An intermolecular N-HN interaction between amine groups is observed only in (I). This might be the reason for the pyramidalization of the amine group. Crystallization experiments on 2-amino-6-methylpyrimidin-4-one yielded two isostructural pseudopolymorphs, namely 2-amino-6-methylpyrimidin-4(3H)-one-2-amino-6-methylpyrimidin-4(1H)-one-dimethylacetamide (1/1/1), C₅H₇N₃O·C₅H₇N₃O·C₄H₉NO, (IIa), and 2-amino-6-methylpyrimidin-4(3H)-one-2-amino-6-methylpyrimidin-4(1H)-one-N-methylpyrrolidin-2-one (1/1/1), C₅H₇N₃O·C₅H₇N₃O·C₅H₉NO, (IIb). In both structures, a 1:1 mixture of 1H- and 3H-tautomers is present, which are linked by three hydrogen bonds similar to a Watson-Crick C-G base pair.

On the symmetry of wulfenite (Pb[MoO₄]) from Mezica (Slovenia)

I. Cora, M. Czugler, I. Dódony and A. Recnik

Wulfenite [lead(II) molybdate(VI)] is known as a scheelite structure in the I4₁/a space group. The structure of the unusual `hemimorphic' wulfenite crystals from the Mezica mine was refined in the noncentrosymmetric space group I using a Pb/Mo exchange disorder model with the approximate composition Pb_0.94Mo_0.06[MoO₄]. Pb atoms in the 2b positions are substituted by Mo at about 12%. The crystal is shown to be twinned by inversion. Hemimorphism may result from the short-range chemical ordering of the metal atoms at the 2b positions.

Poly[aqua[₂-1,4-bis(imidazol-1-ylmethyl)benzene-²N³:N^3'](₂-5-hydroxybenzene-1,3-dicarboxylato-⁴O¹,O^1':O³,O^3')cadmium(II)], a twofold interpenetrated CdSO₄-like metal-organic polymer

S. Zhou, C.-B. Li, Q.-W. Wang and S. W. Ng

In the title cadmium(II) complex, [Cd(C₈H₄O₅)(C₁₄H₁₄N₄)(H₂O)]_n, the 5-hydroxybenzene-1,3-dicarboxylate (5-OH-1,3-bdc) and 1,4-bis(imidazol-1-ylmethyl)benzene (1,4,-bix) ligands bridge water-coordinated Cd^II atoms to generate a three-dimensional network. Two carboxylate groups from different ligands function as O,O'-chelates, while two imidazole N atoms from different ligands coordinate in a monodentate fashion, and one water molecule completes the seven-coordinate pentagonal bipyramid around the Cd^II atom, in which the N atoms occupy the axial sites and the O atoms occupy the equatorial sites. The overall architecture is a twofold interpenetrated CdSO₄-type framework. The two crystallographically equivalent frameworks are linked by O-HO hydrogen bonds between the water, hydroxy and carboxylate groups.

Two hydration products of 3,4,5,6-tetrachloro-N-(methyl-2-pyridyl)phthalmic acids

P. G. Waddell, J. O. S. Hulse and J. M. Cole

In 2-amino-6-methylpyridin-1-ium 2-carboxy-3,4,5,6-tetrachlorobenzoate, C₆H₉N₂⁺·C₈HCl₄O₄^-, there are two perpendicular chains of hydrogen-bonded ions, one arising from the interaction between 2-carboxy-3,4,5,6-tetrachlorobenzoate ions and the other from the interaction between the 2-amino-6-methylpyridin-1-ium and 2-carboxy-3,4,5,6-tetrachlorobenzoate ions. These chains combine to form a two-dimensional network of hydrogen-bonded ions. Cocrystals of bis(2-amino-3-methylpyridin-1-ium) 3,4,5,6-tetrachlorophthalate-3,4,5,6-tetrachlorophthalic acid (1/1), 2C₆H₉N₂⁺·C₈Cl₄O₄^2-·C₈H₂Cl₄O₄, form finite aggregates of hydrogen-bonded ions. - interactions are observed between 2-amino-3-methylpyridin-1-ium cations. Both structures exhibit the characteristic R₂²(8) motif as a result of the hydrogen bonding between the 2-aminopyridinium and carboxylate units.

Extensive hydrogen and halogen bonding, and absence of intramolecular hydrogen bonding between alcohol and nitro groups in a series of endo-nitronorbornanol compounds

A. Lemmerer and J. P. Michael

The influence of the substituent at the C2 position on the hydrogen-bonding patterns is compared for a series of five related compounds, namely (±)-3-exo,6-exo-dibromo-5-endo-hydroxy-3-endo-nitrobicyclo[2.2.1]heptane-2-exo-carbonitrile, C₈H₈Br₂N₂O₃, (II), (±)-3-exo,6-exo-dibromo-6-endo-nitro-5-exo-phenylbicyclo[2.2.1]heptan-2-endo-ol, C₁₃H₁₃Br₂NO₃, (III), (±)-methyl 3-exo,6-exo-dibromo-5-endo-hydroxy-3-endo-nitrobicyclo[2.2.1]heptane-2-exo-carboxylate, C₉H₁₁Br₂NO₅, (IV), (±)-methyl 3-exo,6-exo-dibromo-7-diphenylmethylidene-5-endo-hydroxy-3-endo-nitrobicyclo[2.2.1]heptane-2-exo-carboxylate, C₂₂H₁₉Br₂NO₅, (V), and (±)-methyl 3-exo,6-exo-dibromo-5-endo-hydroxy-3-endo-nitro-7-oxabicyclo[2.2.1]heptane-2-exo-carboxylate, C₈H₉Br₂NO₆, (VI). The hydrogen-bonding motif in all five compounds is a chain, formed by O-HO hydrogen bonds in (III), (IV), (V) and (VI), and by O-HN hydrogen bonds in (II). All compounds except (III) contain a number of BrBr and BrO halogen bonds that connect the chains to each other to form two-dimensional sheets or three-dimensional networks. None of the compounds features intramolecular hydrogen bonding between the alcohol and nitro functional groups, as was found in the related compound (±)-methyl 3-exo,6-exo-dichloro-5-endo-hydroxy-3-endo-nitrobicyclo[2.2.1]heptane-2-exo-carboxylate, (I) [Boeyens, Denner & Michael (1984b). J. Chem. Soc. Perkin Trans. 2, pp. 767-770]. The crystal structure of (V) exhibits whole-molecule disorder.

Two W/Cu/S clusters: tetraethylammonium bromidodi-₂-sulfido-sulfido[tris(3,5-dimethylpyrazol-1-yl)borato]copper(I)tungsten(VI) and tetraethylammonium dibromido-₃-sulfido-di-₂-sulfido-[tris(3,5-dimethylpyrazol-1-yl)borato]dicopper(I)tungsten(VI)

Z. Wei and X. You

The reaction of (Et₄N)[Tp*WS₃] [Tp* = hydrogen tris(3,5-dimethylpyrazol-1-yl)borate] with one or two equivalents of CuBr afforded the [1 + 1] and [1 + 2] addition products (Et₄N)[Tp*WS(-S)₂(CuBr)] {or (C₈H₂₀N)[CuWBr(C₁₅H₂₂BN₆)S₃], (I)} and (Et₄N)[Tp*W(₃-S)(-S)₂(CuBr)₂] {or (C₈H₂₀N)[Cu₂WBr₂(C₁₅H₂₂BN₆)S₃], (II)}. The anion of (I) contains a [W(-S)₂Cu] core formed by the addition of one CuBr unit to the [Tp*WS₃] species. The anion of (II) has a butterfly-shaped [W(₃-S)(-S)₂Cu₂] core formed by the addition of two CuBr units to the [Tp*WS₃] species. The [Tp*WS₃] sections of each complex exhibit approximate C_3v point symmetry and have closely comparable geometry. In (II), both the anion and cation lie on a crystallographic mirror plane. The structure of (I) is noncentrosymmetric and polar.

A tetragonal form of dysprosium orthomolybdate at room temperature

S. Dorzhieva, I. Chumak, A. Sarapulova, D. Mikhailova, J. Bazarova and H. Ehrenberg

In the present tetragonal modification of dysprosium orthomolybdate, Dy₂(MoO₄)₃, the Dy, one Mo and one O atom are located on a mirror plane with Wyckoff symbol 4e, while another Mo atom is located on a fourfold inverse axis, Wyckoff symbol 2a. A single crystal was selected from a polycrystalline mixture of the Dy₂O₃-ZrO₂-MoO₃ system and was stable at room temperature for at least three months. The structure refinement does not indicate the presence of Zr on the Dy sites (to within 1% accuracy). Thus, the stabilization of the tetragonal form is due to disordered positions for a second O atom and split positions for a third O atom that also maintain the DyO₇ coordination, which is not expected for short Dy-O distances [2.243 (6)-2.393 (5) Å].

(⁵-Cyclopentadienyl)(⁶-phenoxathiin 10,10-dioxide)iron(II) hexafluoridophosphate and phenoxathiin 10,10-dioxide

A. D. Hendsbee, J. D. Masuda and A. Piórko

In the structure of the title complex salt, [Fe(C₅H₅)(C₁₂H₈O₃S)]PF₆, the coordinated cyclopentadienyl (Cp) and benzene ring planes are almost parallel, with a hinge angle between the planes of 0.8 (2)°. The hinge angle between the planes of the peripheral (coordinated and uncoordinated) benzene rings in the coordinated phenoxathiin 10,10-dioxide molecule is 169.9 (2)°, and the FeCp moiety is located inside the shallow fold of the heterocycle. The hinge angle between the benzene ring planes in the free heterocycle, C₁₂H₈O₃S, is 171.49 (6)°.

A square two-dimensional polymer of cobalt citrate cubanes

L. R. Falvello, E. Forcén-Vázquez, I. Mayoral, M. Tomás and F. Palacio

The structure of the title complex, poly[dicaesium(I) hexaaquacobalt(II) [octaaquatetra--citrato-hexacobalt(II)] dodecahydrate], {Cs₂[Co(H₂O)₆][Co₆(C₆H₄O₇)₄(H₂O)₈]·12H₂O}_n, at 100 (1) K is formed by layers of a square two-dimensional polymer composed of Co^II citrate cubanes bridged by magnetically active six-coordinate Co^II cations. The polymer has plane symmetry p4mm in the c-axis projection. The cubanes reside on sites of crystallographic symmetry , while the bridging Co^II centres lie on twofold axes. The basic polymeric unit has a charge of 4-, balanced by two Cs⁺ and a [Co(H₂O)₆]²⁺ (symmetry ) cation, which lie in channels between the polymeric layers. Unligated water molecules, of which there are 12 per cubane, enter into an extended intralayer and layer-bridging hydrogen-bond pattern, which can be described in detail even though not all of the H atoms of the water molecules were located.

Comparison of racemic epi-inosose and (-)-epi-inosose

S. Krishnaswamy, M. T. Patil and M. S. Shashidhar

The conversion of myo-inositol to epi-inositol can be achieved by the hydride reduction of an intermediate epi-inosose derived from myo-inositol. (-)-epi-Inosose, (I), crystallized in the monoclinic space group P2₁, with two independent molecules in the asymmetric unit [Hosomi et al. (2000). Acta Cryst. C56, e584-e585]. On the other hand, (2RS,3SR,5SR,6SR)-epi-inosose, C₆H₁₀O₆, (II), crystallized in the orthorhombic space group Pca2₁. Interestingly, the conformation of the molecules in the two structures is nearly the same, the only difference being the orientation of the C-3 and C-4 hydroxy H atoms. As a result, the molecular organization achieved mainly through strong O-HO hydrogen bonding in the racemic and homochiral lattices is similar. The compound also follows Wallach's rule, in that the racemic crystals are denser than the optically active form.

Cocrystals of 6-propyl-2-thiouracil: N-HO versus N-HS hydrogen bonds

M. Tutughamiarso and E. Egert

In order to investigate the relative stability of N-HO and N-HS hydrogen bonds, we cocrystallized the antithyroid drug 6-propyl-2-thiouracil with two complementary heterocycles. In the cocrystal pyrimidin-2-amine-6-propyl-2-thiouracil (1/2), C₄H₅N₃·2C₇H₁₀N₂OS, (I), the `base pair' is connected by one N-HS and one N-HN hydrogen bond. Homodimers of 6-propyl-2-thiouracil linked by two N-HS hydrogen bonds are observed in the cocrystal N-(6-acetamidopyridin-2-yl)acetamide-6-propyl-2-thiouracil (1/2), C₉H₁₁N₃O₂·2C₇H₁₀N₂OS, (II). The crystal structure of 6-propyl-2-thiouracil itself, C₇H₁₀N₂OS, (III), is stabilized by pairwise N-HO and N-HS hydrogen bonds. In all three structures, N-HS hydrogen bonds occur only within R₂²(8) patterns, whereas N-HO hydrogen bonds tend to connect the homo- and heterodimers into extended networks. In agreement with related structures, the hydrogen-bonding capability of C=O and C=S groups seems to be comparable.

Polymorphs of anhydrous theophylline: stable form IV consists of dimer pairs and metastable form I consists of hydrogen-bonded chains

D. Khamar, R. G. Pritchard, I. J. Bradshaw, G. A. Hutcheon and L. Seton

The structure of a previously unreported polymorph of anhydrous theophylline (1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione), C₇H₈N₄O₂, has been determined at 100 K and shown to have monoclinic symmetry with Z' = 2. The structure is named form IV and experimental observation indicates that this is the stable form of the material. The molecular packing consists of discrete hydrogen-bonded dimers similar to that observed in the monohydrate structure. The structure of form I has also been determined and consists of hydrogen-bonded chains.

2,5-Diaryl-1,3,4-selenadiazoles prepared from Woollins' reagent

D. B. Cordes, G. Hua, A. M. Z. Slawin and J. D. Woollins

Two polymorphs of 2,5-diphenyl-1,3,4-selenadiazole, C₁₄H₁₀N₂Se, denoted (Ia) and (Ib), and a new polymorph of 2,5-bis(thiophen-2-yl)-1,3,4-selenadiazole, C₁₀H₆N₂S₂Se, (IIb), form on crystallization of the compounds, prepared using Woollins' reagent (2,4-diphenyl-1,3-diselenadiphosphetane 2,4-diselenide). These compounds, along with 2-(4-chlorophenyl)-5-phenyl-1,3,4-selenadiazole, C₁₄H₉ClN₂Se, (III), and 2-(furan-2-yl)-5-(p-tolyl)-1,3,4-selenadiazole, C₁₃H₁₀N₂OSe, (IV), show similar intermolecular interactions, with - stacking, C-H interactions and weak hydrogen bonds typically giving rise to molecular chains. However, the combination of interactions differs in each case, giving rise to different packing arrangements. In polymorph (Ib), the molecule lies across a crystallographic twofold rotation axis, and (IV) has two independent molecules in the asymmetric unit.

2-Ammonio-5-chloro-4-methylbenzenesulfonate, its 1-methyl-2-pyrrolidone and dimethyl sulfoxide monosolvates and a corrected structure of 2,2'-(1,4-phenylene)di(4,5-dihydroimidazolium) bis(4-aminobenzenesulfonate) dihydrate

S. L. Bekö, J. W. Bats and M. U. Schmidt

2-Ammonio-5-chloro-4-methylbenzenesulfonate, C₇H₈ClNO₃S, (Ia), is an intermediate in the synthesis of lake red azo pigments. The present structure determination from single-crystal data confirms the results of a previous powder diffraction determination [Bekö, Thoms, Brüning, Alig, van de Streek, Lakatos, Glaubitz & Schmidt (2010). Z. Kristallogr. 225, 382-387]. The zwitterionic tautomeric form is confirmed. During a polymorph screening, two additional pseudopolymorphs were obtained, viz. 2-ammonio-5-chloro-4-methylbenzenesulfonate 1-methyl-2-pyrrolidone monosolvate, C₇H₈ClNO₃S·C₅H₉NO, (Ib), and 2-ammonio-5-chloro-4-methylbenzenesulfonate dimethyl sulfoxide monosolvate, C₇H₈ClNO₃S·C₂H₆OS, (Ic). The molecules of (Ib) have crystallographic m symmetry. The 1-methyl-2-pyrrolidone solvent molecule has an envelope conformation and is disordered around the mirror plane. The structure shows hydrogen-bonded ladders of molecules [graph-set notation C₂²(6)R₂²(12)] in the [010] direction. The benzene groups of adjacent ladders are also stacked in this direction. A different type of hydrogen-bonded ladder [graph-set notation C(6)R₂²(4)R₄⁴(12)] occurs in (Ic). In (Ia), (Ib) and (Ic), the molecules correspond to the zwitterionic tautomer. The structure of the cocrystal of 4-aminobenzenesulfonic acid with 1,4-bis(4,5-dihydroimidazol-2-yl)benzene [Shang, Ren, Wang, Lu & Yang (2009). Acta Cryst. E65, o2221-o2222] is corrected; it actually contains 4-aminobenzenesulfonate anions and 2,2'-(1,4-phenylene)di(dihydroimidazolium) dications, i.e. 2,2'-(1,4-phenylene)di(4,5-dihydroimidazolium) bis(4-aminobenzenesulfonate) dihydrate, C₁₂H₁₆N₄²⁺·2C₆H₆NO₃S^-·2H₂O. Hence, all known structures of aminobenzenesulfonic acid complexes contain ionic or zwitterionic molecules; there is no known structure with a neutral aminobenzenesulfonic acid molecule.

Mixed crystals of 2-carbamoylguanidinium with hydrogen fluorophosphonate and hydrogen phosphite in the ratios 1:0, 0.76 (2):0.24 (2) and 0.115 (7):0.885 (7)

J. Fábry, M. Fridrichová, M. Dusek, K. Fejfarová and R. Krupková

The title compounds, 2-carbamoylguanidinium hydrogen fluorophosphonate, C₂H₇N₄O⁺·HFO₃P^-, (I), 2-carbamoylguanidinium-hydrogen fluorophosphonate-hydrogen phosphite (1/0.76/0.24), C₂H₇N₄O⁺·0.76HFO₃P^-·0.24H₂O₃P^-, (II), and 2-carbamoylguanidinium-hydrogen fluorophosphonate-hydrogen phosphite (1/0.115/0.885), C₂H₇N₄O⁺·0.115HFO₃P^-·0.885H₂O₃P^-, (III), are isostructural with guanylurea hydrogen phosphite, C₂H₇N₄O⁺·H₂O₃P^- [Fridrichová, Nemec, Císarová & Nemec (2010). CrystEngComm, 12, 2054-2056]. They constitute structures where the hydrogen phosphite anion has been fully or partially replaced by hydrogen fluorophosphonate. The title structures are the fourth example of isostructural compounds which differ by the presence of hydrogen fluorophosphonate and hydrogen phosphite or fluorophosphonate and phosphite anions. Moreover, the present study reports structures with these mixed anions for the first time. In the reported mixed salts, the P and O atoms of either anion overlap almost exactly, as can be judged by comparison of their equivalent isotropic displacement parameters, while the P-F and P-H directions are almost parallel. There are strong O-HO hydrogen bonds between the anions, as well as strong N-HO hydrogen bonds between the 2-carbamoylguanidinium cations in the title structures. Altogether they form a three-dimensional hydrogen-bond pattern. Interestingly, rare N-HF interactions are also present in the title structures. Another exceptional feature concerns the P-O(H) distances, which are about as long as the P-F distance. The dependence of P-F distances on the longest P-O distances in FO₃P^2- or HFO₃P^- is presented. The greater content of hydrogen phosphite in the mixed crystals causes a larger deformation of the cations from planarity.

Trimethylurea

C. Döring, C. Taouss and P. G. Jones

The title compound, C₄H₁₀N₂O, crystallizes with two independent molecules in the space group Cmc2₁. The first molecule lies in a crystallographic mirror plane with x = 0, whereas the second molecule lies on a general position with x . Each molecule forms classical N-HO=C hydrogen bonds, thereby leading to chains of molecules parallel or antiparallel, respectively, to the polar c axis.

C-HX (X = O, N or ) interactions in benzyl carbamate

I. Mata, E. Molins, M. Amat, N. Llor and B. Checa

The crystal packing and interaction energy of benzyl carbamate, C₈H₉NO₂, have been analysed in detail by the PIXEL method. Benzyl carbamate forms layers of hydrogen-bonded molecules, with the layers connected by weaker C-H interactions. According to the PIXEL analysis, combinations of C-HX (X = O, N or ) interactions are comparable in energy with hydrogen bonding. These interactions are necessary for explaining the geometry and the assembly of the layers.

6-Bromoindigo dye

D. J. Szalda, K. Ramig, O. Lavinda, Z. C. Koren and L. Massa

6-Bromoindigo (MBI) [systematic name: 6-bromo-2-(3-oxo-2,3-dihydro-1H-indol-2-ylidene)-2,3-dihydro-1H-indol-3-one], C₁₆H₉BrN₂O₂, crystallizes with one disordered molecule in the asymmetric unit about a pseudo-inversion center, as shown by the Br-atom disorder of 0.682 (3):0.318 (3). The 18 indigo ring atoms occupy two sites which are displaced by 0.34 Å from each other as a result of this packing disorder. This difference in occupancy factors results in each atom in the reported model used to represent the two disordered sites being 0.08 Å from the higher-occupancy site and 0.26 Å from the lower-occupancy site. Thus, as a result of the disorder, the C-Br bond lengths in the disordered components are 0.08 and 0.26 Å shorter than those found in 6,6'-dibromoindigo (DBI) [Süsse & Krampe (1979). Naturwissenschaften, 66, 110], although the distances within the indigo ring are similar to those found in DBI. The crystals are also twinned by merohedry. Stacking interactions and hydrogen bonds are similar to those found in the structures of indigo and DBI. In MBI, an interaction of the type C-BrC replaces the C-BrBr interactions found in DBI. The interactions in MBI were calculated quantum mechanically using density functional theory and the quantum theory of atoms in molecules.

3,5-Bis{4-[(benzimidazol-1-yl)methyl]phenyl}-4H-1,2,4-triazol-4-amine and its one-dimensional polymeric complex with HgCl₂

Y. Li, Q.-K. Liu, J.-P. Ma and Y.-B. Dong

The molecule of 3,5-bis{4-[(benzimidazol-1-yl)methyl]phenyl}-4H-1,2,4-triazol-4-amine (L), C₃₀H₂₄N₈, has an antiperiplanar conformation of the two terminal benzimidazole groups and forms two-dimensional networks along the crystallographic b axis via two types of intermolecular hydrogen bonds. However, in catena-poly[[[dichloridomercury(II)]--3,5-bis{4-[(benzimidazol-1-yl)methyl]phenyl}-4H-1,2,4-triazol-4-amine] dichloromethane hemisolvate], {[HgCl₂(C₃₀H₂₄N₈)]·0.5CH₂Cl₂}_n, synthesized by the combination of L with HgCl₂, the L ligand adopts a synperiplanar conformation. The Hg^II cation lies in a distorted tetrahedral environment, which is defined by two N atoms and two Cl atoms to form a one-dimensional zigzag chain. These zigzag chains stack via hydrogen bonds which expand the dimensionality of the structure from one to two.

Hydrogen bis[tris(4-fluorophenyl)phosphane oxide] triiodide

F. Haghjoo, N. A. Barnes, R. Pritchard, S. M. Godfrey and S. Ratcliffe

In the title compound, C₃₆H₂₅F₆O₂P₂⁺·I₃^-, hydrogen-bonded [{(p-FC₆H₄)₃PO}₂H]⁺ dimers assemble along the crystallographic c axis to form channels that house extended chains of triiodide anions. Although the I-I bond lengths of 2.9452 (14) and 2.9023 (15) Å are typical, the inter-ion II distance of 3.5774 (10) Å is unusually short. A posteriori modelling of nonmerohedral twinning about (100) has been only partially successful, achieving a reduction in the maximum residual electron density from 5.28 to 3.24 e Å^-3. The inclusion of two low-occupancy I-atom sites (total 1.7%), which can be interpreted as translational disorder of the triiodide anions along the channels, reduced the maximum residual electron density to 2.03 e Å^-3. The minor fractional contribution volume of the nonmerohedral twin domains refined to 0.24 and simultaneous refinement of the inversion twin domains showed the crystal to be a 0.5:0.5 inversion twin.

An example of the refinement of positional disorder modeled as compositional disorder in [5-(2-formylphenyl)-10,15,20-triphenylporphyrinato]nickel(II)

L. C. Spencer, S. A. Yao, J. F. Berry and I. A. Guzei

The title compound, [Ni(C₄₅H₂₈N₄O)], crystallizes in the space group I2d and resides on a crystallographic fourfold rotoinversion axis with only a quarter of the complex in the asymmetric unit. The complex displays positional disorder as the one aldehyde group on the ligand can be located at four different positions. It was necessary to model this as compositional disorder to obtain a correct model and refinement. The practical approach to the refinement is explained.

4-Carboxypyridinium perchlorate 18-crown-6 dihydrate clathrate and 4-carboxypyridinium tetrafluoroborate 18-crown-6 dihydrate clathrate

P. Shi, L. Zhang and Q. Ye

Mixtures of 4-carboxypyridinium perchlorate or 4-carboxypyridinium tetrafluoroborate and 18-crown-6 (1,4,7,10,13,16-hexaoxacyclooctadecane) in ethanol and water solution yielded the title supramolecular salts, C₆H₆NO₂⁺·ClO₄^-·C₁₂H₂₄O₆·2H₂O and C₆H₆NO₂⁺·BF₄^-·C₁₂H₂₄O₆·2H₂O. Based on their similar crystal symmetries, unit cells and supramolecular assemblies, the salts are essentially isostructural. The asymmetric unit in each structure includes one protonated isonicotinic acid cation and one crown ether molecule, which together give a [(C₆H₆NO₂)(18-crown-6)]⁺ supramolecular cation. N-HO hydrogen bonds between the protonated N atoms and a single O atom of each crown ether result in the 4-carboxypyridinium cations `perching' on the 18-crown-6 molecules. Further hydrogen-bonding interactions involving the supramolecular cation and both water molecules form a one-dimensional zigzag chain that propagates along the crystallographic c direction. O-HO or O-HF hydrogen bonds between one of the water molecules and the anions fix the anion positions as pendant upon this chain, without further increasing the dimensionality of the supramolecular network.

Competing intermolecular interactions in some `bridge-flipped' isomeric phenylhydrazones

W. H. Ojala, T. M. Arola, A. M. Brigino, J. D. Leavell and C. R. Ojala

To examine the roles of competing intermolecular interactions in differentiating the molecular packing arrangements of some isomeric phenylhydrazones from each other, the crystal structures of five nitrile-halogen substituted phenylhydrazones and two nitro-halogen substituted phenylhydrazones have been determined and are described here: (E)-4-cyanobenzaldehyde 4-chlorophenylhydrazone, C₁₄H₁₀ClN₃, (Ia); (E)-4-cyanobenzaldehyde 4-bromophenylhydrazone, C₁₄H₁₀BrN₃, (Ib); (E)-4-cyanobenzaldehyde 4-iodophenylhydrazone, C₁₄H₁₀IN₃, (Ic); (E)-4-bromobenzaldehyde 4-cyanophenylhydrazone, C₁₄H₁₀BrN₃, (IIb); (E)-4-iodobenzaldehyde 4-cyanophenylhydrazone, C₁₄H₁₀IN₃, (IIc); (E)-4-chlorobenzaldehyde 4-nitrophenylhydrazone, C₁₃H₁₀ClN₃O₂, (III); and (E)-4-nitrobenzaldehyde 4-chlorophenylhydrazone, C₁₃H₁₀ClN₃O₂, (IV). Both (Ia) and (Ib) are disordered (less than 7% of the molecules have the minor orientation in each structure). Pairs (Ia)/(Ib) and (IIb)/(IIc), related by a halogen exchange, are isomorphous, but none of the `bridge-flipped' isomeric pairs, viz. (Ib)/(IIb), (Ic)/(IIc) or (III)/(IV), is isomorphous. In the nitrile-halogen structures (Ia)-(Ic) and (IIb)-(IIc), only the bridge N-H group and not the bridge C-H group acts as a hydrogen-bond donor to the nitrile group, but in the nitro-halogen structures (III) (with Z' = 2) and (IV), both the bridge N-H group and the bridge C-H group interact with the nitro group as hydrogen-bond donors, albeit via different motifs. The occurrence here of the bridge C-H contact with a hydrogen-bond acceptor suggests the possibility that other pairs of `bridge-flipped' isomeric phenylhydrazones may prove to be isomorphous, regardless of the change from isomer to isomer in the position of the N-H group within the bridge.

A new potential NLO compound with a supramolecular layered structure: aqua(hexamethylenetetramine-N)(iminodiacetato-³O,N,O')copper(II)

J.-J. He, W.-X. Chai, L. Song, F. Niu and X.-B. Fang

In the noncentrosymmetric title compound, [Cu(C₄H₅NO₄)(C₆H₁₂N₄)(H₂O)] or [Cu(IDA)(HMTA)(H₂O)], where IDA is iminodiacetate and HMTA is hexamethylenetetramine, the asymmetric unit consists of a whole mononuclear neutral molecule, where the Cu^II cation is coordinated by two carboxylate O atoms and one N atom from the IDA ligand, by one N atom from the HMTA ligand and by the O atom of the coordinated water molecule, giving rise to a CuN₂O₃ distorted square-pyramidal coordination geometry. The IDA and HTMA ligands adopt terminal tri- and monocoordinated modes, respectively. All adjacent molecules within the ac plane are connected to each other via two pairs of O-HO and one N-HO hydrogen bond, forming a (4,4) supramolecular two-dimensional network. In the unit cell, these layers stack alternately in an ...ABABAB... sequence along the b axis. The optical absorption properties of this compound have been studied on powder samples, which had previously been examined by powder X-ray diffraction.

Enantiomerically pure (1S,5R) and racemic 3-(1-benzothiophen-2-yl)-8-azoniabicyclo[3.2.1]oct-2-ene acetate

B. Frøstrup, D. Peters and A. D. Bond

The title compound, C₁₅H₁₆NS⁺·C₂H₃O₂^-, has been crystallized as both a pure enantiomer (1S,5R) and a racemate. The racemate crystallizes in the space group Cc, with molecules of opposite handedness related to each other by the action of the c-glide. The enantiomer is essentially isostructural with the racemate, except that the glide symmetry is violated by interchange of CH and CH₂ groups within the seven-membered ring. The space-group symmetry is reduced to P1 with two molecules in the asymmetric unit. The enantiomer structure shows disorder of the thiophene ring for one of the molecules in the asymmetric unit. The major component of the disorder has the thiophene ring in the same position as in the racemate, but generates a higher-energy molecular conformation. The minor disorder component has different intermolecular interactions but retains a more stable molecular conformation.

Structures of benzoxazine-fused triazoles as potential diuretic agents

K. Ravikumar, B. Sridhar, J. B. Nanubolu, V. Hariharakrishnan and A. N. Singh

6,8-Dinitro-2,4-dihydro-1H-benzo[b][1,2,4]triazolo[4,3-d][1,4]oxazin-1-one, C₉H₅N₅O₆, (I), a potential diuretic, and its acetylacetone derivative (E)-2-(2-hydroxy-4-oxopent-2-en-3-yl)-6,8-dinitro-2,4-dihydro-1H-benzo[b][1,2,4]triazolo[4,3-d][1,4]oxazin-1-one, C₁₄H₁₁N₅O₈, (II), both crystallize from methanol but in centrosymmetric and noncentrosymmetric space groups, respectively. To the best of our knowledge, this is the first report of crystal structures of benzoxazine-triazole fused systems. The acetylacetone group in (II) exists as the keto-enol tautomer and is oriented perpendicular to the triazol-3-one ring. Of the two nitro groups present, one is rotated significantly less than the other in both structures. The oxazine ring adopts a screw-boat conformation in (II), whereas it is almost planar in (I). N-HN and N-HO hydrogen bonds form centrosymmetric dimers in (I), while C-HO interactions associate the molecules into helical columns in (II).

1,1'-Methylenedipyridinium tetrachloridocuprate(II) and bis[tetrachloridoaurate(III)] hybrid salts by X-ray powder diffraction

M. Al-Ktaifani and M. Rukiah

In order to explore the potential propensity of the 1,1'-methylenedipyridinium dication to form organic-inorganic hybrid ionic compounds by reaction with the appropriate halide metal salt, the organic-inorganic hybrid salts 1,1'-methylenedipyridinium tetrachloridocuprate(II), (C₁₁H₁₂N₂)[CuCl₄], (I), and 1,1'-methylenedipyridinium bis[tetrachloridoaurate(III)], (C₁₁H₁₂N₂)[AuCl₄]₂, (II), were obtained by treatment of 1,1'-methylenedipyridinium dichloride with CuCl₂ and Na[AuCl₄], respectively. Both hybrid salts were isolated as pure compounds, fully characterized by multinuclear NMR spectroscopy and their molecular structures confirmed by powder X-ray diffraction studies. The crystal structures consist of discrete 1,1'-methylenedipyridinium dications and [CuCl₄]^2- and [AuCl₄]^- anions for (I) and (II), respectively. As expected, the dications form a butterfly shape; the Cu^II centre of [CuCl₄]^2- has a distorted tetrahedral configuration and the Au^III centre of [AuCl₄]^- shows a square-planar coordination. The ionic species of (I) and the dication of (II) each have twofold axial symmetry, while the two [AuCl₄]^- anions are located on a mirror-plane site. Both crystal structures are stabilized by intermolecular C-HCl hydrogen bonds and also by Cl interactions. It is noteworthy that, while the average intermolecular centroid-centroid pyridinium ring distance in (I) is 3.643 (8) Å, giving strong evidence for noncovalent - ring interactions, for (II), the shortest centroid-centroid distance between pyridinium rings of 5.502 (9) Å is too long for any significant - ring interactions, which might be due to the bulk of the two [AuCl₄]^- anions.

The weakly coordinating perchlorate group in bis(N,N'-dimethylethylenediamine-²N,N')bis(perchlorato-O)copper(II) studied at 100, 250 and 400 K

S. Schnitzler, M.-D. Serb and U. Englert

The crystal structure of the title compound, [Cu(ClO₄)₂(C₄H₁₂N₂)₂], (I), is reported at 100, 250 and 400 K. The Cu^II cation in this complex is coordinated in a distorted octahedral mode characteristic of Jahn-Teller systems. The coordination of the perchlorate ligands via longer, and presumably weaker, axial Cu-O distances varies significantly as a function of temperature. One of the Cu-O distances increases between 100 and 250 K, and one of the Cu-O-Cl angles expands between 250 and 400 K. At all temperatures, the complex forms a two-dimensional N-HO hydrogen-bond network in the (001) plane.

The heterobifunctional ligand 5-[4-(1,2,4-triazol-4-yl)phenyl]-1H-tetrazole and its role in the construction of a Cd^II metal-organic chain structure

A. B. Lysenko

5-[4-(1,2,4-Triazol-4-yl)phenyl]-1H-tetrazole, C₉H₇N₇, (I), an asymmetric heterobifunctional organic ligand containing triazole (tr) and tetrazole (tz) termini linked directly through a 1,4-phenylene spacer, crystallizes in the polar space group Pc. The heterocyclic functions, serving as single hydrogen-bond donor (tz) or acceptor (tr) units, afford hydrogen-bonded zigzag chains with no crystallographic centre of inversion. In the structure of catena-poly[[diaquacadmium(II)]bis{₂-5-[4-(1,2,4-triazol-4-yl)phenyl]tetrazol-1-ido-²N¹:N^1'}], [Cd(C₉H₆N₇)₂(H₂O)₂]_n, (II), the Cd^II dication resides on a centre of inversion in an octahedral {N₄O₂} environment. In the equatorial plane, the Cd^II polyhedron is built up from four N atoms of two kinds, namely of trans-coordinating tr and tz fragments [Cd-N = 2.2926 (17) and 2.3603 (18) Å], and the coordinating aqua ligands occupy the two apical sites. The metal centres are separated at a distance of 11.1006 (7) Å by means of the double-bridging tetrazolate anion, L^-, forming a chain structure. The water ligands and tz fragments interact with one another, like a double hydrogen-bond donor-acceptor synthon, leading to a hydrogen-bonded three-dimensional array.

Isoquinolin-5-amine

A. M. Atria, M. T. Garland and R. Baggio

The title compound, C₉H₈N₂, presents two almost identical independent molecules in the asymmetric unit, both of them exhibiting an extremely planar isoquinoline core (maximum r.m.s. deviation = 0.014 Å). The most significant deviation is found in the -NH₂ groups, which present a noticeable pyramidalization around the N atom, a feature also present in related structures containing the molecule as a ligand. The supramolecular structure is based on pairs of parallel hydrogen-bonded chains formed by just one molecular type each, defined by the strongest hydrogen bonds in the structure, which are of the N-HN type. These parallel chains are linked into pairs (or strips) via weaker C-HN hydrogen bonds. Related strips generated by the c-glide plane define two families running along [10] and [110], giving rise to an interesting system of interwoven chains stabilized by a number of weaker contacts of the C-H type.

Eight isostructural 4,4'-disubstituted N-phenylbenzenesulfonamides

T. Gelbrich, T. L. Threlfall and M. B. Hursthouse

The isostructural crystals of 4-cyano-N-(4-methoxyphenyl)benzenesulfonamide, C₁₄H₁₂N₂O₃S, (I), N-(4-methoxyphenyl)-4-(trifluoromethyl)benzenesulfonamide, C₁₄H₁₂F₃NO₃S, (II), 4-iodo-N-(4-methoxyphenyl)benzenesulfonamide, C₁₃H₁₂INO₃S, (III), 4-bromo-N-(4-methoxyphenyl)benzenesulfonamide, C₁₃H₁₂BrNO₃S, (IV), 4-chloro-N-(4-methoxyphenyl)benzenesulfonamide, C₁₃H₁₂ClNO₃S, (V), 4-fluoro-N-(4-methoxyphenyl)benzenesulfonamide, C₁₃H₁₂FNO₃S, (VI), N-(4-chlorophenyl)-4-methoxybenzenesulfonamide, C₁₃H₁₂ClNO₃S, (VII), and 4-cyano-N-phenylbenzenesulfonamide, C₁₃H₁₀N₂O₂S, (VIII), contain infinite chains composed of N-HO(sulfonyl) hydrogen-bonded molecules. The crystal structures of (I)-(VIII) have been compared using the XPac software and quantitative descriptors of isostructurality were generated [Gelbrich, Threlfall & Hursthouse (2012). CrystEngComm, 14, 5454-5464]. Certain isostructural relationships in this series involve molecules with substantially different spatial demands, e.g. (VI) and (VIII) are related by the simultaneous interchange of FCN on the benzenesulfonamide ring and OMeH on the N-phenyl ring, which indicates that the geometry of the three-dimensional crystal-packing mode of (I)-(VIII) is unusually adaptable to different molecular shapes.

2-Propynyl 2,3,4,6-tetra-O-acetyl--D-mannopyranoside

H. Al-Mughaid, K. N. Robertson, U. Werner-Zwanziger, M. D. Lumsden, T. S. Cameron and T. B. Grindley

The 2-propynyl group in the title compound, C₁₇H₂₂O₁₀, adopts an exoanomeric conformation, with the acetylenic group gauche with respect to position C1. Comparison of ¹³C NMR chemical shifts from solution and the solid state suggest that the acetylenic group also adopts a conformation anti to C1 in solution. The pyranose ring adopts a ⁴C₁ conformation. Of the three secondary O-acetyl groups, that on position O4, flanked by two equatorial groups, adopts a syn conformation, in agreement with recent generalizations [González-Outeiriño, Nasser & Anderson (2005). J. Org. Chem. 70, 2486-2493]. The acetyl group on position O3 adopts a gauche conformation, also in agreement with the recent generalizations, but that on position O2 adopts a syn conformation, not in agreement with the recent generalizations.

4-(2,5-Dioxo-2,5-dihydro-1H-pyrrol-1-yl)benzoic acid: X-ray and DFT-calculated structure

R. Moreno-Fuquen, J. C. Tenorio, J. Ellena, C. A. De Simone and L. Ribeiro

In the title compound, C₁₁H₇NO₄, there is a dihedral angle of 45.80 (7)° between the planes of the benzene and maleimide rings. The presence of O-HO hydrogen bonding and weak C-HO interactions allows the formation of R₃³(19) edge-connected rings parallel to the (010) plane. Structural, spectroscopic and theoretical studies were carried out. Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) and 6-31++G(d,p) levels are compared with the experimentally determined molecular structure in the solid state. Additional IR and UV theoretical studies allowed the presence of functional groups and the transition bands of the system to be identified.

Four stereoisomers of the novel -opioid receptor agonist tapentadol hydrochloride

K. Ravikumar, B. Sridhar, N. Pradhan and M. Khunt

The crystal and molecular structures of four stereoisomers of tapentadol hydrochloride [systematic name: 3-(3-hydroxyphenyl)-N,N,2-trimethylpentan-1-aminium chloride], C₁₄H₂₄NO⁺·Cl^-, a novel analgesic agent, have been determined by X-ray crystal structure analysis. Resolution of the isomers was carried out by reverse-phase and chiral high-performance liquid chromatographic (HPLC) methods. Stereoisomers (I) and (II) crystallize in the monoclinic space group P2₁, each with two tapentadol cations and two chloride anions in the asymmetric unit, while stereoisomers (III) and (IV) crystallize in the orthorhombic space group P2₁2₁2₁, with one tapentadol cation and one chloride anion in the asymmetric unit. The absolute configurations of the four enantiomers were determined unambiguously by X-ray crystallography. The crystal structures reveal the stereochemistries at the 3-ethyl and 2-methyl groups to be R,R, S,S, S,R and R,S in stereoisomers (I)-(IV), respectively. The ethyl and aminopropyl groups adopt different orientations with respect to the phenol ring for (I) and (IV). In all four structures, the chloride ions take part in N-HCl and O-HCl hydrogen bonds with the tapentadol molecules, resulting in one-dimensional helical chains in the crystal packing in each case.

Optically active diaryl tetrahydroisoquinoline derivatives

T. Naicker, T. Govender, H. G. Kruger and G. E. M. Maguire

In (1R,3S)-6,7-dimethoxy-3-(methoxydiphenylmethyl)-1-phenyl-1,2,3,4-tetrahydroisoquinoline, C₃₁H₃₁NO₃, (I), and (1R,3S)-2-benzyl-3-[diphenyl(trimethylsiloxy)methyl]-6,7-dimethoxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline, C₄₀H₄₃NO₃Si, (II), the absolute configurations have been confirmed to be R and S at the isoquinoline 1- and 3-positions, respectively, by NMR spectroscopy experiments. Both structures have monoclinic (P2₁) symmetry and the N-containing six-membered ring assumes a half-chair conformation. The asymmetric unit of (I) contains one molecule, while (II) has two molecules within the asymmetric unit. These structures are of interest with respect to the conformation around the exocyclic C-C bond: (I) displays an ap (antiperiplanar) conformation, while (II) displays an sc-exo (synclinal) conformation around this bond. These conformations are significant for stereocontrol when these compounds are used as catalysts. Various C-H and C-HO bonds link the molecules together in the crystal structure of (I). In the crystal structure of (II), three intermolecular C-H hydrogen bonds help to establish the packing.

1,N⁶-Etheno-2'-deoxytubercidin hemihydrate

F. Seela, P. Ding, P. Leonard, H. Eickmeier and H. Reuter

The title compound [systematic name: 7-(2-deoxy--D-erythro-pentofuranosyl)-7H-imidazo[1,2-c]pyrrolo[2,3-d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N-glycosylic bonds of both conformers show an almost identical anti conformation with = -107.7 (2)° for conformer (I-1) and -107.0 (2)° for conformer (I-2). The sugar moiety adopts an unusual N-type (C3'-endo) sugar pucker for 2'-deoxyribonucleosides, with P = 36.8 (2)° and _m = 40.6 (1)° for conformer (I-1), and P = 34.5 (2)° and _m = 41.4 (1)° for conformer (I-2). Both conformers and the solvent molecule participate in the formation of a three-dimensional pattern with a `chain'-like arrangement of the conformers. The structure is stabilized by intermolecular O-HO and O-HN hydrogen bonds, together with weak C-HO contacts.

(+)-Geodin from Aspergillus terreus

M. H. Rønnest, M. T. Nielsen, B. Leber, U. H. Mortensen, A. Krämer, M. H. Clausen, T. O. Larsen and P. Harris

The fungal metabolite (+)-geodin [systematic name: (2R)-methyl 5,7-dichloro-4-hydroxy-6'-methoxy-6-methyl-3,4'-dioxospiro[benzofuran-2,1'-cyclohexa-2',5'-diene]-2'-carboxylate], C₁₇H₁₂Cl₂O₇, was isolated from Aspergillus terreus. The crystal structure contains two independent molecules in the asymmetric unit. Molecules denoted 1 interact through O-HO hydrogen bonds creating chains of molecules parallel to the crystallographic 2₁ screw axis. Molecules denoted 2 interact through an OCl halogen bond, also creating chains of molecules parallel to the crystallographic 2₁ screw axis. Molecules 1 and 2 interact through another OCl halogen bond. The two molecules are similar but molecules 2 have a slightly more planar cyclohexadiene ring than molecules 1. The absolute structure of (+)-geodin has been unequivocally assigned with the spiro centre having the R configuration in both molecules. The structurally related (+)-griseofulvin has an S configuration at the spiro centre, a difference of potential biological and biosynthetic relevance.

A dynamic disorder-linked reversible phase transition in a new chloroform solvate of cis-dichloridobis(triethylphosphane)platinum(II)

K. B. Dillon, J. A. K. Howard, P. K. Monks, M. R. Probert and H. J. Shepherd

The title compound, cis-dichloridobis(triethylphosphane)platinum(II) chloroform monosolvate, [PtCl₂(C₆H₁₅P)₂]·CHCl₃, has been obtained from ligand scrambling in the cis-[PtCl₂(Cyp₂PCl)(PEt₃)] (Cyp = cyclopentyl) system in CHCl₃ solvent. Unlike the two previously reported unsolvated polymorphs, which are both monoclinic, the compound crystallizes in an orthorhombic setting. Furthermore, the system exhibits a reversible temperature-dependent structural phase transition, coupling a reduction in anisotropic displacement parameters and a reduction in crystallographic symmetry on cooling. The high-temperature phase adopts space group Pnma with the complex and solvent molecules sitting across a crystallographic mirror plane (Z' = 0.5). The low-temperature phase adopts the space group P2₁2₁2₁ with Z' = 1.

L-Cysteinium semioxalate: a new monoclinic polymorph or a hydrate?

V. S. Minkov and E. V. Boldyreva

The title compound, C₃H₈NO₂S⁺·C₂HO₄^-, (I), crystallizes in the monoclinic C2 space group and is a new form (possibly a hydrate) of L-cysteinium semioxalate with a stoichiometric cation-anion ratio of 1:1. In contrast to the previously known orthorhombic form of L-cysteinium semioxalate, (I) has a layered structure resembling those of monoclinic L-cysteine, as well as of DL-cysteine and its oxalates. The conformations of the cysteinium cation and the oxalate anion in (I) differ substantially from those in the orthorhombic form. The structure of (I) has voids with a size sufficient to incorporate water molecules. The residual density, however, suggests that if water is in fact present in the voids, it is strongly disordered and its amount does not exceed 0.3 molecules per void. The difference in conformation of the cysteinium cations in (I) and in the orthorhombic form is similar to that in DL-cysteine under ambient conditions and in DL-cysteine under high pressure or at low temperature.

Methyl 2-acetamido-2-deoxy--D-glucopyranoside dihydrate and methyl 2-formamido-2-deoxy--D-glucopyranoside

X. Hu, W. Zhang, A. G. Oliver and A. S. Serianni

Methyl 2-acetamido-2-deoxy--D-glucopyranoside (-GlcNAcOCH₃), (I), crystallizes from water as a dihydrate, C₉H₁₇NO₆·H₂O, containing two independent molecules [denoted (IA) and (IB)] in the asymmetric unit, whereas the crystal structure of methyl 2-formamido-2-deoxy--D-glucopyranoside (-GlcNFmOCH₃), (II), C₈H₁₅NO₆, also obtained from water, is devoid of solvent water molecules. The two molecules of (I) assume distorted ⁴C₁ chair conformations. Values of for (IA) and (IB) indicate ring distortions towards B_C2,C5 and ^C3,O5B, respectively. By comparison, (II) shows considerably more ring distortion than molecules (IA) and (IB), despite the less bulky N-acyl side chain. Distortion towards B_C2,C5 was observed for (II), similar to the findings for (IA). The amide bond conformation in each of (IA), (IB) and (II) is trans, and the conformation about the C-N bond is anti (C-H is approximately anti to N-H), although the conformation about the latter bond within this group varies by 16°. The conformation of the exocyclic hydroxymethyl group was found to be gt in each of (IA), (IB) and (II). Comparison of the X-ray structures of (I) and (II) with those of other GlcNAc mono- and disaccharides shows that GlcNAc aldohexopyranosyl rings can be distorted over a wide range of geometries in the solid state.

-Acetato--aqua--hydroxido-bis[(1,10-phenanthroline)copper(II)] dinitrate monohydrate

J. E. Abud, R. P. Sartoris, R. Calvo and R. Baggio

The triply bridged title dinuclear copper(II) compound, [Cu₂(C₂H₃O₂)(OH)(C₁₂H₈N₂)₂(H₂O)](NO₃)₂·H₂O, (I), consists of a [Cu₂(₂-CH₃COO)(₂-OH)(phen)₂(₂-OH₂)]²⁺ cation (phen is 1,10-phenanthroline), two uncoordinated nitrate anions and one water molecule. The title cation contains a distorted square-pyramidal arrangement around each metal centre with a CuN₂O₃ chromophore. In the dinuclear unit, both Cu^II ions are linked through a hydroxide bridge and a triatomic bridging carboxylate group, and at the axial positions through a water molecule. The phenanthroline groups in neighbouring dinuclear units interdigitate along the [010] direction, generating several - contacts which give rise to planar arrays parallel to (001). These are in turn connected by hydrogen bonds involving the aqua and hydroxide groups as donors with the nitrate anions as acceptors. Comparisons are made with isostructural compounds having similar cationic units but different counter-ions; the role of hydrogen bonding in the overall three-dimensional structure and its ultimate effect on the cell dimensions are discussed.

Poly[tetra-₂-L-lactato-indium(III)sodium(I)]

J.-J. Wei, N. Zhang, Y.-L. Wang and Q.-Y. Liu

The asymmetric unit of the title compound, [InNa(C₃H₅O₃)₄]_n, consists of one In^III ion, one Na^I ion and four crystallographically independent L-lactate monoanions. The coordination of the In^III ion is composed of five carboxylate O and two hydroxy O atoms in a distorted pentagonal-bipyramidal coordination geometry. The Na^I ion is six-coordinated by four carboxylate O atoms and two hydroxy O atoms from four L-lactate ligands in a distorted octahedral geometry. Each In^III ion is coordinated by four surrounding L-lactate ligands to form an [In(L-lactate)₄]^- unit, which is further linked by Na^I ions through Na-O bonds to give a two-dimensional layered structure. Hydrogen bonds between the hydroxy groups and carboxylate O atoms are observed between neighbouring layers.

trans-Dichloridobis(4,8-dimethyl-2-phenyl-2-phosphabicyclo[3.3.1]nonane-P)platinum(II)

P. N. Bungu, L. Kirsten and S. Otto

The crystal structure of the title compound, trans-[PtCl₂(C₁₆H₂₃P)₂], has been determined at 100 K. The Pt atom is located on a twofold axis and adopts a distorted square-planar coordination geometry. The structure is only the second example of a coordination complex containing a derivative of the 4,8-dimethyl-2-phosphabicyclo[3.3.1]nonane (Lim) phosphine ligand family. The ligand contains four chiral C atoms, with the stereochemistry at three of these fixed during synthesis, therefore resulting in two possible ligand stereoisomers. The compound crystallizes in the chiral space group P4₃2₁2 but is racemic, comprising an equimolar mixture of both stereoisomers disordered on a single ligand site. The effective cone angles for both isomers are the same at 146°.

(2R*,4S*)-2-(Pyridin-3-yl)-2,3,4,5-tetrahydro-1H-1-benzazepin-4-ol: a three-dimensional framework built from O-HN, C-HO and C-H(arene) hydrogen bonds

S. L. Gómez, A. Palma, J. Cobo and C. Glidewell

The title compound, C₁₅H₁₆N₂O, crystallizes in the space group P2₁2₁2₁ with Z' = 1. The seven-membered ring adopts a chair-type conformation with the hydroxy and pyridyl substituents in equatorial sites. Molecules are linked into a three-dimensional framework structure by a combination of O-HN, C-HO and C-H(arene) hydrogen bonds, but N-HO and N-H(arene) interactions are absent from the structure. Comparisons are made with some related compounds.

Acidic and anionic forms of 1,3-cyclic dihydroxyacetone phosphate (cDHAP) dimethyl acetal

K. Slepokura and I. Mitaszewska

The six-membered cyclic phosphate diester, 5,5-dimethoxy-2-hydroxy-1,3,2-dioxaphosphorinan-2-one, C₅H₁₁O₆P or (MeO)₂cDHAP, which is the dimethyl acetal of cyclic dihydroxyacetone phosphate (cDHAP), has been obtained in the form of two new cyclohexylammonium (cha) salts, cyclohexylammonium 5,5-dimethoxy-2-oxo-1,3,2-dioxaphosphorinan-2-olate monohydrate, (cha)[(MeO)₂cDHAP]·H₂O or C₆H₁₄N⁺·C₅H₁₀O₆P^-·H₂O, and cyclohexylammonium 5,5-dimethoxy-2-oxo-1,3,2-dioxaphosphorinan-2-olate, (cha)[(MeO)₂cDHAP] or C₆H₁₄N⁺·C₅H₁₀O₆P^-, as well as in the form of the anhydrous free acid, (MeO)₂cDHAP. It is shown that protonation of the cyclic phosphate group influences the chair conformation of the P/O/C/C/C/O 1,3,2-dioxaphosphorinane ring, and that differences in the ring conformation correlate with different deformations observed in the ionized and protonated phosphate groups. The ring is more evenly puckered in the anions, in contrast with the flattening observed in the structure of the free acid.

A novel Janus-type AT nucleoside with benzoyl protecting groups forming a pleated-sheet structure

M.-Y. Pan, X.-H. Wu, D.-B. Luo, W. Huang and Y. He

The title compound, 5-amino-8-(2,3,5-tri-O-benzoyl--D-ribofuranosyl)pyrimido[4,5-d]pyrimidine-2,4(3H,8H)-dione methanol monosolvate, C₃₂H₂₅N₅O₉·CH₄O, which crystallized slowly from methanol, exhibits an anti conformation with a glycosyl-bond torsion angle of = -141.28 (17)°. The furanose moiety adopts an N-type sugar puckering (³T₄). The corresponding pseudorotation phase angle and maximum amplitude are P = 24.5 (2)° and _m = 38.3 (2)°, respectively. In the solid state, one methanol molecule acts as a bridge joining adjacent nucleoside molecules head-to-head, leading to a pleated-ribbon supramolecular structure, with the base moieties located in the centre of the ribbon and the sugar residues protruding to the outside of the layers, as in a DNA helix. The pleated-ribbon supramolecular structure is tethered together into a two-dimensional infinite pleated-sheet structure through aromatic stacking between the nucleobase planes and the benzene rings of the benzoyl protecting groups on the 5'-OH group of furanose.

(R)-4-(4-Aminophenyl)-2,2,4-trimethylchroman and (S)-4-(4-aminophenyl)-2,2,4-trimethylthiachroman

C. S. Frampton, D. D. MacNicol and D. R. Wilson

The title compounds, C₁₈H₂₁NO and C₁₈H₂₁NS, in their enantiomerically pure forms are isostructural with the enantiomerically pure 4-(4-hydroxyphenyl)-2,2,4-trimethylchroman and 4-(2,4-dihydroxyphenyl)-2,2,4-trimethylchroman analogues and form extended linear chains via N-HO or N-HS hydrogen bonding along the [100] direction. The absolute configuration for both compounds was determined by anomalous dispersion methods with reference to both the Flack parameter and, for the light-atom compound, Bayesian statistics on Bijvoet differences.

An X-ray powder diffraction study of cis-dichloridobis(2-methyl-2H-tetrazol-5-amine-N⁴)platinum(II), a tetrazole-containing analogue of cisplatin

L. S. Ivashkevich, T. V. Serebryanskaya, A. S. Lyakhov and P. N. Gaponik

The structure of the title compound, cis-[PtCl₂(C₂H₅N₅)₂], was analysed using in-house X-ray powder diffraction data at room temperature. The structure was solved by direct methods and refined using Rietveld analysis. A slightly distorted square-planar coordination geometry is formed around the Pt atom by two Cl atoms and two ring N atoms of the 2-methyl-2H-tetrazol-5-amine ligands, which are in a cis configuration. The planes of the tetrazole rings are inclined at 79.7 (7) and 73.8 (6)° with respect to the coordination plane, with their substituents oriented in such a way that the complex as a whole has approximate C₂ symmetry. Intermolecular N-HCl hydrogen bonds mediate the formation of a three-dimensional supramolecular network.

The pentacoordinated [Cr(CO)₅]^2- dianion in [2,2,2-crypt-K]₂[Cr(CO)₅] ethylenediamine monosolvate

J. Zhai and L. Xu

Bis[(4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane)potassium(+)] pentacarbonylchromate(2-) ethylenediamine monosolvate, [K(C₁₈H₃₆N₂O₆)]₂[Cr(CO)₅]·C₂H₈N₂, was obtained from the reaction between K₃Cd₂Sb₂ and Cr(CO)₆ in ethylenediamine in the presence of the macrocyclic 2,2,2-crypt ligand. The structure provides the first crystallographic characterization of the pentacoordinated [Cr(CO)₅]^2- dianion. The central Cr^III atom is coordinated by five carbonyl ligands in a distorted trigonal-bipyramidal geometry. The distribution of the Cr-C bond lengths indicates a greater degree of back bonding from Cr^III to the equatorial carbonyl ligands compared with the axial carbonyl ligands.

Sodium tris(acetato-²O,O')dioxidoamericate(VI) and guanidinium tris(cyclopropanecarboxylato-²O,O')dioxidoamericate(VI)

M. S. Grigoriev and A. M. Fedosseev

The title compounds, Na[{AmO₂}(C₂H₃O₂)₃], (I), and (CH₆N₃)[{AmO₂}(C₄H₅O₂)₃], (II), contain complex anions in which AmO₂²⁺ cations are surrounded by three bidentate-chelating carboxylate groups. The atoms of the AmO₂ group and the Na atoms in (I) are situated on threefold axes. All the atoms in (II) occupy general positions. Both compounds are isomorphous with earlier studied analogous compounds of previous members of the actinide (An) series.

Two polymorphs of (2-carboxyethyl)(phenyl)phosphinic acid

Q.-S. Hu, X.-Z. Zhang, S.-F. Luo, Y.-H. Sun and Z.-Y. Du

Two polymorphs of (2-carboxyethyl)(phenyl)phosphinic acid, C₉H₁₁O₄P, crystallize in the chiral P2₁2₁2₁ space group with similar unit-cell parameters. They feature an essentially similar hydrogen-bonding motif but differ slightly in their detailed geometric parameters. For both polymorphs, the unequivocal location of the hydroxy H atoms together with the expected differences in the P-O bond lengths establish unequivocally that both forms contain the S isomer; the protonated phosphinic acid and carboxy O atoms serve as hydrogen-bond donors, while the second phosphinic acid O atom acts as a double hydrogen-bond acceptor and the remaining carboxy O atom is not involved in hydrogen bonding. Thus, an undulating two-dimensional supramolecular layer aggregate is formed based on an R₄³(20) ring unit. Such polymorphism derives from the rotation of the C-C single bonds between the two hydrogen-bond-involved carboxy and phosphinic acid moieties.

The molecular conformation of pentan-3-one studied in cholic acid pentan-3-one solvate

I. Kalf and U. Englert

The crystal structure of cholic acid-pentan-3-one (1/1), C₅H₁₀O·C₂₄H₄₀O₅, has been determined in order to deduce the molecular conformation of the small volatile ketone. Data were collected at 100 K to a resolution of (sin )/ = 0.91 Å^-1. The structure contains a hydrogen-bonded cholic acid host network, forming only van der Waals interactions with the guest pentan-3-one molecules. The ketone molecules are disordered on general positions, with two clearly identifiable conformations. The majority conformer exhibits approximate C₂ symmetry and is similar to that recently observed by microwave spectroscopy in the gas phase.

A chiral interdigitated supramolecular network assembled from single-stranded helical tubes

L. Han, L.-P. Xu and W.-N. Zhao

The amino-functionalized helical chiral one-dimensional coordination polymer catena-poly[[bis(pyridine-N)zinc(II)]--2-aminobenzene-1,4-dicarboxylato-⁴O¹,O^1':O⁴,O^4'], [Zn(C₈H₅NO₄)(C₅H₅N)₂]_n, has an extended structure that is assembled from 2-aminobenzene-1,4-dicarboxylate anions and Zn²⁺ cations and which presents a left-handed 4₃ helix with a pitch of 25.6975 (9) Å. All the pyridine rings and all the amino groups point away from the helix to generate a hollow tube with a cross-section of approximately 8 × 8 Å running parallel to the crystallographic c direction. Each single-stranded helix is interdigitated with four neighbouring helices via N-HO hydrogen bonds, which gives rise to a dense homochiral three-dimensional supramolecular network.

Planarity of heteroaryldithiocarbazic acid derivatives showing tuberculostatic activity. III. Mono- and diesters of 3-(pyrazin-2-ylcarbonyl)dithiocarbazic acid

M. Szczesio, A. Olczak, J. Golka, K. Gobis, H. Foks and M. L. Glówka

Methyl 2-(pyrazin-2-ylcarbonyl)hydrazinecarbodithioate, C₇H₈N₄OS₂, (E1), N'-[bis(methylsulfanyl)methylidene]pyrazine-2-carbohydrazide, C₈H₁₀N₄OS₂, (F1), N'-[bis(methylsulfanyl)methylidene]-6-methoxypyrazine-2-carbohydrazide, C₉H₁₂N₄O₂S₂, (F2), and methyl 1-methyl-2-(pyrazin-2-ylcarbonyl)hydrazinecarbodithioate, C₈H₁₀N₄OS₂, (G1), can be considered as derivatives of classical (thio)amide-type tuberculostatics, and all are moderately active against Mycobacterium tuberculosis. This study was undertaken in a search for relationships between activity and specific intramolecular interactions, especially conjugations and hydrogen-bond contacts, and the molecular structures were compared with respective amine analogues, also active against the pathogen. Despite the differences between the amine and carbonyl groups with opposite functions in the hydrogen bond, the two types of structure show a surprisingly similar planar geometry, mostly due to the conjugations aided by the bifurcated intramolecular hydrogen-bond contact between the N-H group of the central hydrazide group as donor and a pyrazine N atom and an S atom of the dithio function as acceptors. Planarity was suggested to be crucial for the tuberculostatic activity of these compounds. The N-methylated derivative (G1) showed a significant twist at the N-N bond [torsion angle = -121.9 (3)°] due to the methyl substitution, which precludes an intramolecular N-HS contact and the planarity of the whole molecule. Nonetheless, the compound shows moderate tuberculostatic activity.

-Carboline (norharman)

R. J. Thatcher and R. E. Douthwaite

The structure of -carboline, also called norharman (systematic name: 9H-pyrido[3,4-b]indole), C₁₁H₈N₂, has been determined at 110 K. Norharman is prevalent in the environment and the human body and is of wide biological interest. The structure exhibits intermolecular N-HN hydrogen bonding, which results in a one-dimensional herringbone motif. The three rings of the norharman molecule collectively result in a C-shaped curvature of 3.19 (13)° parallel to the long axis. The diffraction data show shorter pyridyl C-C bonds than those reported at the STO-3G level of theory.

Polysulfonylamines. CXCI. The `almost' polymorphs rac-trans-2-aminocyclohexan-1-aminium di(methanesulfonyl)azanide and its 0.11-hydrate

C. Wölper, N. Anwar, N. Gulzar, P. G. Jones and A. Blaschette

The title compound, C₆H₁₅N₂⁺·C₂H₆NO₄S₂^-, crystallizes as a 0.11-hydrate, (I), in the space group C2; the asymmetric unit consists of two cations (one of each enantiomer), one anion on a general position, two half anions, each with the N atom on a twofold axis, and approximately one fifth of a water molecule. The general anion departs significantly from the usual conformation: it lacks one of the typical `W'-shaped sequence of O-S-N-S-O atoms. The compound also crystallizes in the solvent-free form, (II), in the space group P2₁/c, with one formula unit in the asymmetric unit. Both compounds form ribbons of hydrogen-bonded cation dimers parallel to the b axis. In (I), there are two independent ribbons of opposite chirality, each involving one anion on a special position, and these ribbons are connected by hydrogen bonds to the anion on a general position, resulting in a layer structure parallel to (100). In (II), the chains are connected by hydrogen bonds, and again a layer structure parallel to (100) results.

N-(tert-Butoxycarbonyl)-L-valyl-L-valine methyl ester: a twisted parallel -sheet in the crystal structure of a protected dipeptide

Ø. Jacobsen, H. G. Gebreslasie, J. Klaveness, P. Rongved and C. H. Görbitz

The title compound, C₁₆H₃₀N₂O₅, crystallizes with three molecules in the asymmetric unit, each adopting a -strand/polyproline II backbone conformation. The main-chain functional groups are hydrogen bonded into tapes having the characteristics of parallel -sheets. Each tape has a left-handed twist and thus forms a helix, with six peptide molecules needed to complete a full 360° rotation. A comparison of hydrogen-bond lengths and twisting modes is made with other related structures of protected dipeptides and with a hexapeptide derived from amyloid- containing the Val-Val segment. Additionally, a comparison of the backbone conformation is made with that of the Val141-Val142 segment of the water channel aquaporin-4 (AQP4).

2,3-Dimethoxy-10-oxostrychnidinium 2-(2,4,6-trinitroanilino)benzoate monohydrate: a 1:1 proton-transfer salt of brucine with o-picraminobenzoic acid

G. Smith and U. D. Wermuth

In the structure of the title 1:1 proton-transfer compound of brucine with 2-(2,4,6-trinitroanilino)benzoic acid, C₂₃H₂₇N₂O₄⁺·C₁₃H₇N₄O₈^-·H₂O, the brucinium cations form classic undulating ribbon substructures through overlapping head-to-tail interactions, while the anions and the three related partial solvent water molecules (having occupancies of 0.73, 0.17 and 0.10) occupy the interstitial regions of the structure. The cations are linked to the anions directly through N-HO_COO^- hydrogen bonds and indirectly by the three water molecules, which form similar conjoint cyclic bridging units [graph set R²₄(8)] through O-HO_C=O and O-HO_COO^- hydrogen bonds, giving a two-dimensional layered structure. Within the anion, intramolecular N-HO_COO^- and N-HO_nitro hydrogen bonds result in the benzoate and picrate rings being rotated slightly out of coplanarity [inter-ring dihedral angle = 32.50 (14)°]. This work provides another example of the molecular selectivity of brucine in forming stable crystal structures, and also represents the first reported structure of any form of the guest compound 2-(2,4,6-trinitroanilino)benzoic acid.

catena-Poly[[[-1,3-bis(diphenylphosphanyl)propane-²P:P'][O-ethyl (4-methoxyphenyl)phosphonodithioato-²S,S']silver(I)] chloroform monosolvate]

D. Sun and R.-B. Huang

Reaction of a mixture of AgOAc, Lawesson's reagent [2,4-bis(4-methoxyphenyl)-1,3-dithiadiphosphetane-2,4-disulfide] and 1,3-bis(diphenylphosphanyl)propane (dppp) under ultrasonic treatment gave the title compound, {[Ag(C₉H₁₂O₂PS₂)(C₂₇H₂₆P₂)]·CHCl₃}_n, a novel one-dimensional chain based on the in situ-generated bipodal ligand [ArP(OEt)S₂]^- (Ar = 4-methoxyphenyl). The compound consists of bidentate bridging 1,3-bis(diphenylphosphanyl)propane (dppp) and in situ-generated bidentate chelating [ArP(OEt)S₂]^- ligands. The dppp ligand links the [Ag{ArP(OEt)S₂}] subunit to form an achiral one-dimensional infinite chain. These achiral chains are packed into chiral crystals by virtue of van der Waals interactions. No - interactions are observed in the crystal structure.

Tosyl esters of cinchonidine and cinchonine alkaloids: the structure-reactivity relationship in the hydrolysis to 9-epibases

Z. Karczmarzyk, T. M. Lipinska, W. Wysocki, M. Denisiuk and K. Piechocka

In the crystal structures of the diastereoisomers of O-tosylcinchonidine [(9R)-cinchon-9-yl 4-methylbenzenesulfonate], (I), and O-tosylcinchonine [(9S)-cinchon-9-yl 4-methylbenzenesulfonate], (II), both C₂₆H₂₈N₂O₃S, both molecules are in an anti-closed conformation and, in each case, the position of the aryl ring of the tosylate system is influenced by an intramolecular C-HO hydrogen bond. The molecular packing in (I) is influenced by weak intermolecular C-HO and C-H interactions. The crystal structure of (II) features C-H interactions and van der Waals forces only. The computational investigations using RHF/6-31G** ab initio and AM1 semi-empirical methods performed for (I) and (II) and their protonated species show that the conformational and energetic parameters of the molecules are correlated with differences in their reactivity in hydrolysis to the corresponding 9-epibases.

N-(tert-Butoxycarbonyl)-O-allyl-L-seryl--aminoisobutyryl-L-valine methyl ester: a protected tripeptide with an allylated serine residue

H. G. Gebreslasie, Ø. Jacobsen and C. H. Görbitz

The title compound [systematic name (6S,12S)-methyl 6-(allyloxymethyl)-12-isopropyl-2,2,9,9-tetramethyl-4,7,10-trioxo-3-oxa-5,8,11-triazatridecan-13-oate], C₂₁H₃₇N₃O₇, containing the little studied O-allyl-L-serine residue [Ser(All)], crystallizes in the monoclinic space group C2 with one molecule in the asymmetric unit. The compound is an analogue of the Ser140-Val142 segment of the water channel aquaporin-4 (AQP4). It forms a distorted type-II -turn with a P_II-3_10L-P_II backbone conformation (P_II is polyproline II). The overall backbone conformation is markedly different from that of the CO(Pro139)-Val142 stretch of rat AQP4, but is quite similar to the corresponding segment of human AQP4, despite significant differences at the level of the individual residues. The side chain of the Ser(All) residue adopts a gauche conformation relative to the backbone CO-C and C-N bonds. The H atoms of the two CH₂ groups in the Ser(All) side chain are almost eclipsed. The crystal packing of the title compound is divided into one-molecule-thick layers, each layer having a hydrophilic core and distinct hydrophobic interfaces on either side.

(E)-4-[2-(3,4,5-Trimethoxyphenyl)ethenyl]nitrobenzene and its `bridge-flipped' analogues

A. Collas and F. Blockhuys

The solid-state structures of three push-pull acceptor--donor (A--D) systems differing only in the nature of the -spacer have been determined. (E)-1-Nitro-4-[2-(3,4,5-trimethoxyphenyl)ethenyl]benzene, C₁₇H₁₇NO₅, (I), and its `bridge-flipped' imine analogues, (E)-3,4,5-trimethoxy-N-(4-nitrobenzylidene)aniline, C₁₆H₁₆N₂O₅, (II), and (E)-4-nitro-N-(3,4,5-trimethoxybenzylidene)aniline, C₁₆H₁₆N₂O₅, (III), display different kinds of supramolecular networks, viz. corrugated planes, a herringbone pattern and a layered structure, respectively, all with zero overall dipole moments. Only (III) crystallizes in a noncentrosymmetric space group (P2₁2₁2₁) and is, therefore, a potential material for second-harmonic generation (SHG).

Water-induced pseudo-quadruple hydrogen-bonding motifs in xanthine-inorganic acid complexes

B. Sridhar

In xanthinium nitrate hydrate [systematic name: 2,6-dioxo-1,2,3,6-tetrahydro-9H-purin-7-ium nitrate monohydrate], C₅H₅N₄O₂⁺·NO₃^-·H₂O, (I), and xanthinium hydrogen sulfate hydrate [systematic name: 2,6-dioxo-1,2,3,6-tetrahydro-9H-purin-7-ium hydrogen sulfate monohydrate], C₅H₅N₄O₂⁺·HSO₄^-·H₂O, (II), the xanthine molecules are protonated at the imine N atom with the transfer of an H atom from the inorganic acid. The asymmetric unit of (I) contains a xanthinium cation, a nitrate anion and one water molecule, while that of (II) contains two crystallographically independent xanthinium cations, two hydrogen sulfate anions and two water molecules. A pseudo-quadruple hydrogen-bonding motif is formed between the xanthinium cations and the water molecules via N-HO and O-HO hydrogen bonds in both structures, and leads to the formation of one-dimensional polymeric tapes. These cation-water tapes are further connected by the respective anions and aggregate into two-dimensional hydrogen-bonded sheets in (I) and three-dimensional arrangements in (II).

Weak C-HO hydrogen bonds in anisaldehyde, salicylaldehyde and cinnamaldehyde

M. T. Kirchner, D. Bläser, R. Boese, T. S. Thakur and G. R. Desiraju

In situ cryocrystallization has been employed to grow single crystals of 4-methoxybenzaldehyde (anisaldehyde), C₈H₈O₂, 2-hydroxybenzaldehyde (salicylaldehyde), C₇H₆O₂, and (2E)-3-phenylprop-2-enal (cinnamaldehyde), C₉H₈O, all of which are liquids at room temperature. Several weak C-HO interactions of the types C_aryl-HO, C_formyl-HO and Csp³-HO are present in these related crystal structures.

Plumeridoid C from the Amazonian traditional medicinal plant Himatanthus sucuuba

B. Waltenberger, J. M. Rollinger, U. J. Griesser, H. Stuppner and T. Gelbrich

The stereochemistry of the iridoid plumeridoid C, C₁₅H₁₈O₇, was established by X-ray single-crystal structure analysis, giving (2'R,3R,4R,4aS,7aR)-methyl 3-hydroxy-4'-[(S)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate. The absolute structure of the title compound was determined on the basis of the Flack x parameter and Bayesian statistics on Bijvoet differences. The hydrogen-bond donor and acceptor functions of the two hydroxy groups are employed in the formation of O-HO-bonded helical chains.

New organic-inorganic frameworks incorporating iso- and heteropolymolybdate units and a 3,3',5,5'-tetramethyl-4,4'-bi-1H-pyrazole-2,2'-diium multiple hydrogen-bond donor

L. V. Lukashuk, A. B. Lysenko, H. Krautscheid and K. V. Domasevitch

Poly[bis(3,3',5,5'-tetramethyl-4,4'-bi-1H-pyrazole-2,2'-diium) -octamolybdate(VI) dihydrate], {(C₁₀H₁₆N₄)₂[Mo₈O₂₆]·2H₂O}_n, (I), and bis(3,3',5,5'-tetramethyl-4,4'-bi-1H-pyrazole-2,2'-diium) -dodecamolybdo(VI)silicate tetrahydrate, (C₁₀H₁₆N₄)₂[SiMo₁₂O₄₀]·4H₂O, (II), display intense hydrogen bonding between the cationic pyrazolium species and the metal oxide anions. In (I), the asymmetric unit contains half a centrosymmetric -type [Mo₈O₂₆]^4- anion, which produces a one-dimensional polymeric chain by corner-sharing, one cation and one water molecule. Three-centre bonding with 3,3',5,5'-tetramethyl-4,4'-bi-1H-pyrazole-2,2'-diium, denoted [H₂Me₄bpz]²⁺ [NO = 2.770 (4)-3.146 (4) Å], generates two-dimensional layers that are further linked by hydrogen bonds involving water molecules [OO = 2.902 (4) and 3.010 (4) Å]. In (II), each of the four independent [H₂Me₄bpz]²⁺ cations lies across a twofold axis. They link layers of [SiMo₁₂O₄₀]^4- anions into a three-dimensional framework, and the preferred sites for pyrazolium/anion hydrogen bonding are the terminal oxide atoms [NO = 2.866 (6)-2.999 (6) Å], while anion/aqua interactions occur preferentially via ₂-O sites [OO = 2.910 (6)-3.151 (6) Å].

[⁶-1-Chloro-2-(pyrrolidin-1-yl)benzene](⁵-cyclopentadienyl)iron(II) hexafluoridophosphate and (⁵-cyclopentadienyl){2-[⁶-2-(pyrrolidin-1-yl)phenyl]phenol}iron(II) hexafluoridophosphate

A. D. Hendsbee, J. D. Masuda and A. Piórko

In the complex salt [⁶-1-chloro-2-(pyrrolidin-1-yl)benzene](⁵-cyclopentadienyl)iron(II) hexafluoridophosphate, [Fe(C₅H₅)(C₁₀H₁₂ClN)]PF₆, (I), the complexed cyclopentadienyl and benzene rings are almost parallel, with a dihedral angle between their planes of 2.3 (3)°. In a related complex salt, (⁵-cyclopentadienyl){2-[⁶-2-(pyrrolidin-1-yl)phenyl]phenol}iron(II) hexafluoridophosphate, [Fe(C₅H₅)(C₁₆H₁₇NO)]PF₆, (II), the analogous angle is 5.4 (1)°. In both complexes, the aromatic C atom bound to the pyrrolidine N atom is located out of the plane defined by the remaining five ring C atoms. The dihedral angles between the plane of these five ring atoms and a plane defined by the N-bound aromatic C atom and two neighboring C atoms are 9.7 (8) and 5.6 (2)° for (I) and (II), respectively.

Two tautomeric polymorphs of 2,6-dichloropurine

M. E. García-Rubiño, D. Choquesillo-Lazarte, M. C. Núñez and J. M. Campos

Two polymorphs of 2,6-dichloropurine, C₅H₂Cl₂N₄, have been crystallized and identified as the 9H- and 7H-tautomers. Despite differences in the space group and number of symmetry-independent molecules, they exhibit similar hydrogen-bonding motifs. Both crystal structures are stabilized by intermolecular N-HN interactions that link adjacent molecules into linear chains, and by some nonbonding contacts of the C-Cl type and by - stacking interactions, giving rise to a crossed two-dimensional herringbone packing motif. The main structural difference between the two polymorphs is the different role of the molecules in the - stacking interactions.

Disorder and conformational analysis of methyl -D-galactopyranosyl-(14)--D-xylopyranoside

W. Zhang, A. G. Oliver and A. S. Serianni

Methyl -D-galactopyranosyl-(14)--D-xylopyranoside, C₁₂H₂₂O₁₀, (II), crystallizes as colorless needles from water with positional disorder in the xylopyranosyl (Xyl) ring and no water molecules in the unit cell. The internal glycosidic linkage conformation in (II) is characterized by a ' torsion angle (C2'_Gal-C1'_Gal-O1'_Gal-C4_Xyl) of 156.4 (5)° and a ' torsion angle (C1'_Gal-O1'_Gal-C4_Xyl-C3_Xyl) of 94.0 (11)°, where the ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (-CH₂OH) C atoms in the -Xyl and -Gal residues, respectively. By comparison, the internal linkage conformation in the crystal structure of the structurally related disaccharide, methyl -lactoside [methyl -D-galactopyranosyl-(14)--D-glucopyranoside], (III) [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719-1721], is characterized by ' = 153.8 (2)° and ' = 78.4 (2)°. A comparison of -(14)-linked disaccharides shows considerable variability in both ' and ', with the range in the latter (38°) greater than that in the former (28°). Inter-residue hydrogen bonding is observed between atoms O3_Xyl and O5'_Gal in the crystal structure of (II), analogous to the inter-residue hydrogen bond detected between atoms O3_Glc and O5'_Gal in (III). The exocyclic hydroxymethyl conformations in the Gal residues of (II) and (III) are identical (gauche-trans conformer).

Magnesium, calcium and strontium salts of phenylacetic acid

J.-B. Arlin, A. R. Kennedy and K. Shankland

Three alkaline earth metal salts of phenylacetic acid were examined and all were found to have similar structural types to analogous salts of benzoic and halobenzoic acids. Thus, a synchrotron study shows that the cations in catena-poly[[[tetraaquamagnesium(II)]--phenylacetato-²O:O'] phenylacetate], {[Mg(C₈H₇O₂)(H₂O)₄](C₈H₇O₂)}_n, form a one-dimensional coordination polymer that propagates through Mg-O-C-O-Mg interactions involving both crystallographically independent Mg centres (Z' = 2) and through translation along the a axis. The polymeric chains pack to give alternate inorganic layers and organic bilayers. The Ca and Sr species catena-poly[[[diaqua(phenylacetato-²O,O')calcium(II)]-₃-phenylacetato-1':1:1''⁴O:O,O':O'] monohydrate], {[Ca(C₈H₇O₂)₂(H₂O)₂]·H₂O}_n, and catena-poly[[[diaqua(phenylacetato-²O,O')strontium(II)]-₃-phenylacetato-1':1:1''⁴O:O,O':O'] monohydrate], {[Sr(C₈H₇O₂)₂(H₂O)₂]·H₂O}_n, are essentially isostructural. Both form one-dimensional coordination polymers through a carboxylate group that forms four M-O bonds. The polymeric chains propagate via 2₁ screw axes parallel to the b axis and are further linked in the bc plane by hydrogen bonding involving the non-metal-bound water molecule. Similarly to the Mg salt, both have inorganic layers that alternate with organic bilayers.

1-Ferrocenylmethyl-3-(2,4,6-trimethylbenzyl)-1H-imidazolidin-3-ium iodide and trans-bis(3-benzyl-1-ferrocenylmethyl-1H-imidazolidin-2-ylidene)diiodidopalladium(II)

J.-C. Daran, F. Demirhan, Ö. Yildirim and B. Çetinkaya

Owing to increasing interest in the use of N-heterocyclic carbenes (NHCs) based on imidazolidinium ions as ligands in the design of highly efficient transition-metal-based homogeneous catalysts, the characterizations of the 1-ferrocenylmethyl-3-(2,4,6-trimethylbenzyl)imidazolidin-3-ium iodide salt, [Fe(C₅H₅)(C₁₉H₂₄N₂)]I, (I), and the palladium complex trans-bis(3-benzyl-1-ferrocenylmethyl-1H-imidazolidin-2-ylidene)diiodidopalladium(II), [Fe₂Pd(C₅H₅)₂(C₁₆H₁₇N₂)₂I₂], (II), are reported. Compound (I) has two iodide anions and two imidazolidinium cations within the asymmetric unit (Z' = 2). The two cations have distinctly different conformations, with the ferrocene groups orientated exo and endo with respect to the N-heterocyclic carbene. Weak C-H donor hydrogen bonds to both the iodide anions and the system of the mesitylene group combine to form two-dimensional layers perpendicular to the crystallographic c direction. Only one of the formally charged imidazolidinium rings forms a near-linear hydrogen bond with an iodide anion. Complex (II) shows square-planar coordination around the Pd^II metal, which is located on an inversion centre (Z' = 0.5). The ferrocene and benzyl substituents are in a trans-anti arrangement. The Pd-C bond distance between the N-heterocyclic carbene ligands and the metal atom is 2.036 (7) Å. A survey of related structures shows that the lengthening of the N-C bonds and the closure of the N-C-N angle seen here on metal complexation is typical of similar NHCs and their complexes.

Clarithromycin form I determined by synchrotron X-ray powder diffraction

S. Noguchi, K. Miura, S. Fujiki, Y. Iwao and S. Itai

The structure of the metastable form I polymorph of the macrolide antibiotic clarithromycin, C₃₈H₆₉NO₁₃, was determined by a powder diffraction method using synchrotron radiation. The space group of form I is P2₁2₁2. The initial model was determined by a molecular replacement method using the structure of clarithromycin form 0 as a search model, and the final structure was obtained through Rietveld refinements. In the form I crystal structure, the clarithromycin molecules are aligned parallel along the a axis in a head-to-tail manner with intermolecular hydrogen bonds between the hydroxy O atoms. The dimethylamine groups of the clarithromycin molecule interdigitate between neighbouring head-to-tail clarithromycin alignments. The novel crystal packing found in form I provides a mechanism that describes the transformation of form 0 to form I.

Conformational studies of hydantoin-5-acetic acid and orotic acid

V. Gerhardt, M. Tutughamiarso and M. Bolte

Hydantoin-5-acetic acid [2-(2,5-dioxoimidazolidin-4-yl)acetic acid] and orotic acid (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid) each contain one rigid acceptor-donor-acceptor hydrogen-bonding site and a flexible side chain, which can adopt different conformations. Since both compounds may be used as coformers for supramolecular complexes, they have been crystallized in order to examine their conformational preferences, giving solvent-free hydantoin-5-acetic acid, C₅H₆N₂O₄, (I), and three crystals containing orotic acid, namely, orotic acid dimethyl sulfoxide monosolvate, C₅H₄N₂O₄·C₂H₆OS, (IIa), dimethylammonium orotate-orotic acid (1/1), C₂H₈N⁺·C₅H₃N₂O₄^-·C₅H₄N₂O₄, (IIb), and dimethylammonium orotate-orotic acid (3/1), 3C₂H₈N⁺·3C₅H₃N₂O₄^-·C₅H₄N₂O₄, (IIc). The crystal structure of (I) shows a three-dimensional network, with the acid function located perpendicular to the ring. Interestingly, the hydroxy O atom acts as an acceptor, even though the carbonyl O atom is not involved in any hydrogen bonds. However, in (IIa), (IIb) and (IIc), the acid functions are only slightly twisted out of the ring planes. All H atoms of the acidic functions are directed away from the rings and, with respect to the carbonyl O atoms, they show an antiperiplanar conformation in (I) and synperiplanar conformations in (IIa), (IIb) and (IIc). Furthermore, in (IIa), (IIb) and (IIc), different conformations of the acid O=C-C-N torsion angle are observed, leading to different hydrogen-bonding arrangements depending on their conformation and composition.

Planarity of heteroaryldithiocarbazic acid derivatives showing tuberculostatic activity. IV. Diesters of benzoylcarbonohydrazonodithioic acid

M. Szczesio, A. Olczak, K. Gobis, H. Foks and M. L. Glówka

Dimethyl (3,4-dichlorobenzoyl)carbonohydrazonodithioate, C₁₀H₁₀Cl₂N₂OS₂, (D1), dibenzyl (3,4-dichlorobenzoyl)carbonohydrazonodithioate, C₂₂H₁₈Cl₂N₂OS₂, (D2), dimethyl (3,4-dichlorobenzoyl)-1-methylcarbonohydrazonodithioate, C₁₁H₁₂Cl₂N₂OS₂, (D3), 3,4-dichloro-N'-(1,3-dithiolan-2-ylidene)-N-methylbenzohydrazide, C₁₁H₁₀Cl₂N₂OS₂, (D4), were synthesized as potential tuberculostatics. Compound (D1) (with two molecules in the asymmetric unit) was the only one showing tuberculostatic activity of the same range as the common drugs isoniazid and pyrazinamide. The molecular structures of the studied compounds depend on the substitution at the N atom adjacent to the carbonyl group. In the case of the unsubstituted derivatives (D1) and (D2), their central frames are generally planar with a twist of the 3,4-dichlorophenyl ring by 30-40°. Until now, coplanarity of the aromatic ring with the (methylene)carbonohydrazone fragment has been considered a prerequisite for tuberculostatic activity. The N-methylated derivatives (D3) and (D4) show an additional twist along the N-C(=O) bond by 20-30° due to the spatial repulsion introduced by the methyl substituent.

Absolute configuration of strictosidinic acid

R. de P. Castro, C. da S. Matos, C. A. do Nascimento, C. M. A. Oliveira, L. Kato, L. M. Lião and J. R. Sabino

The absolute configuration of strictosidinic acid, (2S,3R,4S)-3-ethenyl-2-(-D-glucopyranosyloxy)-4-{[(1S)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-1-yl]methyl}-3,4-dihydro-2H-pyran-5-carboxylate, was determined from its sodium chloride trihydrate, poly[[diaqua((2S,3R,4S)-3-ethenyl-2-(-D-glucopyranosyloxy)-4-{[(1S)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-2-ium-1-yl]methyl}-3,4-dihydro-2H-pyran-5-carboxylate)sodium] chloride monohydrate], {[Na(C₂₆H₃₂N₂O₉)(H₂O)₂]Cl·H₂O}_n. The strictosidinic acid molecule participates in intermolecular hydrogen bonds of the O-HO and O-HCl types. The solid-state conformation was observed as a zwitterion, based on a charged pyridine N atom and a carboxylate group, the latter mediating the packing through coordination with the sodium cation.

Alkyl-chain disorder in tetraisohexylammonium bromide

M. A. Kelland and A. L. Thompson

Tetraisohexylammonium bromide [systematic name: tetrakis(4-methylpentyl)azanium bromide], C₂₄H₅₂N⁺·Br^-, is a powerful structure II clathrate hydrate crystal-growth inhibitor. The crystal structure, in the space group P3₂21, contains one ammonium cation and one bromide anion in the asymmetric unit, both on general positions. At 100 K, the ammonium cation exhibits one ordered isohexyl chain and three disordered isohexyl chains. At 250 K, all four isohexyl chains are disordered. In an effort to reduce the disorder in the alkyl chains, the crystal was thermally cycled, but the disorder remained, indicating that it is dynamic in nature.

Two new XP(O)[NHC(CH₃)₃]₂ phosphoramidates, with X = (CH₃)₂N and [(CH₃)₃CNH]₂P(O)(O)

M. Pourayoubi, A. Tarahhomi, F. Karimi Ahmadabad, K. Fejfarová, A. van der Lee and M. Dusek

In N,N'-di-tert-butyl-N'',N''-dimethylphosphoric triamide, C₁₀H₂₆N₃OP, (I), and N,N',N'',N'''-tetra-tert-butoxybis(phosphonic diamide), C₁₆H₄₀N₄O₃P₂, (II), the extended structures are mediated by P(O)(H-N)₂ interactions. The asymmetric unit of (I) consists of six independent molecules which aggregate through P(O)(H-N)₂ hydrogen bonds, giving R₂¹(6) loops and forming two independent chains parallel to the a axis. Of the 12 independent tert-butyl groups, five are disordered over two different positions with occupancies ranging from to . In the structure of (II), the asymmetric unit contains one molecule. P(O)(H-N)₂ hydrogen bonds give S(6) and R₂²(8) rings, and the molecules form extended chains parallel to the c axis. The structures of (I) and (II), along with similar structures having (N)P(O)(NH)₂ and (NH)₂P(O)(O)P(O)(NH)₂ skeletons extracted from the Cambridge Structural Database, are used to compare hydrogen-bond patterns in these families of phosphoramidates. The strengths of P(O)[H-N]_x (x = 1, 2 or 3) hydrogen bonds are also analysed, using these compounds and previously reported structures with (N)₂P(O)(NH) and P(O)(NH)₃ fragments.

A 2'-deoxycytidine long-linker click adduct forming two conformers in the asymmetric unit

F. Seela, H. Xiong, S. Budow, H. Eickmeier and H. Reuter

The title compound {systematic name: 4-amino-1-(2-deoxy--D-erythro-pentofuranosyl)-5-[6-(1-benzyl-1H-1,2,3-triazol-4-yl)hex-1-ynyl]pyrimidin-2(1H)-one}, C₂₄H₂₈N₆O₄, shows two conformations in the crystalline state, viz. (I-1) and (I-2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N-glycosylic bonds of both conformers adopt similar anti conformations, with = -168.02 (12)° for conformer (I-1) and = -159.08 (12)° for conformer (I-2). The sugar residue of (I-1) shows an N-type (C3'-endo) conformation, with P = 33.1 (2)° and _m = 29.5 (1)°, while the conformation of the 2'-deoxyribofuranosyl group of (I-2) is S-type (C3'-exo), with P = 204.5 (2)° and _m = 33.8 (1)°. Both conformers participate in hydrogen-bond formation and exhibit identical patterns resulting in three-dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N-HN, N-H O, O-HN and O-HO).

Four Ni^II complexes with the new cyclam-methylimidazole ligand 1-[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane

A. G. De Candia, M. Molnar, L. D. Slep and R. Baggio

Although it has not proved possible to crystallize the newly prepared cyclam-methylimidazole ligand 1-[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane (L^Im1), the trans and cis isomers of an Ni^II complex, namely trans-aqua{1-[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane}nickel(II) bis(perchlorate) monohydrate, [Ni(C₁₅H₃₀N₆)(H₂O)](ClO₄)₂·H₂O, (1), and cis-aqua{1-[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane}nickel(II) bis(perchlorate), [Ni(C₁₅H₃₀N₆)(H₂O)](ClO₄)₂, (2), have been prepared and structurally characterized. At different stages of the crystallization and thermal treatment from which (1) and (2) were obtained, a further two compounds were isolated in crystalline form and their structures also analysed, namely trans-{1-[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane}(perchlorato)nickel(II) perchlorate, [Ni(ClO₄)(C₁₅H₃₀N₆)]ClO₄, (3), and cis-{1,8-bis[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane}nickel(II) bis(perchlorate) 0.24-hydrate, [Ni(C₂₀H₃₆N₆)](ClO₄)₂·0.24H₂O, (4); the 1,8-bis[(1-methyl-1H-imidazol-2-yl)methyl]-1,4,8,11-tetraazacyclotetradecane ligand is a minor side product, probably formed in trace amounts in the synthesis of L^Im1. The configurations of the cyclam macrocycles in the complexes have been analysed and the structures are compared with analogues from the literature.

catena-Poly[[[(oxamide dioxime-²N,N')copper(II)]--L-tartrato-⁴O¹,O²:O³,O⁴] tetrahydrate]: a chiral nanochannel framework hosting solvent water molecules

M. M. Bélombé, J. Nenwa, J. S. T. Wankap Kouamo, S. Ponou and A. Fischer

The crystal structure of the title compound, {[Cu(C₄H₄O₆)(C₂H₆N₄O₂)]·4H₂O}_n, contains the central Cu^II cation in a distorted octahedral coordination, symmetrically chelated by the two imine N atoms of a neutral oxamide dioxime (H₂oxado) ligand [Cu-N = 1.9829 (16) Å] and unsymmetrically bis-chelated by two halves of the L-(+)-tartrate(2-) (tart) ligands, each half being linked to the Cu^II cation via the deprotonated carboxylate group and protonated hydroxy group [Cu-O = 1.9356 (14) and 2.4674 (13) Å, respectively]. The extended asymmetric unit is defined by twofold axes, one passing through the Cu^II cation and the centre of the oxamide dioxime (H₂oxado) ligand and the another two (symmetry related) bisecting the central C-C bonds of the tartrate ions. The structure is chiral, consisting of enantiomeric linear-chain polymers oriented along [001], with virtual monomeric {Cu(tart_0.5)₂(H₂oxado)} repeat units and with the chains interleaved face-to-face into `twin pillars'. Nanochannels exist, running parallel to the c axis and bisecting a and b, which host `double strings' of solvent water molecules. Extensive hydrogen bonding (O-HO and N-HO) between the chains and solvent water molecules, together with extended - interactions, consolidate the bulk crystal structure.

Chiral crystals from an achiral molecule: 4,6-di-O-benzyl-1,3-O-benzylidene-2-O-(4-methoxybenzyl)-myo-5-inosose

B. P. Gurale, R. G. Gonnade and M. S. Shashidhar

The title achiral compound, C₃₅H₃₄O₇, crystallizes in the chiral monoclinic space group P2₁. The molecules are densely packed to form a helical assembly along the crystallographic twofold screw axis via C-HO and C-H interactions. Interestingly, the unit-translated helical chains are loosely connected via a rather uncommon edge-to-edge Ph-HH-Ph short contact (HH = 2.33 Å).

Structural study of six cycloalkylammonium cinnamate salt structures featuring one-dimensional columns and two-dimensional hydrogen-bonded networks

A. Lemmerer and M. A. Fernandes

Six ammonium carboxylate salts, namely cyclopentylammonium cinnamate, C₅H₁₂N⁺·C₉H₇O₂^-, (I), cyclohexylammonium cinnamate, C₆H₁₄N⁺·C₉H₇O₂^-, (II), cycloheptylammonium cinnamate form I, C₇H₁₆N⁺·C₉H₇O₂^-, (IIIa), and form II, (IIIb), cyclooctylammonium cinnamate, C₈H₁₈N⁺·C₉H₇O₂^-, (IV), and cyclododecylammonium cinnamate, C₁₂H₂₆N⁺·C₉H₇O₂^-, (V), are reported. Salts (II)-(V) all have a 1:1 ratio of cation to anion and feature three N⁺-HO^- hydrogen bonds forming one-dimensional hydrogen-bonded columns consisting of repeating R₄³(10) rings, while salt (I) has a two-dimensional network made up of alternating R₄⁴(12) and R⁶₈(20) rings. Salt (III) consists of two polymorphic forms, viz. form I having Z' = 1 and form II with Z' = 2. The latter polymorph has disorder of the cycloheptane rings in the two cations, as well as whole-molecule disorder of one of the cinnamate anions. A similar, but ordered, Z' = 2 structure is seen in salt (IV).

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

B. Wicher, K. Pyta, P. Przybylski, E. Tykarska and M. Gdaniec

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975). Acta Cryst. B31, 1454-1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol -OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C₄₃H₅₈N₄O₁₂·5H₂O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O-HO and N-HN hydrogen bonds. Four of the symmetry-independent water molecules are arranged via hydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interact via O-HO hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

Two androsterone derivatives as inhibitors of androgen biosynthesis

G.-B. Djigoue, M. Simard, L.-C. Kenmogne and D. Poirier

The title compounds, (3R,5S,5'R,8R,9S,10S,13S,14S)-10,13-dimethyl-5'-(2-methylpropyl)tetradecahydro-6'H-spiro[cyclopenta[a]phenanthrene-3,2'-[1,4]oxazinane]-6',17(2H)-dione, C₂₆H₄₁NO₃, (I), and methyl (2R)-2-[(3R,5S,8R,9S,10S,13S,14S)-10,13-dimethyl-2',17-dioxohexadecahydro-3'H-spiro[cyclopenta[a]phenanthrene-3,5'-[1,3]oxazolidin-3'-yl]]-4-methylpentanoate, C₂₈H₄₃NO₅, (II), possess the typical steroid shape (A-D rings), but they differ in their extra E ring. The azalactone E ring in (I) shows a half-chair conformation, while the carbamate E ring of (II) is planar. The orientation of the E-ring substituent is clearly established and allows a rationalization of the biological results obtained with such androsterone derivatives.

XRD and VCD: a marriage of love or convenience? Honeymoon around a cyclic urea derivative

D. Gherase, J.-V. Naubron, C. Roussel and M. Giorgi

The structures and absolute configurations of the enantiomers (3aR,8aR)-2,2-dimethyl-4,4,8,8-tetraphenyl-4,5,6,7,8,8a-hexahydro-3aH-1,3-dioxolo[4,5-e][1,3]diazepin-6-one 0.33-hydrate, C₃₂H₃₀N₂O₃·0.33H₂O, (Ia), and (3aS,8aS)-2,2-dimethyl-4,4,8,8-tetraphenyl-4,5,6,7,8,8a-hexahydro-3aH-1,3-dioxolo[4,5-e][1,3]diazepin-6-one 0.39-hydrate, C₃₂H₃₀N₂O₃·0.39H₂O, (Ib), have been elucidated unambiguously using the complementary power of single-crystal X-ray diffraction (XRD) and vibrational circular dichroism (VCD). The enantiomers crystallize in the Sohncke space group P2₁2₁2 and pack as dimers stabilized by two symmetric hydrogen bonds involving one amide group each of the cyclic urea moiety. This double interaction is capped by a water molecule that partially occupies a site lying on the twofold axis and forms an uncommon hydrogen bond between the two monomers. A comparison between the solid-state VCD characterizations and the Bayesian statistics on Bijvoet differences determined from the XRD measurements reveals a tendency towards the correct determination of the absolute configuration by this latter method.

KCo(H₂O)₂BP₂O₈·0.48H₂O and K_0.17Ca_0.42Co(H₂O)₂BP₂O₈·H₂O: two cobalt borophosphates with helical ribbons and disordered (K,Ca)/H₂O schemes

A. Guesmi and A. Driss

The two title compounds, potassium diaquacobalt(II) borodiphosphate 0.48-hydrate and potassium-calcium(0.172/0.418) diaquacobalt(II) borodiphosphate monohydrate, were synthesized hydrothermally. They are new members of the borophosphate family characterized by [BP₂O₈]^3- helices running along [001] and constructed of boron (Wyckoff position 6b, twofold axis) and phosphorus tetrahedra. The [CoBP₂O₈]^- anionic frameworks in the two materials are structurally similar and result from a connection in the ab plane between the CoO₄(H₂O)₂ coordination octahedra (6b position) and the helical ribbons. Nevertheless, the two structures differ in the disorder schemes of the K,Ca and H₂O species. The alkali cations in the structure of the pure potassium compound are disordered over three independent positions, one of them located on a 6b site. Its framework is characterized by double occupation of the tunnels by water molecules located on twofold rotation axes (6b) and a fraction of alkali cations; its cell parameters, compared with those for the mixed K,Ca compound, show abnormal changes, presumably due to the disorder. For the K,Ca compound, the K and Ca cations are on twofold axes (6b) and the channels are occupied only by disordered solvent water molecules. This shows that it is possible, due to the flexibility of the helices, to replace the alkali and alkaline earth cations while retaining the crystal framework.

Pseudosymmetry in a cyclopalladated compound

W. Raven, I. Kalf and U. Englert

The enantiomerically pure title complex, [SP-4-4]-(R)-[2-(1-aminoethyl)phenyl-²C¹,N]chlorido(quinoline-N)palladium(II) acetone hemisolvate, [Pd(C₈H₁₀N)Cl(C₉H₇N)]·0.5C₃H₆O, crystallizes with four molecules of the organopalladium complex and two molecules of acetone in the asymmetric unit. This corresponds to a discrete hydrogen-bonded aggregate and to the content of the unit cell in the space group P1. Pronounced pseudo-inversion symmetry relates pairs of these objects in the asymmetric unit.

The first 3':5'-cyclic nucleotide-amino acid complex: L-His-cIMP

K. Slepokura

In the crystal structure of the L-His-cIMP complex, i.e. L-histidinium inosine 3':5'-cyclic phosphate [systematic name: 5-(2-amino-2-carboxyethyl)-1H-imidazol-3-ium 7-hydroxy-2-oxo-6-(6-oxo-6,9-dihydro-1H-purin-9-yl)-4a,6,7,7a-tetrahydro-4H-1,3,5,2⁵-furo[3,2-d][1,3,2⁵]dioxaphosphinin-2-olate], C₆H₁₀N₃O₂⁺·C₁₀H₁₀N₄O₇P^-, the Hoogsteen edge of the hypoxanthine (Hyp) base of cIMP and the Hyp face are engaged in specific amino acid-nucleotide (HiscIMP) recognition, i.e. by abutting edge-to-edge and by - stacking, respectively. The Watson-Crick edge of Hyp and the cIMP phosphate group play a role in nonspecific HiscIMP contacts. The interactions between the cIMP anions (anti/C3'-endo/trans-gauche/chair conformers) are realized mainly between riboses and phosphate groups. The results for this L-His-cIMP complex, compared with those for the previously reported solvated L-His-IMP crystal structure, indicate a different nature of amino acid-nucleotide recognition and interactions upon the 3':5'-cyclization of the nucleotide phosphate group.

Cinerin C: a macrophyllin-type bicyclo[3.2.1]octane neolignan from Pleurothyrium cinereum (Lauraceae)

E. D. Coy-Barrera, L. E. Cuca-Suárez, M. Sefkow and U. Schilde

The structure of naturally-occurring cinerin C [systematic name: (7S,8R,3'R,4'S,5'R)-^8'-4'-hydroxy-5,5',3'-trimethoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan], isolated from the ethanol extract of leaves of Pleurothyrium cinereum (Lauraceae), has previously been established by NMR and HRMS spectroscopy, and its absolute configuration established by circular dichroism measurements. For the first time, its crystal strucure has now been established by single-crystal X-ray analysis, as the monohydrate, C₂₂H₂₆O₇·H₂O. The bicyclooctane moiety comprises fused cyclopentane and cyclohexenone rings which are almost coplanar. An intermolecular O-HO hydrogen bond links the 4'-OH and 5'-OCH₃ groups along the c axis.

(1S)-1-Phenylethanaminium 4-{[(1S,2S)-1-hydroxy-2,3-dihydro-1H,1'H-[2,2'-biinden]-2-yl]methyl}benzoate

C. S. Frampton, T. Zhang, G. A. Scalabrino, N. Frankish and H. Sheridan

The title molecular salt, C₈H₁₂N⁺·C₂₆H₂₁O₃^-, contains a dimeric indane pharmacophore that demonstrates potent anti-inflammatory activity. The indane group of the anion exhibits some disorder about the -C atom, which appears common to many structures containing this group. A model to account for the slight disorder was attempted, but this was deemed unsuccessful because applying bond-length constraints to all the bonds about the -C atom led to instability in the refinement. The absolute configuration was determined crystallographically as S,S,S by anomalous dispersion methods with reference to both the Flack parameter and Bayesian statistics on Bijvoet differences. The configuration was also determined by an a priori knowledge of the absolute configuration of the (1S)-1-phenylethanaminium counter-ion. The molecules pack in the crystal structure to form an infinite two-dimensional hydrogen-bond network in the (100) plane of the unit cell.

A novel one-dimensional Co^II coordination polymer: catena-poly[[hexaaquacobalt(II)] [[diaquabis(sulfato-O)cobalt(II)]--4,4'-bipyridine-²N:N'] [[triaqua(sulfato-O)cobalt(II)]--4,4'-bipyridine-²N:N']]

K.-L. Zhong and M.-Y. Qian

The title compound, {[Co(H₂O)₆][Co(SO₄)(C₁₀H₈N₂)(H₂O)₃][Co(SO₄)₂(C₁₀H₈N₂)(H₂O)₂]}_n, contains three crystallographically unique Co^II centres, all of which are in six-coordinated environments. One Co^II centre is coordinated by two bridging 4,4'-bipyridine (4,4'-bipy) ligands, one sulfate ion and three aqua ligands. The second Co^II centre is surrounded by two N atoms of two 4,4'-bipy ligands and four O atoms, i.e. two O atoms from two monodentate sulfate ions and two from water molecules. The third Co^II centre forms part of a hexaaquacobalt(II) ion. In the crystal structure, there are two different one-dimensional chains, one being anionic and the other neutral, and adjacent chains are arranged in a cross-like fashion around the mid-point of the 4,4'-bipy ligands. The structure features O-HO hydrogen-bonding interactions between sulfate anions and water molecules, resulting in a three-dimensional supramolecular network.

Hydrogen bonding in cyclic imides and amide carboxylic acid derivatives from the facile reaction of cis-cyclohexane-1,2-carboxylic anhydride with o- and p-anisidine and m- and p-aminobenzoic acids

G. Smith and U. D. Wermuth

The structures of the open-chain amide carboxylic acid rac-cis-2-[(2-methoxyphenyl)carbamoyl]cyclohexane-1-carboxylic acid, C₁₅H₁₉NO₄, (I), and the cyclic imides rac-cis-2-(4-methoxyphenyl)-3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione, C₁₅H₁₇NO₃, (II), chiral cis-3-(1,3-dioxo-3a,4,5,6,7,7a-hexahydroisoindol-2-yl)benzoic acid, C₁₅H₁₅NO₄, (III), and rac-cis-4-(1,3-dioxo-3a,4,5,6,7,7a-hexahydroisoindol-2-yl)benzoic acid monohydrate, C₁₅H₁₅NO₄·H₂O, (IV), are reported. In the amide acid (I), the phenylcarbamoyl group is essentially planar [maximum deviation from the least-squares plane = 0.060 (1) Å for the amide O atom] and the molecules form discrete centrosymmetric dimers through intermolecular cyclic carboxy-carboxy O-HO hydrogen-bonding interactions [graph-set notation R₂²(8)]. The cyclic imides (II)-(IV) are conformationally similar, with comparable benzene ring rotations about the imide N-C_ar bond [dihedral angles between the benzene and isoindole rings = 51.55 (7)° in (II), 59.22 (12)° in (III) and 51.99 (14)° in (IV)]. Unlike (II), in which only weak intermolecular C-HO_imide hydrogen bonding is present, the crystal packing of imides (III) and (IV) shows strong intermolecular carboxylic acid O-HO hydrogen-bonding associations. With (III), these involve imide O-atom acceptors, giving one-dimensional zigzag chains [graph-set C(9)], while with the monohydrate (IV), the hydrogen bond involves the partially disordered water molecule which also bridges molecules through both imide and carboxy O-atom acceptors in a cyclic R₄⁴(12) association, giving a two-dimensional sheet structure. The structures reported here expand the structural database for compounds of this series formed from the facile reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with substituted anilines, in which there is a much larger incidence of cyclic imides compared to amide carboxylic acids.

An optically resolved crystal of thiomalate: (S)-1-phenylethanaminium (R)-thiomalate

K. Igawa, N. Yoshinari and T. Konno

The asymmetric unit of the optically resolved title salt, C₈H₁₂N⁺·C₄H₅O₄S^-, contains a 1-phenylethanaminium monocation and a thiomalate (3-carboxy-2-sulfanylpropanoate) monoanion. The absolute configurations of the cation and the anion are determined to be S and R, respectively. In the crystal, cation-anion N-HO hydrogen bonds, together with anion-anion O-HO and S-HO hydrogen bonds, construct a two-dimensional supramolecular sheet parallel to the ab plane. The two-dimensional sheet is linked with the upper and lower sheets through C-H interactions to stack along the c axis.

3,4,6-Tri-O-acetyl-1,2-O-[1-(exo-ethoxy)ethylidene]--D-mannopyranose 0.11-hydrate

Y.-L. Liu, P. Zou, H. Wu, M.-H. Xie and S.-N. Luo

The title compound, C₁₆H₂₄O₁₀·0.11H₂O, is a key intermediate in the synthesis of 2-deoxy-2-[¹⁸F]fluoro-D-glucose (¹⁸F-FDG), which is the most widely used molecular-imaging probe for positron emission tomography (PET). The crystal structure has two independent molecules (A and B) in the asymmetric unit, with closely comparable geometries. The pyranose ring adopts a ⁴C₁ conformation [Cremer-Pople puckering parameters: Q = 0.553 (2) Å, = 16.2 (2)° and = 290.4 (8)° for molecule A, and Q = 0.529 (2) Å, =15.3 (3)° and = 268.2 (9)° for molecule B], and the dioxolane ring adopts an envelope conformation. The chiral centre in the dioxolane ring, introduced during the synthesis of the compound, has an R configuration, with the ethoxy group exo to the mannopyranose ring. The asymmetric unit also contains one water molecule with a refined site-occupancy factor of 0.222 (8), which bridges between molecules A and B via O-HO hydrogen bonds.

Novel pseudopolymorph of the active metabolite of perindopril

J. Bojarska, W. Maniukiewicz, L. Sieron, A. Fruzinski, P. Kopczacki, K. Walczynski and M. Remko

The dimethyl sulfoxide hemisolvate of perindoprilat [systematic name: (1S)-2-((S)-{1-[(2S,3aS,7aS)-2-carboxyoctahydro-1H-indol-1-yl]-1-oxopropan-2-yl}azaniumyl)pentanoate dimethyl sulfoxide hemisolvate], C₁₇H₂₈N₂O₅·0.5C₂H₆OS, an active metabolite of perindopril, has been synthesized, structurally characterized by single-crystal X-ray diffraction and compared with its ethanol disolvate analogue [Pascard et al. (1991). J. Med. Chem. 34, 663-669]. Both compounds crystallize in the orthorhombic P2₁2₁2₁ space group in the same zwitterionic form, with a protonated alanine N atom and an anionic carboxylate group at the n-alkyl chain. The three structural units present in the unit cell (two zwitterions and the solvent molecule) are held together by a rich system of O-HO, N-HO and C-HO hydrogen-bond contacts.

Reinterpretation of the monohydrate of clarithromycin from X-ray powder diffraction data as a trihydrate

J. van de Streek

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst. (2012), E68, o667-o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X-ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules. After successful location of the two additional water molecules, the Rietveld refinement still showed minor problems. These were resolved by noticing that one of the chiral centres in the molecule had been inverted. The corrected crystal structure of clarithromycin trihydrate, refined against the original data, is now reported. Dispersion-corrected density functional theory calculations were used to check the final crystal structure and to position the H atoms.

5-Ethynyl-2'-deoxycytidine: a DNA building block with a `clickable' side chain

F. Seela, H. Mei, H. Xiong, S. Budow, H. Eickmeier and H. Reuter

The title compound [systematic name: 4-amino-1-(2-deoxy--D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C₁₁H₁₃N₃O₄, shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with = -149.2 (1)° for conformer (I-1) and -151.4 (1)° for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2'-endo envelope conformation (²E, S-type), with P = 164.7 (1)° and _m = 36.9 (1)°, while (I-2) shows a major C3'-exo sugar pucker (C3'-exo-C2'-endo, ₃T², S-type), with P = 189.2 (1)° and _m = 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.

Three derivatives of 4-fluoro-5-sulfonylisoquinoline

S. Ohba, N. Gomi, T. Ohgiya and K. Shibuya

In 4-fluoroisoquinoline-5-sulfonyl chloride, C₉H₅ClFNO₂S, (I), one of the two sulfonyl O atoms lies approximately on the isoquinoline plane as a result of minimizing the steric repulsion between the chlorosulfonyl group and the neighbouring F atom. In (S)-(-)-4-fluoro-N-(1-hydroxypropan-2-yl)isoquinoline-5-sulfonamide, C₁₂H₁₃FN₂O₃S, (II), there are two crystallographically independent molecules (Z' = 2). The molecular conformations of these two molecules differ in that the amine group of one forms an intramolecular bifurcated hydrogen bond with the F and OH groups, whilst the other forms only a single intramolecular N-HF hydrogen bond. The N-HF hydrogen bonds correspond to weak coupling between the N(H) and ¹⁹F nuclei, observed in the ¹H NMR solution-state spectra. In (S)-(-)-4-[(4-fluoroisoquinolin-5-yl)sulfonyl]-3-methyl-1,4-diazepan-1-ium chloride, C₁₅H₁₉FN₃O₂S⁺·Cl^-, (III), the isoquinoline plane is slightly deformed, suggestive of a steric effect induced by the bulky substituent on the sulfonyl group.